Zoonotic Coronavirus Literature Review

United States Department of Agriculture

Animal and Plant Health Inspection Service

Revised June 15, 2023

This report was prepared by Rose Li and Associates, Inc., under contract to USDA. 

The views expressed in this document do not necessarily reflect those of USDA. 

Contributions to this report by the following individuals are gratefully 

acknowledged: Gina Castelvecchi, Dana Carluccio, Jessica Dade, Rebecca Fuldner, 

Cooper Roache, and Nancy Tuvesson.
Zoonotic Coronavirus Literature Review

Acronyms Definitions Page ii

Acronym Definitions

3CLpro 3C-like protease

ACE2 angiotensin-converting enzyme 2

ADAR adenosine deaminases acting on RNAs

ADE antibody-dependent enhancement

APHIS Animal and Plant Health Inspection Service

APOBEC apolipoprotein B mRNA editing enzyme, catalytic polypeptides

ARDS acute respiratory distress syndrome

ARP American Rescue Plan Act

ASGR1 asialoglycoprotein receptor 1

AURKB aurora kinase B

BAL bronchoalveolar lavage

BLAST Basic Local Alignment Search Tool

Bov-CoV bovine coronavirus

BPL β-propiolactone

BSL-2 biosafety level 2

BSL-3 biosafety level 3

CCL2 chemokine ligand 2

CD147 cluster of differentiation 147

CDC Centers for Disease Control and Prevention 

COBALT Constraint-based Multiple Alignment Tool

CPE cytopathic effect

CRISPR clustered regularly interspaced short palindromic repeats

CT computed tomography

cVNT conventional virus neutralization test

CXCL10 C-X-C motif chemokine ligand 10

DC-SIGN dendritic cell-specific intercellular adhesion molecule-3-grabbing 

non-integrin

DPI days post infection

DPP4 dipeptidyl peptidase-4

EGCG epigallocatechin gallate

ELISA enzyme-linked immunosorbent assays

G-CSF granulocyte colony stimulating factor

GRAMM-X Global Range Molecular Matching X

hACE2 human angiotensin I converting enzyme 2

HADDOCK High Ambiguity Driven protein-protein DOCKing

HIV human immunodeficiency virus

HPAI highly pathogenic avian influenza

I-TASSER Iterative Threading ASSEmbly Refinement

ID Innovation Diagnostics

IFN Interferon

IFN-α interferon alpha
Acronym Definitions Page iii

Ig Immunoglobulin

IHC Immunohistochemistry

IL Interleukin

IL28RA/IL10Rβ Interleukin 28 receptor alpha/beta

IP-10 interferon gamma-induced protein 10

IRF3 interferon regulatory factor 3

ISG interferon stimulated genes

JAK janus kinase

LIPS luciferase immunoprecipitation system

L-SIGN liver/lymph node-specific intracellular adhesion molecules-3-

grabbing non-integrin

mAb monoclonal antibody

MAFFT Multiple Alignment using Fast Fourier Transform

MAVS mitochondrial antiviral signaling

MCP-1 monocyte chemoattractant protein 1

MEGA Molecular Evolutionary Genetics Analysis

MERS-CoV Middle East respiratory syndrome coronavirus

MERSr MERS-related

MCP-1 monocyte chemoattractant protein 1

mg/kg milligrams per kilogram

MHV murine hepatitis virus

MIA microsphere immunoassay

miSARS-CoV mink-associated coronavirus 2

MLV murine leukemia virus

MNA microneutralization assay

MUSCLE Multiple Sequence Comparison by Log- Expectation

NAHRS National Animal Health Reporting System

NET neutrophil extracellular trap

NFκB nuclear factor kappa-light-chain enhancer

NHP non-human primate

NK natural killer

NRP1 neuropilin 1

PISA Proteins, Interfaces, Structures and Assemblies

PPE personal protective equipment

ppNT pseudoparticle neutralization test

PRNT plaque reduction neutralization test

RBD receptor binding domain

RdRp RNA-dependent RNA polymerase

RSCU relative synonymous codon usage

RT-PCR reverse transcription-polymerase chain reaction

S spike protein

SARS-CoV-1 severe acute respiratory syndrome coronavirus 1

SARS-CoV-2 severe acute respiratory syndrome coronavirus 2

SARSr SARS-related
Acronym Definitions Page iii

SCID severe combined immunodeficient

sVNT surrogate virus neutralization test

TGEV transmissible gastroenteritis virus

TGFβ transforming growth factor beta

TIM1 T-cell immunoglobulin and mucin domain 1

TLR-7 toll-like receptor-7

TLR-8 toll-like receptor-8

TMPRSS transmembrane protease, serine

TMPRSS2 transmembrane protease, serine 2

TNF tumor necrosis factor

TNFα tumor necrosis factor alpha

TRACE Tracking Resistance and Coronavirus Evolution 

UAE United Arab Emirates

USDA United States Department of Agriculture

VSV vesicular stomatitis virus

WOAH World Organisation for Animal Health
Table of Contents Page iv 

Table of Contents

Acronym Definitions................................................................................................................ ii

Executive Summary ................................................................................................................. 1

Report................................................................................................................................... 10

Introduction .................................................................................................................................. 10

Approach....................................................................................................................................... 10

Epidemiology................................................................................................................................. 12

Coronavirus Ecology ........................................................................................................................... 12

Evidence Types for Determining Species Susceptibility ..................................................................... 19

Species Interfaces Relevant to Coronavirus Transmission................................................................. 23

Molecular Biology and Virology ..................................................................................................... 47

Molecular Biology Implications for Intermediate Hosts .................................................................... 47

Mutations that Affect Host Range...................................................................................................... 47

Recombination Events........................................................................................................................ 49

Molecular Determinants of SARS-CoV-1 and SARS-CoV-2 Host Ranges............................................49

Immunology .................................................................................................................................. 51

Innate Immune Response................................................................................................................... 51

Adaptive Immune Response............................................................................................................... 53

SARS-CoV-1, MERS-CoV, and SARS-CoV-2 Immune Responses in Select Susceptible Species...........53

Pathogenesis ................................................................................................................................. 58

Hamster.............................................................................................................................................. 58

Mouse................................................................................................................................................. 61

Non-Human Primates......................................................................................................................... 62

Ferret.................................................................................................................................................. 65

Civet.................................................................................................................................................... 66

Companion Animals ........................................................................................................................... 67

Mink.................................................................................................................................................... 69

Sheep and Swine ................................................................................................................................ 70

Camelid............................................................................................................................................... 70

Surveillance ................................................................................................................................... 71

Types of Surveillance Systems............................................................................................................ 74

Diagnostics.................................................................................................................................... 75

Viral RNA Detection............................................................................................................................ 75

Virus-Specific Antibody Detection...................................................................................................... 80

Vaccines ........................................................................................................................................ 86

Research Tools for Vaccine Development.......................................................................................... 86

Vaccines Tested in Susceptible Animals............................................................................................. 87

Vaccines Designed for Veterinary Use ............................................................................................... 87

Therapeutics.................................................................................................................................. 94

FDA-Approved Antivirals.................................................................................................................... 94

Biologics.............................................................................................................................................. 96

Other FDA-Approved Drugs................................................................................................................ 97

Biosecurity................................................................................................................................... 100

Vaccines............................................................................................................................................ 101

Surveillance ...................................................................................................................................... 101

Disinfection, Decontamination, and Personal Protective Equipment..............................................101
Acronym Definitions Page iii

Reducing Animal Contact ................................................................................................................. 102

Land Use Changes ............................................................................................................................ 103

Policy on Markets and Trade............................................................................................................ 103

Depopulation and Culling................................................................................................................. 103

Appendix A: References....................................................................................................... 104
Zoonotic Coronavirus Literature Review

Executive Summary Page 1

Executive Summary

This report presents the results of a comprehensive literature review regarding research and 

public health progress on emerging coronaviruses—specifically severe acute respiratory 

syndrome coronavirus 1 and 2 (SARS-CoV-1 and SARS-CoV-2) and Middle East respiratory 

syndrome coronavirus (MERS-CoV)—in various animal species. The report is intended as a tool 

to supplement future in-depth gap analyses to identify areas for research funding with 

maximum potential impact on animal health. 

Understanding Emerging Coronaviruses in Animals

Epidemiology

SARS-CoV-1, SARS-CoV-2, and MERS-CoV most commonly spread via airborne droplets, and 

their airborne travel distance depends heavily on environmental conditions that affect virus 

stability in droplets (e.g., colder temperatures, high or low relative humidity). Virus stabilizing 

conditions can therefore partially dictate disease spread or lack thereof at different population 

densities. While these three coronaviruses can survive on some solid surfaces (i.e., fomites), 

transmission via fomites is poorly understood. Moreover, little is known about the 

transmissibility of these emerging coronaviruses in feces (including fecal-contaminated water)

and animal products. Although coronaviruses and other RNA viruses have been isolated from 

these potential sources, their concentrations may be insufficient to infect additional hosts.

Many emerging coronaviruses can be traced to Chiropterans as both origin and primary 

reservoir species. SARS-related (SARSr), MERS-related (MERSr), and other related coronaviruses 

have been detected in diverse Chiropteran species across multiple continents. Unique aspects 

of Chiropteran immunity enable coronavirus coinfections and frequent recombination events 

that can result in novel viruses with broader species tropisms, ultimately spreading these 

viruses to additional potential reservoirs living proximally to Chiropteran colonies. Such

reservoir species include dromedary camels, palm civets, raccoon dogs, and some mustelid 

species. Significant proportions of dromedary camel populations have been infected with 

MERS-CoV in both the Middle East and Africa. Based on surveillance studies of live animal 

markets, palm civets and raccoon dogs were identified as SARS-CoV-1 reservoirs. Although no 

definitive reservoir has been identified for SARS-CoV-2, palm civets, racoon dogs, and certain 

mustelid species, especially American mink, represent potential current and future reservoirs 

for this virus. 

Identification of additional reservoir species and tracing of close interspecies contacts can help 

inform emerging coronavirus surveillance and disease control to proactively prevent viral 

spread to additional animal species. Novel approaches using computational methods have 

rapidly predicted species susceptible to SARS-CoV-2 infection based on models of spike proteinangiotensin converting enzyme (ACE2) protein interactions. However, some of these predicted 

species cannot be infected with SARS-CoV-2 and sometimes SARS-CoV-1 and MERS-CoV, as 

evidenced by in vitro and in vivo infection experiments, studies of host receptor expression, and 

detection of natural infections. Ultimately, even species that can be infected experimentally 
Zoonotic Coronavirus Literature Review

Executive Summary Page 2

need to be exposed to these viruses either by living in close proximity to or preying upon other 

infected species to naturally contract these infectious diseases. The susceptibility of select 

species and groups of species detailed in this literature review are briefly summarized below.

Based on computational studies, multiple mustelid species appear moderately to highly

susceptible to SARS-CoV-2. These findings have been corroborated with experimental infection 

and surveillance studies, particularly in ferrets and American mink. Therefore, mustelids 

preying on Chiropterans or residing near Chiropteran roosts are at high risk for contracting 

SARS-CoV-2. Farmed mustelids and those traded at live animal markets are also at particularly

high risk for SARS-CoV-2 infection from humans as well as other infected species housed in 

close proximity.

Computational modeling predicts moderate to high susceptibility to SARS-CoV-2 for a diverse 

set of non-human primates (NHPs). New World monkeys and great apes appear to have similar 

susceptibility as humans to SARS-CoV-2, while Old World monkeys, lemurs, and lorises are 

moderately susceptible, as evidenced by a combination of computational modeling, in vitro and 

in vivo experimental infections, and detection of natural infections. Some NHP models have 

also been successfully infected with SARS-CoV-1 in laboratory settings. NHPs living near or 

opportunistically preying upon Chiropterans (e.g., New World Cebidae monkeys and Old World 

Cercopithecus monkeys) may be especially at risk for coronavirus spillover events. 

Various computational studies have predicted that domesticated dogs and cats have variable 

susceptibility to SARS-CoV-2, and in vitro studies indicate that dogs may be susceptible to SARSCoV-1. Natural infections of SARS-CoV-1 have not been detected in dogs and cats, but 

numerous surveillance studies across the globe have detected active infection or antibodies to 

SARS-CoV-2 in both animals. Some of these cases were traced to infected owners, and other 

cases identified likely interspecies transmission events from American mink farms. The 

collective data suggest that dogs and cats are generally susceptible to SARS-CoV-2 infection. 

Computational studies have also identified variable SARS-CoV-2 susceptibilities in farmed 

ungulates. Different SARS-CoV-2 in vitro infection confirmatory studies were also inconsistent 

with one another, except for white-tailed deer, which were susceptible to in vitro infection in 

multiple experimental contexts. Due to the animals’ overall size, few in vivo experimental 

infection studies have been performed. Natural SARS-CoV-2 infections have been detected in 

white-tailed deer across the United States, and individual studies have reported very low rates 

of SARS-CoV-2 in goats, pigs, and sheep. MERS-CoV infections present an overall larger threat 

than SARS-CoV infections in farmed ungulates, with numerous reports of infections in 

dromedary and Bactrian camels, cattle, goats, sheep, and alpacas, as well as a small number of 

infections in donkeys and horses. Overall, multiple farmed ungulate species are at risk for 

spillover infections with emerging coronaviruses, especially those with regular contact with 

humans, Chiropterans, and other susceptible farmed ungulate species. 

Molecular Biology and Virology

Identifying molecular similarities and differences observed between SARS-CoV-1, SARS-CoV-2, 

and MERS-CoV can help improve overall understanding of the factors that can enhance or 
Zoonotic Coronavirus Literature Review

Executive Summary Page 3

depress infectivity and pathogenesis in animals. SARS-CoV-1, SARS-CoV-2, and MERS-CoV have 

similar host cell entry mechanisms based on their spike proteins. These spike (S) proteins 

engage with host cell surface receptors, and with the assistance of cell surface proteases, 

promote fusion at the plasma membrane for cellular entry. SARS-CoVs engage with different 

host cell receptors and proteases than MERS-CoV, and host receptor binding domains differ 

across all three coronaviruses. Although SARS-CoV-1 and SARS-CoV-2 interact with the same 

host receptor, their S protein amino acid sequences are distinct. These variations in S protein 

sequence affect overall viral transmission and host range. 

The host ACE2 receptor, a key component for SARS-CoV-1 and SARS-CoV-2 entry, is conserved 

across a variety of animal species. Host susceptibility is impacted by the presence or absence of 

amino acids that are key for binding to the ACE2-receptor binding domain (RBD). Researchers 

have used these key ACE2 residues to identify species susceptible to SARS-COV-2. Animal 

susceptibility to SARS-CoV-2 is also impacted by the expression of different ACE2 isoforms, 

some of which do not support SARS-CoV-2 binding.

SARS-CoV-1, SARS-CoV-2, and MERS-CoV likely originated from recombination events in 

Chiropterans. With the global spread of SARS-CoV-2, recombination events with MERS-CoV may

occur due to (1) co-circulation of viruses in the same regions and species, (2) co-infection of 

type II alveolar cells, (3) high overall recombination rates, and (4) high sequence homology. 

Immunology

Immunity to MERS-CoV-1, SARS-CoV-1, and SARS-CoV-2 induced after viral infection involves 

both the innate and adaptive immune systems. Protective immunity (i.e., immunological 

memory) against subsequent reinfections involves the production of neutralizing antibodies in 

addition to the generation of antigen specific CD8+

T cells. Many detailed studies have 

characterized the immune response to these coronaviruses in both humans and in animal 

species such as ferrets, hamsters, marmosets and other NHPs that are susceptible to infection. 

The robustness of these immune responses varies based on viral strain and host species, but 

much has been learned through cross-species comparisons about the role of different 

immunological factors.

Studies of SARS-CoV-1, MERS-CoV-1, and SARS-CoV-2 have demonstrated that these 

betacoronaviruses can evade the innate immune system by inhibiting interferon (IFN) 

responses. This dysregulation of IFN responses can result in more severe disease. In addition, 

inflammatory cell infiltration by macrophages, neutrophils, and activated T cells, as well as 

enhanced release of cytokines (i.e., cytokine storm), often result in acute respiratory distress 

syndrome (ARDS) which is observed in humans and some animal species to a lesser degree. 

Studies in animal models are needed to better understand the roles of the IFN and innate 

immune responses to SARS-CoV-2, and the various proteins used by coronaviruses to evade this 

response, in order to develop therapeutics for treatment of disease.
Zoonotic Coronavirus Literature Review

Executive Summary Page 4

Pathogenesis

Pathogenesis data on coronaviruses primarily comes from species used for research on

mechanisms and treatment of SARS-CoV-2 infection, such as laboratory hamsters, mice, and 

NHP. Findings from experimental species provide more detail about clinical symptoms, viral 

loads, histopathology, and genetic and epigenetic factors, compared to data from other species 

for which data come primarily from population surveillance. Overall, hamsters, NHPs, and 

ferrets are readily infected by SARS-CoV-2 and SARS-CoV-1, while companion animals and mice 

show comparatively less susceptibility to infection. In addition, these species show varying 

degrees of susceptibility to MERS-CoV infection, with dromedary camels being the primary 

reservoir for the virus.

Pathogenesis data on coronaviruses in hamsters are primarily generated in Golden Syrian 

hamsters used as a model for human disease. Multiple studies suggest that Golden Syrian 

hamsters’ susceptibility to SARS-CoV-2 infection depends on both sex and SARS-CoV-2 variant. 

For Golden Syrian hamsters inoculated with SARS-CoV-1, high viral titers were detected in the 

upper and lower respiratory tracts, but hamsters remained asymptomatic. In contrast, 

Roborovskii hamsters develop severe or fatal disease from SARS-CoV-2 inoculation and are 

substantially more susceptible to infection than Golden Syrian hamsters. However, MERS-CoV 

cannot effectively replicate in Golden Syrian hamsters: animals show a lack of clinical 

symptoms, viral replication, histopathological lesions in the lungs, cytokine upregulation, and

seroconversion of antibodies.

Laboratory mice inoculated with SARS-CoV-2 (WA1/2020) do not show significant signs of 

infection because of insufficient binding affinity between the SARS-CoV-2 S protein and murine 

ACE2 receptors. However, multiple variants containing an N501Y substitution in the S protein 

have infectious potential in mice. When inoculated with SARS-CoV-1, BALB/c mice showed agedependent signs of infection. In addition, older mice showed a higher number of differentially 

regulated host cellular genes than their younger counterparts.

Multiple studies of rhesus macaques, cynomolgus macaques, and African green monkeys 

inoculated with SARS-CoV-2 report changes in respiratory pattern, increased body temperature, 

reduced appetite, hunched posture, pale appearance, and dehydration. Compared to rhesus 

macaques, African green monkeys and cynomolgus macaques showed more severe pulmonary 

lesions in lung tissue. In addition, compared to rhesus macaques inoculated with SARS-CoV-1, 

which showed no clinical symptoms of illness, cynomolgus macaques inoculated with SARSCoV-1 showed similar symptoms to SARS-CoV-2 infection and more severe histological findings. 

When inoculated with MERS-CoV, rhesus macaques exhibited transient clinical symptoms; in 

contrast, marmosets displayed more severe clinical symptoms than rhesus macaques, with 

increased antigen detection and severe histopathological changes in lung tissues.

Similarly to mice, ferrets have shown age-dependent pathogenic characteristics of SARS-CoV-2 

infection, with older ferrets containing higher viral titers from nasal turbinates compared to 

younger ferrets. In addition, older ferrets had more severe histopathological changes in lung 

tissue compared to younger ferrets. Interestingly, ferrets rechallenged with SARS-CoV-2 
Zoonotic Coronavirus Literature Review

Executive Summary Page 5

showed more severe clinical symptoms that were not observed during the initial challenge. In 

contrast, multiple studies of SARS-CoV-2 in mink populations report mixed findings, with some 

reporting positive cases associated with clinical symptoms and others reporting no viral 

detection. In addition, reports from mink that died on farms reveal histopathological changes in 

lung tissues. For sheep and swine farms, no evidence currently indicates susceptibility to SARSCoV-2 infection.

Companion animals, such as dogs and cats, show varying susceptibility to SARS-CoV-2 infection. 

Cats inoculated with SARS-CoV-2 are typically asymptomatic, but readily shed virus orally, 

nasally, and rectally. However, some variants of SARS-CoV-2 have caused symptoms in cats, 

with more severe histopathological changes in lung tissue. Similarly, cats inoculated with SARSCoV-1 do not show any clinical symptoms, but only shed virus from the pharynx. Dogs 

inoculated with or exposed to SARS-CoV-2 have shown clinical presentations ranging from 

asymptomatic to increases in body temperature, decreases in weight, and respiratory 

symptoms. However, multiple studies provide evidence that dogs are less susceptible to overall 

SARS-CoV-2 infection than cats and do not shed any virus. 

Dromedary camels are commonly known as a primary reservoir for the MERS-CoV virus. MERSCoV infection in camelids is characterized by minor clinical symptoms composed of mild to 

moderate nasal discharge. MERS-CoV is primarily shed in these nasal secretions, but has not 

been detected in urine, whole blood, or serum. Primary histopathological lesions are limited to 

the upper respiratory tract and are associated with ciliocytophthoria (i.e., ciliary loss) and 

depletion of dipeptidyl peptidase 4 (DPP4). Identifying mechanisms in which cilia presence and 

function are lost may be a key focus for future investigations in upper respiratory infections.

Controlling Emerging Coronaviruses in Animals

Surveillance

Asymptomatic and pre-symptomatic cases of SARS-CoV-1, SARS-CoV-2, and MERS-CoV in 

animals pose a risk of undetected intraspecies and interspecies infection spread. When not 

properly controlled, even detected symptomatic infections of wildlife, farmed, captive, and 

companion animals can spread due to close proximity to other infected animals, which may 

stem from changes in land use, wildlife trade, climate change, and domestic species 

introductions (e.g., establishment of farms near wildlife populations). Sufficient infection rates 

within a species increases the likelihood of spillover events. 

Emerging coronavirus infections in animals can be detected through clinical evaluations and 

monitoring as well as diagnostic tests (e.g., viral nucleic acid- and serology-based assays). 

Detection of viral nucleic acids provides active infection data, while serology assays provide 

historic data of past infections. Serology and nucleic acid assays are performed using blood and 

other biological samples (e.g., oral, nasal, respiratory, anal, and fecal swabs), respectively. To 

reduce the cost of surveillance, nucleic acid assays can also be performed on pooled biological 

samples and environmental samples (e.g., air, water, fomite surfaces).
Zoonotic Coronavirus Literature Review

Executive Summary Page 6

Surveillance strategies should be tailored to available resources and information to answer 

specific questions regarding pathogen spread. Passive surveillance strategies rely on mandatory 

or voluntary broad case reports of many different pathogens, while active surveillance 

strategies are more targeted to surveil for a specific pathogen in a specific species in a 

particular area. Syndromic surveillance can detect only pathogens that result in symptomatic 

infection and will therefore overlook asymptomatic cases. Laboratory-based surveillance is 

more resource-intensive but can detect both symptomatic and asymptomatic cases. Sentinel 

and targeted active surveillance strategies can also reduce required resources compared to 

whole population surveillance. 

Diagnostics

Current coronavirus diagnostics detect either viral nucleic acids or serum antibodies. Viral RNA 

detection methods are used to identify active infections, while serologic methods detect past 

infections. Importantly, certain detection methods may be more or less feasible, depending on 

the type of animal. Further optimization of diagnostic methods can enable surveillance of 

additional animal species.

Metagenomics techniques are used to broadly identify pathogenic nucleic acids. While these 

techniques may be appropriate for broad pathogen surveillance, they are unsuitable for highlyscaled surveillance of specific pathogens or groups of pathogens. RT-PCR amplification of 

conserved regions followed by next-generation sequencing (i.e., targeted sequencing) is used to 

detect various related betacoronaviruses. Targeted sequencing strategies for emerging 

coronaviruses most often amplify conserved RNA-dependent RNA polymerase (RdRp), while 

other strategies amplify RBD or spike. These targeted sequencing strategies have been used 

successfully in Chiropteran species, dromedary camels, Sunda pangolins, and domestic cats. 

RT-PCR for rapid and relatively inexpensive detection of emerging coronaviruses uses virusspecific primers for one or more target regions. To achieve virus-specific detection, some 

amplifications involve nested, heminested, or multiple sequence targets. SARS-CoV-1 RT-PCR 

detection strategies have been deployed in masked palm civets, while MERS-CoV RT-PCR 

detection strategies have been used in various species, including camelids, farmed ungulates, 

and Chiropterans. SARS-CoV-2 RT-PCR strategies have detected SARS-CoV-2 in domestic dogs 

and cats and white-tailed deer as well as other feline and small carnivore species. 

Serological methods used to detect emerging coronaviruses include assays that detect the 

presence of antigen-binding antibodies as well as those that detect neutralizing antibodies. 

Importantly, antibody binding does not always correlate with virus neutralization and 

immunity. In addition, highly specific antibody assays are needed because antibodies specific to 

one coronavirus may cross-react with other coronaviruses.

Enzyme-linked immunosorbent assays (ELISAs), protein microarrays, microsphere 

immunoassays (MIAs), and luciferase immunoprecipitation system (LIPS) protocols have already 

been developed and used to detect antibodies to emerging coronaviruses in animals. ELISA

methods have detected MERS-CoV antibodies in camelids; SARS-CoV-1 antibodies in palm 

civets; and SARS-CoV-2 antibodies in domestic dogs and cats, some farmed ungulate species, 
Zoonotic Coronavirus Literature Review 

Executive Summary Page 7 

some mustelids, white-tailed deer, and some small carnivores. Protein microarrays enable 

multiplexing for multiple antigens, enabling design of antibody assays with high specificity. 

Protein microarrays have detected SARS-CoV-2 antibodies in cats and in one beech marten. 

MIAs can also use multiplexing with a shorter preparation time. MIAs have detected SARS-CoV2 antibodies in domestic cats, dogs, and rabbits. LIPS is a relatively new method for antibody 

detection has only been used to detect SARS-CoV-2 antibodies in cats. 

Live virus neutralization assays (e.g., plaque reduction neutralization tests (PRNTs) and 

microneutralization assays (MNAs)), and pseudoparticle neutralization tests (ppNTs) have been 

used to detect coronavirus neutralizing antibodies in animals. Live virus neutralization assays 

require more rigorous biosafety regulations and compliance, while ppNTs and sVNTs are more 

accessible to laboratories without biosafety level 3 (BSL-3) certifications. At least one 

neutralizing assay method has successfully detected MERS-CoV antibodies in dromedary 

camels, alpacas, goats, cattle, and donkeys; SARS-CoV-1 antibodies in pigs, palm civets, raccoon 

dogs, and Chinese ferret-badgers; and SARS-CoV-2 antibodies in white-tailed deer, domestic 

cats and dogs, and some mustelid and feline species. 

Vaccines

The development of vaccines to protect susceptible host species from infections with 

coronaviruses has been at the forefront of efforts to control the spread of SARS-CoV-1, MERSCoV-1 and more recently SARS-CoV-2. Different inactivated and attenuated vaccine 

formulations as well as recombinant protein, mRNA, and DNA vaccines have been developed 

and approved for use. The S protein on the surface of coronaviruses is particularly 

immunogenic and therefore has been used in many of these vaccine formulations. 

Most vaccines have been approved only for use in humans, and very few formulations have 

been approved for use as veterinary vaccines in susceptible species such as mink, cats, and 

captive animals residing in zoos. However, vaccine studies typically involve small animal models 

as a first step to evaluate immunogenicity and antibody response; further testing and efficacy 

studies have relied on the use of NHPs such as rhesus macaques whose immune systems are 

closely related to those of humans and may therefore shed light on correlates of protection. 

Therefore, although these vaccines may not be officially approved for use in animals, they may 

still be effective and safe for use in some small animal models and NHPs. 

A major challenge in developing vaccines against coronaviruses has been the lack of durability 

of the vaccine response, as evidenced by a decrease of neutralizing titers and T cell responses. 

Continued development of vaccine formulations that offer more prolonged protection is

ongoing. In addition, emerging coronaviruses are especially prone to genetic evolution that 

enables adaptation to new hosts and evasion of the host immune response. The mutated 

viruses can often escape the immunological response generated by current vaccines, 

necessitating the continuous development of new vaccine formulations. Current vaccine 

development efforts thus focus on generating vaccines with broader protection against 

multiple variants. 
Zoonotic Coronavirus Literature Review

Executive Summary Page 8

Animal protection strategies against coronaviruses will require vaccines that can protect various 

species, including companion, farmed, captive, and wild animals from infection. Several of the 

FDA-approved and emergency use vaccines for humans are not useful for large scale 

immunization of animal species due to their expense and difficult administration. Specific 

veterinary vaccine formulations that can be rapidly disseminated during an outbreak are also 

being formulated and tested. One such vaccine is an S protein vaccine developed by Zoetis that 

has been supplied for use in animals in zoos and mink farms. 

Therapeutics

Laboratory animal models used in therapeutic efficacy studies for SARS-CoV-2, SARS-CoV-1, and 

MERS-CoV in humans provide insight on how mice, ferrets, rhesus macaques, hamsters, 

marmosets, and other similar wildlife and companion animals could be treated to reduce 

severity and transmission of these viruses. Drugs assessed in this literature review include 

antivirals that target RdRp, reverse transcriptase inhibitors, protease inhibitors, antibiotics, cas 

proteins, microbicides, antidepressants, polyphenols, aldehyde dehydrogenase inhibitors, nonstructural protein targets, fatty acid synthesis, statins, and anti-inflammatory and anti-parasitic 

drugs.

Antivirals targeting RdRp include remdesivir, molnupiravir, GS-441524, GS-621762, galidesivir, 

and favipiravir. Some of these RdRp antivirals have demonstrated efficacy against SARS-CoV-2 

in rhesus macaques, mice, ferrets, and Golden Syrian hamsters. Reverse transcriptase 

inhibitors, specifically emtricitabine-tenofovir, are effective against SARS-CoV-2 in ferrets, while 

other protease inhibitors—ensitrelvir and nirmatrelvir—were effective against this virus in mice 

and Golden Syrian hamsters. Prophylactic and therapeutic antibodies have shown efficacy in 

marmosets for MERS-CoV and hamsters for SARS-CoV-2. Drugs that target essential cellular 

processes and components of SARS-CoV-2, such as fatty acid synthesis, DNA replication, and 

cell membrane structure are effective in treating SARS-CoV-2 in rodents. 

Drugs that are effective in limiting the inflammatory response to coronaviruses include

baricitinib, loratadine, glucocorticoids, 1% astronomer sodium, and fluoxetine. Some of these 

anti-inflammatory drugs have successfully reduced SARS-CoV-2 inflammatory responses in 

rhesus macaques and some rodents. Notably, antimalarial drugs hydroxychloroquine (HCQ) and 

chloroquine were ineffective against SARS-CoV-2 in hamsters and rhesus macaques despite 

positive in vitro results. 

Biosecurity

Humans are a primary reservoir of coronaviruses, with the potential for zoonosis and 

subsequent reverse zoonosis. In addition, many species-specific coronaviruses cause respiratory 

disease and are transmitted through droplets and/or aerosol, similar to SARS-CoV-1, MERS-CoV, 

and SARS-CoV-2. Therefore, human infection prevention, not only animal biosecurity measures 

for species-specific coronaviruses, should be considered as relevant strategies for SARS-CoV-1, 

MERS-CoV, and SARS-CoV-2 animal biosecurity.
Zoonotic Coronavirus Literature Review

Executive Summary Page 9

Vaccines are one of the most effective methods for controlling the spread of infectious diseases 

from coronaviruses. However, because vaccines are currently approved only for use in humans 

and have been tested on a limited number of species, other biosecurity measures should also 

be considered, such as surveillance strategies. Surveillance of coronaviruses within animal 

populations is necessary for early viral detection and diagnosis, which can facilitate 

implementation of other biosecurity measures, such as quarantine of infected animals. 

Quarantining animals can reduce contact between animals and humans or other animals and 

should be highly prioritized to substantially reduce coronavirus exposures. Both the Centers for 

Disease Control and Prevention (CDC) and the United States Department of Agriculture (USDA) 

Animal and Plant Health Inspection Service (APHIS) provide guidance for wildlife researchers 

and farmers on reducing animal contact. In addition, USDA APHIS provides guidance on proper 

disinfection, decontamination, personal protective equipment (PPE) usage, and carcass 

disposal, all of which can significantly reduce viral spread.

Other biosecurity measures for consideration include modifying land use and policy on live 

markets and trade. Land use changes (e.g., logging, mining) can alter the movement of wildlife 

and create new habitats for species, allowing contact between previously isolated species.

Reducing land use changes can help keep ecosystems with high species diversity intact, leading 

to enhanced wildlife immune function and prevention of high viral prevalence and 

transmission. In addition, policy changes for live animal markets can reduce viral transmission 

between animals that are otherwise isolated from each other, and thus reduce the emergence 

of novel recombinant viruses. Depopulation/culling of coronavirus-positive animals is not 

recommended as a biosecurity measure because this method raises ethical concerns for both 

animal rights and welfare.
Report Page 10

Report 

Introduction 

On March 11, 2021, President Joseph R. Biden, Jr. signed the American Rescue Plan Act of 2021 

(ARP), a $1.9 trillion COVID-19 stimulus plan, into law. Under the Act, the U.S. Department of 

Agriculture (USDA) was provided $300 million to conduct monitoring and surveillance of 

susceptible animal species for incidence of SARS-CoV-2 and designated the Animal and Plant 

Health Inspection Service (APHIS) as the lead Agency in this charge.

In response, APHIS developed a Strategic Framework focused on actions to prevent, detect, 

investigate, and respond to new and emerging zoonotic disease threats including SARS-CoV-2. A 

key component of APHIS’ effort is acknowledging known gaps in its current One Health 

infrastructure and identifying specific actions to address them. 

To meet the charge set by Congress, APHIS must understand how SARS-CoV-2 moves between 

people and animals as well as how to take a One Health approach to the problems the global 

SARS-CoV-2 pandemic has highlighted. This understanding includes a need to learn more about 

the virus, which animals it affects, and how it is spreading to new locations or species, as well as 

other potential emerging coronaviruses that could pose a threat to both people and animals. 

As a first step in this work, APHIS commissioned a research report on emerging zoonotic 

coronaviruses based on scientific literature, other publications, and outreach to researchers. 

The scope of the report extended across any research deemed vital in the fields of biology and 

disease control, including surveillance, virology, diagnostics, pathogenesis, immunology, 

vaccinology, and epidemiology, concerning SARS-CoV-2 and other potential emerging 

coronaviruses that could pose a threat to both people and animals. This report is a first step 

toward a gap analysis that will determine where APHIS can optimize its efforts to meet the 

priorities set forth in its Strategic Framework. Such an analysis will add validity to the ARP 

projects, provide context for future decision-making, and advance APHIS’ ability to quantify and 

predict zoonotic disease dynamics and human risk.

Approach

This literature review was conducted in the PubMed (https://pubmed.ncbi.nlm.nih.gov/) and 

SCOPUS (https://www.scopus.com/) databases, using the search terms “SARS-CoV-2,” OR 

“SARS-CoV-1”, OR “MERS” combined with MeSH terms focusing on the prioritized research 

categories. Results were limited to studies that were published in English and that addressed 

research in non-human animal species (initial searches were not limited by date because the 

relative recency of the viruses created natural date ranges). This search returned a list of 2,883 

papers. These papers were manually screened for relevance to SARS-CoV-1, MERS-CoV, or 

SARS-CoV-2 (e.g., that those viruses were not mere context or analogies). The remaining papers 

were allocated to the following topic areas and reviewed in detail to develop this report.
Report Page 11

Table 1: Literature Search Results Categorization

Research Category Papers (n)

Epidemiology 469

Molecular Biology and 

Virology

128

Immunology 136

Pathogenesis 135

Surveillance 29

Diagnostics 168

Vaccines 123

Therapeutics 50

Biosecurity 20

Total 1,258

These studies formed the main structure of the report and were supplemented by 140 recently 

published studies identified as the literature review progressed and through participation in the 

May 2023 International Conference on Livestock, Companion Animals and Wildlife 

Coronaviruses. Additional literature searches were performed during writing to provide 

appropriate citation for all material and, where needed, useful background. Studies were 

selected for inclusion based on the authors’ impressions of their relevance and quality to the 

goals of controlling emerging zoonotic coronaviruses. More recent studies were given priority 

within the report. In total, 817 studies are referenced herein.

This review aimed primarily to define trends in the coronavirus literature to inform subsequent 

identification of knowledge gaps at an APHIS-sponsored workshop taking place in 2023. The 

literature review thus focuses on presenting both well-established patterns across the literature 

and novel findings that require further investigation. 

Interpretation of literature review results and definition of trends was aided by conversations 

with coronavirus researchers and experts who were contacted by email and invited to 

participate in brief interviews about trends in SARS-CoV-1, MERS-CoV, SARS-CoV-2, or pancoronavirus research. These individuals were selected from participation in the National 

Institutes of Health Tracking Resistance and Coronavirus Evolution (TRACE) Working Group, 

through presentation at a related conference, or through being among the list of most prolific 

authors within the “SARS-CoV-2,” or “SARS-CoV-1,” or “MERS” database search (defined as 
Report Page 12

having contributed to at least 3 of the publications selected for inclusion in the review). 

Information provided by these researchers and experts is incorporated only as corroborated by 

independent citations within the appropriate report sections.

Epidemiology

Coronavirus Ecology

Reservoirs

Chiropterans as Reservoirs for Related Coronaviruses

The origins of emerging coronaviruses of interest, including SARS-CoV-1, MERS-CoV, and SARSCoV-2, can be bioinformatically traced back to various species of the order Chiroptera.5,6

Chiropteran immune systems support long-term, asymptomatic viral infections through two 

main mechanisms: (1) viral host receptors lacking full compatibility with some viruses and (2) 

constitutive expression of interferon alpha (IFN-α).7–11 While constitutive expression of IFN-α 

would trigger detrimental inflammatory responses in other mammals, Chiropterans appear 

unaffected; other research groups have hypothesized that this adaptation increases 

Chiropteran tolerance to increased DNA damage during prolonged flights.12–16 Chiropterans are 

often co-infected with multiple viruses, which enables recombination events and the potential 

creation of novel viruses with broader species tropisms.17 Researchers have recently 

recapitulated these characteristics of viral propagation in Chiropteran cell lines.18

Certain Chiropteran social behaviors further facilitate the propagation of viral pathogens. 

Chiropterans reside in close quarters with their colony mates, and breeding and migration can 

affect their proximity to one another.19–21 In addition, Chiropteran echolocation is produced 

from vibrations that may trigger airborne release of viral pathogens.20,21 The unique 

combination of high-density social behaviors and immune system characteristics of 

Chiropterans makes these mammals a large reservoir of coronaviruses, along with other 

potentially zoonotic pathogens.

SARS-related (SARSr) and MERS-related (MERSr) viral RNAs have been detected in Chiropterans, 

and some Chiropterans have tested positive for SARSr or MERSr antibodies (Table 2). Most 

prevalence studies of Chiropterans included in this review assayed for viral RNA, and a minority 

of studies tested for relevant antibodies. Evidence of SARSr infections in Chiropterans was 

detected in Australia,22,23 Bulgaria,24 Cambodia,25 China,5,26–34 Japan,35 Laos,36 Nigeria,37 and 

Vietnam,38 while evidence of MERSr was detected in Australia,23 China,39–42 Italy,43 Saudi Arabia,

44

South Africa,45,46 Switzerland,47 and Thailand.

48 Other betacoronavirus RNAs were previously 

detected in Ethiopia,49 Ghana,50 Romania,50 and Ukraine.50 Notably, the Rhinolophus genus 

frequently tested positive for SARSr infections.5,25–33,51

Table 2: Locations of Chiropterans Infected with Emerging Coronaviruses

Virus Location Species

SARSr Australia22,23 Rhinonicteris aurantia22
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Austronomous australis23**

Chalinolobus gouldii23**

Chalinolobus morio23**

Nyctophilus gouldi23**

Nyctophilus major23**

Vespadelus regulus23**

Bulgaria24

Rhinolophus blasii24

Rhinolophus euryale24

Rhinolophus ferrumequinum24

Rhinolophus mehelyi24

Cambodia25 Rhinolophus shameli25

China5,26

–34

Rhinolophus ferrumequinum5,26

–28

Rhinolophus macrotis5,27

–29*

 

Rhinolophus pearsoni

5*

Rhinolophus affinis26,30

Rhinolophus sinicus26,28,31

–33

Miniopterus schreibersi34

Aselliscus stoliczkanus26

Rhinolophus marshalli29

Rhinolophus pusillus29,51

*

Rhinolophus thomasi29

Chaerephon plicatus51

Rousettus leschenaulti

5**

Japan35 Rhinolophus cornutus35

Laos36

Rhinolophus malayanus36

Rhinolophus marshalli36

Rhinolophus pusillus36

Nigeria37 Hipposideros commersoni37

Vietnam38 Rhinolophus acuminatus38

MERSr

Australia23

Chalinolobus gouldii23**

Chalinolobus morio23**

Vespadelus regulus23**

China39

–42

Vespertilio superans39

–41

Ia io40

Pipistrellus abramus40

Pipistrellus pipistrellus40

Hypsugo pulveratus42

Italy43 Eptesicus serotinus43

Saudi Arabia44 Taphozous perforates44

South Africa45,46 Neoromicia zuluensis45

Neromicia capensis46

Switzerland47 Vespertilio murinus47

Thailand48 Tadarida plicata48

Other 

Betacoronaviruses

Ethiopia49

Chaerephon pumilus49

Neoromicia somalica49

Rhinopoma hardwickii49

Ghana50 Nycteris gambiensis50

Romania50

Pipistrellus nathusii50

Pipistrellus pipistrellus50

Pipistrellus pygmaeus50
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Ukraine50 Pipistrellus nathusii50

* Detected via viral RNA and serology. ** Only detected via serology.

Dromedaries

A large proportion of dromedary camels (Camelus dromedarius) in the Middle East and parts of 

Africa are currently or have been previously infected with MERS-CoV, particularly in larger 

herds.52–56 However, C. dromedarius MERS-CoV-specific antibodies are short-lived, resulting in 

potential reinfections;57 for example, approximately 25% of C. dromedarius calves had been 

reinfected with MERS-CoV.58 Trade routes and import and export of C. dromedarius impact the 

spread of MERS-CoV in different Middle Eastern and African geographies.56 

MERS-CoV RNA surveillance studies have identified active infections in C. dromedarius in 

Burkina Faso,54 Djibouti,59 Egypt,53,60 Ethiopia,54 Kenya,58,61 Morocco,54 Oman,62 Qatar,63,64 Saudi 

Arabia,59,65–68 Somalia,65 Sudan,59,65 Tunisia,69 and United Arab Emirates (Table 3).70 Notably, a 

surveillance study in Egypt identified much higher rates of infection in camels located on farms 

or in slaughterhouses compared to those in live animal markets or raised in free herds.53 

Table 3: Rates of MERS-CoV Infection in Camelus dromedarius

Country Rate of Infection

Burkina Faso 5%54

Djibouti 11%59

Egypt 4%60

15%53

Ethiopia 10%54

Kenya <1%61

34%58*

Morocco 2%54

Oman 100%62**

Qatar 59%63

21%64

Saudi Arabia 15%65

13%59

3%66

45%67

25%68

Somalia 7%65

Sudan 6%65

14%59

Tunisia 80%69

United Arab Emirates 5%70

*Calves only.

**Camels with respiratory symptoms.
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Masked Palm Civets

SARS-CoV-1 has been traced back to spillover from bats to the masked palm civet (Paguma 

larvata).71,72 P. larvata likely experience asymptomatic SARS-CoV-1 infections73 and are thought 

to have transmitted SARS-CoV-1 to humans during human–animal contacts during wildlife 

farming practices and at wet markets.74–77 Consistent with detection of SARS-CoV-1 RNA and 

antibodies in P. larvata, in vitro experiments have shown that exogenous masked palm civet 

angiotensin-converting enzyme 2 (ACE2) supports SARS-CoV viral entry.78 Although SARS-CoV-2 

infections have not been detected in P. larvata, a variety of in silico predictive studies of 

infection risk, including modeling of ACE2-receptor binding domain (RBD) binding79–85 and ACE2 

homology,80,83–98 as well as exogenous in vitro viral entry studies,91,95–97,99,100 suggest that P. 

larvata may be susceptible to SARS-CoV-2 infection. 

Raccoon Dogs

Similar to P. larvata, raccoon dogs (Nyctereutes procyonoides) at live animal markets tested 

positive for SARS-CoV-1 infection.75,101 In addition, in vitro experiments have shown that 

exogenous N. procyonoides ACE2 supports SARS-CoV viral entry.78 

N. procyonoides may also be susceptible to SARS-CoV-2 infection based on in silico analysis of 

ACE2 homology83,86,87,89,91,96 and predictive ACE2-RBD binding.82,83 In vitro experiments 

exogenously expressing N. procyonoides ACE2 demonstrated that this viral receptor can 

support both ACE2-RBD binding91 of SARS-CoV-2 as well as viral entry.91,96 Althogh N. 

procyonoides can also be experimentally infected with SARS-CoV-2 and transmit the virus to 

other N. procyonoides via direct contact,102 no evidence of SARS-CoV-2 infection was detected 

in 11 N. procyonoides in Germany.103 More definitive prevalence studies are needed to 

determine whether N. procyonoides significantly contribute to the spread of SARS-CoV-2. 

Candidate Reservoirs for SARS-CoV-2 

The animal reservoir for SARS-CoV-2 remains unknown, with evidence suggesting snakes or 

pangolins as candidate reservoirs. Sequence analysis and relative synonymous codon usage 

(RSCU) biases suggested snake as a potential SARS-CoV-2 reservoir. RSCU biases for the manybanded krait (Bungarus multicinctus) and Chinese cobra (Naja atra) were more similar to SARSCoV-2 than the Chinese rufous horseshoe bat (Rhinolophus sinicus), chicken (Gallus gallus), 

Sunda pangolin (Manis javanica), and the European hedgehog (Erinaceus europaeus).

17

However, multiple research groups strongly disagree that RSCU analysis was sufficient to 

identify B. multicinctus and N. atra as potential SARS-CoV-2 reservoirs.104,105 SARS-CoV-2 has 

also not been identified in any snake species.

While closely related viruses (e.g., RaTG13) circulate in Chiropterans, these viruses still lack 

critical features present in SARS-CoV-2, including a furin cleavage site at the S1/S2 junction. This 

furin cleavage site facilitates conformational changes to promote interaction with ACE2. 

Researchers have suggested that SARS-CoV-2 arose after recombination events between 

RaTG13 and another coronavirus containing the furin cleavage site.106,107 Other coronaviruses 
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containing sites recognized by furins include MERS-CoV108,109 and bovine coronavirus (BovCoV).110 

SARS-CoV-2 viruses detected in other species also lack this furin cleavage site. M. javanica was 

previously suspected as a SARS-CoV-2 reservoir, but sequence analysis confirmed the absence 

of this furin cleavage site, and further evolutionary analysis indicated that RaTG13 from 

Chiropterans was more closely related to SARS-CoV-2 than pangolin coronaviruses.107 The origin 

of this furin cleavage site remains unclear but may provide further insight into potential SARSCoV-2 reservoirs. 

Potential Future Reservoir for SARS-CoV-2: Mustelids

Multiple countries have reported SARS-CoV-2 outbreaks on American mink (Neogale vison) 

farms, including those in Canada,111 Denmark,112,113 France,114 Greece,111 Italy,115 Lithuania,111

Netherlands,116–118 Poland,119 Spain,120 Sweden,111 and United States.

121–123 These outbreaks 

likely originated from humans working on these farms,

124 and spillover events likely occurred 

from farmed N. vison to wild N. vison121 as well as cats (Felis catus) and possibly dogs (Canis 

lupus familiaris) residing nearby.125,126 As a result of N. vison infections on farms, the Danish 

government opted to depopulate infected farms, institute mandatory reporting of symptoms, 

and quarantine and disinfect infected farms.127 Because of its susceptibility and transmission 

among populations, N. vison may become a SARS-CoV-2 reservoir with global impact, as 

millions of N. vison are farmed across China, Europe, North America, and Russia.128

SARS-CoV-2 viral RNA has also been detected in other mustelids, particularly in Spain, including 

ferrets (Mustela putorius furo),129 and Eurasian river otters (Lutra lutra).130 Previous SARS-CoV-2 

infections are likely in mustelids as indicated by antibody detection in European pine martens

(Martes martes) and European badgers (Meles meles) in France131 and M. purotrius furo in 

Spain.132 Further research is required to determine whether farmed and wild mustelids have 

the potential to become SARS-CoV-2 reservoirs. 

Possible Modes of Coronavirus Transmission

Airborne Droplets

Coronaviruses are often spread through airborne droplets, and the distance a virus can travel 

depends on external environmental factors, including air flow, temperature, and humidity.133–

138 Colder temperatures paired with either low or high levels of relative humidity promote 

overall coronavirus stability.138,139 This stability of coronaviruses within droplets can therefore 

dictate maximum transmission distances. Therefore, transmission of coronaviruses among 

animals under human care and captive wildlife may depend on their housing conditions, 

including population density. 

Animals with the potential to transmit coronaviruses via airborne droplets will likely shed 

coronavirus oronasally. Detection of viral RNA in oropharyngeal or oronasal swabs is often used 
Report Page 17

as a readout for viral shedding as well as a common diagnostic tool (see “Diagnostics” for more 

details).

Fomites

Extensive prior research has demonstrated that MERS-CoV can survive on both plastic and steel 

surfaces for more than 48 hours, which may play a critical role in transmission, at least among 

humans.140–146 SARS-CoV-1 RNA can be detected on hospital surfaces near infected patients, 

and computational modeling suggests that fomite transmission has contributed to previous 

outbreaks of SARS-CoV-1 among humans.147,148 Although fomite transmission of SARS-CoV-2 

has been overshadowed by the threat of airborne transmission, replication-competent SARSCoV-2 is detectable on fomites; however, infectivity of SARS-CoV-2 on fomites is poorly 

understood.149 Similar to viruses in droplets, the stability of coronaviruses on fomites can be 

influenced by environmental conditions.139 Animals shedding coronaviruses via any route (e.g., 

oronasal, ocular, fecal) can contaminate nearby fomites, resulting in intraspecies and possibly 

interspecies transmission. 

Feces

Recently, surveillance efforts of SARS-CoV-2 have transitioned from clinical sampling to 

wastewater sampling. SARS-CoV-2 RNA is readily detectable in wastewater as well as fecal 

samples isolated from various species, but little is known about whether live, infectious SARSCoV-1, MERS-CoV, or SARS-CoV-2 can survive digestion. Although previous research has shown 

that SARS-CoV-1 is inactivated by gastric juices, live coronaviruses have been occasionally 

isolated from fecal swabs.150 Researchers have proposed that certain gastrointestinal

conditions that reduce gastric pH may enable survival of SARS-CoV-2 in the stomach.151,152

MERS-CoV can survive and retain infectivity following passage through the human digestive 

tract.153 In addition, SARS-CoV-1 has been isolated once from a farmed pig (Sus scrofa) fecal 

sample154 and twice from fecal/anal swabs from R. sinicus.

155,156 Consistent with the potential of 

fecal shedding of SARS-CoV-1 and SARS-CoV-2, the corresponding viral host receptor, ACE2, is 

expressed in the gastrointestinal tract of S. scrofa,

157,158 F. catus,159 tiger (Panthera tigris),158,159

lion (Panthera leo), Eurasian lynx (Lynx lynx), common marmoset (Callithrix jacchus), gorilla 

(Gorilla gorilla), golden-headed lion tamarin (Leontopithecus chrysomelas), horse (Equus 

caballus), and sheep (Ovis aries).158

If emerging coronaviruses can indeed survive digestion, inadequate wastewater treatment 

could result in live coronavirus contamination of coastal waters, although coronaviruses may 

not survive certain aquatic conditions at sufficient concentrations for transmission.160–164 Some 

respiratory viruses (e.g., cetacean morbillivirus) can transmit from terrestrial animals to 

pinnipeds, and from pinnipeds to cetaceans for sustained circulation.165 

Animal Products

Some animal species that can contract and transmit SARS-CoV-1, MERS-CoV, or SARS-CoV-2 are 

common livestock species raised for meat and other animal products, such as milk. Although 
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MERS-CoV RNA is detectable in camel milk, further research has not adequately determined 

whether milk from an infected camel can transmit MERS-CoV.166,167 China’s Centers for Disease 

Control reported on tracing efforts that linked a SARS-CoV-2 outbreak to seafood products in 

2020.168 A recent study investigated the stability of SARS-CoV-2 in meat, poultry, and seafood 

via multiple surrogates: murine hepatitis virus (MHV), transmissible gastroenteritis virus (TGEV), 

and phi 6 RNA bacteriophage. At least one surrogate was detectable in both refrigerated and 

frozen meat, poultry, and seafood after 30 days of storage. Post-isolation, these viral particles 

were likely infectious, because cell culture assays resulted in cytopathic effects.169 In addition, a 

recent study demonstrated that SARS-CoV-2 spike (S) protein could bioaccumulate in Pacific 

oysters; this finding, combined with frequent detection of SARS-CoV-2 RNA in wastewater, 

indicates that oysters have the potential to transmit SARS-CoV-2.170 Further research is required 

to determine whether viral particles detected in animal products retain their infectivity and are 

present at high enough concentrations to successfully infect a host after consumption. 

Arthropods

Although coronavirus-like organisms have been identified in sea bird tick and cat fleas,171,172

arthropods likely do not biologically or mechanically transmit coronaviruses. Despite expression 

of SARS-CoV-2 host receptors in ticks (Ixodes scapularis and Ixodes ricinus) and cat fleas 

(Ctenocephalides felis),172–176 extensive epidemiological studies of wild-caught arthropods did 

not detect SARS-CoV-2 in mosquitoes (i.e., Anopheles and Culex species), as well as arthropods 

from the following taxonomic families: Asilidae (robber flies), Blattidae (cockroaches), 

Calliphoridae (blow flies), Ulidiidae (picture-winged flies), Dolichopodidae (long-legged flies), 

Drosophilidae (pomace flies), Muscidae (houseflies), Phoridae (hump-backed flies), Psychodidae 

(drain flies), Sarcophagidae (flesh flies, Syrphidae (hoverflies), and Tabanidae (horse flies).177,178

In addition, no MERS-CoV RNA was detected in Hyalomma dromedarii (camel ticks) that 

previously fed on infected dromedary camels.179 Researchers in laboratory settings have 

attempted to infect arthropod species to assess their potential for transmission of SARS-CoV-2; 

mosquitoes, houseflies (Musca domestica) and midges (Culicoides sonorensis) cannot 

mechanically or biologically transmit SARS-CoV-2 in this setting.180–183 Notably, computation 

modeling of ectoparasite ACE predicted that body louse, deer tick, and water flea ACE can bind 

SARS-CoV-2 RBD.176 

Mechanisms of Coronavirus Evolution

As coronaviruses continue to evolve, mutations may arise that affect their infectivity, 

transmissibility, severity, and species tropism. Notably, SARS-CoVs have a high level of genetic 

diversity and rate of recombination, which increases the likelihood of cross-species 

transmission and expanded species tropism.184 These intrinsic aspects of SARS-CoVs, paired 

with the unique Chiropteran immune system (see “Chiropterans” for more details) can facilitate 

the rapid development of viral threats to other species. For example, researchers suggest that 

multiple recombination events involving Bat-CoV-RaTG13 resulted in SARS-CoV-2 containing the 

S1/S2 cleavage site seen in humans.185 
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The mutation rate of RNA viruses Is relatively high compared to other pathogens because of the 

absence of the corrective function of RNA-dependent RNA polymerase.74 In addition, because 

of their larger genomes, coronaviruses are more tolerant of deletion mutations compared to 

other pathogens.186 Indeed, the evolutionary rates of SARS-CoV-1, MERS-CoV, and SARS-CoV-2 

are similarly high at a magnitude of 10-3 mutations per site per year.187–190 However, these 

evolutionary rates are not evenly distributed; the SARS-CoV-2 spike gene has a higher 

evolutionary rate compared to the rest of its genome.191 Mutation acquisition has expanded 

SARS-CoV-2’s species tropism to include mouse (Mus musculus) and N. vison.

192

The presence and activity of certain host innate immune proteins may be impacting the types 

of mutations seen in SARS-CoV-2. After detecting an overabundance of C-to-U mutations in 

SARS-CoV-2, researchers proposed a model by which two classes of innate immune proteins—

adenosine deaminases acting on RNAs (ADARs) and apolipoprotein B mRNA editing enzyme, 

catalytic polypeptides (APOBECs)—induce point mutations in foreign genetic material, including 

SARS-CoV-2 to create a C-to-U mutational bias, impacting the virus’s evolution.193–196

Evidence Types for Determining Species Susceptibility

This section summarizes the evidence types commonly described in the emerging coronavirus 

epidemiology literature. The contexts of different evidence types should be considered when 

making determinations about the vulnerability of a particular species to coronavirus infection; 

for example, exogenous expression of a viral host factor in vitro may not recapitulate natural 

infection risk in vivo of a particular species. A combination of evidence types can help identify 

species at risk for coronavirus infection, which are identified in the “Species Interfaces Relevant 

to Coronavirus Transmission” section. 

Risk of Interspecies Exposure

Various species-intrinsic and species-extrinsic factors place certain species at risk of exposure to 

emerging coronaviruses. 

Species-Intrinsic Factors

Species that prey on various Chiropterans may be at higher risk for contracting coronavirus 

infections due to direct interspecies contacts, while highly social species and those living in 

dense groups may also be at high risk for contracting coronavirus infections due to direct 

intraspecies contacts.197 Although birds that prey on Chiropterans have tested positive for 

betacoronaviruses,1 these have not been identified as closely related to SARS-CoV-1, MERSCoV, or SARS-CoV-2.198 In addition, social grooming behaviors in Japanese macaques (Macaca 

fuscata yakui) facilitate transmission of parasitic infections.199 Mating behaviors and seasonality 

can also impact direct contact between farmed and wild animals of the same species. For 

example, wild boar and farmed pig mating interactions may have caused a brucellosis spillover 

event.200

1 Avian species are mainly hosts for deltacoronaviruses and gammacoronaviruses, not betacoronaviruses. 
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Species-Extrinsic Factors

Legal and illegal wildlife trade bring various species in direct contact that would not otherwise 

meet in natural conditions.201–203 Interspecies contacts have also been disrupted over time due 

to habitat loss204 and agricultural practices that increase contact between livestock and 

wildlife.205 For example, in Malaysia and Singapore, farmed pigs were sometimes housed near 

fruit trees that attracted flying foxes (Pteropus spp.) that carry Nipah virus. This close contact 

resulted in transmission of Nipah virus from bats to farmed pigs and then to humans.206,207 In 

addition, computational modeling has suggested that transmission of Hendra virus from black 

flying foxes (Pteropus alecto) to E. caballus occurs through prolonged exposure to 

contaminated urine at the base of bat tree roosts.207,208 In both instances, adjustments to 

farming practices dramatically reduced interspecies contacts and viral spread.206–208

Ongoing climate change can also drastically affect virus transmissibility139 as well as animal life 

cycles.209 Changes in temperature and humidity can impact the transmissibility of coronaviruses 

via different routes (see “Possible Modes of Coronavirus Transmission”). Climate change greatly 

impacts seasonality across the globe, which has already been shown to impact interspecies 

interactions facilitated by factors such as migratory patterns,210 foraging and predation,211 and 

lifecycle synchronicity.209,212 

Expression of Coronavirus Host Factors

Specific host factors are required for efficient viral entry of different viruses. Although 

expression of host factors can be used to predict species susceptibility and routes of 

transmission, expression of canonical viral host factors may not be sufficient to accurately 

predict host susceptibility.213 Expression and function of other host factors should be 

considered, among other evidence types. For further information on the molecular mechanisms 

of coronavirus host factors, see “Molecular Biology and Virology.” 

Receptors

ACE2 serves as the canonical viral receptor for SARS-CoV-1 and SARS-CoV-2,214,215 while 

dipeptidyl peptidase-4 (DPP4) is the main viral receptor for MERS-CoV.216 Because these 

receptors play major roles in facilitating viral entry, many research articles investigated the 

expression levels and patterns of these proteins as part of assessing potential risk of infection in 

different species. In addition, some species express soluble extracellular domain isoforms of 

ACE2 that do not support RBD binding and viral entry.217,218 A soluble extracellular domain of 

DPP4 has been extensively studied in the context of metabolic diseases and cancer, but it is 

unclear whether this form of DPP4 is due to alternative splicing or protein cleavage events.219

However, a soluble form of DPP4 likely does not support viral entry because of a lack of 

tethering to cells. 

In the absence of canonical viral receptors, coronaviruses may use alternative receptors to 

infect cells. Notably, species susceptibility research has not thoroughly investigated the 

expression of these alternative receptors and their relation to susceptibility to coronaviruses. 

Dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) and 
Report Page 21

liver/lymph node-specific intracellular adhesion molecules-3-grabbing non-integrin (L-SIGN) 

(i.e., C-type lectins)220–223 as well as T-cell immunoglobulin and mucin domain 1 (TIM1)220,224 and 

AXL220,225 can support SARS-CoV-2 viral entry in vitro; however further research has indicated 

that these proteins cannot support SARS-CoV-2 viral entry in the absence of ACE2.220,226,227

Therefore, although expression of C-type lectins, TIM1, and AXL are not sufficient to assess 

whether a species is susceptible to SARS-CoV-1 or SARS-CoV-2 infection, the presence of these 

factors may still improve the rate of viral entry. Another proposed alternative receptor for 

SARS-CoVs, cluster of differentiation 147 (CD147), cannot directly bind to the spike (S) protein 

of SARS-CoV-2, and therefore likely also does not support viral entry in the absence of 

ACE2.220,228–230 In addition, neuropilin 1 (NRP1) enhances transmembrane protease, serine 2 

(TMPRSS2)-dependent SARS-CoV-2 entry231,232 and has been proposed to form a complex with 

ACE2 and SARS-CoV-2.233 No additional research indicates that NRP1 can facilitate ACE2-

dependent viral entry. 

A recent genomic receptor screen identified 12 proteins with affinity for SARS-CoV-2. Of these 

proteins, Kremen1 and ASGR1 supported SARS-CoV-2 viral entry independent from ACE2 in 

vitro and in mice. Notably, both of these alternative receptors did not support viral entry of 

SARS-CoV-1 or MERS-CoV in the absence of ACE2. In addition, the presence of Kremen1 or 

asialoglycoprotein receptor 1 (ASGR1) on certain cell types correlated with cellular 

susceptibility to SARS-CoV-2 infection.234 Therefore, further research on the expression of 

Kremen1 and ASGR1 may provide additional information on the susceptibility of different 

species to SARS-CoV-2 infection.

Proteases

Prior to viral entry, host cell proteases are required to cleave S protein of SARS-CoV-1 or SARSCoV-2. Both SARS-CoVs contain two cleavage sites; SARS-CoV-2 contains a furin cleavage site 

and a site cleaved either by TMPRSS2 or cathepsin L, while SARS-CoV-1 contains two cleavage 

sites, both of which are cleaved by TMPRSS2 or cathepsin L.235–237 Other serine proteases help 

promote infection by respiratory viruses in airway cells, and additional research may identify 

specific proteases that may indicate increased susceptibility to infection.220,238 

Computational Modeling of Host Factors

Computational modeling methods have been used extensively to predict species susceptibility 

to SARS-CoV-2, but not SARS-CoV-1 or MERS-CoV. The main modeling strategies present in the 

literature are protein sequence alignments, ACE2-RBD docking simulations, and molecular 

dynamics simulations. 

Protein Sequence Alignments

ACE2 protein sequence alignment data available in current literature were generated using 

versions of Clustal,83,87,90,92,93,96,98,239–246 Multiple Sequence Comparison by Log- Expectation 

(MUSCLE),90,93,247–251 Multiple Alignment using Fast Fourier Transform 

(MAFFT),82,84,85,252,253,253,254 BioEdit,94,255 Molecular Evolutionary Genetics Analysis 

(MEGA),250,256–259 Constraint-based Multiple Alignment Tool (COBALT),93 and Basic Local 
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Alignment Search Tool (BLAST).260 Importantly, the types and locations of amino acid 

substitutions likely have different effects on ACE2-RBD binding, and individual substitutions 

should ultimately be considered within the context of the full ACE2 protein. 

Docking Simulations

ACE2-RBD docking simulation data in the current literature were generated using combinations 

of High Ambiguity Driven protein-protein DOCKing (HADDOCK),82,84,255,260,261 AlphaFold,85

Rosetta,247,251,253,253 Iterative Threading ASSEmbly Refinement (I-TASSER),85,87,258,260 Modeller,81–

85,239,243,245,257,261 Proteins, Interfaces, Structures and Assemblies (PISA),85 SWISSMODEL,79,80,86,94,241,242,244,246,256,259,262 Chimera,89,90,93,241,256,261 Phyre2,

96,98 HDOCK,81,242,246 Global 

Range Molecular Matching X (GRAMM-X),244 PyMOL,88,90 ClusPro,259 PRISM,258 and Visual 

Molecular Dynamics.240 Most docking simulations were based on the X-ray crystallography 

structures of human ACE2-RBD. These data were used to predict the capacity for binding of 

SARS-CoV-2 RBD by ACE2 from various species.

Molecular Dynamics Simulations

Molecular dynamics simulations have been used to determine the potential stability of ACE2-

RBD complexes using GROMACS,80,81,239,242,255,262 Visual Molecular Dynamics,241 AMBER,79,243,257

and Desmond.241 Researchers have posited that more stable ACE2-RBD interactions are 

predictive of infection susceptibility.

In Vitro Experimental Infection Capacity

Multiple in vitro assays have been used to assess species susceptibility to coronavirus infection: 

host receptor-virus binding, viral entry, and viral replication. These assays were performed 

either in non-permissive cells overexpressing ACE2 (i.e., exogenous) or cell lines derived from 

the species of interest (i.e., endogenous). Although in vitro assay results do not always 

recapitulate in vivo risks of infection, these assays can be useful for rapid screening of multiple 

species.

In Vivo Experimental Infection Capacity

Experimental infections of live animals have been used to identify species capable of sustaining 

coronavirus infection. Although these infection experiments are performed in live animals, the 

viral titers and routes of infection may not reflect real-world coronavirus exposures. In addition, 

experimental infection studies may not be feasible in larger animals. Oral and nasal inoculations 

more closely mimic respiratory virus exposures than intratracheal and intravenous inoculations. 

In Vivo Experimental Transmission Studies

Experimental transmission studies of live animals have been used to determine (1) whether a 

species sheds sufficient viral loads to infect another, co-housed animal and (2) the level of 

contact between animals required for viral transmission. For example, SARS-CoV-2 transmitted 

from separately housed, infected ferrets to naïve ferrets via shared airflow at distances greater 

than 1 meter, indicating the possibility of airborne transmission among M. putorius furo.

263
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Although these transmission studies require a large number of animals and specialized housing, 

they can closely recapitulate real-world infection and transmission scenarios. 

Detection of Natural Infections

Active and past infections can be detected through viral RNA detection methods and serological 

methods, respectively. Positive coronavirus RNA and antibody assay results from a particular 

species indicate a risk of infection in other animals of the same species. Detection of viral RNA 

is indicative of active infection, while detection of specific antibodies suggests previous 

infection. Specific methods for detecting viral RNA and antibodies are described in detail in 

“Diagnostics.” 

Species Interfaces Relevant to Coronavirus Transmission

Interactions with Chiropterans

Because Chiropterans harbor a wide variety of viruses (see “Chiropterans as Reservoirs for 

Related Coronaviruses”), animals in close contact with them are at risk for zoonotic spillover 

events. One such contact event is predation of Chiropterans. Although most specialized 

predators of bats are birds264 (e.g., bat hawk [Macheiramphus alcinus]

265–267 and bat falcons 

[Falco rufigularis]

268), opportunistic predators include other raptors264,269–273 as well as raccoons 

(Procyon lotor),274,275 F. catus,

276 Cebidae monkeys,277–279 Cercopithecus monkeys,280 otters 

(Lutra lutra),281 N. vison,

282 long-tailed weasels (Neogale frenata),283 and Siberian weasels 

(Mustela sibirica).284 Another contact event involves exposure of animals to Chiropteran saliva, 

which is known to spread various Chiropteran viruses such as rabies, lyssavirus, Hendra virus, 

and Nipah virus. Animals that have contracted viruses originating from Chiropterans include E. 

caballus,

285–287 mules (Equus mulus),288 donkeys (Equus asinus),288 goats (Capra hircus),288 O. 

aries,

286,288 S. scrofa,288,289 C. lupus familiaris,288 poultry,288 F. catus,286,288,290 Vulpes vulpes,286

skunks (Mephitis mephitis),286,291 cows (Bos taurus),286 and stone martens (Martes foina).292

These spillover events indicate close contacts, and therefore animals that have contracted 

Chiropteran viruses are at risk for future spillover events of coronaviruses. The susceptibilities 

of these species (i.e., avian, mustelid, NHP, and farmed ungulate species) to SARS-CoV-1, MERSCoV, and SARS-CoV-2 are outlined below, and susceptibilities of companion animals are 

outlined in “Interactions with Humans.” 

Avian Susceptibility

Avian species that prey on Chiropterans have tested positive for betacoronaviruses, despite 

normally only contracting gamma- and deltacoronaviruses.198 However, most computational 

modeling data predicted low susceptibility of avian species, which is consistent with the 

inability to infect avians in vivo and in vitro. Computational modeling data of 94 avian species 

analyzed across 19 computational modeling publications are summarized in Table 4. Very few 

publications reported any avian species with ACE2-RBD affinity comparable to humans except 

for Kaushik et al., 2022 and Fischhoff et al., 2021. 
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Table 4: Summary of Computational Modeling Data on Avian Susceptibility to SARS-CoV-2

Evidence Types

Species Common 

Name

ACE2 Homology ACE2-RBD Affinity ACE2-RBD Molecular 

Dynamics

Accipiter nisus Eurasian 

sparrowhawk

Low245 Low245 Not assessed

Amazona collaria Yellow-billed 

amazon

Low245 Low245 Not assessed

Anas platyrhynchos Mallard Low83,84,86,87,93,245,250,257 Low82–85,244,245,257 Not assessed

Anser brachyrhynchus Pink-footed 

goose

Low245 Low245 Not assessed

Anser cygnoides Swan goose Low93,245 Low,82 High245 Not assessed

Antrostomus carolinensis Chuck-will’s 

widow

Low93 Low,82 Moderate85 Not assessed

Apaloderma vittatum Bar-tailed 

trogon

Low93 Not assessed Not assessed

Aptenodytes forsteri Emperor 

penguin

Low83,87,93 Low82,83 Not assessed

Apteryx haastii Great spotted 

kiwi

Low245 Low245 Not assessed

Apteryx owenii Little spotted 

kiwi

Low245 Low245 Not assessed

Apteryx rowi Okarito kiwi Low83,93,245 Low,82,245 High85 Not assessed

Aquila chrysaetos Golden eagle Low83,93,245 Low,82,83,244,245 High85 Not assessed

Athene cunicularia Burrowing 

owl

Low83,93,245 Low82,83,245 Not assessed

Aythya fuligula Tufted duck Low83,93,253 Low82,83,253 Low253

Buceros rhinoceros Rhinoceros 

hornbill

Low83,93 Low,83 High82 Not assessed

Calidris pugnax Ruff Low83,93,245 Low82,83,245 Not assessed

Calidris pygmaea Spoon-billed 

sandpiper

Low245 Low245 Not assessed

Calypte anna Anna’s 

hummingbird

Low83,93 Low,82,83 Moderate85 Not assessed

Camarhynchus parvulus Small tree 

finch

Low83,93 Low,82,83 High85 Not assessed

Cariama cristata Red-legged 

seriema

Low93 Low82 Not assessed

Cathartes aura Turkey 

vulture

Low86 Not assessed Not assessed

Catharus ustulatus Swainson’s 

thrush

Low83 Low82,83 Not assessed

Centrocercus urophasianus Greater sagegrouseNot assessed Moderate85 Not assessed

Chaetura pelagica Chimney swift Low83,93 Low,83 High82 Not assessed

Charadrius vociferus Killdeer Low83,93 Low82,83 Not assessed

Chiroxiphia lanceolata Lance-tailed 

manakin

Low83 Low,83 High82 Not assessed

Chlamydotis macqueenii MacQueen’s 

bustard

Low83,93 Low,83 High82 Not assessed

Chloebia gouldiae Gouldian 

finch

Low245 High245 Not assessed

Columba livia Rock dove Low93 Not assessed Not assessed

Corapipo altera White-ruffed 

manakin

Low83,93 Low,82,83 High85 Not assessed
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Corvus brachyrhynchos American 

crow

Low93, Moderate83 Low83 Not assessed

Corvus cornix Hooded crow Low83,93 Low,82,83 High85 Not assessed

Corvus kubaryi Mariana crow Not assessed High85 Not assessed

Corvus moneduloides New 

Caledonian 

crow

Low83,93 Low,82,83 Moderate85 Not assessed

Coturnix japonica Japanese 

quail

Low83,93,245 Low,82,83,245 Moderate85 Not assessed

Cuculus canorus Common 

cuckoo

Low93 Low82 Not assessed

Cyanistes caeruleus Eurasian blue 

tit

Low83,93,245 Low,82 Moderate,83

High85,245

Not assessed

Cygnus atratus Black swan Low83 Low,83 Moderate85 Not assessed

Cygnus olor Mute swan Not assessed Moderate85 Not assessed

Dromaius novaehollandiae Emu Low93,245 Low,82,245 High85 Not assessed

Egretta garzetta Little egret Low93 Not assessed Not assessed

Empidonax traillii Willow 

flycatcher

Low83,93 Low,82,83 High85 Not assessed

Eurypyga Helias Willow 

flycatcher

Low83,93 Low82,83 Not assessed

Falco cherrug Saker falcon Low83,93 Low,82,83 Moderate85 Not assessed

Falco naumanni Lesser kestrel Not assessed Moderate85 Not assessed

Falco peregrinus Peregrine 

falcon

Low93 Not assessed Not assessed

Falco rusticolus Gyrfalcon Not assessed Moderate85 Not assessed

Ficedula albicollis Collared 

flycatcher

Low83,93,245 Low82,83,245 Not assessed

Fulmarus glacialis Northern 

fulmar

Low83,93 Low82,83 Not assessed

Gallus gallus Red 

junglefowl

Low,83,84,87,90,93,95–

97,240,245,253,257

Moderate86,98,250

Low,82–84,244,245,253,257

High85

Low253

Gavia stellata Red-throated 

loon

Low83,93 Low82,83 Not assessed

Geospiza fortis Medium 

ground finch

Low93 Low82 Not assessed

Haliaeetus albicilla White-tailed 

eagle

Low83,93 Low,83 Moderate244 Not assessed

Haliaeetus leucocephalus Bald eagle Low83,93 Low82,83 Not assessed

Junco hyemalis Dark-eyed 

junco

Low245 Low245 Not assessed

Lepidothrix coronate Blue-capped 

manakin

Low83,93,245 Low82,83,245 Not assessed

Leptosomus discolor Cuckoo-roller Low93 High82 Not assessed

Lonchura striata Whiterumped 

munia

Low83,93,245 Low,82,83 Moderate,85

High245

Not assessed

Manacus vitellinus Goldencollared 

manakin

Low83,93,245 Low,82,83,245 High85 Not assessed

Meleagris gallopavo Wild turkey Low,83,93,245

Moderate86,250

Low,83,245 High244 Not assessed

Melopsittacus undulatus Budgerigar Low83,93,245 Low,82,83,245 High85 Not assessed

Merops nubicus Northern 

carmine beeeater

Low,93 Moderate83 Low,83 High82 Not assessed
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Mesitornis unicolor Brown mesite Low83,93 Low,83 High82 Not assessed

Molothrus ater Brownheaded 

cowbird

Not assessed High85 Not assessed

Motacilla alba White wagtail Not assessed Moderate85 Not assessed

Neopelma chrysocephalum Saffroncrested 

tyrantmanakin

Low83,93 Low,83 High82,85 Not assessed

Nipponia nippon Crested ibis Low83,93 Low,83 High82 Not assessed

Nothoprocta perdicaria Chilean 

tinamou

Low,83,245 Moderate93 Low,82,83 Moderate,85

High245

Not assessed

Numida meleagris Helmeted 

guineafowl

Low83,93,245 Low,82,83,245 High85 Not assessed

Onychostruthus 

taczanowskii

Whiterumped 

snowfinch

Not assessed Moderate85 Not assessed

Opisthocomus hoazin Hoatzin Low83,93 Low,83 High82 Not assessed

Oxyura jamaicensis Ruddy duck Low83 Low,83 Moderate85 Not assessed

Parus major Great tit Low83,93,245 Low,82,83 High85,245 Not assessed

Passer montanus Eurasian tree 

sparrow

Not assessed Moderate85 Not assessed

Pelecanus crispus Dalmatian 

pelican

Low93 Low82 Not assessed

Phaethon lepturus White-tailed 

tropicbird

Low83,93 Low82,83 Not assessed

Phalacrocorax carbo Great 

cormorant

Low93 Low82 Not assessed

Phasianus colchicus Ring-necked 

pheasant

Low83,93,245 Low,82,83,245 High85 Not assessed

Pipra filicauda Wire-tailed 

manakin

Low83,93 Low,82,83 High85 Not assessed

Pseudopodoces humilis Ground tit Low83,93 Low82,83 Not assessed

Pterocles gutturalis Yellowthroated 

sandgrouse

Low93 Low82 Not assessed

Pyrgilauda ruficollis Rufousnecked 

snowfinch

Not assessed High85 Not assessed

Pygoscelis adeliae Adélie 

penguin

Low83,93 Low82,83 Not assessed

Serinus canaria Atlantic 

canary

Low,93,245

moderate83,84

Low,82–84,245 High85 Not assessed

Strigops habroptila Kākāpō Low83,93,245 Low,82,83,245 High85 Not assessed

Struthio camelus Common 

ostrich

Low83,93,245 Low82,83,245 Not assessed

Sturnus vulgaris Common 

starling

Low83,93 Low,83 High82 Not assessed

Taeniopygia guttata Australian 

zebra finch

Low83,93,245 Low,83,245 High82,85 Not assessed

Tauraco erythrolophus Red-crested 

turaco

Low93 High82 Not assessed

Tinamus guttatus Whitethroated 

tinamou

Low93 Low82 Not assessed

Tyto alba Barn owl Low83,93 Low,82,83 High85 Not assessed
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Zonotrichia albicollis Whitethroated 

sparrow

Low83,93,245 Low,82,83,245 Moderate85 Not assessed

Previous experiments determined that all avian species tested (i.e., mallard [Anas 

platyrhynchos],293,294 swan goose [Anser cygnoides],293 Japanese quail [Coturnix japonica],293 G. 

gallus,

293–296 and wild turkey [Meleagris gallopavo]293) could not be successfully infected with 

MERS-CoV or SARS-CoV-2. Exogenous expression of ACE2 from G. gallus91,95,97,100 and M. 

gallopavo100 in vitro also failed to facilitate ACE2-SARS-CoV RBD binding and viral entry. 

However, one in vitro study demonstrated that G. gallus ACE2-expressing cells did manage to 

support some SARS-CoV-2 replication but at a much lower rate than highly susceptible 

species.100 In addition seroprevlance studies of more than 400 pintails (Anas acuta), Eurasian 

wigeon (Anas penelope), and G. gallus did not detect any MERS-CoV antibodies.297,298 Serology 

and viral RNA testing also failed to detect evidence of SARS-CoV-1 infections in A. platyrhynchos

and G. gallus. Together, computational modeling, experimental infection, and surveillance 

studies indicate that most avian species are at minimal risk for SARS-CoV-1, MERS-CoV, and 

SARS-CoV-2 infections. However, because of some species’ close contact events with 

Chiropterans, researchers should consider adding screening for these coronaviruses to existing 

avian surveillance studies.

Mustelid Susceptibility

SARS-CoV-2 infections on fur farms of N. vison have been widely reported during the pandemic, 

and other research evidence, including computational modeling data, suggests that other 

mustelids may be susceptible to coronavirus infections. Computational modeling data of 14 

mustelid species analyzed across 30 publications are summarized in Table 5. 

Table 5: Summary of Computational Modeling Data on Mustelid Susceptibility to SARS-CoV-2 

Evidence Types

Species Common 

Name

ACE2 Homology ACE2-RBD Affinity Evidence ACE2-RBD Molecular 

Dynamics

Arctonyx collaris Greater hog 

badger

Moderate96 Not assessed Not assessed

Lontra canadensis North 

American 

river otter

Moderate,83 High259 Low,259 High83,85,244 Not assessed

Lutra lutra Eurasian otter Moderate90 Not assessed Not assessed

Mellivora capensis Honey badger Moderate93 Not assessed Not assessed

Melogale moschata Chinese 

ferret-badger

Moderate96 Not assessed Not assessed

Mustela erminea Stoat Moderate,83,86,93

High88,89,248,259

Low,259 High82,83,85 Not assessed

Mustela lutreola European 

mink

Moderate,93,247 High248 Moderate247 Not assessed

Mustela nigripes Black-footed 

ferret

Moderate93 Not assessed Not assessed
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Mustela putorius furo Ferret Low,240 Moderate,83–

85,90,92,98,245,250–253,261

High86,88,259

Low,259 Moderate,81 High82–

85,90,244,245,253,260,261

Moderate,255 High253

Neogale vison American 

mink

Moderate,85,245 High88 Low,79 Moderate,85 High82,245 Not assessed

Pteronura brasiliensis Giant otter Moderate93 Not assessed Not assessed

Taxidea taxus American 

badger

Moderate93 Not assessed Not assessed

While M. putorius furo DPP4-expressing cells did not support MERS-CoV viral entry,299

expression of ACE2 did support moderate SARS-CoV-1 binding, entry, and replication.99,100,300

Intratracheal inoculation of M. putorius furo was also sufficient for symptomatic SARS-CoV-1 

infection, and direct contact was sufficient to transmit SARS-CoV-1.301,302 For SARS-CoV-2, 

similar in vitro overexpression experiments showed that M. putorius furo ACE2 supported 

minimal to some viral binding,99,240,248 entry,99,100,248 and replication.303 Endogenous M. putorius 

furo cells supported some SARS-CoV-2 replication304 but resulted in no cellular lysis.304 Similarly, 

N. vison ACE2-expressing cells did not support SARS-CoV-2 binding and supported some viral 

entry.248 Additional overexpression in vitro studies demonstrated moderate SARS-CoV-2 binding 

and viral entry in greater hog badger (Arctonyx collaris) and Chinese ferret-badger (Melogale 

moschata) ACE2-expressing cells.96

Strong in vivo evidence indicates that M. putorius furo are susceptible to SARS-CoV-2 infection. 

In vivo intranasal inoculation resulted in minimally symptomatic SARS-CoV-2 infections in M. 

putorius furo with nasal shedding.263,294,295,305–312 In addition, these animals transmitted the 

infection to others via direct contact295,309,311,312 as well as airborne respiratory 

droplets.263,309,310,312 Consistent with these results, M. putorius furo respiratory tract tissue 

samples expressed both ACE2158,303,313 and TMPRSS2.303 Based on computational data, M. 

putorius furo only expresses full-length ACE2 and not truncated forms possibly capable of 

binding SARS-CoV-2 without facilitating viral infection (see “Receptors” for more detail on ACE2 

isoforms).256 Additional experimental infection and transmission experiments are needed for 

other mustelids to more accurately assess whether their susceptibility to these coronaviruses is 

similar to M. putorius furo. 

Some mustelids have been tested for both active and previous infections of SARS-CoV-1 and 

SARS-CoV-2. A. collaris and M. moschata found at live markets in China tested negative for 

SARS-CoV-1 infection, but surveillance for SARS-CoV-1 in animals has only been performed at 

small scales. Seropositivity and viral RNA studies have identified active or previous SARS-CoV-2 

infections in Asian small-clawed otter (Aonyx cinereus), L. lutra, M. martes, M. putorius furo, 

and N. vison, although at relatively low rates. Consistent with detection in N. vison, these 

animals also express ACE2 in the respiratory tract.158

A viral RNA and seropositivity study of 87 and 12 M. meles, respectively, found no evidence of 

SARS-CoV-2 infection. However, ACE2 was detected in respiratory tracts of M. meles, indicating 

risk of SARS-CoV-2 infection.158 In addition, 57 M. mephitis samples, 59 European mink (Mustela 

lutreola) samples, and 2 least weasel (Mustela nivalis) samples all tested negative for SARS-CoV-
Report Page 29

2 RNA. No SARS-CoV-2 antibodies were detected in 101 M. lutreola, 3 M. nivalis, and 3 M. 

putorius2 samples. Overall, because of the susceptibility of mustelids to SARS-CoV-1 and SARSCoV-2 as determined by computational modeling, in vitro and in vivo infection studies, and 

surveillance data, mustelids with habitats near known Chiropteran roosts are at risk for 

contracting emerging coronaviruses. 

Non-Human Primate Susceptibility

Because of close evolutionary ties, non-human primate (NHP) susceptibilities to SARS-CoV-1, 

MERS-CoV, and SARS-CoV-2 likely reflect human susceptibilities. Computational modeling 

presented across 31 publications for 89 species predicted high susceptibility for most NHPs, and 

these data are summarized in Table 6. Great apes, lesser apes, Old World monkeys, and New 

World monkeys were mostly predicted as highly susceptible for SARS-CoV-2; notably, lemurs 

and lorises were mostly predicted as moderately susceptible. 

Table 6: Summary of Computational Modeling Data on Non-Human Primate Susceptibility to 

SARS-CoV-2 

Evidence Types

Species Common 

Name 

ACE2 Homology ACE2-RBD Affinity ACE2-RBD 

Molecular 

Dynamics

Great Apes

Gorilla gorilla Western 

gorilla

High83,85,86,88,93,94,241,245,248,252,258,259 Low,259 High82,83,85,239,245,260 High239

Pan paniscus Bonobo High83,86,88,93,241,245,248,252,259 Low,259,260 High82,83,85,245 Not assessed

Pan troglodytes Chimpanzee Low,257 Moderate,85

High83,84,86,88,89,93,243,245,248,252,259

Low,259 High82–85,243–

245,257,260

Not assessed

Pongo abelii Sumatran 

orangutan

High83–86,88,89,93,241,245,248,252,259 Low,259 High82–85,245,260 Not assessed

Lesser Apes

Hylobates moloch Silvery gibbon High83,85,88,241,252,259 Low,259 Moderate,85

High82,83

Not assessed

Nomascus leucogenys Northern 

whitecheeked 

gibbon

High83,86,88,93,241,245,248,252,259 Low,259 High82,83,85,245 Not assessed

Old World

Cercocebus atys Sooty 

mangabey

High83,86,88,93,245,248,252,259 Low,259 High82,83,245 Not assessed

Chlorocebus aethiops Grivet High86,88 High82,85 Not assessed

Chlorocebus sabaeus Green 

monkey

High83,86,88,93,245,248,252,259 Low,259 High82,83,85,245,260 Not assessed

Colobus angolensis Angola 

colobus

High93,245 High245 Not assessed

Erythrocebus patas Common 

patas monkey

High93 Not assessed Not assessed

Macaca fascicularis Crab-eating 

macaque

High83,86–88,93,96,240,245,248,252,259 Moderate,259 High81–

83,244,245

Not assessed

2 European polecat, the likely ancestor of now domesticated M. putorius furo
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Macaca mulatta Indochinese 

rhesus 

macaque

Low,257 Moderate,85 High83,84,86–

90,93,94,96,98,240,243,245,248,251–253,259

Low,259 Moderate,85,243

High82–84,239,244,245,253,257,260

High239,253

Macaca nemestrina Southern pigtailed 

macaque

High83,86,88,93,245,248,252,258,259 Low,259 Moderate,85

High82,83,244,245

Not assessed

Mandrillus leucophaeus Drill High83,86,93,245,248,252,259 Low,259 High82,83,245 Not assessed

Mandrillus sphinx Mandrill High88 Not assessed Not assessed

Nasalis larvatus Proboscis 

monkey

High93 Not assessed Not assessed

Papio anubis Olive baboon High83,85,86,88,89,93,245,248,252,259 Low,259 High82,83,85,244,245 Not assessed

Piliocolobus 

tephrosceles

Ugandan red 

colobus

Moderate85, 

High83,88,93,245,248,252,259

Low,259 High82,83,85,245 Not assessed

Pygathrix nemaeus Red-shanked 

douc

High93 Not assessed Not assessed

Rhinopithecus bieti Black-andwhite snubnosed 

monkey

Low,248 High88,259 High259 Not assessed

Rhinopithecus 

roxellana

Golden snubnosed 

monkey

High83,85,88,89,93,245,248,252,259 Low,259 High83,85,245 Not assessed

Theropithecus gelada Gelada High83,85,88,93,245,248,252,259 Low,259 High82,83,85,245 Not assessed

Trachypithecus 

francoisi

Francois’ leaf 

monkey

High259 Low259 Not assessed

New World

Alouatta palliata Mantled 

howler 

monkey

High93,252 Not assessed Not assessed

Aotus nancymaae Nancy Ma’s 

night monkey

High83,86,88,93,245,248,252,259 Low,259 Moderate,83,85

High82,245

Not assessed

Ateles geoffroyi Black-handed 

spider 

monkey

High93 Not assessed Not assessed

Callicebus donacophilus White-eared 

titi monkey

High93 Not assessed Not assessed

Callithrix jacchus Common 

marmoset

Moderate,85

High83,86,88,89,93,245,248,251,252,259

Low,259 Moderate,83,85

High82,245

Not assessed

Cebus capucinus Columbian 

white-faced 

capuchin

High86,88,93,245,248,252 High82,245 Not assessed

Cebus imitator Panamanian 

white-faced 

capuchin

High259 Low,259 Moderate85 Not assessed

Pithecia pithecia White-faced 

saki

High93 Not assessed Not assessed

Saguinus imperator Emperor 

tamarin

High93 Not assessed Not assessed

Saimiri boliviensis Black-capped 

squirrel 

monkey

High83,86,88,93,245,248,252,259 Low,259 Moderate,83,85

High82,245

Not assessed

Sapajus apella Tufted 

capuchin

High83,88,93,248,252,259 Low,259 Moderate,83,85

High82

Not assessed

Lemurs and Lorises
Report Page 31

Arctocebus 

calabarensis

Calabar 

angwantibo

Moderate254 Moderate254 Not assessed

Avahi laniger Woolly indri High254 High254 Not assessed

Avahi peyrierasi Peyrieras’s 

woolly lemur

High254 High254 Not assessed

Cheirogaleus major Greater 

dwarf lemur

Moderate254 Low254 Not assessed

Cheirogaleus medius Fat-tailed 

dwarf lemur

Moderate,254 High93 Low254 Not assessed

Daubentonia 

madagascariensis

Aye-aye High93,252,254 High254 Not assessed

Eulemur albifrons Whiteheaded lemurHigh254 Moderate254 Not assessed

Eulemur collaris Collared 

brown lemur

High254 Moderate254 Not assessed

Eulemur coronatus Crowned 

lemur

High254 Moderate254 Not assessed

Eulemur flavifrons Blue-eyed 

black lemur

High93,252,254 Moderate254 Not assessed

Eulemur fulvus Common 

brown lemur

High254 Moderate254 Not assessed

Eulemur macaco Black lemur High254 Moderate254 Not assessed

Eulemur mongoz Mongoose 

lemur

High254 Moderate254 Not assessed

Eulemur rubriventer Red-bellied 

lemur

High254 Moderate254 Not assessed

Eulemur rufus Red lemur High254 Moderate254 Not assessed

Eulemur sanfordi Sanford’s 

brown lemur

High254 Moderate254 Not assessed

Hapalemur alaotrensis Lac Alaotra 

bamboo 

lemur

High254 Moderate254 Not assessed

Hapalemur gilberti Bamboo 

lemur

High254 Moderate254 Not assessed

Hapalemur griseus Eastern lesser 

bamboo 

lemur

High254 Moderate254 Not assessed

Hapalemur 

meridionalis

Southern 

lesser 

bamboo 

lemur

High254 Moderate254 Not assessed

Hapalemur occidentalis Western 

lesser 

bamboo 

lemur

High254 Moderate254 Not assessed

Indri indri Indri High93 Not assessed Not assessed

Lemur catta Ring-tailed 

lemur

High254 Moderate254 Not assessed

Lepilemur ankaranensis Ankarana 

sportive 

lemur

Moderate254 Moderate254 Not assessed

Lepilemur dorsalis Gray-backed 

sportive 

lemur

Moderate254 Moderate254 Not assessed

Lepilemur ruficaudatus Red-tailed 

sportive 

lemur

Moderate254 Moderate254 Not assessed
Report Page 32

Lepilemur 

septentrionalis

Northern 

sportive 

lemur

Moderate254 Moderate254 Not assessed

Loris lydekkerianus Gray slender 

loris

Moderate254 Moderate254 Not assessed

Loris tardigradus Red slender 

loris

Moderate254 Moderate254 Not assessed

Microcebus murinus Gray mouse 

lemur

Low,248 Moderate,83,93,245,254

High252,259

Low,259 Moderate,83,254

High245

Not assessed

Mirza coquereli Coquerel’s 

giant mouse 

lemur

High93 Not assessed Not assessed

Mirza zaza Northern 

giant mouse 

lemur

Moderate254 Moderate254 Not assessed

Nycticebus bengalensis Bengal slow 

loris

Moderate254 Moderate254 Not assessed

Nycticebus pygmaeus Pygmy slow 

loris

Moderate254 Moderate254 Not assessed

Otolemur 

crassicaudatus

Brown 

greater 

galago

Moderate254 Moderate254 Not assessed

Otolemur garnetti Northern 

greater 

galago

Low,248 Moderate,83,86,93,245,252,254

High259

Low,259 Moderate,83,254

High82,85,245

Not assessed

Otolemur Monteiro Silvery 

greater 

galago

Moderate254 Moderate254 Not assessed

Perodicticus ibeanus East African 

potto

Moderate254 Moderate254 Not assessed

Perodicticus potto Potto Moderate254 Moderate254 Not assessed

Protolemur simus Greater 

bamboo 

lemur

High245,254 Moderate,254 High245 Not assessed

Propithecus coquereli Coquerel’s 

sifaka

High83,86,88,93,245,248,252,254,259 Low,259 High82,83,245,254 Not assessed

Propithecus coronatus Crowned 

sifaka

High254 High254 Not assessed

Propithecus diadema Diademed 

sifaka

High254 High254 Not assessed

Propithecus edwardsi MilneEdwards’s 

sifaka

High254 High254 Not assessed

Propithecus perrieri Perrier’s 

sifaka

High254 High254 Not assessed

Propithecus tattersalli Goldencrowned 

sifaka

High254 High254 Not assessed

Propithecus verreauxi Verreaux’s 

sifaka

High254 High254 Not assessed

Varecia rubra Red ruffed 

lemur

High254 Moderate254 Not assessed

Varecia variegata Black-andwhite ruffed 

lemur

High254 Moderate254 Not assessed

Other
Report Page 33

Carlito syrichta Philippine 

tarsier

Low,248 Moderate,245

High83,88,89,252,259

Low,259 Moderate,83

High82,85,245

Not assessed

Galago moholi Mohol 

bushbaby

Moderate254 Moderate254 Not assessed

Galago senegalensis Senegal 

bushbaby

Moderate254 Moderate254 Not assessed

Galagoides demidovii Prince 

Demidoff’s 

bushbaby

Moderate254 Moderate254 Not assessed

Numerous NHP species have been tested in vitro for viral susceptibility. Grivet (Chlorocebus 

aethiops)-derived cells supported lytic viral replication of SARS-CoV-1,155,156,314 MERS-CoV entry 

and replication,108,315 and SARS-CoV-2 replication,100 indicating susceptibility to all three viruses. 

Rhesus macaque (Macaca mulatta)-derived cells supported viral entry of SARS-CoV-1156 as well 

as lytic cell replication of SARS-CoV-2.304 Exogenous expression of M. mulatta ACE2 also 

supported binding, entry, and replication of SARS-CoV-2.96,304 The ACE2 of another closely 

related species, crab-eating macaque (Macaca fascicularis), also supported binding and entry of 

SARS-CoV-1 and SARS-CoV-2.91,248 Additional screening of NHP ACE2 proteins demonstrated 

that the following species supported SARS-CoV-2 binding and entry: G. gorilla, northern whitecheeked gibbon (Nomascus leucogenys), chimpanzee (Pan troglodytes), olive baboon (Papio 

anubis), Ugandan red colobus (Piliocolobus tephrosceles), Sumatran orangutan (Pongo abelii), 

golden snub-nosed monkey (Rhinopithecus roxellana), and gelada (Theropithecus gelada). 

Additional studies are required to further explore the susceptibility of great apes to SARS-CoV2; preliminary studies identified TMPRSS2 and ACE2 expression in P. abelii respiratory tract,303

but not in the respiratory tract of G. gorilla.

158 Notably, based on sequence data, P. abelii—and 

other NHPs (i.e., M. fascicularis, M. mulatta, drill [Mandrillus leucophaeus], bonobo [Pan 

paniscus], chimpanzee [Pan troglodytes], and R. roxellana)—ACE2 isoforms all support SARSCoV-2 infection.256 Conversely, ACE2 from C. jacchus, black-capped squirrel monkey (Saimiri 

boliviensis), and tufted capuchin (Sapajus apella) did not support SARS-CoV-2 binding or 

entry.248 Notably, all NHP species that supported SARS-CoV-2 binding and entry are New World 

primates and great apes, while the species that did not support binding and entry are Old 

World primates.

In vivo experimental infection experiments largely agree with in vitro infection results. The 

following species experienced symptomatic SARS-CoV-2 infections after combination 

inoculation (e.g., intratracheal plus intranasal, intratracheal plus intranasal plus conjunctival, 

etc.): C. aethiops,

316–318 M. fascicularis,319,320 M. mulatta,316,318,319,321 and southern pig-tailed 

macaque (Macaca nemestrina).318 Although computational modeling predicted Callithrix and 

Saimiri species as highly susceptible, both C. jacchus319 and S. sciureus318 were mostly 

asymptomatic after experimental infection with minimal viral shedding. Consistent with these 

lack of symptoms, C. jacchus ACE2 expression was absent from the respiratory tract but 

detectable in the small intestine.158 Both C. aethiops and M. mulatta are also susceptible to 

aerosol-based SARS-CoV-2.316 Notably, the degree of viral shedding does not always correlate 

with severity of symptoms. M. fascicularis experienced asymptomatic infections after 

combination inoculation with SARS-CoV-1 or MERS-CoV. These monkeys seroconverted for both 
Report Page 34

viruses, but these antibodies were not always protective against reinfection with SARS-CoV1.322,323 324 M. mulatta was susceptible to MERS-CoV combination inoculation but experienced 

no symptoms following combination inoculation with SARS-CoV-1. Monkeys infected with 

MERS-CoV or SARS-CoV-1 seroconverted, but this was not protective against SARS-CoV-1 

reinfection.322–324 C. aethiops also remained asymptomatic after infection with SARS-CoV-1 but 

did seroconvert.324

Some NHPs have been tested for active and previous SARS-CoV-2 coronaviruses. No evidence of 

natural active or previous infections of SARS-CoV-2 was detected in Alouatta palliata,

325 C. 

jacchus,

325 collared mangabey (Cercocebus torquatus),326 M. mulatta,327 P. troglodytes,326 and 

pied tamarin (Saguinus bicolor).

325 However, some captive NHPs have been naturally infected 

with SARS-CoV-2, including sun-tailed monkey (Allochrocebus solatus),326 G. gorilla, mandrill 

(Mandrillus sphinx), and Guianan squirrel monkey (Saimiri sciureus).328 

Farmed Ungulate Susceptibility

Depending on farm location, farmed ungulates can be at risk for spillovers from Chiropterans, 

other wild animals, and even farmers. The computational modeling data for 13 farmed 

ungulates are summarized in Table 7. 

Table 7: Summary of Computational Modeling Data for Farmed Ungulates 

Evidence Types

Species Common 

Name 

ACE2 Homology ACE2-RBD Affinity ACE2-RBD 

Molecular 

Dynamics

Bos grunniens Domestic yak Moderate245 High245 Not assessed

Bos indicus Zebu High83,87,93,248,259 High82,83,244,259 Not assessed

Bos taurus Domestic 

cattle

Low,240,257 Moderate,85,245,246

High80,83,84,86,87,89,90,93,95–

97,242,243,248,250,253,259

Low,81,84

Moderate,85,239,253

High80,82,83,85,90,243–

245,257,259,260

Moderate239,253

Bubalus bubalis Domestic 

water buffalo

Moderate,246 High83,93,248,259 Low,82 High83,244,259,260 Not assessed

Camelus bactrianus Bactrian 

camel

Low,248 High83,93,95–97,253,259 Low,82,253,259

Moderate,83 High244

High253

Camelus 

dromedarius

Dromedary 

camel

Low,89,248 Moderate,241,245,246

High83,84,86,93,253,259

Low,82,84,253,259

Moderate,83

High85,244,245

Moderate253

Capra hircus Goat Low,240 Moderate,245,246

High83,84,86,87,90,93,95–97,248,253,259

Low,84,259

High82,83,90,244,245,253,260

High253

Equus asinus Donkey Low,240 Moderate,83,93,95,97,245,246

High84,248,259

Low,82,259 High83,84,244,245 Not assessed

Equus caballus Horse Low,240

Moderate,83,85,86,90,95,97,241,243,245,246

High80,84,87–89,93,96,248,253,259

Low,80,82,243,259

Moderate,81,85,253

High83,84,90,244,245

High253

Odocoileus 

virginianus

White-tailed 

deer

High93,250,259 Low,259 High82,83,85,257 Not assessed

Ovis aries Sheep Low,240,257 Moderate,85,245,246

High80,83,84,86,87,89,90,93,95–

97,241,243,248,253,259

Low,243,244,259

Moderate,80,85,239

High82–84,90,245,253,257,260

Moderate,239

High253
Report Page 35

Sus scrofa Pig Low,240,246,257

Moderate,85,90,98,241,245

High80,83,84,86,87,89,93,96,243,248,250–

253,259

Low,80,84,243,244,259

Moderate,85,239

High82,83,90,245,253,257,260

Moderate239,253

Vicugna pacos Alpaca Low,248 Moderate,90,241

High83,88,93,96,250,259

Low,82,259 Moderate,83

High85

Not assessed

Overexpression of ACE2 proteins from different farmed ungulates identified that following 

species as potentially susceptible to SARS-CoV-1 based on ACE2 binding and entry: B. taurus,

97

Bactrian camel (Camelus bactrianus),91,95 C. hircus,

91,95,97,100 E. caballus,91,95,97,100,329 O. 

aries,

91,95,97,100 S. scrofa,91,99,100,314 and alpaca (Vicugna pacos).91 Notably, E. asinus ACE2 did not 

support SARS-CoV-1 binding or entry,95,97 while S. scrofa-derived cells with endogenous ACE2 

supported viral replication.155,156 In addition, C. dromedarius-derived315 and E. caballus-derived 

cells330 both supported MERS-CoV infection, while O. aries-derived cells did not.156,315

Exogenous and endogenous in vitro results were inconsistent for some farmed ungulate species 

(i.e., B. taurus, C. hircus, E. caballus, O. aries, S. scrofa, V. pacos). Overexpression of speciesspecific ACE2 mostly indicated susceptibility, while species-derived cell culture models mostly 

showed minimal susceptibility. Importantly, results for white-tailed deer (Odocoileus 

virginianus) were consistent across both experimental contexts. These differing results are 

summarized in Table 8. Because in vivo experimental infection studies of B. taurus331 and S. 

scrofa294,295,311,332,333 indicated low susceptibility as well, using species-derived cell culture 

models to assess susceptibility may provide results more relevant to in vivo contexts. 

Table 8: Summary of In Vitro Data for Farmed Ungulates

Exogenous Results Endogenous Results

Species ACE2 Binding Viral Entry Viral 

Replication

ACE2 

Binding

Viral 

Entry

Viral Replication

Bos taurus High91,97,240,248 High91,95,97,100,248 Moderate303 Not 

assessed

Not 

assessed

None,100 Moderate304

Camelus 

bactrianus

Moderate91,97 Moderate91,95,97 Low303 Not 

assessed

Not 

assessed

Low304

Capra hircus High91,97,248 High91,95,97,100,248,334,335 Not assessed Not 

assessed

Not 

assessed

None304

Equus asinus None95,97 None95,97 Not assessed Not 

assessed

Not 

assessed

Not assessed

Equus 

caballus

High91,97,248,329 Moderate91,95,97,100,248,334 Not assessed Not 

assessed

Not 

assessed

None100

Odocoileus 

virginianus

Not assessed High336 Not assessed Not 

assessed

Not 

assessed

High337

Ovis aries High91,97,248 High91,95,97,100,248 Not assessed Not 

assessed

Not 

assessed

None100

Sus scrofa High91,99,248 High91,99,100,248,335 High100 Not 

assessed

Not 

assessed

None,303Moderate100,304

Vicugna 

pacos

Moderate91 Moderate91 Not assessed Not 

assessed

Not 

assessed

Low303
Report Page 36

In vivo expression studies identified the following farmed ungulates as having ACE2 and 

TMPRSS2 expression in respiratory tracts: B. taurus,

158,303,313 C. bactrianus,303 C. hircus,303,338

and O. aries.

158,303 Studies of ACE2 expression in E. caballus158,303 and V. pacos158,303 obtained 

mixed results of ACE2 in the respiratory tract, and S. scrofa contains low ACE2 expression in 

respiratory organs. Notably, E. caballus and S. scrofa158 also express ACE2 in the small intestine, 

suggestive of potential gastrointestinal symptoms and fecal shedding.

Most experimental infection studies in farmed ungulates focused on MERS-CoV. As expected, C. 

dromedarius can be infected with MERS-CoV intranasal inoculation,339 which correlates well 

with high expression of the viral receptor DPP4 in the upper respiratory tract.340 Although no 

studies have identified natural MERS-CoV infections in C. bactrianus, these camels can also be 

intranasally infected.341 After intranasal inoculation, E. caballus and O. aries experience minimal 

symptoms and viral shedding that do not result in seroconversion.342,343 C. hircus,

342 S. 

scrofa,

343,344 and V. pacos339,345,346 also experience minimal symptoms from intranasal 

inoculation, but these animals develop MERS-CoV antibodies. One experimental infection study 

of farmed ungulates for SARS-CoV-1 demonstrated that only combination inoculation including 

the intravenous route resulted in seroconversion without symptoms.296

Recent surveillance studies have detected evidence of SARS-CoV-2 in O. virginianus. 

Experimental infection studies have demonstrated that O. virginianus can be infected 

intranasally, resulting in subclinical infection and seroconversion.336,337,347 In addition, these 

animals can transmit SARS-CoV-2 via close contact347 and can transmit the virus to fetuses.337 In 

agreement with these experimental studies, surveillance studies have identified evidence of 

active and past SARS-CoV-2 infections in O. virginianus in Illinois,348 Iowa,349 Michigan,348 New 

York,348,350 Ohio,351,352 Pennsylvania,348,353 South Carolina,354 and Texas.355–357 Both free-roaming 

and captive O. virginianus tested positive for current or previous SARS-CoV-2 infections,349,355

and further study of viral sequences isolated from Ohio identified multiple likely human-to-deer 

spillover events as well as deer-to-deer transmission.

351,352,358 In addition, further sequence 

analysis demonstrated the SARS-CoV-2 evolutionary rate in O. virginianus is three times faster 

than the rate in humans with different mutational biases and selection pressures, suggesting 

that O. virginianus may become a significant SARS-CoV-2 reservoir. Although no phenotypic 

changes were observed for SARS-CoV-2 in O. virginianus, the faster evolutionary rate may result 

in phenotypic changes with significant impacts on virulence and species tropism.352 Additional 

surveillance studies have identified evidence of SARS-CoV-2 in C. hircus and O. aries at very low 

rates in Italy359 as well as seropositivity in S. scrofa in one animal in Gabon and six animals in 

Croatia.326,360 Consistent with these low infection rates, C. hircus ACE2 has two isoforms, only 

one of which can support SARS-CoV-2 infection. Similarly, S. scrofa ACE2 has three isoforms, but 

only one can fully bind and facilitate SARS-CoV-2 infection.90,256

While only one study identified SARS-CoV-1 antibodies in S. scrofa but not B. taurus in China,154

numerous MERS-CoV surveillance studies have been conducted in farmed ungulates in mostly 

Middle Eastern regions. For a summary of MERS-CoV surveillance studies in C. dromedarius, see 

“Dromedaries.” Notably, some farmed ungulates positive for MERS-CoV RNA or antibodies 

were housed in close proximity with C. dromedarius, suggesting transmission from infected C. 
Report Page 37

dromedarius. Neutralizing antibodies for MERS-CoV in B. taurus were identified in Egypt,361 but 

not in Jordan,362 Netherlands,363 Saudi Arabia,298 Tunisia,361 and United Arab Emirates (UAE).

364

and In C. bactrianus, evidence of MERS-CoV neutralizing antibodies was only found in China,365

but not Japan,366 Kazakhstan,367 and Mongolia.368 Neutralizing antibodies in C. hircus were 

detected in Egypt and Tunisia, and one active infection was found in Senegal;361 however, no 

evidence of current or previous MERS-CoV infections in C. hircus was found in Jordan,362

Netherlands,363 Saudi Arabia,68,298 Spain,

363 and UAE.364 Only one active infection in E. asinus 

was detected in Egypt,361 but no evidence of infection was found in Spain330 and Tunisia.

361 One 

E. caballus animal had neutralizing antibodies in Tunisia,361 but no other evidence of infection 

was found in Egypt,60,361 Spain,

330 and UAE.330 Ovis aries animals in Egypt,60,361 Jordan,362

Senegal,361 Tunisia,361 and UAE364 had very low rates of current or past MERS-CoV infections, 

while O. aries in Netherlands363 and Saudi Arabia68,298 were negative for MERS-CoV infections 

and antibodies. In addition, V. pacos in Israel369 and Qatar370 had MERS-CoV neutralizing 

antibodies, while S. scrofa in China showed no evidence of current or past MERS-CoV 

infections.297

Interactions with Humans

Humans that contract zoonotic viruses can transmit them to other animals as well. Multiple 

reports have shown that Chiropterans have transmitted to humans Henipavirus in Cameroon,371

Melaka and Pulau viruses in Malaysia,372 and Filovirus in India.373 Human–Chiropteran 

interactions facilitated these zoonoses, and emerging coronaviruses could also transmit from 

Chiropteran to human. In addition, avian species have transmitted multiple avian influenza 

subtype A viruses to humans,374 and C. dromedarius have transmitted MERS-CoV to humans.375

Reverse zoonoses can also occur when infected humans are in close contact with naïve animals. 

Examples of reverse zoonoses of respiratory viruses include H1N1 transmission to farmed S. 

scrofa,

376–378 companion M. putorius furo,379 and farmed M. gallopavo;380 metapneumovirus to 

wild P. troglodytes;

381 and adenoviruses to captive M. fascicularis, M. mulatta, and mantled 

guereza (Colobus guereza).

382 The susceptibilities of animals with close contacts to humans (i.e., 

captive animals, companion animals, and other wildlife) to SARS-CoV-1, MERS-CoV, and SARSCoV-2 are outlined below, and susceptibilities of farmed animals are summarized in

“Interactions with Chiropterans.” 

Companion Animal Susceptibility

Companion animals that spend time outdoors are at risk for close Chiropteran contacts, 

especially if left unattended, and they are also at risk because of close contact with humans. 

Common companion animal species include C. lupus familiaris, F. catus, birds, and small 

mammals (e.g., rodents, rabbits [Oryctolagus cuniculus], M. putorius furo). Susceptibilities of C. 

lupus familiaris, F. catus, and O. cuniculus are described in this section, while birds (see “Avian 

Susceptibility”), rodents (see “Rodent Susceptibility”), and M. putorius furo (see “Mustelid 

Susceptibility”) are described elsewhere. Computational modeling data for C. lupus familiaris, F. 

catus, and O. cuniculus are summarized in Table 9.
Report Page 38

Table 9: Summary of Computational Modeling Data for Select Companion Animals

Evidence Types

Species Common 

Name

ACE2 Homology ACE2-RBD Affinity ACE2-RBD 

Molecular 

Dynamics

Canis lupus 

familiaris

Dog Low,240,249,257

Moderate,85,94,241,246,252,258,261

High80,83,84,86–90,93,96,243,245,248,250,253,259

Low,243,249,253,259–261

Moderate,80,239 High81–

85,89,90,244,245,257

Low,249,253

Moderate,255

High239

Felis catus Cat Low,240,257 Moderate,241,246,249

High80,83–

98,243,245,248,250,252,253,258,259,261

Low,257,259

Moderate,81,239,249,253

High80,82–85,89,90,243–

245,260–262

Low,249,253

Moderate,239,255

High262

Oryctolagus 

cuniculus

Rabbit Low,240,250,257 Moderate,85,241,246

High80,83,84,86–90,93–97,243,245,248,251,259

Low,82,243,259

Moderate,80,85

High83,84,244,245,257,260

Not assessed

In vitro experimental infection data indicate potential companion animal susceptibilities to 

some emerging coronaviruses. Exogenous expression of C. lupus familiaris ACE2 supported 

moderate to high viral binding and high viral entry of both SARS-CoV-191,100 and SARS-CoV2.91,96,100,248,335 In vitro studies of C. lupus familiaris-derived cells resulted in mixed results of 

either no SARS-CoV-2 replication100 or some replication.303,304 In addition, overexpression of F. 

catus ACE2 resulted in moderate to high viral binding and entry but no viral replication of both 

SARS-CoV-191,95,97,100,314,383 and SARS-CoV-2.91,95–97,100,240,248,334,335,384 However, F. catus-derived 

cells did support SARS-CoV-2 replication that resulted in cell lysis.304 For O. cuniculus, 

overexpression of ACE2 supports high viral binding and entry for SARS-CoV-191,95,97,100,314 and 

SARS-CoV-2, but replication only occurred for SARS-CoV-2.91,95–97,100,248 O. cuniculus-derived 

cells supported MERS-CoV385 infection as well as some SARS-CoV-2 replication.304

Some viral receptor and protease expression studies detected ACE2 and TMPRSS2 in the 

respiratory tracts of C. lupus familiaris,

303,313,338,386 F. catus,158,313,338 and O. cuniculus.303

However, other studies failed to detect expression of these genes in C. lupus familiaris158 and O. 

cuniculus313,338 respiratory tracts. C. lupus familiaris ACE2 isoforms include one truncated 

isoform that may actually block ACE2-SARS-CoV-2 binding, impeding infection, while all 

isoforms predicted for F. catus and O. cuniculus ACE2 can facilitate SARS-CoV-2 infection.90,256 In

addition, ACE2 was detected in F. catus digestive tracts, suggesting potential gastrointestinal 

symptoms and fecal shedding.159 Consistent with these expression data, experimental infection 

with SARS-CoV-2 resulted in seroconversion in C. lupus familiaris,

294,387 F. catus,294,387–391 and O. 

cuniculus.

392 In addition, O. cuniculus can be infected with MERS-CoV via combination 

inoculation, resulting in viral shedding and seroconversion.385 F. catus can also be infected with 

SARS-CoV-1 via intratracheal inoculation,301,302 and similar to SARS-CoV-2,387,390,391 F. catus can 

transmit SARS-CoV-1 via direct contact.302

Consistent with experimental infection results, surveillance studies have found evidence of 

natural SARS-CoV-2 infections in C. lupus familiaris, F. catus, and O. cuniculus. Evidence of 

active or previous SARS-CoV-2 infections in C. lupus familiaris were reported in Croatia,393,394
Report Page 39

Ecuador,395 Egypt,396 Poland,397 France,398 Gabon,326 Italy,399–401 Spain,402–404 Thailand,405 and 

United States,406–408 but not in France,409 Indonesia,410 Mexico,411 or Turkey.412 For F. catus, 

SARS-CoV-2 infections were detected in Colombia,413 China,414,415 Croatia,393 Ecuador,395

Egypt,396 France,398,409,416 Germany,417,418 Iran,419 Israel,420 Italy,399,401,421 Mexico,411 Peru,422

Poland,397 Spain,404,423,424 Switzerland,425 United States,406–408 Thailand,405 and Turkey,426 but 

not Gabon.

326. Multiple case study reports detailed evidence of human-to-animal transmission 

events for both C. lupus familiaris396,407,427–433 and F. catus,

395,407,416,425,428,431,434–442 and one 

study provided evidence of potential transmission from M. putorius furo.

126 Fewer surveillance 

studies were performed for O. cuniculus, but one such study identified a very low rate of 

seropositivity in France.

Rodent Susceptibility 

A diverse set of rodents were analyzed for susceptibility to SARS-CoV-1, MERS-CoV, and SARSCoV-2. Importantly, different rodent species interact with humans in multiple ways as 

companion animals, research subjects, and wildlife encounters. Computational modeling data 

for 59 rodent species from 41 articles are summarized in Table 10. 

Table 10: Summary of Computational Modeling Data for Rodent Species

Evidence Types

Species Common 

Name 

ACE2 Homology ACE2-RBD Affinity ACE2-RBD 

Molecular 

Dynamics

Acomys cahirinus Cairo spiny 

mouse

Moderate93 Not assessed Not assessed

Allactaga bullata Gobi jerboa High93 Not assessed Not assessed

Arvicanthis niloticus African grass 

rat

Moderate,83 High259 Low,83,259 High85 Not assessed

Arvicola amphibius European 

water vole

High259 Low,259 Moderate85 Not assessed

Cavia porcellus Guinea pig Low,89,248 Moderate,93,95–97,245,259

High84,86,87

Low,82 High84,245,259 Not assessed

Cavia tschudii Montane 

guinea pig

Moderate93 Not assessed Not assessed

Chinchilla lanigera Long-tailed 

chinchilla

Low,248,257 Moderate,245

High83,86,88,93,259

Low,257,259,260

Moderate,83 High82,245

Not assessed

Cricetomys gambianus Gambian 

pouched rat

High93 Not assessed Not assessed

Cricetulus griseus Chinese 

hamster

Low,240

High83,85,86,88,89,92,93,245,248,258,259,261

Low,259,261

High82,83,85,89,244,245

Not assessed

Ctenodactylus gundi Common gundi High93 Not assessed Not assessed

Ctenomys sociabilis Social tucotucoModerate93 Not assessed Not assessed

Cynomys marmota Prairie dog Low257 High257 Not assessed

Dasyprocta punctata Central 

American 

agouti

Moderate93 Not assessed Not assessed

Dipodomys ordii Ord’s kangaroo 

rat

Low,89,248 High83,86,88,93,245,259 Low,82,259 Moderate,83

High245

Not assessed

Dipodomys spectabilis Banner-tailed 

kangaroo rat

Not assessed High85 Not assessed
Report Page 40

Dipodomys stephensi Stephens’s 

kangaroo rat

High93 Not assessed Not assessed

Dolichotis patagonum Patagonian 

mara

Moderate93 Not assessed Not assessed

Ellobius lutescens Transcaucasian 

mole vole

High93 Not assessed Not assessed

Fukomys damarensis Damara moleratLow,248 Moderate,245

High83,88,93,259

Low,259

High79,82,83,85,245

Not assessed

Grammomys surdaster African 

woodland 

thicket rat

Low,248 Moderate,83,93 High259 Low,83,259 High82,85 Not assessed

Graphiurus murinus Woodland 

dormouse

High93 Not assessed Not assessed

Heterocephalus glaber Naked moleratLow,248 Moderate,245

High83,86,88,89,93,259

Low,259

High82,83,85,245,260

Not assessed

Hydrochoerus 

hydrochaeris

Capybara High93 Not assessed Not assessed

Hystrix cristata Crested 

porcupine

High93 Not assessed Not assessed

Ictidomys 

tridecemlineatus

Thirteen-lined 

ground squirrel

Low,248 Moderate,245

High83,86,88,89,93,259

Low,82,259 High83,85,245 Not assessed

Jaculus jaculus Lesser Egyptian 

jerboa

Moderate,245 High83,88,93,248,259 Low,259 High82,83,245 Not assessed

Marmota flaviventris Yellow-bellied 

marmot

Low,248 High83,88,93,259 Low,82,259 High83,85 Not assessed

Marmota marmota Alpine marmot Low,248 Moderate,245

High83,88,93,259

Low,82,259 High83,245 Not assessed

Mastomys coucha Southern 

multimammate 

mouse

Low,248 Moderate,83,93 High259 Low,82,83,259

Moderate85

Not assessed

Meriones unguiculatus Mongolian 

gerbil

Moderate93 Not assessed Not assessed

Mesocricetus auratus Golden 

hamster

Low,240 Moderate,85 High83,84,86–

89,92,93,241,245,247,248,251,253,259

Low,259 High81–

85,245,247,253,260

Moderate253

Microtus ochrogaster Prairie vole Low,248 Moderate,92,245

High83,88,93,259

Moderate,79

High82,83,85,245,259

Not assessed

Microtus oregoni Creeping vole High259 Moderate,85 High259 Not assessed

Mus caroli Ryukyu mouse Low,245,248 Moderate,83,93 High259 Low,79,82,83,245

High85,259

Not assessed

Mus musculus House mouse Low,89,240,245,246,248,257

Moderate,80,83,84,86,87,90–

98,243,250,251,253,258 High259

Low,79–84,239,243–

245,257,262 Moderate,253

High85,90,259,260

Low,239,262

Moderate253

Mus pahari Gairdner’s 

shrewmouse

Low,245,248 Moderate,83,93 High259 Low,83,245,259

Moderate,79 High82,85

Not assessed

Mus spicilegus Steppe mouse Low245 Low245 Not assessed

Mus spretus Algerian 

mouse

Low,245 Moderate93 High245 Not assessed

Myocastor coypus Nutria Moderate93 Not assessed Not assessed

Nannospalax 

ehrenbergi

Middle East 

blind mole-rat

High245 High245 Not assessed

Nannospalax galili Upper Galilee 

mountains 

blind mole rat

High259 Low259 Not assessed

Octodon degus Common degu Low,248 Moderate,93,245

High83,88,259

Low,259,260 Moderate,83

High82,245

Not assessed

Ondatra zibethicus Muskrat High93 Not assessed Not assessed
Report Page 41

Onychomys torridus Southern 

grasshopper 

mouse

High259 Low,259 High85 Not assessed

Perognathus 

longimembris

Little pocket 

mouse

High93 Not assessed Not assessed

Peromyscus leucopus White-footed 

mouse

High83,85,92,93,248,259 Moderate,85

High82,83,259

Not assessed

Peromyscus 

maniculatus

Deer mouse Moderate,245

High83,85,88,92,93,248,259

Low,259 High82,83,85,245 Not assessed

Petromus typicus Dassie rat Moderate93 Not assessed Not assessed

Phodopus campbelli Campbell’s 

dwarf hamster

High86,89,241 High82 Not assessed

Phodopus roborovskii Roborovski 

dwarf hamster

High247 High247 Not assessed

Psammomys obesus Fat sand rat Moderate93 Not assessed Not assessed

Rattus norvegicus Brown rat Low,89,245,248

Moderate,80,83,86,90,91,93–97,250,251

High84,259

Low,79,80,82–

84,239,244,245,259 High85

Low239

Rattus rattus Black rat Low,246 Moderate,83,98 High259 Low83,259 Not assessed

Rhizomys pruinosus Hoary bamboo 

rat

High79 Not assessed Not assessed

Spermophilus dauricus Daurian 

ground squirrel

Moderate,245 High93 High245 Not assessed

Thryonomys 

swinderianus

Greater cane 

rat

Moderate93 Not assessed Not assessed

Urocitellus parryii Arctic ground 

squirrel

Low,248 Moderate,85,245

High83,88,93,259

Low,82,259 Moderate,85

High83,245

Not assessed

Zapus hudsonius Meadow 

jumping mouse

Moderate93 Not assessed Not assessed

In vitro experimental data using rodent ACE2 and rodent-derived cell culture models indicate a 

diverse set of susceptibilities across species to SARS-CoV-1, MERS-CoV, and SARS-CoV-2. For 

guinea pigs (Cavia porcellus), overexpression of DPP4 supported only minimal MERS-CoV 

entry,

299 and overexpression of ACE2 resulted in minimal to no viral binding and moderate to 

no viral entry for both SARS-CoV-1 and SARS-CoV-2,91,95,97,99 indicating a general lack of 

susceptibility of this species to these coronaviruses. A similar lack of susceptibility was 

concluded for brown rats (Rattus norvegicus) for SARS-CoV-1 and SARS-CoV-2 as well.96,97,99,100

In vitro results for M. musculus viral receptor overexpression studies provided varied results. 

Although DPP4 overexpression resulted in minimal viral entry,299 ACE2 overexpression 

supported varied levels of SARS-CoV-191,95,97,99 and SARS-CoV-291,95–97,99,248,335,384 binding and 

viral entry. Ultimately, however, M. musculus-derived cells did not support viral replication of 

SARS-CoV-1 or SARS-CoV-2,100,314 indicating overall low susceptibility. Similarly, overexpression 

of Chinese hamster (Cricetulus griseus) and Syrian hamster (Mesocricetus auratus) ACE2s 

supported high viral entry of both SARS viruses,100,248,334 but infection of corresponding speciesderived cells did not yield any viral replication.100,155,314

Other rodent species ACE2s supported binding and viral entry for either SARS-CoV-1 or SARSCoV-2. Long-tailed chinchilla (Chinchilla lanigera)

100 and Arctic ground squirrel (Urocitellus 

parryii)

99 ACE2s supported high viral entry for both SARS-CoV-1 and SARS-CoV-2. Lesser jerboa 

(Jaculus jaculus) and white-footed mouse (Peromyscus leucopus) ACE2s were only tested for 
Report Page 42

SARS-CoV-2, and both supported high viral entry.248 Notably, no species-derived cell lines for 

these four species (i.e., C. lanigera, U. parryii, J. jaculus, and P. leucopus) have been used to 

confirm these susceptibility findings. However, in vivo infection studies of two related species—

Wyoming ground squirrel (Urocitellus elegans) and eastern deer mouse (Peromyscus 

maniculatus)—determined that P. maniculatus was susceptible to intranasal infection of SARSCoV-2 resulting in seroconversion and the ability to transmit to other animals via direct contact;

92,443,444 Urocitellus elegans could not be intranasally infected with SARS-CoV-2.444 In addition to 

P. maniculatus, bank vole (Myodes glareolus),

445 black-tailed prairie dog (Cynomys 

ludovicianus),446 and fox squirrel (Sciurus niger)

447 also live in close proximity to O. virginianus 

and other likely susceptible ungulates (see “Farmed Ungulate Susceptibility”), but only M. 

glareolus could be intranasally infected with SARS-CoV-2.444,448

While no in vivo SARS-CoV-2 infection studies of R. norvegicus have been published, low 

expression of ACE2 and TMPRSS2449 further confirm low susceptibility findings from in vitro 

infection studies. In vivo infection studies of M. musculus demonstrated an inability to infect 

intranasally with SARS-CoV-2,444 which confirmed the lack of susceptibility findings from in vitro 

experiments. Minimal expression of ACE2 and TMPRSS2 in mice likely contributes to this lack of 

susceptibility.449 M. musculus cannot be intranasally infected with MERS-CoV, likely due to low 

DPP4 lung expression.450

Four different hamster species (i.e., M. auratus,

251,451–453 Campbell’s dwarf hamster [Phodopus 

campbelli], Roborovski hamster [Phodopus roborovskii], and winter white dwarf hamster 

[Phodopus sungorus]

454) can all be intranasally infected with SARS-CoV-2. All four species 

experience symptoms, although P. roborovskii reportedly had more severe symptoms than the 

other two Phodopus species.454 Transmission studies using M. auratus further demonstrated 

SARS-CoV-2 transmission to other animals via direct contact, aerosol, and fomites.251,452

Consistent with M. auratus in vivo susceptibility, ACE2 and TMPRSS2 were coexpressed in the 

same lung cells as demonstrated by single cell RNA-sequencing,338 and all predicted M. auratus 

ACE2 isoforms can facilitate SARS-CoV-2 infection.256 Notably, the susceptibility of M. auratus in 

vivo was not recapitulated in M. auratus-derived cell lines, suggesting that all in vitro infection 

studies for SARS-CoV-2 susceptibility should be confirmed with in vivo testing when possible.

Researchers in some countries have performed sporadic surveillance studies for SARS-CoV-1 

and SARS-CoV-2 in rodent species. For SARS-CoV-1, Eurasian beavers (Castor fiber) in a live 

market as well as chestnut white-bellied rats (Niviventer fulvescens), black rats (Rattus rattus), 

and Sikkim rats (Rattus sikkimensis) in China tested negative.33 75 Also in China, SARS-CoV-2 

remains at a low rate of positivity in hamsters, although individual species were not 

specified.247,455 In addition, a study of R. norvegicus in Belgium found no evidence of SARS-CoV2 infection,456 while a case study of one C. porcellus found no evidence of SARS-CoV-2 

transmission from its positive owner.434 Of rodent species tested near a mink farm containing 

SARS-CoV-2-positive N. vison, only one M. musculus tested positive for SARS-CoV-2, and both 

rock squirrel (Otospermophilus variegatus) and P. maniculatus animals tested negative.121
Report Page 43

Non-Farmed Ungulate and Ursid Susceptibility

Large mammals can encounter humans in farm and captive contexts as well as wildlife 

encounters. For a summary of susceptibilities of farmed large mammals, see “Farmed Ungulate 

Susceptibility.” Susceptibilities of other large mammals are summarized within this section, 

including computational modeling data for 31 species summarized in Table 11. 

Table 11: Summary of Computational Modeling Data for Large Mammals, Excluding Farmed 

Ungulates 

Evidence Types

Species Common 

Name

ACE2 Homology ACE2-RBD Affinity ACE2-RBD Molecular 

Dynamics

Ailuropoda melanoleuca Giant panda Moderate,90,245,246

High80,83,86–88,93,248,259

Low,259 Moderate,80

High83,245

Not assessed

Ammotragus lervia Barbary sheep High93 Not assessed Not assessed

Antilocapra americana Pronghorn High93 Not assessed Not assessed

Beatragus hunter Hirola High93 Not assessed Not assessed

Bison bison American 

bison

High83,90,93,248,259 Low,244 High83,259 Not assessed

Bos mutus Wild yak Moderate,245

High83,86,87,93,248,259

Low,259 High82,83,245,260 Not assessed

Camelus ferus Wild Bactrian 

camel

Low,248 Moderate,85

High83,87,88,93,259

Low,82,259 Moderate,83

High85

Not assessed

Capra aegagrus Wild goat High93 Not assessed Not assessed

Catagonus wagneri Chacoan 

peccary

Moderate,245 High93 High245 Not assessed

Ceratotherium simum White 

rhinoceros

High83,88,93,93,248,259 Low,259 High82,83 Not assessed

Dicerorhinus sumatrensis Sumatran 

rhinoceros

High93 Not assessed Not assessed

Diceros bicornis Black 

rhinoceros

High93 Not assessed Not assessed

Elaphurus davidianus Père David's 

deer

High93 Not assessed Not assessed

Equus przewalskii Przewalski’s 

horse

Moderate,83,241

High88,93,248,259

Low,82,259 High83 Not assessed

Giraffa camelopardalis Masai giraffe High93 Not assessed Not assessed

Hemitragus hylocrius Nilgiri tahr High93 Not assessed Not assessed

Hippopotamus amphibius Hippopotamus High93 Not assessed Not assessed

Loxodonta africana African bush 

elephant

Low,89,246,248

Moderate,87,93,245

High83,86,259

Low,82,244,259 Moderate,83

High245

Not assessed

Moschus moschiferus Siberian musk 

deer

Moderate,245 High93 High245 Not assessed

Muntiacus muntjak Southern red 

muntjac

High87 High82 Not assessed

Nanger dama Dama gazelle High93 Not assessed Not assessed

Okapia johnstoni Okapi High93 Not assessed Not assessed

Oryx dammah Scimitar oryx High93,259 Low,259 High85 Not assessed

Pantholops hodgsonii Tibetan 

antelope

High93 Not assessed Not assessed

Rangifer tarandus Reindeer High93 Not assessed Not assessed

Tapirus indicus Malayan tapir High93 Not assessed Not assessed
Report Page 44

Tapirus terrestris South 

American 

tapir

High93 Not assessed Not assessed

Tragulus javanicus Java mousedeerHigh93 Not assessed Not assessed

Ursus americanus American 

black bear

Moderate,245 High86 High245 Not assessed

Ursus arctos Brown bear High83,86–88,93,248,259 Low,259 High82,83,85,260 Not assessed

Ursus maritimus Polar bear Moderate,85,245

High83,86–88,93,162,248,259

Low,162,259 High82,83,85,245 Not assessed

The only experimental infection studies in large mammals have been performed in vitro. Similar 

to O. virginianus, mule deer (Odocoileus hemionus)-derived cells supported replication of SARSCoV-2.337 However, cells from another cervid, elk (Cervus canadensis), cannot support SARSCoV-2 replication.337 ACE2 overexpression from the moose (Alces alces) cervid also cannot 

support SARS-CoV-2 replication.303 Respiratory tissues from A. alces303 and sika deer (Cervus 

nippon)

338 expressed ACE2 and TMPRSS2, suggesting that both species may still be susceptible 

to SARS-CoV-2 infections despite in vitro results.303 Overexpression of two bovid ACE2s—from 

wild yak (Bos mutus)

248 and nyala (Tragelaphus angasii)303—support high viral binding of SARSCoV-2 and minimal viral replication, respectively; T. angasii lung tissue also expressed ACE2 and 

TMPRSS2.303 In addition, overexpression of ACE2s from giant panda (Ailuropoda melanoleuca),

brown bear (Ursus arctos), and white rhinoceros (Ceratotherium simum) supported SARS-CoV-2 

binding and viral entry,248 while overexpression of northern giraffe (Giraffa camelopardalis)

ACE2 overexpression only supported minimal SARS-CoV-2 replication.303 However, because of

ACE2 and TMPRSS2 positivity in G. camelopardalis respiratory tracts, these animals may still be 

susceptible to SARS-CoV-2 infections.303 Although no ACE2 or TMPRSS2 expression data have

been published for ursids, polar bear (Ursus maritimus) ACE2 consists of nine isoforms, and 

multiple truncated isoforms cannot fully interact with SARS-CoV-2 RBD, which may reduce 

susceptibility.256 Similar to its domesticated counterpart, wild camel (Camelus ferus) ACE2 

overexpression supported SARS-CoV-2 as well as SARS-CoV-1 binding and viral entry.99

Surveillance studies of large mammals for SARS-CoV-2 have been conducted for chital (Axis

axis) in a captive U.S. facility;355 roe deer (Capreolus capreolus) in Austria,457 Germany,458 and

United Kingdom;

459 C. canadensis in the United States;354 red deer (Cervus elaphus) in 

Austria,457 Germany,458 Poland,460 and United Kingdom;

459 C. nippon in the United Kingdom;459

European fallow deer (Dama dama) in the United Kingdom;459 water deer (Hydropotes inermis)

in the United Kingdom;459 Reeve’s muntjac (Muntiacus reevesi) in the United Kingdom;459 and 

mouflon (Ovis gmelina) in Germany.458 A low rate of seropositivity in C. capreolus and C. 

elaphus was detected in Germany, although these data are likely due to cross-reactivity with 

other coronavirus antibodies;458 a low rate of seropositivity in these animals was also reported 

for the United Kingdom.459 Both D. dama and M. reevesi animals in the United Kingdom also 

were seropositive for SARS-CoV-2.459
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Small and Medium-Sized Carnivore and Omnivore Susceptibility

As small carnivores and omnivores, P. larvata, N. procyonoides, mustelids, F. catus, and C. lupus 

familiaris are highly susceptible to emerging coronaviruses (see “Reservoirs,” “Mustelid 

Susceptibility,” and “Companion Animal Susceptibility” for more details); other small and 

medium-sized carnivores and omnivores could be at similar risk levels for contracting viruses 

through contact with infected prey. Susceptibility data from other small carnivores and 

omnivores are summarized in this section, including computational modeling data for 26 

species in Table 12. 

Table 12: Summary of Computational Modeling Data for Small and Medium-Sized Carnivores 

and Omnivores

Evidence Types

Species Common 

Name 

ACE2 Homology ACE2-RBD Affinity ACE2-RBD 

Molecular 

Dynamics

Acinonyx jubatus Cheetah High83,88,93,248,259 Low,82,259 High83,85 Not assessed

Canis lupus dingo Dingo Moderate,241,245

High83,87,93,248,259

Low,259 High82,83,85,245 Not assessed

Chrysocyon brachyurus Maned wolf High93 Not assessed Not assessed

Crocuta Crocuta Spotted 

hyena

Moderate,87 High88 High82 Not assessed

Cryptoprocta ferox Fossa Moderate93 Not assessed Not assessed

Helogale parvula Common 

dwarf 

mongoose

Moderate93 Not assessed Not assessed

Hyaena hyaena Striped hyena Moderate,93 High259 Low,259 High85 Not assessed

Lynx canadensis Canada lynx Moderate,85

High83,88,93,245,248,259

Low,82,259 High83,85,245 Not assessed

Lynx pardinus Iberian lynx High86,88 High82 Not assessed

Mungos mungo Banded 

mongoose

Moderate93 Not assessed Not assessed

Neofelis diardi Sunda 

clouded 

leopard

High93 Not assessed Not assessed

Neofelis nebulosa Clouded 

leopard

High93 Not assessed Not assessed

Nyctereutes 

procyonoides

Common 

raccoon dog

Low,89 Moderate83,86,87,96 High82,83 Not assessed

Paguma larvata Masked palm 

civet

Moderate,80,83–87,90–98 High88,89 Low,79–81 Moderate,83

High82,84,85

Not assessed

Panthera leo Lion High88,253 Moderate253 Moderate253

Panthera onca Jaguar High93 Not assessed Not assessed

Panthera pardus Leopard Moderate,85

High83,88,93,245,248,259

Low,259 Moderate,85

High82,83,245

Not assessed

Panthera tigris Tiger Low,257 Moderate,241,246

High80,83,84,87,88,90,93,248,253,259,261

Low,81,259

Moderate,80,253 High82–

84,244,257,260,261

Low253

Paradoxurus 

hermaphroditus

Asian palm 

civet

Moderate93 Not assessed Not assessed

Procyon lotor Raccoon Low,89 Moderate86,87 Low82 Not assessed

Puma concolor Cougar Low,257 Moderate,85

High83,87,88,93,248,259

Low,259 High82,83,85,257 Not assessed
Report Page 46

Puma yagouaroundi Jaguarundi High259 Low,259 High85 Not assessed

Speothos venaticus Bush dog High93 Not assessed Not assessed

Suricata suricatta Meerkat Low,89,245,248

Moderate,83,86,87,93 High259

Low,82,259 Moderate,83

High85,245

Not assessed

Vulpes lagopus Arctic fox High93,259 Low,259 High85 Not assessed

Vulpes vulpes Red fox Moderate,85,87,245

High83,86,89,93,96,248,259

Low,259,260 Moderate,85

High82,83,244,245

Not assessed

Most in vitro studies of carnivores and omnivores utilized overexpression of species-specific 

ACE2s and not species-derived cell lines. Similar to F. catus, ACE2s from four other feline 

species—Canada lynx (Lynx canadensis), leopard (Panthera pardus), cheetah (Acinonyx 

jubatus), and cougar (Puma concolor)—also supported high SARS-CoV-2 binding and viral 

entry.248 ACE2 and TMPRSS2 expression in respiratory tracts and small intestines of P. leo and P. 

tigris further suggest feline susceptibility to SARS-CoV-2 and potential fecal 

shedding.158,159,303,313,338 P. larvata ACE2 overexpression supported SARS-CoV-1 binding and 

entry,91,95,97,99,100 but multiple studies for this species reported varied results for SARS-CoV-2 

ranging from no viral binding and entry to moderate binding and entry;91,95–97,99,100 P. larvata 

ACE2 overexpression also supported SARS-CoV-1 replication.155,156 Exogenous V. vulpes and N. 

procyonoides ACE2s also supported viral binding and entry of both SARS-CoV-1 and SARS-CoV2.78,91,99,248

In vivo infection studies of carnivores and omnivores have only utilized N. procyonoides and P. 

lotor. In agreement with in vitro data, N. procyonoides was susceptible to intranasal infection 

with SARS-CoV-2 and could transmit the virus via direct contact with other naïve animals.102

Despite low ACE2 expression in the respiratory tract,303 P. lotor was susceptible to 

asymptomatic, intranasal SARS-CoV-2 infection resulting in seroconversion.461 However, P. lotor 

could not transmit SARS-CoV-2 to other animals via direct contact,461 and a second study 

determined that this species could not be infected with SARS-CoV-2 via the intranasal route.444

Globally, sporadic reports of natural infections in captive carnivores and omnivores indicated 

anecdotal SARS-CoV-2 infections in binturong (Arctictis binturong),462 spotted hyena (Crocuta 

crocuta), L. canadensis, white-nosed coati (Nasua narica),462 P. leo,

462–468 P. tigris,462–464,469–472

snow leopard (Panthera uncia),462,473 P. concolor,

468 and fishing cat (Prionailurus viverrinus).462

In addition, India reported one SARS-CoV-2 infection in a wild P. pardus.

474 Low seropositivity 

rates for wild golden jackel (Canis aureus) and V. vulpes were reported in Croatia, although 

Canis aureus antibodies failed to neutralize SARS-CoV-2.360 Screening of Asian palm civet 

(Paradoxurus hermaphroditus) in Cambodia25 and Vietnam,475 P. lotor in the United States121

and Canada,476 large-spotted civet (Viverra megaspila) in Cambodia,25 V. vulpes in 

Netherlands,118 and P. larvata and N. procyonoides in Cambodia25 did not detect any evidence 

of SARS-CoV-2 infections. However, past surveillance studies for SARS-CoV-1 detected high 

rates of active infections in N. procyonoides and P. larvata in live animal markets in 

China.71,73,75,77
Report Page 47

Molecular Biology and Virology

SARS-CoV-1 and SARS-CoV-2 enter cells via S protein (i.e., a class I viral fusion protein) 

interaction with the host ACE2 receptor found on pulmonary and extra-pulmonary cell types.

477

MERS-CoV gains access to host cells by engaging the S protein with transmembrane 

dipeptidylpeptidase (DPP4), also referred to as CD26.478 MERS-CoV-1, SARS-CoV-1, and SARSCoV-2 fuse at the plasma membrane and depend on cell surface proteases—such as endosomal 

cathespins, cell surface transmembrane proteases/serine proteases (TMPRSS), furin, and 

trypsin—to activate viral fusion proteins and prime the S protein at the S1 and S2 

interface.220,479,480 Interestingly, the cleavage efficiency of the S protein in the S1 and S2 

subunits modulates the SARS-CoV-2 infection.481,482 Only SARS-CoV-2 utilizes the furin protease, 

as this virus has a polybasic furin cleavage motif, unlike MERS-CoV and SARS-CoV-1.250 The RBD

position also differs between SARS-CoV-1 and SARS-CoV-2. The position of the RBD in SARSCoV-2 is frequently angled at a position that favors evasion of the host immune response, while 

the RBD in SAR-CoV-1 is frequently in the “up” conformation and demonstrates a lower binding 

affinity to ACE2 compared to SARS-CoV-2.

220,483,484 Notably, the Omicron SARS-CoV-2 variant 

enters host cells via the endocytic route, has reduced TMPRSS usage, and enhanced usage of 

membrane-type matrix metalloproteinase, leading to weaker cell-cell fusion activity.220,485

Molecular Biology Implications for Intermediate Hosts

SARS-CoV-1, MERS-CoV, and SARS-CoV-2 genomes share similarity, with SARS-CoV-2 sharing 

79% genome sequence identity with SARS-CoV and 50% with MERS-CoV.486 All three viruses 

have high sequence homologies to Chiropteran coronaviruses, and therefore likely originated 

from these animals. SARS-CoV-2 shares more than 90% and 93.3% sequence identity with the 

Chiropteran coronaviruses RaTG13 and RmYN02, respectively.486 For SARS-CoV-1 and MERSCoV, the over 99% genome sequence identity to coronaviruses isolated from palm civets and 

camels, respectively, indicates that these animals were the intermediate hosts. Pangolin-CoV is 

linked to SARS-CoV-2 with 90.7-92.6% overall sequence identity and one amino acid variation 

from SARS-CoV-2 in the RBD.

487 However, pangolins are not considered an intermediate host 

for SARS-CoV-2, in part because SARSr-CoV sequences isolated from pangolins lack the 

polybasic furin cleavage motif.107

The S protein of SARS-CoV-2 is distinct from MERS-CoV and SARS-CoV-1 and known bat SARSrCoVs. It shares 76.7-77% amino acid sequence with SARS-CoVs from civets and humans, 75-

97.7% with bat coronaviruses, and 90.7-92.6% with pangolin coronaviruses.483 Additionally, 

SARS-CoV-2 spike contains a distinct four amino acid insertion between the S1 and S2 domains 

at the priming loop,, which is seen in other SARSr-CoVs of the betacoronavirus lineage.484

Molecular surveillance, molecular dynamic simulations, and comparative in silico analyses for 

genetic diversity, particularly at the S protein level, provide clues to the origin, early evolution, 

intermediate hosts, and host adaptation and predictive range of SARS-CoV-1, MERS-CoV, and 

SARS-Cov-2 (See “Computational Modeling of Host Factors”).241,250,488

Mutations that Affect Host Range

The S protein is the key to SARS-CoV-2 receptor binding and cell membrane fusion, making it 

also a molecular determinant for host tropism and viral transmission.484 Mutations in the 
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receptor binding motif of the S protein promote adaptive diversity and increase the host range 

of SARS-CoV-2; this motif is the structural determinant that engages with the ACE2 host 

receptor. S protein mutations can also enhance binding to the host ACE2 receptor. More than 

3,561 viral S protein mutations have been identified. However, mutations that enhance 

infectivity, replication, transmissibility, and resistance to neutralization are found within five

variants, known as alpha (B.1.1.7), beta (B.1.351; mutations include L18F, D80A, D215G, Δ242–

244, K417N, E484K, N501Y, D614G, A701V), gamma (P.1; mutations include L18F, T20N, P26S, 

D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F), omicron (B.1.529; 

mutations include D614G, E484A, N501Y, Q493K, K417N, S477N, Y505H G496S) and delta 

(B.1.617.2; mutations include T19R, G142D, Δ156–157, R158G, L452R, T478K, D614G, P681R, 

D950N).489–491

The original strain of SARS-CoV-2 was unable to employ murine and non-mammalian ACE2 

receptors for viral entry.

100,492 However, SARS-CoV-2 spike mutations can expand the host range 

of infectivity, thereby creating new viral reservoirs. Thakur et al. (2022) assessed whether the S

protein of four different variants (alpha, beta, gamma, and delta) could broaden the host range 

to M. musculus, R. norvegicus, and P. larvata ACE2.489 The alpha, beta, gamma, and delta strains 

demonstrated increased usage of M. musculus ACE2 compared to the wildtype Wuhan strain 

(D614).489 The N501Y-containing variants (alpha, beta, and gamma) permitted binding to the rat 

ACE2 receptor, and the beta variant of concern conferred a small increase in binding to the 

civet ACE2.489 Other studies observed similar results with strains containing the N501Y 

mutation (present in all omicron sublineages) in the RBD. 

Mutant strains with either a single N501Y mutation or combination of N501Y, K417N, and 

K417N in the RBD also acquired the ability to interact with the M. musculus and N. vison ACE2 

receptors in vitro.192 Additionally, laboratory studies generated mouse adapted SARS-CoV-2 

strains through serial infections, and these strains contained K417N and/or N501Y mutations 

(See “SARS-CoV-1, SARS-CoV-2, and MERS-CoV Immune Responses in Select Susceptible 

Species”, “Mouse”).493 The N501Y mutation combined with the T4781 mutation in a 

pseudovirus enables utilization of G. gallus ACE2. The delta variant, which lacks the N501Y 

mutation, was unable to utilize G. Gallus ACE2, but the N501Y-containing omicron variant was 

able to employ M. gallopavo and G. gallus ACE2 receptors. The T4781 mutation combined with 

the A262A mutation increased utilization of the ACE2 receptors in S. scrofa, B. taurus, O. 

cuniculus, F. catus, C. lupus familiaris, C. hircus, and Equus caballus; however, fish and reptilian 

ACE2 receptors remained incompatible with these mutations.492 The D614G mutation is present 

in all SARS-CoV-2 variants and when combined with either A262S or T4781 mutations, 

enhanced utilization for human and NHP ACE2 has been observed.492

The Y453F and N501T SARS-CoV-2 mutations increased M. putorius furo ACE2 usage. The 

experiments that yielded this result also identified a new genetic variant, Y453F, with five 

amino acid changes in the S protein. Notably, a reverse zoonotic event has already occurred 

from humans to minks, and subsequently the mink-associated coronavirus 2 (miSARS-CoV-2) 

was transmitted back to humans containing a Y453F spike mutation in the RBD, which 

enhanced cell entry and ACE2 binding in minks, other mustelid species, and humans.

494,495 (This 
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transmission is the source of one of 76 SARS-CoV-2 variants found in humans.496) Prolonged 

interspecies contacts may result in acquisition of new mutations that further increase host 

species tropism.

Recombination Events

Recombination events of betacoronaviruses in wild and domestic animals are the evolutionary 

driving force in the emergence of SARS-CoV-1, MERS-CoV, and SARS-CoV-2, and provide an 

opportunity for zoonosis, reverse zoonosis, and creation of novel lineages. Frequent 

recombination events can take place during coinfections, which commonly occur in 

Chiropterans (see “Chiroptorans”). Both SARS-CoV-1 and SARS-CoV-2 arose after recombination 

events among Chiropteran coronaviruses. In contrast to SARS-CoV-1 and SARS-CoV-2, MERSCoV arose from recombination events in both C. dromedarius and Chiropterans.497

So et al. (2019) analyzed an example of recombination events occurring between coronaviruses 

in dromedary camels. They found evidence of recombination of DcCov-HKU23 dromedary 

isolates with viruses from rodents, O. cuniculus, and B. taurus in Nigeria, Morocco, and 

Ethiopia,

498 and identified several genomic positions indicative of cross-species virus active 

recombination events among betacoronaviruses. Recombination signals were observed with: 

(1) BcoV-DB2 at the NS2a gene, (2) rabbit coronavirus (RbCoV-HKU14) at the hemagglutinin 

esterase gene, and (3) rodentCoV-IM2014 at ORFa, ORFb, and NS5a genes.

To date, there is no evidence that MERS-CoV-2 and SARS-CoV-2 have recombined.499 However, 

future recombination events are likely to occur because: (1) both viruses are co-circulating in 

the same region, (2) both viruses can infect type II alveolar cells, (3) SARS-CoV-2 has a high 

recombination rate, and (4) SARS-CoV-2 RBD is compatible with ACE2 receptors of diverse 

species. Recombination events between MERS-CoV-2 and SARS-CoV-2 are also possible due to 

their identical transcription regulatory sequences and clusters of high sequence homology at 

ORF1a and ORF1b. 

Molecular Determinants of SARS-CoV-1 and SARS-CoV-2 Host Ranges

ACE2 receptor recognition is a necessary component of viral entry for SARS-CoV-1 and SARSCoV-2, and this receptor is conserved across a variety of species with high similarities identified 

at major binding sites.252 The ACE2 receptor has a signal sequence at the N terminus, a 

transmembrane sequence at the C terminus, and an extracellular region that contains a zinc 

metallopeptidase domain.252 The polymorphism of ACE2 receptors contributes to differences in 

SARS-CoV-2 susceptibility across various species. However, high compatibility between the 

SARS-CoV-2 S protein and various host ACE2 receptors highlights adaptive diversity and leads to 

reverse zoonosis as observed between minks and humans. Six amino residues within the 

receptor-binding domain of the S protein are important for species tropism as well as 

progression.

253

Host susceptibility is impacted by the presence or absence of amino acids that are key for ACE2-

RBD binding. Analysis of amino acid differences in the RBM can help researchers identify host 

ranges (see “Computational Modeling of Host Factors”). For example, the host ranges of SARS-
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CoV-1 and SARS-CoV-2 are dissimilar due to distinct ACE2-interacting residues within the RBD

and differences in host proteases required for activation and virus uptake.

500 Palm civets are 

thought to be an unlikely intermediate host due to the absence of amino acids needed to 

interact with ACE2.86However, substitution of the two amino acid residues of SARSr-CoV 

isolated from palm civets made it capable of infecting human ACE2-expressing cells.

501

Yet ACE2 RBD homology is not sufficient to determine host range. For example, there are 18 

interacting amino acids between human ACE2 and RBD of SARS-CoV-2; although nine of these 

sites differ in the ferret ACE2, the latter still supports SARS-CoV-2 infection.502 A comparative 

analysis revealed the differing key amino acids between RBD of SARS-CoV-1 and SARS-CoV-2 for 

interaction with the ACE2 receptor: the amino acids needed for SARS-CoV-1-ACE2 binding are 

Y442, L472, N479, D480, T487, and Y491, whereas the key amino acids needed for SARS-CoV-2 

are L455, F486, Q493, S494, N501, and Y505. Alexander et al. identified ACE2 residues in SARSCoV-2 that distinguish susceptible from non-susceptible species (Leu79, HIS34, Tyr83, Gln24, 

Lys31, Asp30, and Glu329).253 In silico analysis also suggests that species with K31, Y41, N90, 

and K353 are likely to be susceptible to SARS-CoV-2 infection.98 The authors examined amino 

acid substitutions in 14 species of mammals, birds, reptiles, and amphibians that were

proposed to be intermediate hosts for SARS-CoV-2, and discovered that N90 is possibly a critical 

position in ACE2 for SARS-CoV-2 binding, because the substitution of N90T destroys a major Nglycosylation site.98 There is a high correlation between in silico analysis of ACE2 binding 

prediction and in vivo SARS-CoV-2 infection in human, NHPs, F. catus, M. putorius furo, and S. 

scrofa (although SARS-CoV-2 replicates poorly in S. scrofa). Researchers have determined that 

ACE2 genetic diversity is broader among bat species compared to humans and other mammals 

susceptible to SARS-CoV related viruses, which aligns with Chiropterans serving as coronavirus 

reservoirs. 

Different animal species express various ACE2 isoforms, some of which do not support SARSCoV-2-ACE2 binding and impact overall infection susceptibility.256 Researchers have 

demonstrated that the cytoplasmic tail of ACE2 is not critical for SARS-CoV-2 infection. There 

are five canine isoforms, including one that lacks a transmembrane domain and a soluble 

canine ACE2; soluble ACE2 proteins impede the interaction between full-length ACE2 and SARSCoV-2. The ACE2 isoform found in S. scrofa lacks the first 122 residues in the N terminus, which 

is crucial for binding. In contrast, M. mulatta, M. fascicularis, and M. putorius furo have one 

ACE2 isoform that retains the critical amino acids for interaction with the SARS-CoV-2 S protein. 

Notably, the only ACE2 isoform found in O. aries, R. roxellana, M. leucophaeus, Physeter 

macrocephalus, and Delphinapterus leucas contains the key residues in human ACE2 needed for 

binding to SARS-CoV-2.256

Host range is also determined by host proteins that are required for infection. Poston et al.

demonstrated that a vacuolar protein sorting gene, VPS20, is required for infectivity for human 

and animal CoVs.

503 Shang et al. (2020) demonstrated that the host furin protease increases the 

types of cells, such as lung epithelial and lung fibroblast cells, that SARS-CoV-2 can infect, 

because the virus becomes less dependent on target cells to highly express other host 

proteases such as TMPRSS2 and/or lysosomal cathepsins that are used for viral entry.504
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Codon usage bias, or preferential selection for a codon in highly expressed genes, changes 

based on the host environment of a virus.505 Structural proteins of SARS-CoV-2 showed codon 

usage patterns similar to coronaviruses that infect horseshoe bats.107 Interestingly, the codon 

usage pattern of the S protein in SARS-CoV-2 is closely related to the SARSr-CoV-BtKY72 found 

in Kenya.506 This finding correlates with affinity binding and molecular dynamic simulation data.

A group led by Yuzhou Gong reported that snakes were suspected to be a likely source of 

coronaviruses. However, codon usage bias has not been shown to be useful for successful viral 

infection; in fact, several studies have disproved this utility by demonstrating that the similarity 

of RSCU between virus and host is not sufficient to identify host species.105,192

Immunology

Natural immunity to SARS-CoV-1, MERS-CoV, and SARS-CoV-2 induced after viral infection 

involves both the innate and adaptive immune systems. The robustness of these immune 

responses varies greatly based on both the viral strain and the host species.294,507–509 The 

generation of protective immunity (i.e., immunological memory) against subsequent 

reinfections with the same or related strain consists of both antigen-specific memory B and T 

lymphocytes as well as the production of neutralizing antibodies. In addition, T cells contribute 

to protection against reinfection, and tissue resident memory T cells play an important role in 

the immune response to both SARS-CoV-1 and SARS-CoV-2. 

Many detailed studies have characterized human immune responses to SARS-CoV-2, in 

particular. In the early phases of the SARS-CoV-2 pandemic, therapeutic strategies and vaccine 

formulations were inadequate, so animal models susceptible to SARS-CoV-2 were studied to 

further characterize immune responses and symptoms; current research studies focus largely 

on how viral infections and vaccination provide protection against subsequent reinfections with 

newly mutated variants of SARS-CoV-2.510 Although such studies are typically not designed to 

address coronavirus in animals per se, they have generated data relevant to understanding 

coronavirus in animals. While studies of less commonly used animal models have helped 

evaluate vaccine and therapeutic efficacy, most immunological studies have used rodents and 

NHP animal models. In addition, in the past 3 years, new SARS-CoV-2 variant lineages have 

emerged including alpha, beta, gamma, delta, and most recently, omicron—each of which has 

different pathogenic characteristics in different species, which must be considered when 

assessing animal susceptibilities. The immunological response of several species to infection 

with SARS-CoV-1, MERS-CoV, and SARS-CoV-2 are summarized below. 

Innate Immune Response

Upon viral infection, the host’s innate immune system recognizes the pathogenic singlestranded RNA via the toll-like receptor-7 (TLR-7) and toll-like receptor-8 (TLR-8). These 

receptors activate downstream signaling cascades to activate IFN regulatory factor 3 (IRF3) and 

nuclear factor kappa-light-chain enhancer (NFκB) of activated cells, which regulate both type I 

and type III IFN responses. Activation of these IFN responses results in upregulation of IFN 

stimulated genes (ISGs) and the production of various cytokines and chemokines to eliminate 

the viral infection. Earlier studies of SARS-CoV-1, MERS-CoV, and other coronaviruses 

demonstrated that betacoronaviruses have the capacity to evade the innate immune system by 
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inhibiting NFκB signaling.511,512 Because SARS-CoV-1 and SARS-CoV-2 proteins are homologous, 

ongoing analyses are focused on the roles of different SARS-CoV-2 proteins to determine 

whether they modulate the IFN response similar to SARS-CoV-1. Type I IFNs (IFN-α and 

interleukin 28 receptor alpha/beta [IL28RA/IL10Rβ]) lead to the formation of both STAT1-STAT2 

heterodimers and STAT1 homodimers, which induce transcription of ISGs. Type III IFN (i.e., IFNγ) signaling results in the formation of additional STAT1 homodimers. ORF-10 of SARS-CoV-2 

has been found to suppress the type I IFN expression and downstream ISGs through a 

mitochondrial antiviral signaling (MAVS) protein.513 Ongoing research aims to elucidate the 

roles of these overlapping IFN signaling cascades and their roles in the immune response to 

SARS-CoV-2 infection.514 

SARS-CoV-2 viral infection of lung cells results in the recruitment of both macrophages and 

monocytes to the alveolar tissue, resulting in the production of various cytokines that prime the 

adaptive immune response. Most individuals infected with SARS-CoV-2 eventually clear the 

viral infection; their immune response dampens and resolves, allowing recovery. However, 

some individuals develop more severe infections with more exaggerated innate immune 

responses than individuals who more rapidly resolve SARS-CoV-2 infections. This heightened 

response involves increased levels of inflammatory monocyte-derived macrophages (CD14+

CD16+ double positive). These macrophages are recruited to the lung tissue where they secrete 

various inflammatory cytokines including IP-10, macrophage inflammatory protein 1 α (MIP1α), and monocyte chemoattractant protein 1 (MCP-1).515,516 Inflammatory cell infiltration by 

macrophages, neutrophils, and activated T cells is associated with lung tissue damage. This 

infiltration as well as enhanced release of cytokines often results in acute respiratory distress 

syndrome (ARDS) in many cases.517,518 Individuals with severe COVID-19 disease often have 

either autoimmune diseases that elevate levels of autoantibodies to IFN-1 or mutations that 

disrupt IFN responses to infection, which highlights the importance of IFN responses for timely 

clearance of SARS-COV-2.519,520 

Numerous studies have shown that early IFN responses are critical in the innate immune 

response and are important in the early stages of disease.512 Dysregulation of IFN response 

timing may lead to more severe disease due to higher plasma levels of pro-inflammatory 

cytokines including interleukin (IL)-2, IL-7, IL-10, granulocyte colony stimulating factor (G-CSF), 

IFN gamma-induced protein 10 (IP-10), MCP-1, MIP1α, and tumor necrosis factor (TNF).521,522 In 

addition, elevated systemic levels of the pro-inflammatory cytokine IL-6 correlate with severe 

COVID-19 disease. Additional studies have suggested that inflammasome activation can elevate 

levels of IL-1 and IL-18, which can also promote inflammation.523 These pro-inflammatory 

responses contribute to the cytokine storm that is observed in severe COVID-19 disease in 

some individuals, and targeted immunosuppressive treatments can help modulate production 

of these inflammatory cytokines.517 Studies in animal models are ongoing to better understand 

the role of the IFN response in SARS-CoV-2 replication and lung pathology. 

Similar to SARS-CoV-1 and -2, infection with MERS-CoV affects the respiratory tract. MERS-CoV 

infection in camels typically causes mild symptoms including nasal and ocular discharge. 

Analysis of sera from camels revealed the presence of MERS-CoV neutralizing antibodies that 
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did not cross-react with the SARS-CoV-1 antigen.362,363 One hundred immune-response genes 

were analyzed in 121 camels that had been infected with the MERS-CoV-1 virus. 

Transcriptional profiling of 121 MERS-CoV-infected camels identified several genes with 

adaptive immune system functions (major histocompatibility complex class I and II) and innate 

immune functions. The results suggested that MERS-CoV infection involves multiple host factor

pathways that are seen in other coronavirus infections in other host species.524 In addition, type

I IFNs have been identified as critical to the innate immune response to MERS-CoV in 

camels.525,526

Adaptive Immune Response

The generation of immunological memory against subsequent SARS-CoV-1, MERS-CoV, and 

SARS-CoV-2 reinfections involves the adaptive immune response, which consists of virus 

specific memory B and T lymphocytes functions. B cells generate the humoral response by 

producing neutralizing antibodies that can prevent reinfection with the same or related strains 

of the virus.

527 In addition, both CD4+

T cells and CD8+T cells contribute to viral clearance. CD8+

cytotoxic T cells kill infected cells, while CD4+ helper T cells prime the B cell response as well as 

produce cytokines for immune cell recruitment. Immunological memory involves several 

immune cell types including memory B cells, plasma B cells, and tissue resident memory T cells 

that allow for a rapid immune response and accelerated clearance of infection when the host 

encounters the virus in a subsequent infection. SARS-CoV-2 elicits a robust B cell response, and 

most individuals seroconvert and produce antibodies 7 to 10 days post infection (dpi). 

Antibodies include virus-specific immunoglobulin (Ig)M, IgG, and IgA that recognize the external 

S protein or internal N protein. Neutralizing antibodies against the RBD can prevent viral entry 

into cells and subsequent infection.

528,529 Neutralizing antibodies that bind RBDs of SARS-CoV-1, 

MERS-CoV, and SARS-CoV-2 are distinct for each virus. However, there is some degree of crossreactivity between antibodies to the S and N proteins of the coronaviruses. These cross-reactive 

antibodies target the stem helix portion of the spike S2 fusion subunit, which is present in the 

prefusion conformation in different viruses.

530,531 

The longevity of protection afforded post-infection for SARS-CoV-1, MERS-CoV, and SARS-CoV-2

in animals is poorly understood. However, studies of human patients who have recovered from 

SARS-CoV-2 infection determined that while specific plasma and memory B cells are present, 

they begin to decline approximately 3 months post-infection. In addition, SARS-CoV-1 

neutralizing antibodies decrease significantly within a few years of infection to nearly 

undetectable levels in some individuals.532 Studies conducted on camel serum have shown the 

presence of antibodies highly specific for the MERS-CoV S protein.363 The durability of this 

antibody protection is poorly understood; however, a study of calves identified reinfections 

with a median time between infections of only 59 days.58

SARS-CoV-1, MERS-CoV, and SARS-CoV-2 Immune Responses in Select Susceptible 

Species

Because NHP immune systems closely recapitulate human innate immune responses to 

pathogens, most immunological studies are performed in these animal models rather than 

rodent models. As a result, information about immune responses to SARS-CoV-1, MERS-CoV, 
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and SARS-CoV-2 in animals is limited primarily to NHPs. However, additional studies of SARSCoV-2 have been performed in cats, hamsters, ferrets, and transgenic mice expression human 

angiotensin I converting enzyme 2 (hACE2).507,508,533,534 The immune response elicited by 

infection with SARS-CoV-1 and SARS-CoV-2 will be summarized for several host species below.

Non-Human Primates

Immunology research on SARS-CoV-1, MERS-CoV, and SARS-CoV-2 has been performed in 

multiple different NHPs (e.g., M. mulatta, M. fascicularis, P. anubis, C. sabaeus). M. mulatta are 

susceptible to SARS-CoV-1 infection535 as well as MERS-CoV infection.323,536,537 M. mulatta have 

also been used in numerous studies of SARS-CoV-2 and its emerging variants.316,320,538,539 In 

response to SARS-CoV-2 infection, M. mulatta develop clinical symptoms including systemic 

inflammation and elevation of cytokines accompanied by interstitial and alveolar pneumonitis

within the first week of infection. Analysis of BAL samples collected from infected M. mulatta

indicates that they mount an early antiviral response including an inflammatory phenotype with 

the presence of both innate and adaptive immune cells, myeloid cells, and a type I IFN

response. Cytokines including IFN-α, IFN-γ, IL-6, IL-8, perforin, IP-10, MIP1-α, and MIP1-β were 

elevated in these BAL samples as well. Both type I IFNs and IL-6 are signatures of a cytokine 

storm that contributes to the development of ARDS (see “Innate Immune Response”). In 

addition, IFN-α was elevated, which resulted in downstream expression of the type I ISG IP-10 

(i.e., CXCL-10); increased IP-10 can facilitate recruitment of T regulatory CXCR3+ Th1 T cells, 

which are found at sites of inflammation. Further analysis of lung tissue revealed extensive 

infiltration of interstitial lymphocytes, macrophages, plasma cells, and eosinophils, which led to 

an expansion of the alveolar space. Both CD4+T cells and CD8+T cells exhibited both proliferative 

and memory cell markers that increased after infection with the virus. By contrast, markers of 

naive T cells and effector T cells were reduced, indicating that an induction of robust CD4+ and 

CD8+ T cell responses had taken place after infection and was maintained up to 9 dpi.540 Viral 

antigens were detected in alveolar epithelial cells and alveolar macrophages, suggesting 

engulfment of infected cells. Following infection with SARS-CoV-2, CD4+T cells isolated from BAL 

samples expressed high levels of PD-1 and LAG-3, indicating a high level of T cell exhaustion. 

Additionally, CD8+T cells in BAL fluid had increased PD-1 and LAG-3 expression, which was

correlated with the BAL viral titer load. It appears that rapid recruitment of myeloid cells 

expressing Type I IFNs aids in controlling the viral replication of SARS-CoV-2, but the remaining 

viral antigens promote the recruitment of effector T lymphocytes. M. mulatta also developed T 

cell memory for SARS-CoV-2.540 

In SARS-CoV-2 challenge experiments using previously infected M. mulatta, the animals had a 

marked reduction in median viral loads compared to the primary infection with a concomitant 

increase in B and T cell responses. This protective adaptive immune response involving both B 

and T cells was elicited by 21 days after infection and afforded a full protection against 

reinfection,539 indicating that SARS-CoV-2 infection induces protective immunity against reexposure in M. mulatta. In addition, the antibodies exhibit a range of effector functions, 

including antibody-dependent complement deposition, antibody-dependent cellular 

phagocytosis, and antibody-dependent natural killer (NK) cell degranulation (NK CD107a).539 

However, many questions remain regarding the durability of protection, and studies are 
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ongoing to determine the level of protection after a several month period. Other studies 

indicate that this protective response is CD8+ T cell-dependent.539 

M. fascicularis infected with SARS-CoV-2 exhibit mild clinical symptoms, including mild fever 

and weight loss, nasal discharge, and high levels of viral RNA present in the respiratory tract. 

Viral loads were lower than those observed in the M. mulatta, and viral clearance occurs more 

quickly in this species.319,320 Infected animals also developed diffuse alveolar damage.541

Additional studies found that P. anubis are generally more susceptible to SARS-CoV-2 infection 

than M. mulatta and display more extensive lung infection (see “Non-Human Primates”). 

Histopathological analysis of BAL samples revealed the presence of plasma cells, interstitial 

lymphocytes, macrophages, the alveolar space. There is also evidence of alveolar wall 

thickening and collagen deposition. P. anubis also exhibit more prolonged viral shedding with 

higher levels of virus being present when compared to rhesus macaques. 

Studies conducted on C. jacchus indicated less severe pathology and limited viral shedding after

SARS-CoV-2 infection when compared to rhesus macaques or baboons.540,542 Histopathologic 

analysis of BAL samples indicated a lower number of interstitial lymphocytes and macrophages 

in the alveolar space, indicating less recruitment to lung tissues (see “Non-Human Primates”). 

SARS-CoV-1-infected marmosets were found to develop interstitial pneumonia and may also 

develop additional pathologies involving liver and renal organs and gastrointestinal 

involvement.543

In SARS-CoV-2 infection studies, C. sabaeus developed moderate viral titers as evidenced by the 

presence of viral RNA and infectious virus in nasal, BAL, oral, and rectal swabs by day 2 postinfection. In addition, the animals developed more severe respiratory disease and exhibited 

interstitial pneumonia with diffuse alveolar damage, hyaline membranes, and multinucleate 

epithelial cells by day 5 post-infection.317 All animals in the study seroconverted at day 5 postinfection and were protected in challenge experiments conducted 2 months after the primary 

infection. Transcriptome analysis of BAL samples demonstrated stimulation of proinflammatory IFN and IL-6 pathways similar to other NHPs. In addition, these animals had 

increased serum concentrations of interleukins as well as other pro-inflammatory cytokines and 

chemokines.317 

The immune responses in aged NHPs have been studied in some NHPs. While both young and 

aged M. mulatta fully recovered by 2 weeks post infection, aged M. mulatta had lower SARSCoV-2 IgG titers compared to their young counterparts. For P. anubis, SARS-CoV-2 infections in 

aged animals yielded higher SARS-CoV-2 viral titers and more severe pathology compared to 

young animals. Although C. jacchus exhibit mild disease when infected with SARS-CoV-2, aged

C. jacchus exhibited some degree of pulmonary inflammation although they still recover 

quickly.540 

Results on these NHPs indicate that different species mount differing immune responses to

SARS-CoV-2, with the P. anubis exhibiting more severe disease than both M. mulatta and C. 
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jacchus. Notably, M. mulatta and P. anubis share multiple SARS-CoV-2 immune response 

features. 

Syrian Hamster

Hamsters are naturally susceptible to infection with SARS-CoV-2, and M. auratus has been used 

extensively as an animal model to study the immune response to SARS-CoV-2 because infection 

with the virus mimics many characteristics of human COVID-19 disease. M. auratus develop 

moderate disease following intranasal infection with low doses of the virus but recover within 2 

weeks.544 SARS-CoV-2 RNA was detected at high levels in nasal turbinates, trachea, and lungs 

with lower levels measured in other organs including intestines, heart, liver, spleen, and kidney. 

Additionally, SARS-CoV-2 was detected in brain tissue of hamsters and acute inflammation of 

the olfactory epithelium is seen with infection of mature and immature olfactory neurons. This 

may relate to the olfactory function impairment seen with COVID-19 in patients.545 

Severity of pulmonary disease correlates with the infectious dose of virus, and the most severe 

pathology is observed at day 5 post-infection, followed by clearance of viral antigen and a 

reduction in inflammation by 2 weeks post infection.251 In addition, infected hamsters display 

both enteric necrosis as well as cardiac myofiber degeneration not observed in other rodent 

species. Neutralizing antibodies were detectable at approximately 1 week post-infection. Viral 

replication in hamsters could be suppressed by administration of early convalescent serum 

collected from previously infected hamsters. However, convalescent serum did not reduce the 

lung pathology observed.

546 

In additional experiments, previously infected Syrian hamsters were protected against 

subsequent reinfection of SARS-CoV-2, as evidenced by absence of viral replication and lung 

pathology.547,548 Additional reinfection experiments with newly emerging Alpha and Beta 

variants showed that previously infected Syrian hamsters were protected against viral 

replication in the lower respiratory tract and severe lung pathology. However, viral replication 

was still observed in the upper respiratory tract, suggesting that these animals could still 

transmit SARS-CoV-2.549 

The role of type I and type III IFNs in controlling SARS-CoV-2 replication was investigated in 

STAT2 knockout hamster lines that lack this key type I and type III IFN downstream signaling 

protein. Viral titers in blood were higher in STAT2-deficient hamsters compared to wildtype 

controls, although the severe lung pathology was not observed in these animals. These results 

suggest that STAT2-dependent IFN responses play a key role in limiting viral dissemination yet 

contribute to the development of lung pathology observed upon infection.550 Additional studies 

have demonstrated the role of the adaptive immune response using RAG2 hamster knockout 

strains551 and IL-2 R deficient hamsters.

544 Studies of both genetic backgrounds showed that 

functional B and/or T cells are required for clearance of the virus. Prolonged viral presence of 

up to 24 days was evident in the IL-2 R knockout hamster strain, which lacked T cells, NK cells, 

and mature B cells, suggesting that the innate immune system plays a role in decreasing viral 

replication, and that the adaptive immune system is needed to completely clear the viral 

infection. Comparison of M. auratus model to other rodent models indicates that the SARS-
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CoV-2 virus replicates to higher levels and for a longer period of time in the respiratory tracts of 

hamsters. In addition, hamsters also display more significant lung pathology with spread of 

virus to other organs and tissues.552,553 

Ferret

M. putorius furo are highly susceptible to SARS-CoV-1 and SARS-CoV-2 (see “Mustelid 

Susceptibility”).

294,309 Upon infection with SARS-CoV-2, ferrets display elevated body 

temperatures and shed the virus through nasal secretions. SARS-CoV-2 is detectable in saliva, 

urine, and fecal specimens. Viral antigens were also detected in nasal turbinate, lung tissues, 

and intestine until 8 days after infection. Infected ferrets could also transmit SARS-CoV-2 to 

naive ferrets via direct contact.309 Analysis of age-related disease severity in ferrets 

demonstrated that aged ferrets older than age 3 years exhibited higher viral loads and longer 

periods of viral shedding accompanied by a more prominent lung inflammatory cell infiltration 

when compared to young animals.312 Lung tissues from SARS-CoV-2-infected, aged ferrets 

showed enhanced type I IFN activity as well as an increase in activated T cells and macrophage 

responses when compared to young animals.

309 Together, these data indicate that age is a 

critical factor in SARS-CoV-2 severity in M. putorius furo. Infected ferrets develop antibodies 

against SARS-CoV-2,

294,309 and challenge of recovered ferrets with SARS-CoV-2 was 

accompanied by a reduction in viral shedding from the upper respiratory tract compared to the 

prior infection, indicating protection from reinfection.

307 

Mink

Previous research has indicated that N. vison can be infected by both SARS-CoV-1554 and SARSCoV-2.116,555,556 SARS-CoV-2 causes severe respiratory disease in N. vison with high mortality 

rates. Virus can be detected in nasal, oral and rectal swabs, and SARS-CoV-2 transmission 

between N. vison and humans has occurred extensively.557,558 Infected minks often exhibit 

labored breathing, with interstitial pneumonia and extensive neutrophil, macrophage and 

lymphocyte infiltration in lung tissue with resulting alveolar damage. 

Mouse

Wildtype mouse susceptibility differs for SARS-CoV-1 and SARS-CoV-2.

559 SARS-CoV-1 can infect 

several laboratory strains of mice including BALB/c and CC57BL/6 mice, and viral replication can 

be detected in the respiratory tract of mice. The mice are asymptomatic and do not display 

severe pathology of lung tissue with infection and exhibit only mild infiltration of inflammatory 

cells. Virus is cleared within 1 week, and neutralizing antibodies can be detected. However, 

these laboratory strains of mice are not readily infected with older strains of SARS-CoV-2. 

Recent reports have investigated newly emerging variants of SARS-CoV-2 and found that the 

B.1.351 variant containing the N501Y mutation in the S protein has allowed recognition of the 

mouse ACE2 receptor, allowing entry of the virus and subsequent infection of wild type mice. In 

addition, the presence of serum SARS-CoV-2 specific neutralizing antibodies was detected at 14 

dpi in mice that had been infected with the variant strain but not in mice infected with wildtype

SARS-CoV-2. Levels of neutralizing antibody increased after rechallenge with the variant species 

of the virus.560
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Numerous mouse models susceptible to SARS-CoV-1 and SARS-CoV-2 infections have been 

generated through various means: (1) adaptation of viruses through serial infections in mice,

561

(2) transgenesis of mice to insert human ACE2,

562–565 and (3) transduction of mice with human 

ACE2 via adenovirus 5.

566,567 Transgenesis has also been used to generate human DPP4 

expressing mice that are susceptible to MERS-CoV infection.

568 Several mouse-adapted strains 

of both the SARS-CoV-1569 and SARS-CoV-2 virus have been generated in the past few years that 

would allow infection and efficient replication of the virus in both the upper and lower 

respiratory tracts in laboratory strains of mice.

570–573 The SARS-CoV-2 WuHan-Hu-1 strain of 

virus was used to intranasally inoculate BALB/c mice, and the virus was passaged for 11 times, 

generating a viral strain that was infective in the mice and caused interstitial pneumonia. 

Sequence analysis of the virus revealed mutations in the RBD of the S protein, which resulted in 

increased binding affinity for the mouse ACE2 receptor.

574 Similar methods have been used to 

generate several different mouse-adapted strains of the virus that accumulate multiple 

mutations at different sites in the RBD with repeated passaging. The more virulent strains of 

the virus result in acute lung injury with significant lung inflammation accompanied by 

infiltrating immune cells.570–573 Ongoing research of SARS-CoV-2 focuses on host immunology 

and its ability to prevent viral infection. However, because these studies have mainly used 

transgenic, humanized mouse models, there is a paucity of immunological studies conducted in 

wildtype rodent species that may actually be susceptible to SARS-CoV-2. 

Pathogenesis

Hamster

Golden Syrian

SARS-CoV-2 

Studies containing pathogenesis data on coronaviruses in hamsters primarily focus on M. 

auratus as a model for human disease. Aside from humans and M. mulatta, M. auratus ACE2 

exhibited the highest binding affinity to the S protein of SARS-CoV-2 from in silico modeling (see 

“Rodent Susceptibility” for more details).251 M. auratus inoculated with SARS-CoV-2 primarily 

lost weight or had reduced weight gain, as well as lethargy, ruffled fur, a hunched posture, and 

dyspnea.251,452,575–577 However, Yuan et al. (2021) found that many female M. auratus showed 

no significant weight loss, while male M. auratus showed up to 9.6 percent mean weight loss 

through 7 dpi.578 In addition, M. auratus inoculated with the Delta variant (B.1.617.3) showed 

the least weight gain compared to those inoculated with the B.1 D614G variant, while M. 

auratus inoculated with the Omicron variant (B.1.1.529) experienced no weight loss.579,580

These data suggest that M. auratus susceptibility to infection of SARS-CoV-2 is dependent on 

both M. auratus sex and SARS-CoV-2 variant.

Viral RNA was detected primarily in the nasal turbinates and lungs of SARS-CoV-2 inoculated M. 

auratus, with males showing the most sensitivity to infection and viral replication compared to 

females.251,452,578 From immunohistochemistry (IHC) analysis of tissue samples, viral antigen was 

detected in bronchial epithelial cells and pneumocytes, nasal epithelial cells, olfactory sensory 
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neurons, and duodenum cells.452 In Delta-inoculated M. auratus, viral RNA was detected in 

nasal turbinates, trachea, and lungs up to 14 dpi, while Omicron-inoculated M. auratus showed 

significantly less viral burden in lung tissue compared to Delta-inoculated M. auratus.

579,580

Blood hematology of SARS-CoV-2-inoculated M. auratus showed significant increases in 

neutrophils, red blood cells, and hemoglobin, as well as intracardiac platelet and fibrin 

aggregates at 8 dpi, which is potentially indicative of hypercoagulation. Blood chemistry 

showed elevated markers of renal disease and blood lipids, such as uric acid, triglyceride, and 

low-density lipoprotein. Furthermore, metabolic markers, such as total protein and albumin, 

significantly decreased. Together, these blood chemistry changes indicate a potential 

dysregulation of extrapulmonary organs during acute infection.575

Histopathological analysis of lung tissues from SARS-CoV-2-inoculated M. auratus showed 

broncho-interstitial pneumonia (correlated with continued weight loss), diffuse alveolar 

damage, protein-rich fluid exudate, hyaline membrane formation, cellular debris in bronchiolar 

lumen, alveolar collapse with hemorrhage, and damage to pulmonary vasculature.251,575,576

Nasal turbinates showed inflammatory cell infiltration and blood vessel congestion, though the 

epithelium was generally intact.251,452 The bronchial and mesenteric lymph nodes show 

subcapsular and medullary lymphatic sinus ectasia, and the trachea shows epithelial cell 

swelling, focal cilia loss, and mononuclear cell infiltration.251 In lung tissue from Omicroninoculated M. auratus, congestion and hemorrhages were absent because of less efficient viral 

replication compared to Delta-inoculated M. auratus, which showed severe pathological 

changes.579,580

One study evaluated M. auratus that lacked the STAT2 gene (STAT2-/- M. auratus) to determine 

the role of STAT2 signaling in SARS-COV-2 pathogenesis.550 After SARS-CoV-2 inoculation,

STAT2-/- M. auratus showed higher viral titers and detectable viral RNA in the blood, spleen, and 

liver not typically found in SARS-CoV-2-inoculated wildtype M. auratus. In contrast, the lung 

pathology in STAT2-/- M. auratus was significantly attenuated compared to wildtype M. auratus. 

Furthermore, pulmonary consolidations were not present in STAT2-/- M. auratus. These findings 

indicate that STAT2 potentially not only restricts the systemic spread of SARS-CoV-2 infection, 

but also drives severe lung injury.550

SARS-CoV-1 

M. auratus inoculated with SARS-CoV-1 (Urbani strain) did not show clinical symptoms; 

however, high viral titers were detected in the upper and lower respiratory tracts for up to 5 

dpi, while lower levels of viral titers were detected in the liver and spleen. At 1 to 2 dpi, viral 

titers could be transiently detected in blood and plasma but are no longer detected by 3 dpi. 

From IHC analysis, viral antigens were found in endothelial cells of the nasal turbinates and 

mucosal glands of the trachea. From histopathological analysis, epithelial cells of the nasal 

turbinates, trachea, and bronchi showed swelling with mononuclear inflammatory cell 

infiltrates in the submucosa of bronchioles, which is indicative of pneumonitis. In addition, the 

nasal passages contained mild ulcers and the trachea had a focal loss of cilia. However, the 

lungs of SARS-CoV-1-inoculated M. auratus recovered without detectable viral antigen by 14 
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dpi. Upon rechallenge of SARS-CoV-1 inoculation, M. auratus showed no clinical symptoms, a 

lack of detectable viral antigen in all tissues, and a lack of pneumonitis.581

Although SARS-CoV-1-inoculated M. auratus developed only mild infections, M. auratus 

immunosuppressed with cyclophosphamide treatment experienced increased weight loss and 

mortality. High viral titers were detected at 2 dpi and were eventually detectable in the lungs, 

liver, spleen, and kidneys by 19 dpi. From histopathological analysis, lungs showed moderate 

bronchointerstitial pneumonia with multifocal infiltrations of macrophages, neutrophils, 

lymphocytes, and plasma cells. In extrapulmonary tissues samples, multifocal myocardial 

inflammation was present, as well as dilation of renal cortical tubules, tubular degeneration, 

and renal necrosis. Together, these findings suggest that immunosuppressed M. auratus are 

susceptible to broader pathogenesis of SARS-CoV-2 infection compared to healthy M. 

auratus.

582

MERS-CoV

M. auratus inoculated with MERS-CoV lacked indications of clinical symptoms, viral replication, 

histopathological lesions in the lungs, cytokine upregulation, or seroconversion of antibodies, 

indicating that MERS-CoV cannot effectively replicate in M. auratus.

323

Roborovski

SARS-CoV-2 

P. roborovskii inoculated with SARS-CoV-2 show severe clinical symptoms, including snuffling, 

dyspnea, cough, sneeze, ruffled fur, reduced activity, hunched posture, and weight loss.454,583

Interestingly, although Zhai et al. (2021) did not find any change in body temperature, Trimpert 

et al. (2020) found that body temperature significantly decreased. In addition, multiple P. 

roborovskii were deemed terminally ill and were euthanized at 3 dpi.454 Viral RNA and titers

were primarily detected in the homogenates of the lung and trachea, with lower levels

detected in the brain, stomach, intestine, liver, heart, kidney, spleen, and blood. From IHC 

analysis, viral antigen was detected in alveolar epithelial cells, bronchial epithelial cells, 

macrophages infiltrating the bronchi, liver cells, subarachnoid cells of the brain, and blood 

leukocytes.

454,583 Blood analysis also revealed elevated levels of fibrin degradation product and 

D-dimer in plasma, suggesting thrombosis and fibrinolysis.583 These viral RNA, IHC, and blood 

analysis data suggest a severe systemic infection in SARS-CoV-2-inoculated P. roborovskii. 

From histopathological analysis, lung tissues showed severe inflammatory lesions, multifocal 

interstitial pneumonia with thickened alveolar septa and infiltration of fibrin and mononuclear 

cells, diffuse alveolar damage, hyaline membrane formation, edema, and cellular debris within 

alveoli.454,583 In extrapulmonary organs, liver tissues showed multifocal fatty changes and portal 

lymphocytic infiltration, and brain tissues showed focal infiltration of lymphocyte and 

subarachnoid hemorrhage. However, despite high levels of viral RNA detected in the trachea, 

tissue damage was not detected. In addition, no obvious histopathological changes were 

observed in the stomach, intestine, heart, kidney, and spleen.583
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Together, these data suggest that P. roborovskii develop severe or fatal disease from SARS-CoV2 inoculation and are substantially more susceptible to infection than M. auratus. From genome 

sequencing analysis, the ACE-2 receptors of P. roborovskii and M. auratus show minor 

differences. However, these differences do not reside in any amino acids associated with SARSCoV-2 binding, and thus cannot account for the viral susceptibility differences between P. 

roborovskii and M. auratus.

454

Mouse

SARS-CoV-2 

M. musculus inoculated with SARS-CoV-2 (WA1/2020) do not show significant signs of infection 

characterized by clinical symptoms or pathological analysis because of insufficient binding 

affinity between the SARS-CoV-2 S protein and murine ACE2 receptors.500 However, multiple 

variants, including Beta (B.1.351) and Alpha (B.1.1.7), showed infectious potential in mice. Both 

variants contain an N501Y substitution in the S protein, which may increase the binding affinity 

of the S protein to murine ACE2 receptors.560,584,585

Both BALB/c and C57BL6/J M. musculus inoculated with the Beta variant lost weight in a dosedependent manner, while older BALB/c M. musculus showed ruffled fur, hunched postures, and 

mortality.584 BALB/c M. musculus also contained higher viral RNA and titer levels in the lungs 

compared to C57BL6/J M. musculus, with IHC analysis showing infection of bronchial epithelial 

cells, macrophages, and stroma cells in BALB/c M. musculus. From histopathology analysis, the 

lungs of BALB/c M. musculus had lesions in both lobes, perivascular and interstitial edema, and 

hemorrhages, as well as alveolar wall thickening due to macrophage infiltration.584,585 Similarly, 

C57BL6/J M. musculus inoculated with the Alpha variant showed viral RNA in the nasal 

turbinates, lungs, spleen, colon tissues, and brain, with alveolar wall congestion, inflammatory 

infiltration, and hemorrhages in the lungs.560

However, Currey et al. (2022) reported conflicting findings when inoculating C57BL6/J M. 

musculus with the Beta variant; C57BL6/J M. musculus did not show clinical symptoms or 

pathological changes in the lungs.586 In addition, BALB/c M. musculus inoculated with the 

Omicron (B.1.1.529) variant (which also contains an N501Y substitution) did not show clinical 

symptoms or changes in pulmonary function on whole-body plethysmography. Omicroninoculated M. musculus also showed significantly lower viral titers in the lungs and nasal 

turbinates compared to Beta variant-inoculated M. musculus.

580 Although mouse-adapted 

SARS-CoV-2 strains similarly contained the N501Y substitution and caused increased virulence 

in M. musculus,

587 these conflicting findings make it unclear whether M. musculus are 

susceptible to infection from N501Y variants.

SARS-CoV-1 

BALB/c M. musculus showed age-dependent signs of infection when inoculated with SARS-CoV1.588,589 Young BALB/c M. musculus experienced mild clinical symptoms and were often 

asymptomatic,590 while older BALB/c M. musculus had clinical symptoms of weight loss, 
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hunched posture, ruffled fur, and mild dehydration.588 In older BALB/c M. musculus, viral titers 

were detected in the lungs, nasal turbinates, and liver, with IHC detecting viral antigen in 

epithelial cells of nasal turbinates and bronchioles and alveolar pneumocytes, but not in whole 

blood or spleen. From histopathological analysis, the lungs had pneumonitis, alveolar damage, 

hyaline membrane formation, intra-alveolar edema, and fibrotic foci.588

Older BALB/c M. musculus inoculated with SARS-CoV-1 also showed a higher number of 

differentially regulated host cellular genes than younger M. musculus. Furthermore, the 

number of differentially expressed genes in lung tissues of older SARS-CoV-1-inoculated M. 

musculus were significantly greater compared to younger M. musculus. A set of genes 

associated with cell cycle (e.g., DNA repair, cell development, and cell death) were 

downregulated in younger M. musculus but upregulated in older M. musculus. The upregulation 

of these cell cycle genes, along with continuous upregulation of genes associated with immune 

response through 7 dpi, may contribute to immunopathology and delays in viral clearance in 

older SARS-CoV-1-inoculated M. musculus.

589

Non-Human Primates 

Rhesus Macaque

SARS-CoV-2 

Studies on M. mulatta inoculated with SARS-CoV-2 report conflicting findings. Some studies 

found that SARS-CoV-2-infected M. mulatta showed no clinical symptoms, including no 

increases in body temperature or decreases in weight,576,591 while others found changes in 

respiratory pattern, increased body temperature, reduced appetite, hunched posture, pale 

appearance, and dehydration.592,593 Choudhary et al. (2022) and Munster et al. (2020) both 

inoculated M. mulatta with WA1/2020 SARS-CoV-2 at similar doses via intratracheal and 

intranasal routes; however, ocular inoculation alone did not affect weight or body 

temperature.321 When inoculated with the Beta (B.1.351) variant, M. mulatta experienced 

weight loss and increased body temperature, as well as hematological changes indicative of 

acute viral infection.594

Studies confer viral shedding is detected from swabs of the nose, oropharyngeal, rectum, and 

bronchoalveolar lavage (BAL), with no viral shedding detected in urine.576,592,593 Viral RNA was

detected transiently in blood, as well as in the gastrointestinal tract and lymphoid tissues.592,593

From IHC analysis, viral antigen was found in type I and II pneumocytes and alveolar 

macrophages in lung tissue, as well as lymphocytes and macrophages in intestinal tract 

tissue.593 Beta variant-inoculated M. mulatta supported more efficient viral replication in the 

lower respiratory tract and lung tissue compared to those inoculated with prototype SARS-CoV2 strain GD108.594 After ocular inoculation of M. mulatta with SARS-CoV-2, viral RNA was 

detected in the conjunctiva, lacrimal gland, nasal cavity, and throat, all of which form a bridge 

between ocular and respiratory tissue.321
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From histopathology analysis, lung tissues contained multifocal lesions, interstitial pneumonia, 

diffuse alveolar damage, thickening of alveolar septa, alveolar oedema, fibrin with formation of 

hyaline membranes, and type II pneumocyte hyperplasia. In addition, some endothelial cells of 

blood vessels were necrotic with edematous vessel walls containing cellular debris, which is 

indicative of both vasculitis and endotheliitis.576,592,593 In extrapulmonary tissues, one M. 

mulatta showed evidence of encephalitis, with brain tissue histopathology revealing multifocal 

inflammatory cell infiltrates and blood vessel cuffing. However, no other SARS-CoV-2-related 

histopathological changes were reported in other organ tissues.576

SARS-CoV-1 

M. mulatta inoculated with SARS-CoV-1 showed no clinical symptoms of illness.324,595 Viral titers 

were detected from nose and throat swabs and tracheal lavage samples, but not in plasma, 

urine, or fecal samples.324 In addition, viral RNA is detected in tissues from lymph nodes, 

trachea, and lungs. Blood hematology and chemistry of infected M. mulatta often revealed low 

platelet counts, but no other remarkable changes. From histopathological analysis, lung tissues 

had lesions, focal consolidation, mild interstitial edema, alveolar inflammation, but no diffuse 

alveolar damage.595

MERS-CoV

M. mulatta inoculated with MERS-CoV displayed clinical symptoms of transient increased body 

temperature and decreased water intake. Viral RNA was detected in tissue homogenates of the 

lungs, but not in nasal turbinate, oropharyngeal, and rectal swabs. From IHC analysis, viral 

antigen was found extensively across type I and II pneumocytes, alveolar macrophages, 

eosinophils, and bronchial epithelial cells. From histopathological analysis, lung tissues had 

focal interstitial pneumonia, focal degeneration and necrosis of pneumocytes and bronchial 

epithelial cells, focal pulmonary oedema, and mild hemorrhage.322,596 Extrapulmonary tissues 

did not exhibit any histopathological changes.322

Cynomolgus Macaque

SARS-CoV-2 

Similar to M. mulatta, studies of M. fascicularis inoculated with SARS-CoV-2 report a range of 

clinical symptoms, with some reporting no changes in weight, body temperature, or adverse 

clinical signs,500,591 and others reporting increased body temperature and decreased 

appetite.597,598 In comparison to M. mulatta, infected M. fascicularis had similar viral RNA levels 

from nasal washes, throat swabs, and bronchiolar lavage, peaking at 3 dpi. Histopathological 

changes in the lungs of M. fascicularis were also comparable to M. mulatta, showing multifocal 

areas of pneumonitis with alveolar necrosis, alveolar wall thickening, alveolar oedema, and 

inflammatory infiltration. However, Bixler et al. (2022) found that lung tissues from M. 

fascicularis showed more severe pulmonary lesions compared to M. mulatta. Furthermore, M. 

fascicularis still contained viral antigen in lung tissues upon IHC analysis at 9 dpi, while most M. 
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mulatta no longer had viral antigen.591 These findings suggest that M. fascicularis are 

potentially susceptible to more severe SARS-CoV-2 infection than M. mulatta. 

SARS-CoV-1 

M. fascicularis inoculated with SARS-CoV-1 show similar clinical symptoms to SARS-CoV-2 

infection, as well as decreased activity, decreased appetite, and dyspnea;595,599,600 however, one 

study reported that M. fascicularis were asymptomatic.324 Viral RNA and titers were detected 

from nasal, throat, and rectal swabs in higher levels than those from M. mulatta, as well as 

urine (unlike SARS-CoV-2) and occasionally blood samples.324,599 Hematology revealed minimal 

change to blood cell counts, and blood chemistry indicated elevated alkaline phosphatase, 

which may or may not necessarily reflect hepatic injury.599 In addition, viral RNA was detected 

in tissues from lymph nodes, trachea, and lungs.595 From histopathological analysis, lung tissues 

showed interstitial pneumonia similar to SARS-CoV-2 infection, with diffuse alveolar damage, 

alveolar edema, and necrosis of alveolar and bronchiolar epithelium.600

Pigtail Macaque

SARS-CoV-2 

M. nemestrina inoculated with SARS-CoV-2 experienced mild clinical symptoms of decreased 

appetite, soft stool, and mild cough and dyspnea, but no change in weight, body temperature, 

or blood oxygen saturation levels. Viral titers in M. nemestrina were found in nasal, pharyngeal, 

and rectal swabs, with M. nemestrina showing higher titers from nasal swabs and lower titers 

from pharyngeal swabs compared to M. mulatta. From histopathological analysis, lung tissues 

had interstitial pneumonia with expanded alveolar septa lined by type II pneumocytes and 

occasional alveolar fibrin rafts, similar to mild histopathological findings in M. mulatta. 

However, mild residual interstitial pneumonia was observed in lung tissue of M. nemestrina

even after viral antigen is no longer detected at 21 dpi, suggesting longer-term respiratory 

complications. In addition, D-dimer levels were elevated in blood samples from M. nemestrina

within the first week of infection, indicating potential coagulopathy. These findings potentially 

suggest a more robust response from SARS-CoV-2 infection in M. nemestrina than M. 

mulatta.

601

African Green

SARS-CoV-2 

C. aethiops inoculated with SARS-CoV-2 exhibited clinical symptoms of decreased appetite and 

activity, increased body temperature, and mild dyspnea.602,603 In both C. aethiops and M. 

mulatta, aerosol inoculation resulted in less severe and delayed onset of symptoms compared 

to multi-route inoculation via intranasal and intratracheal delivery.603 Viral RNA and titers were 

detected from nasal swabs, pharyngeal swabs, rectal swabs, and bronchiolar lavage in 

comparable levels to M. mulatta, but were not detected in whole blood.602,603 Similar to M. 

nemestrina, C. aethiops showed evidence of transient coagulopathy from increases in partial 
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thromboplastin time and circulating levels of fibrinogen. From histopathological analysis, lung 

tissues had mild multifocal pneumonia, characterized by inflammation of terminal bronchioles, 

alveolar edema, alveolar hemorrhage, and alveolar spaces lined with neutrophils, macrophages, 

and fibrin. The trachea also contained ulcerated with multifocal epithelial erosion and 

associated hemorrhage and fibrin. By 34 dpi, lung tissue damage had progressed, showing 

moderate multifocal chronic pneumonia, despite a lack of viral antigen upon IHC analysis.602

These findings suggest that C. aethiops are susceptible to the most severe underlying pathology 

of SARS-CoV-2 infection compared to M. mulatta, M. fascicularis, and M. nemestrina. 

SARS-CoV-1 

C. aethiops inoculated with SARS-CoV-1 displayed no clinical symptoms, except for one 

reported case of transiently increased body temperature. Viral titers were detected in the 

throat, nose, and trachea in C. aethiops at higher levels than either M. mulatta or M. 

fascicularis. However, unlike M. fascicularis, viral RNA was not detected in plasma or urine from

C. aethiops. Upon rechallenge of SARS-CoV-1 inoculation, viral replication was restricted to the 

upper respiratory tract. From IHC analysis, viral antigen was detected in type I pneumocytes 

and macrophages in lung tissues, but not in any extrapulmonary tissues. From histopathological 

analysis, lung tissues showed focal interstitial infiltrates indicative of pneumonia and edema.324

Marmoset

MERS-CoV

C. jacchus inoculated with MERS-CoV exhibited more severe clinical symptoms than M. mulatta, 

including weight loss, severe respiratory symptoms, and decreased water intake. From IHC 

analysis, lung tissues showed moderate levels of antigen in pneumocytes, with increased levels 

of antigen in alveolar macrophages. Compared to M. mulatta, histopathological analysis of C. 

jacchus lung tissues had more widespread pulmonary oedema and diffuse alveolar hemorrhage.

Despite viral antigen levels being slightly lower in lung tissues and comparable infiltration of 

inflammatory cells,596 these findings suggest that C. jacchus are susceptible to more severe 

MERS-CoV infection than M. mulatta. 

Ferret

SARS-CoV-2 

M. putorius furo showed age-dependent pathogenic characteristics from SARS-CoV-2 infection. 

M. putorius furo aged 1-2 years that were inoculated with SARS-CoV-2 exhibited more severe 

clinical symptoms than those aged 6 months, including elevated body temperature and greater 

weight loss, lethargy, and respiratory symptoms.604 Other studies showed that younger M. 

putorius furo developed mild clinical symptoms, such as stagnated weight gain and ruffled fur 

(an indication of lethargy), but did not experience elevated body temperatures.307 Variation in 

clinical symptoms between studies may also be affected by inoculation dose and route, with 

higher doses and intranasal inoculation resulting in more severe symptoms.307,605 Interestingly, 
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M. putorius furo that were rechallenged with SARS-CoV-2 inoculation showed weight loss, 

lethargy, and ruffled fur that were not observed during the initial challenge.307

Older M. putorius furo also contained the highest viral titers from nasal turbinates compared to 

younger M. putorius furo, as well as higher viral RNA levels from fecal samples, indicating higher 

viral loads within the gastrointestinal tract. Younger M. putorius furo also had reduced viral RNA 

levels in the lower respiratory tract compared to older M. putorius furo, which researchers 

concluded was not associated with reduction in ACE2 receptor expression.604 In addition, viral 

RNA has been detected in the BAL, tonsils, trachea, lung, and olfactory bulb, as well as 

cerebrum and cerebellum from intranasal inoculation. Despite showing increased clinical 

symptoms, viral shedding and lung pathology were significantly reduced in M. putorius furo 

rechallenged with SARS-CoV-2 inoculation.307,605

From histopathology of lung tissue, older M. putorius furo contained increased inflammatory 

cell infiltration and widened, edematous, and congested alveolar septa compared to younger 

M. putorius furo.

604 Lung tissue from both older and younger M. putorius furo showed mild 

peribronchitis with infiltrating cells in the sub-mucosa of bronchi.605 Epithelial lining of nasal 

cavities were damaged, characterized by hypertrophy, hyperplasia, and squamous metaplasia, 

especially in M. putorius furo inoculated with higher doses of SARS-CoV-2.307,605 In addition, the 

liver showed multifocal inflammatory cell infiltration, consisting of macrophages, lymphocytes, 

and plasma cells.307

SARS-CoV-1 

M. putorius furo inoculated with SARS-CoV-1 displayed clinical symptoms of lethargy, with 

multiple studies having at least one M. putorius furo die before 4 dpi.301,302 Viral RNA was 

detectable from pharyngeal swabs but not from either nasal or rectal swabs.302 From 

immunofluorescence analysis, SARS-CoV-1 antigen was detected in the alveolus, in which 

antigen appeared in type II pneumocytes and alveolar macrophages. IHC analysis revealed that 

ACE2 receptors were additionally expressed in bronchiole, bronchus, trachea, and pulmonary 

blood vessel tissues, where SARS-CoV-1 antigen was not observed. Lastly, histopathology 

revealed lesions in tissues of the lung, liver, spleen, and bronchial lymph nodes. In lung tissue, 

histopathology revealed multifocal, mild-to-severe diffuse alveolar damage with macrophages 

and neutrophils present, as well as proteinaceous exudate in alveolar and bronchiolar 

lumina.301 Considering the consistency of clinical and pathological features, SARS-CoV-1 

pathogenesis is potentially more severe than SARS-CoV-2 pathogenesis in M. putorius furo. 

Civet

SARS-CoV-1 

P. larvata inoculated with SARS-CoV-1 have shown clinical symptoms of lethargy, reduced 

aggression, and elevated body temperatures starting at 3 dpi and remaining until 7 dpi. Viral 

RNA was detected in the lungs, liver, kidney, spleen, heart, and cerebrum and remained 

detectable in the lymph nodes and spleen up to 35 dpi. In addition, virus was detected in low 
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levels from blood samples, in which leucopenia was also observed. From histopathology 

analysis of lung tissue at 3 dpi, researchers found interstitial inflammatory infiltrates and 

congestion of the alveolar septa. Furthermore, the lumina of alveoli and bronchioles were filled 

with oedema fluid, erythrocytes, cellular debris, and lymphocytes. Findings from other tissues 

include spleens with extensive necrosis and atrophy of white pulp lymphoid aggregates; livers 

with diffuse congestion and renal cortices; and small intestines with focal hemorrhages. In 

addition, tissues from the cerebrum showed evidence of neuronal degeneration and mild 

neuronophagia, in which glial cell apoptosis occured.606,607 Together, these findings suggest that 

P. larvata are highly susceptible to SARS-CoV-1 infection and show substantial disease 

pathogenesis compared to other species.

Companion Animals

Cat

SARS-CoV-2 

F. catus inoculated with SARS-CoV-2 are typically asymptomatic;387,388 however, in one case 

study, a 7-month-old F. catus presented with symptoms of dullness, lethargy, elevated 

temperature, and respiratory signs of coughing, wheezing, and dyspnea. Although no SARSCoV-2 RNA was detected on nasal, oropharyngeal, and rectal swabs, and viral antigen was not 

detected on post-mortem IHC, SARS-CoV-2 antibodies were detected upon serum analysis. The 

F. catus was also positive for feline parvovirus, which typically causes panleukopenia, 

suggesting that a combination of SARS-CoV-2 and parvovirus infection may have contributed to 

death.608 In another case study, an F. catus presented with respiratory and gastrointestinal 

symptoms and tested positive for SARS-CoV-2 infection. The F. catus showed a mild increase in 

red blood cells and reticulocytes and a mild decrease in platelets. After receiving amoxicillin and 

prednisone for 10 days, the cat no longer presented with any clinical symptoms.609

When infected with SARS-CoV-2, F. catus shed virus orally, nasally, and rectally. However, when 

rechallenged with SARS-CoV-2, F. catus did not shed virus. Upon histology analysis, the nasal 

turbinates showed ulcerative, lymphoplasmacytic and neutrophilic rhinitis, and 

lymphoplasmacytic tracheitis. The lungs also had mild histological changes, including interstitial 

pneumonia with peribronchiolar and perivascular lymphocytic cuffing and alveolar 

histiocytosis.

387,390 In the case of the 7-month-old symptomatic cat, computed tomography (CT) 

images of the lungs revealed two heterogenous lesions and bilateral ground-glass opacities. In 

addition, post-mortem histopathology revealed interstitial pneumonia and type II pneumocyte 

hyperplasia, consistent with prior studies of SARS-CoV-2 infection in F. catus.

608

Although F. catus typically do not show clinical symptoms when inoculated with wildtype SARSCoV-2 variants, other variants of SARS-CoV-2 have caused symptoms.610,611 Cats inoculated with 

the Delta (B.1.617.2) variant showed significant clinical symptoms compared to prior studies of 

F. catus inoculated with wildtype SARS-CoV-2, while F. catus inoculated with Omicron (BA.1.1) 

also remained asymptomatic. Similar to wildtype SARS-CoV-2 infection, F. catus infected with 

Delta and Omicron variants shed virus from nasal, oropharyngeal, and rectal swab, but virus 
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was detected at higher levels in F. catus infected with the Delta variant from samples of nasal 

turbinate, tonsil, retropharyngeal lymph node, trachea, lung, mediastinal lymph node, heart, 

liver, spleen, kidney, small intestine, and mesenteric lymph node. Gross post-mortem and 

histopathology findings were also more severe in F. catus inoculated with Delta in the lungs. 

Delta-inoculated F. catus showed dark red pulmonary consolidation, hemorrhage, and 

pulmonary edema, as well as diffuse alveolar damage and disruption of vascular architecture by 

infiltrating neutrophils and lymphocytes.387,388,610

From RNASeq analysis of lung samples from Delta-inoculated F. catus, many genes associated 

with activation of innate immunity and SARS-CoV-2 disease severity were upregulated. In 

addition, analysis of differentially expressed genes identified several clusters of dysregulated 

genes associated with clinical symptoms and lung pathology during the acute phase of 

infection. For example, differentially expressed gene analysis identified the gene encoding 

aurora kinase B (AURKB), which is associated with cell cycle progression and chromosome 

segregation and may contribute to SARS-CoV-2 N-protein mutation. Several genes associated 

with neurodegenerative diseases were also upregulated during the recovery phase of infection 

in Delta-inoculated F. catus.

387,388,610

SARS-CoV-1 

Similar to SARS-CoV-2 infection, F. catus inoculated with SARS-CoV-1 do not show any clinical 

symptoms. Although viral RNA was not detectable from nasal or rectal swabs, SARS-CoV-1-

inoculated F. catus shed virus from the pharynx. In addition, low levels of SARS-CoV-1 antigen 

were detected in the respiratory tract, including titers in lung homogenates, and the intestine. 

In the respiratory tract, SARS-CoV-1 antigen and ACE2 receptor expression were primarily 

detected in type I and II pneumocytes and serous cells of tracheo-bronchial submucosal 

glands.301,302

From post-mortem histology analysis, lesions were observed in tracheo-bronchial submucosal 

glands, spleen, mesenteric lymph nodes, and Peyer’s patches. Similar to SARS-CoV-2 histology, 

SARS-CoV-1-inoculated F. catus had multifocal diffuse alveolar damage in the lungs, 

characterized by cellular debris in the alveolar lumen and epithelial cells with karyorrhexis, 

karyopyknosis, multifocal necrosis, sparse type II pneumocyte hyperplasia, and infiltration with 

few neutrophils in the alveolar septa.

301,302

Dog 

SARS-CoV-2 

C. lupus familiaris inoculated with or exposed to SARS-CoV-2 have shown clinical presentations 

ranging from asymptomatic to increases in body temperature, decreases in weight, and 

respiratory symptoms. Although Bosco-Lauth et al. (2020) did not detect any viral shedding by 

plaque assay at any time point post infection, Lyoo et al. (2023) detected viral RNA from nasal, 

rectal, and urethral swabs and demonstrated the ability to cultivate SARS-CoV-2 from these 

samples.387,396,612 IHC of the lung tissue also showed SARS-CoV-2 antigen in alveolar 
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macrophages and neutrophils.612 However, these studies provide evidence that C. lupus 

familiaris are less susceptible to SARS-CoV-2 infection than cats.387,396,612

Although Bosco-Lauth et al. (2020) reported not observing any gross lesions in SARS-CoVinoculated C. lupus familiaris, post-mortem histopathology analyses from other studies have 

revealed mild interstitial pneumonia and perivascular infiltration of lymphocytes, macrophages, 

and neutrophils.387,396,612 In addition, blood samples revealed decreases in platelet counts and 

increases in inflammatory factors, fibrinolysis, and clotting factors. These parameters are 

indicative of thrombocytopenia and lymphocytopenia, which may occur because of to 

pulmonary embolism, systemic thrombosis, and/or lymphocyte apoptosis.396

In a case study of a West Highland Terrier that presented with hemorrhagic diarrhea, the C. 

lupus familiaris tested positive for SARS-CoV-2 infection (B.1.177) upon next-generation 

sequencing of a fecal sample. The sequencing of the fecal sample also revealed an I402V 

substitution in the S protein of the virus, which the authors speculate may have affected the 

gastrointestinal tract.402

MERS-CoV

Similar to SARS-CoV-2, C. lupus familiaris inoculated with MERS-CoV showed increased body 

temperature and weight loss. MERS-CoV was detected from nasal, rectal, and urethral swabs, 

but not to the level of SARS-CoV-2 detection, indicating that C. lupus familiaris may not shed 

infectious MERS-CoV. Blood samples from MERS-CoV-inoculated C. lupus familiaris showed 

decreases in platelets and increases in lactate dehydrogenase levels, suggesting potential tissue 

damage. Similar to SARS-CoV-2-inoculated C. lupus familiaris, histopathology analysis of lung 

samples from MERS-CoV-inoculated C. lupus familiaris revealed mild interstitial pneumonia and 

focal bronchiolitis with perivascular infiltration of lymphocytes, macrophages, and neutrophils. 

However, MERS-CoV antigen was not detected in lung tissue from IHC analysis. Together, these 

data indicate that C. lupus familiaris are potentially less susceptible to MERS-CoV infection 

compared to SARS-CoV-2.612

Mink

SARS-CoV-2 

Multiple studies of SARS-CoV-2 in mink populations have reported mixed findings of infection 

signals. A study of both wild and captive-bred minks (N. vison and M. lutreola) from Northern 

Spain found no evidence of systemic symptoms from general physical examinations, with no 

detection of SARS-CoV-2 RNA from swab samples nor SARS-CoV-2 antibodies from serum 

samples.613 However, studies of farmed N. vison across Europe and North American have 

reported findings from SARS-CoV-2 positive cases.

614,615 Viral RNA has been detected from 

throat and rectal swab samples, as well as lung, conchae, liver, and intestine tissue samples. 

Clinical symptoms from SARS-CoV-2-positive N. vison include reduced food intake, nasal 

discharge, sneezing, and coughing, as well as respiratory distress.615 N. vison that were 
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experimentally inoculated with SARS-CoV-2 also showed weight loss; however, viral RNA was 

not detected from concha or rectal swabs.310

Post-mortem histopathological findings from N. vison that died on farms revealed acute diffuse 

interstitial pneumonia with hyaline membrane formation and focal micro-hemorrhages in the 

alveolar septa, as well as fibrin thrombi formation in the lungs and other tissues.614,615

Histopathological findings from tissue samples of experimentally inoculated minks showed 

similar results, as well as interstitial inflammatory infiltrates and intra-alveolar edema.310

SARS-CoV-2 genome sequencing from mink farms in Denmark, the Netherlands, and Greece all 

independently revealed a Y453F mutation of the S protein, suggesting that this variant is minkspecific and may have a higher binding affinity to N. vison ACE2 receptors.614,615

Sheep and Swine

Neither O. aries nor S. scrofa are susceptible to infection from SARS-CoV-2.616,617 SARS-CoV-2 

antibodies were not detected in O. aries that were in close contact with a veterinary student 

community from June 2020 to March 2021. However, direct detection of the virus using RT-PCR 

was not performed.616 SARS-CoV-2 can infect porcine kidney and testicle cells, but viral RNA has 

not been detected from any swab or blood samples from inoculated S. scrofa. Gross and 

histopathological analyses of S. scrofa lung tissue did not identify any pathological lesions, 

SARS-CoV-2 antigen, or SARS-CoV-2 RNA. SAR-CoV-2 also failed to replicate in the respiratory 

and digestive tract of inoculated S. scrofa. More refined predictive analysis of the binding 

potential of SARS-CoV-2 with ACE2 receptors of O. aries and S. scrofa could provide insight into 

the lack of infection susceptibility, as well as additional studies on experimental infection.616,617

Camelid

MERS-CoV

C. dromedarius are commonly known as a primary reservoir for the MERS-CoV virus and have 

been studied because of the risk of zoonotic transmission of the virus to humans. MERS-CoV 

infection in camelids is characterized by minor clinical symptoms comprised of mild to 

moderate nasal discharge. MERS-CoV is primarily shed in these nasal secretions, but has not 

been detected in urine, whole blood, or serum. Viral RNA has been detected in feces, but the 

low level of detection indicates that feces are not likely a contributing factor in transmission.618

Viral antigen is primarily detected in the upper respiratory tract, with few reports of viral 

antigen present in the lower respiratory tree. Primary histopathological lesions are limited to 

the upper respiratory tract in MERS-CoV-infected camelids, resulting in epithelial cell necrosis, 

mucosal ulcerations, increased mucous production, and neutrophil accumulation in the nasal 

mucosa. During the acute phase of infection, inflammatory processes in the lower respiratory 

tract are limited to epithelial necrosis, lymphocytic infiltration, and squamous metaplasia.618

One study noted that MERS-CoV infection in both New (i.e., L. glama and V. pacos) and Old 

World camelids (i.e., C. dromedarius and C. bactrianus) was associated with ciliocytophthoria 
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(i.e., ciliary loss) and depletion of DPP4.619 Identifying mechanisms in which cilia presence and 

function are lost may be a key focus for future investigations in upper respiratory infections.618

Surveillance

Future surveillance of various animal species can be used to detect novel coronaviruses as well 

as outbreaks of specific coronaviruses. Optimal surveillance systems should enable early 

detection of coronaviruses while minimizing costs for sample collection and analysis. Different 

components of viral surveillance systems, their advantages and disadvantages, and their 

relevance to different surveillance goals are outlined below. 

Geographies

Regions at high risk for zoonotic coronavirus spillover events should be actively surveilled for 

coronaviruses. Various environmental factors can impact risks for spillover events. Zoonotic 

spillovers to humans are associated with changes in land use that place humans in closer 

proximity to infected animals.620 Therefore, areas of risk for interspecies transmission are those 

where one infected species, particularly a Chiropteran species, comes into contact with another 

species. The geographical distributions of different species are impacted by wildlife trade and 

live markets, climate change, and domestic species introductions (e.g., establishment of farms 

near wildlife populations).621 Species interfaces critical for coronavirus transmission are 

outlined in detail in “Species Interfaces Relevant to Coronavirus Transmission.”

Species

Species at risk for coronavirus infection should be prioritized for regular surveillance activities. 

Risk can be determined based on various criteria, including those outlined in “Evidence Types 

for Determining Species Susceptibility.” Sentinel surveillance strategies can also be employed. 

For example, farm workers can serve as sentinels for cattle coronavirus infection; zookeepers as 

sentinels for captive animals; and veterinarians and veterinary technicians as sentinels for 

companion animals.

Clinical Evaluations and Monitoring

In animals with symptomatic infections, surveillance systems can use symptom data to guide 

additional testing (see “Assays”) or as an early warning system of viral outbreaks. For example, 

biosensors on farmed pigs can detect temperature changes in real time associated with porcine 

reproductive and respiratory syndrome virus622 as well as African swine fever.623 Observations 

of clinical signs in farmed, captive, and companion animals can be reported to a central entity 

as part of a larger surveillance system

Assays

Different detection assays can be used to meet certain surveillance goals. Although sequencing 

methods may require higher monetary investment than reverse transcription-polymerase chain 

reaction (RT-PCR) methods, they do provide the most flexibility for detection of multiple 

pathogens. Metagenomic sequencing paired with strong bioinformatic analysis pipelines can 

detect various novel viruses within even a single sample. Targeted sequencing using conserved 

primers detects multiple viruses within specific viral groups. For example, targeted sequencing 
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of RNA-dependent RNA polymerase (RdRp) is used to detect novel coronaviruses in 

Chiropterans (see “Diagnostics” and “Viral RNA Detection”). When used as part of a surveillance 

system, these sequencing techniques can be used to monitor coronavirus evolution and detect 

mutations that may impact infectivity, transmissibility, and host species tropism. 

RT-PCR methods are used alone to screen for the presence of specific coronavirus RNA. RT-PCR 

alone cannot provide detailed information about acquired viral mutations, but it can serve as a 

scalable, cost-effective method for screening large numbers of samples (see “RT-PCR” in the 

“Diagnostics” Section). Compared to costs between $7.20 to $43.30 per sample and duration of 

20 hours for targeted sequencing of RdRp, RT-PCR costs approximately $12 per sample and 

takes only 4 hours to complete.624 Primers used to detect a specific coronavirus should not 

cross-react with RNA from other coronaviruses or host genetic material to ensure specific and 

exclusive detection. When used as part of a surveillance system, large-scale RT-PCR methods 

can detect local outbreaks of specific coronaviruses in specific species of interest.

RT-PCR and sequencing methods are typically used to detect active infections, while serology 

methods detect past infections. Antibody detection methods are continually improved to 

increase scalability, decrease cost and time investments, and reduce the amount of specialized

expertise required. Specific antibody detection methods used for coronaviruses are outlined in 

“Virus-Specific Antibody Detection.” While serology surveillance systems cannot detect active 

infections, they can identify additional species susceptible to specific coronavirus infections.

Both viral RNA and antibody strategies have inherent advantages and disadvantages. Sample 

type availability often dictates which detection methods are possible; serology tests require 

blood samples, which are more difficult to collect, especially from wild animals, than oral, nasal, 

or fecal samples that can be used for viral RNA detection. Detection of viral RNA indicates 

active infection, and although seropositivity is usually not used to determine infection timing, 

some researchers have quantified antibody levels to roughly estimate infection timing in 

humans and animals.625,626 Overall, because viral infections usually resolve after a period of 

time, the rate of active infections of a coronavirus is much lower than the rate of seropositivity 

for the same coronavirus. Therefore, larger sample sizes are likely required to detect active 

infections compared to sample sizes used for the detection of coronavirus antibodies. 

Sample Types and Sizes

Biological Sample Types

Different biological sample types are required for the detection of different assay readouts. 

Oral, nasal, respiratory, anal, and fecal swabs are used to detect coronavirus viral RNA, while 

blood samples are required for detection of coronavirus antibodies. Different types of samples 

require different levels of contact between researchers and animal subjects. Blood sampling 

requires close, prolonged contact with animals and may not be feasible for certain wildlife 

species. Oral, nasal, and rectal swabs require more limited animal contact, and fecal samples 

can be safely collected well after excretion with minimal to no animal contact. Notably, 
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reported RNA extraction methods used different pre-extraction steps for fecal samples versus 

swab samples, but extraction kits were used across sample types.

Interestingly, scientists created a device called the SnotBot® to collect blowhole samples from 

cetaceans with minimal invasiveness, which could be used to detect respiratory pathogens such 

as coronaviruses.627 

Pooled Sampling Strategies

Pooled sampling methods are currently used to reduce the cost of SARS-CoV-2 surveillance in 

humans at airports. The Centers for Disease Control and Prevention has deployed at select 

airports pooled surveillance strategies using nasal samples from voluntary travelers as well as 

samples collected from aircraft wastewater tanks.628,629 Similar pooled sampling strategies 

could be applied to various animal species for initial detection of coronaviruses in oral, nasal, 

rectal, or fecal samples. However, sequence analysis of pooled samples requires robust 

bioinformatic pipelines capable of data deconvolution to assess the presence of multiple 

mutations within the same viral genome.630 Further streamlining of these pipelines as well as 

adaptation for use in animal species will enable successful pooled sample surveillance systems 

for zoonotic coronaviruses. 

Environmental Sample Types

Environmental sampling requires less invasive procedures compared to more conventional 

biological sampling methods and may represent many different animals, even from different 

species. Sample types include fomites, air, and wastewater. Notably, the lack of detection of 

coronaviruses in air, fomites, or wastewater does not eliminate the possibility of water droplet 

and airborne transmission-dependent coronavirus outbreaks. However, detection of 

coronavirus RNA in environmental samples can identify potential modes of transmission 

threatening certain animal species. Environmental samples positive for coronavirus RNA should 

also be tested for live, infectious virus to further determine the level of risk of transmission. 

Infectious virus can be determined based on successful viral culture and isolation, but these 

methods are very difficult. As an alternative, a research group in Portugal collected air samples 

and pretreated them with RNAse A to destroy any non-encapsulated coronavirus RNA, leaving 

only RNA within intact viral particles.631

Various sampling devices have been described previously for air sample collection and 

surveillance: Coriolis Compact (Bertin Instruments),631 AerosolSenseTM (Thermo Fisher 

Scientific),632 and various in-house sampling devices.633–636 Notably, an air-to-liquid device 

collected air samples in 1-2 minutes, compared to several hours required from traditional air 

sampling devices.633 

Efforts across the globe are using sewershed samples to monitor SARS-CoV-2 RNA in 

wastewater, and this monitoring has proven useful and less expensive than clinical sampling. 

However, multiple published articles detail concerns about discharge of SARS-CoV-2-

contaminated wastewater into bodies of water.161,162 To detect SARS-CoV-2 RNA in 
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contaminated coastal waters, researchers may need to concentrate SARS-CoV-2 and other 

coronaviruses from water samples. One peer-reviewed publication compared five different 

methods for concentrating SARS-CoV-2 in wastewater and found that the elution with beef 

extract and polyethylene glycol precipitation method as well as Amicon filtration robustly 

concentrated SARS-CoV-2 in real-world wastewater samples.637 Notably, although coastal water 

samples may contain coronavirus RNA, this does not necessarily indicate the presence of live, 

infectious virus. In addition, the viral concentration may not be sufficient for transmission to 

cetaceans and other animals. 

Surveillance using fomite samples can provide indications of viral shedding as well as risk to 

nearby animal populations. For example, bedding belonging to a SARS-CoV-2-positive F. catus

tested positive for SARS-CoV-2 RNA in Switzerland.425 However, the utility of fomite-based 

surveillance depends on coronavirus stability on fomite surfaces (see “Fomites”). 

Sample Size

Surveillance systems should also use adequate sample sizes for coronavirus detection. Various 

computational models can be used to estimate sufficient sample sizes for future surveillance 

efforts.638–640 Notably, sample size calculations depend on various factors, including the key 

question for the surveillance project (e.g., virus detection versus variant detection versus 

variant frequencies) and intended sampling frequency (e.g., cross-sectional versus periodic 

surveillance).639 

Types of Surveillance Systems

Passive Versus Active Surveillance

Passive surveillance strategies rely on case reports; for example, the Animal and Plant Health 

Inspection Service (APHIS) of the U.S. Department of Agriculture (USDA) collects animal cases of 

SARS-CoV-2 in the United States.328 The USDA National Animal Health Reporting System 

(NAHRS) is another voluntary disease reporting program for animal diseases.641 An ideal passive 

surveillance strategy, however, would consist of a global effort of animal case reporting to a 

central entity. For example, the World Organisation for Animal Health (WOAH) collects 

voluntary SARS-CoV-2 case reports in animals across the globe.

642 Conversely, active 

surveillance systems are more targeted and designed to surveil for a specific pathogen in a 

specific species in a particular area. Many articles cited within this review containing 

coronavirus incidence or prevalence are examples of active surveillance projects. Their 

diagnostic methods (see “Diagnostics”) were scalable and appropriate for use in animals; these 

methods could inform the design of a global, active surveillance program of emerging 

coronaviruses.

Syndromic Versus Laboratory-Based Surveillance

Syndromic surveillance strategies use symptom data to identify potential cases, while 

laboratory-based surveillance uses specific assays to identify a causative pathogen (see 

“Assays”). Although syndromic surveillance does not involve the identification of a pathogen, it 

does enable non-experts to identify syndromic cases. In a passive surveillance system, everyday 
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citizens can report symptomatic or deceased animals; such a system is used for highly 

pathogenic avian influenza (HPAI) surveillance in the United States, and another for SARS-CoV-2 

is already in development. Individuals can contact local or state wildlife and animal health 

agencies as well as local veterinarians to report deceased birds, while mass die-offs and other 

unusual observations should be reported to the USDA directly via their hotline.643 In contrast, 

laboratory-based surveillance programs are more resource-intensive and require careful 

planning to maximize useful information and minimize costs.

Sentinel and Targeted Active Versus Whole Population Surveillance

Sentinel surveillance focuses on testing fewer animals as representatives of larger animal 

populations. Sentinel strategies can provide critical surveillance information in a shorter period 

of time with a smaller financial investment.644 Sentinel animals are sometimes used as a 

surveillance tool to monitor viruses present in species that are more difficult to sample. For 

example, analysis of potential surveillance strategies for HPAI utilized mute swans (Cygnus olor)

and A. platyrhynchos as sentinel animals for wild birds. Because of H5N1’s high mortality in 

birds, researchers designed a targeted active surveillance strategy to test dead birds, which was 

more cost-effective than capturing live birds.645 Selection of appropriate sentinel species is 

critical for designing a sentinel surveillance system that can adequately answer surveillance 

questions. 

Diagnostics

Viral RNA Detection

Viral RNA detection is used as a proxy for active infection, but the presence of genetic material 

is not always indicative of live virus. One RNA isolation protocol—viral particle-protected 

nucleic acid extraction—uses RNAses to destroy non-encapsulated RNA to subsequently isolate 

genetic material from intact viral particles, but this protocol has not been in widespread use for 

coronavirus surveillance applications.631,646–648 Various methods used for surveillance of SARSCoV-1, MERS-CoV, and SARS-CoV-2 are summarized below.

Next-Generation Sequencing

Next-generation sequencing strategies are often used to screen samples for a variety of viruses. 

Metagenomics techniques screen for pathogenic nucleic acids and have been applied to 

Chiropterans and M. javanica.

29,51,649 Targeted sequencing methods characterize RT-PCRamplified conserved regions of closely related viruses. Targeted sequencing of RdRp is 

commonly used to identify coronaviruses, as summarized in Table 13.

Table 13: Conserved Coronavirus RT-PCR Strategies

Target Viral RNA Detection 

Method Primers Validated Species

RdRp nested RT-PCR650

PCR 1: TTATGGGTTGGGATTATC + 

TGATGGGATGGGACTATC; PCR 2: 

CTTATGGGTTGGGATTATCCTAAGTGTGA + 

CTTATGGGTTGGGATTATCCCAAATGTGA

Various 

Chiropterans,24,26,34,43,5

0,155 Camelus 

dromedarius651
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Target Viral RNA Detection 

Method Primers Validated Species

RT-PCR652 TCCTAAGTGTGATAGAGCTATGCC + 

GTGCACACTCATTTGCTAACCG

Various 

Chiropterans,38,44,49

Manis javanica38,475

Nested RT-PCR with 

degenerative primers37

PCR 1: CGTTGGIACWAAYBTVCCWYTICARBTRGG + 

GGTCATKATAGCRTCAVMASWWGCNACNACATG; 

PCR 2: GGCWCCWCCHGGNGARCAATT + 

GGWAWCCCCAYTGYTGWAYRTC

Various 

Chiropterans,25,38,44

Manis javanica38,475

RT-PCR653 AYAACCAAGATCTTAATGG + 

TGCTTAGAACCCAAAATCAT

Various 

Chiropterans,22 Felis 

catus354

Heminested RT-PCR654

PCR 1: 

GARTTYGATTGGRCKCGKTAYGA/GARTTYGATTGGR

CKAGGTAYGA + GGYTTKACCCACATNCCRAA; PCR 

2: 

CGKTAYGATGGKACKATHCC/AGGTAYGATGGKACK

ATHCC + GGYTTKACCCACATNCCRAA

Various 

Chiropterans654

RT-PCR655 GGTTGGGACTATCCTAAGTGTGA + 

CCATCATCAGATAGAATCATCATA

Various 

Chiropterans30,31

Nested RT-PCR656

PCR 1: CARATGAATYTIAARTAYGC + reverse 

TGYTGWGARCAAAAYTCRTG; PCR 2: 

ATGGGWTGGGAYTAYCCIAARTG-3′+ reverse 

ACRTTRTTYTGRWARTA

Various 

Chiropterans30,31

RT-PCR657

PCR 1: ATGGGITGGGAYTATCCWAARTGTG + 

AATTAT ARCAIACAACISYRTCRTCA; PCR 2: 

ATGGGITGGGAYTATCCWAARTGTG + 

CTAGTICCACCIGGYTTWANRTA

Various Chiropterans48

RT-PCR to conserved 

RdRp658

GGTTGGGACTATCCTAAGTGTGA + 

CCATCATCAGATAGAATCATCATA

Various 

Chiropterans,

33,42

RT-PCR659 ACWCARHTVAAYYTNAARTAYGC + 

TCRCAYTTDGGRTA RTCCCA

Various 

Chiropterans47,660

RBD RT-PCR155

PCR 1: VWGADGTTGTKAGRTTYCCT + 

TAARACAVCCWGCYTGWGT; PCR 2: 

TGTKAGRTTYCCTAAYATTAC + 

ACATCYTGATANARAACAGC

Various Chiropterans26

S RT-PCR661 TGGCWTATAGGTTYAATGGYATTGGAG + 

CCGTCGATTGTGTGWATTTGSACAT Manis javanica661

RT-PCR

Large numbers of samples are readily screened for coronavirus pathogens using various RT-PCR 

amplification methods specific to a coronavirus of interest. Primers selected for RT-PCR should 

be specific and not produce off-target RT-PCR products from host species or other pathogens. 

Nested and heminested RT-PCR strategies improve both sensitivity and specificity to the viral 

gene of interest by using multiple primer pairs.
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SARS-CoV-1 

SARS-CoV-1 viral RNA has been isolated from P. larvata using three different RT-PCR strategies, 

summarized in Table 14. 

Table 14: SARS-CoV-1 RT-PCR Strategies

Target Viral RNA Detection 

Method

Primers Validated Species

P and N RT-PCR kit from

Qiagen662

Not specified Paguma larvata77

ORF1ab and N RT-PCR and nested RTPCR663Nested N PCR 1: 

ATGAATTACCAAGTCAATGGTTAC + 

CATAACCAGTCGGTACAGCTAC

Nested N PCR 2: 

GAAGCTATTCGTCACGTTCG + 

CTGTAGAAAATCCTAGCTGGAG

ORF1ab PCR: TACACACCTCAGCGTTG + 

CACGAACGTGACGAAT

Paguma larvata73

N, M, S RT-PCR71 PCR N: ATGTCTGATAATGGACCCCAAT + 

TTATGCCTGAGTTGAATCAG

PCR M: ATGGCAGACAACGGTACTATT + 

CTTACTGTACTAGCAAAGCAAT

PCR S: ATGTTTATTTTCTTATTATTTC + 

GTCGACATGCTCAGCTCCTAT

Paguma larvata71

MERS-CoV

MERS-CoV viral RNA has been isolated mainly from Chiropterans and C. dromedarius, as well as 

other livestock species. Amplification strategies are summarized in Table 15. 

Table 15: MERS-CoV RT-PCR Strategies 

Target Viral RNA Detection 

Method

Primers Validated Species

UpE RT-PCR664 GCAACGCGCGATTCAGTT + 

GCCTCTACACGGGACCCATA 

Camelus 

dromedarius;

53,59,60,62,6

3,66–70 Llama glama;

369

Vicugna pacos;

369,370

Ovis aries;

361 Capra 

hircus;

361 Bos 

taurus;

361 Equus 

asinus;

361 various 

Chiropterans44

N2 & N3 RT-PCR665 GGCACTGAGGACCCACGTT + 

TTGCGACATACCCATAAAAGCA; 

GGGTGTACCTCTTAATGCCAATTC + 

TCTGTCCTGTCTCCGCCAAT

Camelus 

dromedarius61,67
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Target Viral RNA Detection 

Method

Primers Validated Species

N nested RT-PCR followed 

by sequencing666

PCR 1: CCTTCGGTACAGTGGAGCCA + 

GATGGGGTTGCCAAACACAAAC; 

PCR 2: TGACCCAAAGAATCCCAACTAC; 

GATGGGGTTGCCAAACACAAAC

Camelus 

dromedarius;

53,60,63

Ovis aries;

361 Capra 

hircus;

361 Bos 

taurus;

361 Equus 

asinus;

361 various 

Chiropterans44

ORF1b RT-PCR664 TTCGATGTTGAGGGTGCTCAT + 

TCACACCAGTTGAAAATCCTAATTG

various Chiropterans44

ORF1a RT-PCR666 CCACTACTCCCATTTCGTCAG + 

CAGTATGTGTAGTGCGCATATAAGCA

Camelus 

dromedarius;

53,59,60,62,6

6,68,69 Ovis aries;

361

Capra hircus;

361 Bos 

taurus;

361 Equus 

asinus;

361 various 

Chiropterans44

RdRp RT-PCR followed by 

sequencing666 

TGCTATWAGTGCTAAGAATAGRGC + 

GCATWGCNCWGTCACACTTAGG

Camelus 

dromedarius;

53,60,65

various Chiropterans44

SARS-CoV-2 

SARS-CoV-2 viral RNA has been isolated mainly from F. catus, C. lupus familiaris, and 

Chiropterans, as well as other feline species, small carnivores, and O. virginianus. These 

amplification strategies are outlined in Table 16. 

Table 16: SARS-CoV-2 RT-PCR Strategies

Target Viral RNA Detection 

Method

Primers Validated Species

E 

RT-PCR667 ACAGGTACGTTAATAGTTAATAGCGT + 

ATATTGCAGCAGTACGCACACA

Various 

Chiropterans;25 Felis 

catus;

126,399,404,405,420,421

,425,434,438 Manis

javanica;

475 Canis 

lupus 

familiaris;

126,387,399,403–

405 Neogale vison;

118

COVISure (Genetix) Not provided Panthera pardus474

Bio-T kit TRISTAR COVID-19 

(Biosellal)

Not provided Felis catus409

Allplex 2019-nCoV Assay 

(SeeGene) for RdRp, N, E

Not provided Canis lupus 

familiaris;

430 Puma 

concolor468

RT-PCR E/RP kit (Bio 

Manguinhos) 

Not provided Felis catus;

431 Canis 

lupus familiaris431
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Target Viral RNA Detection 

Method

Primers Validated Species

modular RT-PCR kits for 

multiplexing (TIB MOLBIOL)

Not specified Felis catus;

415,421,442

Panthera leo468

M

Genesig COVID-19 kit Not provided Felis catus436

RT-PCR668 GGYTCTAARTCACCCATTCA + 

TGATACTCTARAAAGTCTTCATA

Felis catus;

415 Canis 

lupus familiaris387

N

RT-PCR667 CACATTGGCACCCGCAATC + 

GAGGAACGAGAAGAGGCTTG

Various 

Chiropterans;25 Felis 

catus;

399,405,420,421

Canis lupus 

familiaris399,405

Viasure RT-PCR kit (certest) Not provided Lutra lutra;

130 Neogale 

vison669

Allplex 2019-nCoV Assay 

(SeeGene) for RdRp, N, E

Not provided Canis lupus 

familiaris;

430 Puma 

concolor468

EURORealTime SARS-CoV-2 

(EUROIMMUN) to ORF1ab 

and N

Not provided Canis lupus 

familiaris430

RT-PCR E/RP kit (Bio 

Manguinhos) 

Not provided Felis catus;

431 Canis 

lupus familiaris431

OPTI SARS-CoV-2 RT-PCR 

(Thermo Fisher Scientific)

Not provided Odocoileus 

virginianus;

349,350 Felis 

catus441

IDT Primer & Probe Kit (IDT) Not specified Felis catus440

modular RT-PCR kits for 

multiplexing (TIB MOLBIOL)

Not specified Felis catus;

415,421,442

Panthera leo468

nsp16 RT-PCR668 GGWCAAATCAATGATATGATTTT + 

GTTGTTAACAAGAACATCACTAGA

Felis catus;

415 Canis 

lupus familiaris387

ORF1ab

Genesig COVID-19 kit Not provided Felis catus436

Viasure RT-PCR kit (certest) Not provided Lutra lutra;

130 Neogale 

vison669

EURORealTime SARS-CoV-2 

(EUROIMMUN) to ORF1ab 

and N

Not provided Canis lupus 

familiaris430

ORF1b RT-PCR670 TGGGGYTTTACRGGTAACCT + 

AACRCGCTTAACAAAGCACTC

Felis catus435

RdRp

RT-PCR667 GTGARATGGTCATGTGTGGCGG + 

CARATGTTAAASACACTATTAGCATA

various 

Chiropterans;25 Felis 

catus;

405,421,425 Canis 

lupus 

familiaris;

387,403,405

Manis javanica;

475

Odocoileus 

virginianus351,355,356

COVISure (Genetix) Not provided Panthera pardus474
Report Page 80

Target Viral RNA Detection 

Method

Primers Validated Species

Bio-T kit TRISTAR COVID-19 

(Biosellal)

Not provided Felis catus409

Allplex 2019-nCoV Assay 

(SeeGene) for RdRp, N, E

Not provided Canis lupus 

familiaris;

430 Puma 

concolor468

RT-PCR E/RP kit (Bio 

Manguinhos) 

Not provided Felis catus;

431 Canis 

lupus familiaris431

IDT Primer & Probe Kit (IDT) Not specified Felis catus440

modular RT-PCR kits for 

multiplexing (TIB MOLBIOL)

Not specified Felis catus;

415,421,442

Panthera leo468

S Genesig COVID-19 kit Not provided Felis catus436

Sample Types

Coronavirus RNA is mainly detected in oral and nasal samples as well as fecal samples. Viral 

detection via fecal samples is only appropriate when the species of interest sheds a virus of 

interest in its fecal matter, which does not always occur for respiratory viruses. Reported RNA 

extraction methods of SARS-CoV-1, MERS-CoV, and SARS-CoV-2 used different pre-extraction 

steps for fecal samples versus swab samples, but extraction kits were used across sample types.

Virus-Specific Antibody Detection

Antibody detection and neutralization methods are frequently used to assess individuals for 

previous exposure to coronaviruses of interest. Because coronaviruses contain similar S

proteins, antibodies to one coronavirus may cross-react and provide protection against 

subsequent infection with another coronavirus. Therefore, antibody detection and 

neutralization assays should be assessed for specificity to the coronavirus of interest, especially 

when used in various animal species vulnerable to infection with other coronaviruses. For 

example, researchers studying SARS-CoV-2 prevalence in F. catus previously demonstrated that 

feline sera with hyperimmunity to feline infectious peritonitis—a feline coronavirus—did not 

cross-react with SARS-CoV-2 enzyme-linked immunosorbent assays (ELISAs) and 

microneutralization assays (MNAs); this increased confidence that positive results were due to 

previous exposure to SARS-CoV-2, not another coronavirus.671 Various antibody detection and

neutralization assays are summarized below.

Antibody Binding Detection

Various serological technologies have been adapted to detect binding antibodies for 

coronaviruses as strategies for discerning prior exposure to specific viruses. Antibody binding 

assays have been developed for SARS-CoV-1, MERS-CoV, and SARS-CoV-2. Although these 

strategies are readily scalable, results are less biologically relevant compared to virus 

neutralization assays. Samples positive for binding antibodies do not always contain 

neutralizing antibodies that confer protection against reinfection with the same virus; 
Report Page 81

therefore, antibody detection methods should be selected based on correlation with 

neutralization assays.

Enzyme-linked Immunosorbent Assay

ELISAs are scalable tests used for detecting various peptides, including antibodies. ELISA 

strategies for coronavirus antibody detection use spike or RBD antigens and indirect and 

double-antigen sandwich strategies. Notably, although the indirect method can be highly 

sensitive, it uses a secondary antibody for binding detection, which may result in nonspecific 

signals. The double-antigen sandwich ELISA retains similar sensitivity while increasing specificity 

at the detection step; rather than a secondary antibody for detection, the bound antigenantibody complex is incubated with tagged (e.g., fluorescence, luminescence, HRP) antigen. In 

addition, previous evidence suggests that for coronaviruses, ELISAs targeted to S and RBD are 

more virus-specific but less sensitive compared to N-targeted ELISAs.651,672,673 Therefore, prior 

to selecting an ELISA for use in animals, the method should be tested for cross-reactivity with 

antibodies to other common pathogens in the species of interest to verify assay specificity.

Both in-house laboratory and commercial indirect ELISA protocols can detect MERS-CoVbinding antibodies (Table 17). Euroimmun manufactures an indirect ELISA kit for MERS-CoV S1 

protein antibodies that has been used successfully in C. dromedarius, V. pacos, and L. 

glama,

69,369 while in-house strategies have only detected MERS-CoV antibodies in C. 

dromedarius.

61,68,70,674 

Table 17: ELISAs for MERS-CoV Antibodies 

Target ELISA Type Laboratory/Company Species with Successful 

Antibody Detection

S1 Indirect

Euroimmun

Camelus 

dromedarius69,369

Vicugna pacos369

Llama glama369

Alexandersen (National Centres for Animal Disease, 

Canada) Camelus dromedarius674

Drosten (University of Bonn, Germany) Camelus dromedarius70

S Indirect

Alagaili (King Saud University, Saudi Arabia) and Briese 

(Columbia University, United States) Camelus dromedarius68

Agwanda (National Museums of Kenya, Kenya) Camelus dromedarius61

N Indirect Alagaili (King Saud University, Saudi Arabia) and Briese

(Columbia University, United States) Camelus dromedarius68

Indirect ELISA methods for SARS-CoV-1 have been mostly used for antibody detection in human 

samples, although an indirect S ELISA has successfully detected SARS-CoV-1 antibodies in palm 

civet.73 Studies in patient samples have demonstrated that an ELISA for N-binding antibodies 

was more sensitive than an ELISA for S-binding antibodies.675,676
Report Page 82

Both indirect and double-antigen sandwich ELISAs have successfully detected SARS-CoV-2-

binding antibodies in some animal species and are summarized in Table 17. Numerous in-house 

ELISAs tested in animals have been used in seroprevalence studies of F. catus and C. lupus 

familiaris. Developers of some methods have previously published cross-reactivity data for 

other coronaviruses. Because of sequence similarities, SARS-CoV-2 ELISAs may cross-react with 

antibodies to SARS-CoV-1 and MERS-CoV. For example, the Sparer laboratory’s indirect RBD 

ELISA cross-reacts with SARS-CoV-1, and Biorad’s SARS-CoV-2 ELISA may cross-react with MERSCoV. 

Developers of other ELISAs have assessed their methods for cross-reactivity with other, less 

similar coronaviruses. The Segalés and Vergara-Alert laboratories tested lions using their 

double-antigen sandwich method for N that was non-reactive with OC43 and Bov-CoV.465 In 

addition, the Sparer laboratory’s indirect RBD ELISA did not cross-react with antibodies for 

turkey coronavirus, porcine respiratory coronavirus, canine coronavirus, feline coronavirus, and 

Bov-CoV.

354 Another ELISA for RBD from the laboratories of Zou, Shi, and Jin demonstrated no 

cross-reactivity for feline coronavirus, making it a suitable method for feline coronavirus 

seroprevalence studies.671 Vircell’s indirect S and N ELISAs show no cross-reactivity to cCoV and 

CRCoV, indicating suitability for canine seroprevalence studies.393 Biorad’s double-antigen ELISA 

for N does not cross-react with antibodies for CoV 229E, CoV NL63, CoV HKU1, and CoV OC43, 

but data on other animal coronaviruses were not found before the completion of this literature 

review.677

Notably, Innovation Diagnostics’ (ID’s) double-antigen ELISA for N (i.e., IDScreen®) has 

successfully detected SARS-CoV-2 antibodies in numerous species including O. aries,359 C.

hircus359, F. catus401,405,406,416,421,435,437,438, S. scrofa,326,360 V. vulpes,360 Canis aureus 

moreoticus,360 M. martes,131 M. meles,131 C. lupus familiaris,326,401,427 and Allochrocebus 

solatus.

326 However, cross-reactivity has only been officially demonstrated for avian and 

porcine coronaviruses. ID stated in assay documentation that the lack of conservation of N 

protein sequences across other coronaviruses suggests that cross-reactivity with other animal 

coronaviruses would be minimal.678 Because of the wide applicability of IDScreen to various 

species, this ELISA may become an important tool for seroprevalence studies in other species 

identified as susceptible to SARS-CoV-2 infection. 

Table 18: ELISAs for SARS-CoV-2 Antibodies

Target ELISA Type Laboratory/Company Species with Successful 

Antibody Detection

RBD Indirect

Gamarnik (Fundación Instituto Leloir-CONICET, 

Buenos Aires, Argentina) Felis catus436,679

Egberink (Utrecht University, Utrecht, Netherlands) Felis catus, Canis lupus 

familiaris680

Raybiotech Felis catus403

Stevanovic, Tabain, Vilibic-Cavlek (University of 

Zagreb and Croatian Institute of Public Health, 

Croatia)

Canis lupus familiaris393,394
Report Page 83

Target ELISA Type Laboratory/Company Species with Successful 

Antibody Detection

Sparer (University of Tennessee, United States) Felis catus, Odocoileus 

virginianus354

Zou (Huazhong Agricultural University, China), Shi 

(Wuhan Institute of Virology, China), and Jin 

(Huazhong Agricultural University and Ministry of 

Agriculture, China)

Felis catus671

Beer (Friedrich-Loeffler-Institut, Germany) Felis catus417,418,681

Fernández (University of Zaragoza, Spain) Felis catus,423,424 Mustela 

putorius furo132

Ly and Liang (University of Minnesota, United States) Felis catus, Canis lupus 

familiaris408

Klaus (University of Zurich, Switzerland) Felis catus,400,425 Canis lupus 

familiaris400

Yilmaz (Istanbul University-Cerrahpasa, Turkey) Felis catus426

S Indirect

Egberink (Utrecht University, Netherlands) Felis catus, Canis lupus 

familiaris680

Huergo (Federal University of Paraná, Brazil) Canis lupus familiaris430

Beer (Friedrich-Loeffler-Institut, Germany) Felis catus417,418,681

Vircell Felis catus, Canis lupus 

familiaris393

N 

Double 

antigen 

Innovation Diagnostics

Ovis aries,359 Capra 

hircus,

359 Felis 

catus401,405,406,416,421,435,437,438, 

Sus scrofa,326,360 Vulpes 

vulpes,360 Canis aureus 

moreoticus,360 Martes 

martes,131 Meles meles,131

Canis lupus 

familiaris,326,401,427

Allochrocebus solatus326

Segalés and Vergara-Alert (Universitat Autónoma de 

Barcelona, Spain) Panthera leo465

Biorad Felis catus441

Indirect

Egberink (Utrecht University, Netherlands) Felis catus680

Huergo (Federal University of Paraná, Brazil) Canis lupus familiaris430

Ly and Liang (University of Minnesota, United States) Felis catus, Canis lupus 

familiaris408

Vircell Felis catus, Canis lupus 

familiaris393

Protein Microarray

Protein microarrays enable multiplexing for multiple antigens, require smaller sample amounts, 

and often provide higher sensitivity compared to ELISAs.682 A quantitative SARS-CoV-2 antibody 

microarray originally used to assess vaccines683 has successfully detected antibodies to S, RBD, 

and N in cats.420 Another protein microarray for multiple coronaviruses (i.e., 229E, NL63, OC43, 

HKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2) developed for use in humans684 detected SARSCoV-2 antibodies in one beech marten (Martens martens).118 Although protein microarrays can 
Report Page 84

potentially provide multiplexed solutions for screening animals for multiple coronaviruses, 

further development is needed to identify applicable species. 

Microsphere Immunoassay

Microsphere immunoassays (MIAs) couple antigens of interest to microspheres instead of 

plates used in ELISAs and microarrays. These coated microspheres are then incubated with 

serum to capture antibodies of interest, followed by a secondary antibody for detection via 

flow cytometry. This immunoassay type can also be used for multiplex assay design with a 

reported higher reproducibility and dynamic range as well as lower preparation time compared 

to ELISAs.685

MIAs have been used to detect SARS-CoV-2 antibodies in select animal species. One multiplex 

MIA for N and two S regions successfully detected SARS-CoV-2 antibodies in F. catus and C. 

lupus familiaris,

428 while another multiplex MIA for N and S was established in cats.416

Microspheres coated with RBD and trimeric S also successfully detected SARS-CoV-2 antibodies 

in C. lupus familiaris and F. catus as well as O. cuniculus.

409,686–688 

Luciferase Immunoprecipitation System

The luciferase immunoprecipitation system (LIPS) uses antigen of interest fused to luciferase, 

and after incubation with a serum sample, serum antibodies are immunoprecipitated and 

luciferase activity is used as a readout of antibodies bound to the antigen of interest. LIPS 

requires less time for completion and can be adapted to various formats according to specific 

needs.689 The Eloit and Schwartz laboratories at the Pasteur Institute developed a LIPS assay for 

multiple SARS-CoV-2 S regions690 that was subsequently used to detect SARS-CoV-2 in cats.441

Antibody Neutralization Assays

Importantly, not all binding antibodies can successfully neutralize a target virus. Neutralization 

assays provide information on the activity of antibodies present in serum and their effects on 

virus replication. Live virus neutralization assays consist of plaque reduction neutralization tests 

(PRNTs) and MNAs to test neutralization activity against a live, intact virus. Because of the 

transmissibility and virulence of emerging coronaviruses, experiments using live viruses require 

biosafety level 3 (BSL-3) laboratory certification and compliance. A report released in August 

2022 identified only 381 BSL-3 laboratories worldwide, with 148 of those located in the United 

States.691 Therefore, laboratories without BSL-3 certification test neutralization of antibodies to 

coronaviruses using either pseudoparticle neutralization tests (ppNTs) or surrogate virus 

neutralization tests (sVNTs) that do not use intact, infectious coronavirus. Antibody 

neutralization methods are described below.

Live Virus Neutralization

PRNTs have been long regarded as a gold standard for detection of neutralizing antibodies and 

are more sensitive than other neutralization assays, but also less scalable. However, these 

assays require advanced expertise and longer timeframes, compared to other neutralization 
Report Page 85

assays.692 PRNTs have been used to assess neutralization activity against MERS-CoV693 and 

SARS-CoV-2.399,668,694–696 These assays have detected MERS-CoV neutralizing antibodies in C. 

dromedarius and Vicugna pacos,

370 as well as C. hircus, B. taurus, and E. asinus.361 PRNTs have 

also successfully detected SARS-CoV-2 neutralizing antibodies in F. catus,

399,431 C. lupus 

familiaris,

399,431,668 and O. virginianus.355,356 

MNAs enable scalable testing of neutralization activity—albeit at lower sensitivity than PRNTs—

compared to conventional virus neutralization tests (cVNTs) by incubating live virus with serum, 

followed by inoculation of a permissive cell line in a 96-well format. After an incubation period, 

wells are analyzed using infection readouts, most often cytopathic effect (CPE).692 MNAs have

been used to assess neutralization activity against MERS-CoV,297,363,651,693,697,698 SARS-CoV1,75,154 and SARS-CoV-2.393,401,417,437,699 MERS-CoV MNAs have successfully detected neutralizing 

antibodies in C. dromedarius,

53,60,61,63,362,369,651,674 C. bactrianus,365 V. pacos,369 llamas (Llama 

glama),369 O. aries,

60,361 C. hircus,361 B. taurus,361 E. caballus,361 and E. asinus.361 SARS-CoV-1 

MNAs have detected neutralizing antibodies in S. scrofa,

154 P. larvata, M. moschata, and N. 

procyonoides.

75 SARS-CoV-2 MNAs have been used to detect neutralizing antibodies in O. 

aries,

359 F. catus,126,393,398,401,407,414,417,418,423,437,441,671 C. lupus familiaris,126,393,394,398,403,407,432,471

ferrets (M. putorius furo),699 N. vison,

121 M. lutreola,116 P. leo,466 and P. tigris.463,464

Pseudovirus Neutralization

ppNTs have increased accessibility of laboratories to neutralization tests, but importantly, not 

all aspects of pseudoviruses recapitulate their corresponding, naturally-occurring viruses. A 

typical ppNT uses a recombinant pseudovirus engineered to block expression of native surface 

proteins, resulting in a virus unable to replicate beyond a single round. Because of their 

reduced virulence, pseudoviruses can be handled in biosafety level 2 (BSL-2) laboratories. These 

pseudoviruses are then used to package surface protein(s) of interest. Common pseudovirus 

packaging systems include the human immunodeficiency virus (HIV)-1-derived lentiviral system, 

murine leukemia virus (MLV)-based system, and vesicular stomatitis virus (VSV)-derived 

system.692 

SARS-CoV-2 pseudoviruses have been developed using HIV-1-derived lentiviral system,36 MLVbased system,428 and VSV-derived system,700,701 while MERS-CoV pseudovirus has been 

developed using the HIV-1-derived lentiviral system.297,298 SARS-CoV-2 VSV and MLV 

pseudovirus systems have been successfully used with serum from C. lupus familiaris408,428 and 

F. catus,

408,409,428,436 and the newly-created SARS-CoV-2 lentiviral system has not been used with 

non-human serum. The MERS-CoV lentivirus system has only detected neutralizing antibodies 

in camels.54,62,66,297,702

Surrogate Virus Neutralization

Genscript has developed the cPass kit, which serves as an sVNT by recreating ACE2-SARS-CoV-2 

interactions under cell-free conditions, eliminating handling of any live virus or pseudovirus. 

When kit contents are incubated with neutralizing antibodies, HRP-conjugated SARS-CoV-2 RBD 

cannot bind to ACE2, resulting in HRP detection.672,703 This sVNT is highly specific to SARS-CoV-2 
Report Page 86

and strongly correlates with MNA and ppNT assay results. In addition, researchers have 

demonstrated that Genscript’s cPass kit is more sensitive than live virus neutralization assays 

and has the potential for further modifications to increase sensitivity.672

Vaccines

Different inactivated and attenuated vaccines, as well as recombinant protein, mRNA, and DNA

vaccines, have been developed over the past several years to provide protection against 

infection from SARS-CoV-1, MERS-CoV, and more recently SARS-CoV-2.

704–706 Numerous studies 

have demonstrated that the S protein on the surface of these three coronaviruses is particularly 

immunogenic and therefore this protein has been targeted in many vaccine formulations. Many 

of the resulting vaccine strategies result in reduced viral titers and some degree of protection 

against severe disease, with less morbidity and mortality when compared to lack of vaccination. 

However, just as many studies to date have shown that infections with SARS-CoV-1, MERS-CoV1, and SARS-CoV-2 do not provide a long-lasting antibody response and wane post 

infection,

707,708 several vaccines developed against SARS-CoV-1 also produced only short-term 

protection against subsequent viral challenges.709,710 These vaccines also caused complications 

related to inflammatory disease and, for vaccines targeting the SARS-CoV-1 S protein, triggered 

antibody-dependent enhancement (ADE).710,711 Inactivated viral vaccines have also produced 

non-neutralizing antibodies that exhibit ADE functions that promote inflammation and tissue 

destruction, with the activation of myeloid cells via Fc receptors.712 Therefore, it remains 

imperative to develop a vaccine with minimal risk of ADE that can provide long-lasting 

protection against potentially emerging variants of the coronavirus. Vaccines that confer longterm protection should elicit both the production of virus-specific neutralizing antibodies as 

well as antigen-specific T and B cell adaptive immune responses. Select vaccines tested in 

animals are summarized in Table 18, and notable vaccines are discussed below.

Research Tools for Vaccine Development

A good deal of data on coronavirus vaccines in animals comes from animal model testing of 

vaccines intended for human use. Initial in vivo tests of vaccine candidates typically involve 

mice, rats, and other small animals that may not be susceptible to infection with SARS-CoV-1, 

MERS-CoV, or SARS-CoV-2. These initial tests are used to determine whether a candidate 

antigen is immunogenic and elicits a humoral response generating antibodies. This approach 

has been used for recombinant protein antigens and inactivated SARS-CoV-2 virus, which can 

generate neutralizing antibodies in mice and rats.713,714 

However, species not susceptible to SARS-CoV-1, MERS-CoV, or SARS-CoV-2 cannot be used in 

follow-up challenge experiments to determine whether these immune responses are

protective. Therefore, transgenic715 and adenovirus transduced mouse strains566,567 expressing 

human ACE2, as well as wildtype species susceptible to infection (e.g., M. auratus, M. putorius 

furo, NHPs) are used to test vaccines’ protective effects. Although these particular models 

cannot shed light on animal protection, mouse-adapted strains of SARS-CoV-2 have also been 

used for vaccine development, and challenge experiments can be conducted on these mouse 

models to determine the degree of protection afforded by a given vaccine. Several subunit 

vaccines have been tested via this method and demonstrate efficacy, with some protection 
Report Page 87

obtained and infected mice developing less severe disease.561 Another vaccine consisting of a 

virus-like particle was tested and also demonstrated efficacy, with lower viral titers observed in 

infected mice.587 

Large animal models such as NHPs have been used extensively to evaluate vaccine candidates 

prior to testing in humans due to their closely related immune systems. These animals have

helped explore the decrease in neutralizing antibody titers and T cell responses over time that 

has been one of the major challenges in developing a vaccine against SARS-CoV-2, with multiple 

studies showing a decrease to low levels within 2-3 years post infection in humans.

707,708 Both 

rhesus macaques and pigtailed macaques have been the most widely used NHPs due to their 

availability and presence of reagents that can be used to evaluate the immune response and 

correlates of protection. 

Vaccines Tested in Susceptible Animals

During the past two years, vaccine development for SARS-CoV-2 has focused on novel mRNA 

vaccines that can be rapidly produced. The two major novel mRNA vaccines used in the U.S., 

both encoding the S protein of SARS-CoV-2, were largely developed and evaluated in rhesus 

macaques prior to human clinical trials. Both achieved 95% efficacy in clinical trials and are in 

use today.716,717

ChAdOx1, an adenovirus vector-based vaccine, has been used in vaccines against MERS-CoV 

and SARS-CoV-2.141,718 The MERS ChAdOx1 spike vaccine induced neutralizing antibodies and 

protected C. dromedarius from future MERS-CoV infections,

719 while the SARS-CoV-2 spikebased vaccine elicited a strong humoral as well as cell-mediated responses in the same species. 

The vaccine was then tested in rhesus macaques and was demonstrated to provide protection 

against infection in challenge experiments prior to being evaluated in clinical trials.

718

PiccoVac, an inactivated SARS-CoV-2 vaccine, elicited a strong immune response involving both 

the production of neutralizing antibodies as well as T cell responses in M. mulatta.

714

Like other RNA viruses, SARS-CoV-2 is prone to genetic evolution and acquires mutations that 

allow the virus to adapt to new hosts and/or evade the host’s immune response. Over the past 

3 years, multiple variants of concern have arisen and many are able to escape the 

immunological response afforded by current vaccines, necessitating the development of new 

formulations. However, although the vaccines may not afford complete protection from 

infection by the newly emerging variants, they do appear to protect animals and humans 

against more severe disease.

720 Current vaccine development efforts focus on generating 

vaccines with broader protection against multiple variants.

Vaccines Designed for Veterinary Use

Animal protection strategies against SARS-CoV-1, MERS-CoV-1, and SARS-CoV-2 require 

effective vaccines in various animal species, including companion, farmed, captive, and wild 

animals. Several of the FDA-approved and emergency use vaccines that have been approved for 

humans may not be useful in the immunization of animal species due to their expense and 

logistically difficult administration (e.g., temperature requirements). Therefore, the 
Report Page 88

development of specific veterinary vaccine formulations that can be disseminated rapidly 

during a pandemic outbreak are still needed. 

Multiple veterinary vaccines are being formulated and tested in animals for this purpose. An 

experimental SARS-CoV-2 S protein vaccine developed by Zoetis was reported to elicit a strong 

immune response in domesticated cats.3 Neutralizing antibody titers were present in cat serum 

of vaccinated animals after the first and second vaccinations with the recombinantly produced 

S protein trimer, and robust levels of these neutralizing antibody titers were induced for both 

the wildtype Wuhan strain and the more severe delta variant. This experimental vaccine has 

been provided to zoos and mink farms to immunize animals at risk for contracting the virus and 

transmitting it to other animals as well as humans. Captive orangutans housed at the San Diego 

Zoo were one of the first NHPs to receive this experimental vaccine and since that time other 

species housed at zoos have been immunized. 

The LinearDNA COVID-19 vaccine is also currently being developed by Applied DNA Sciences 

and EvviVax for use in domestic cats. This vaccine has received regulatory approval from the 

United States Department of Agriculture and is currently undergoing clinical trials to evaluate 

its immunogenicity and efficacy. According to preliminary results reported by the company, the

vaccine is well tolerated and generates high levels of neutralizing antibodies with a single dose 

in domesticated cats.

721 Immunization of cats with this vaccine could prevent SARS-CoV-2 

infections and prevent transmission not only to feral cats that could subsequently transmit the 

virus to wildlife but also to humans.615

An inactivated SARS-CoV-2 vaccine, Carnivac-CoV, has been recently registered as a vaccine 

formulation for animals based on testing in dogs, cats, foxes, and mink. Clinical trial data 

indicate that protective immunity is achieved and has a duration of at least six months after 

vaccination.722

Table 19: Summary of select vaccine studies in animal species

Species Virus Vaccine Type Target Vaccine Name Administration 

Route

Induction of 

neutralizing 

antibodies

T cell 

responses

Protection 

against 

infection

Camelus 

bactrianus

MERSCoV

recombinant, 

nonvirulent 

Newcastle 

disease virus

S rLa-MERS-S723 intramuscular Yes N/A N/A

Camelus 

dromedarius

MERSCoV

adenovirus 

vector S ChAdOx1 MERS719 intramuscular Yes N/A Yes

DNA S not specified724 intramuscular Yes N/A N/A
Report Page 89

modified 

vaccinia virus 

Ankara 

vectored DNA

S not specified725 intranasal Yes N/A Yes

Cavia 

porcellus

SARSCoV-2inactivated 

virus whole virus BBIBP-CorV726 intramuscular Yes N/A N/A

Felis catus SARSCoV-2 Protein

S not specified727 intramuscular Yes N/A Yes

S, trimer Zoetis vaccine3 not specified Yes N/A N/A

Llama glama SARSCoV-2 Protein S1 not specified728 intramuscular Yes N/A Yes

Macaca 

fascicularis

SARSCoV-2

DNA S GX-19729 intramuscular Yes Yes Yes

Sendai virus 

vector N, M, E SeV-NME730 intramuscular; 

intranasal Yes Yes Yes

fusion protein S S1-Fc731 unknown Yes N/A N/A

inactivated 

virus whole virus BBIBP-CorV726 intramuscular Yes N/A N/A

mRNA

S, prefusion 

stabilization 

mutation 

and furin 

cleavage 

site 

mutation

MRT5500732 intramuscular Yes N/A N/A

nanoparticleencapsulated 

mRNA

RBD ARCoV733 intramuscular Yes Yes N/A
Report Page 90

Protein S NVXCoV2373734 intramuscular Yes N/A Yes

Macaca 

mulatta

MERSCoV

DNA S not specified724 intramuscular Yes Yes Yes

DNA priming + 

protein boost

S DNA 

prime + S1 

protein 

boost

not specified735 intramuscular Yes N/A Yes

Protein RBD not specified736 intramuscular Yes Yes Yes

recombinant 

VSV vector S VSVΔGMERS737

intramuscular; 

intranasal Yes Yes N/A

virus-like 

particle whole virus MERS-CoV VLP738 intramuscular Yes Yes N/A

SARSCoV-1

adenovirus 

vector S1 Ad5-SARSCoV739 intramuscular Yes N/A N/A

human 

adenovirus 

vector; 

chimpanzee 

adenovirus 

vector

S not specified740 intramuscular Yes Yes N/A

SARSCoV-2adenovirus 

vector

S ChAdOx1nCoV-19718 intramuscular Yes Yes Yes

S

Sad23L-nCoV-S 

& 

Ad49L-nCoVS741

intramuscular Yes Yes N/A
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S Ad5-nCoV742 nebulization 

inhalation Yes Yes N/A

S not specified743 intramuscular Yes Yes Yes

DNA

S not specified744 intramuscular Yes N/A Yes

S INO-4800745 intradermal Yes Yes Yes

inactivated 

virus

whole virus BBV152746 intramuscular Yes N/A Yes

whole virus PiCoVacc714 intramuscular Yes N/A N/A

whole virus BBIBP-CorV726 intramuscular Yes N/A Yes

whole virus not specified747 intramuscular Yes Yes Yes

modified 

vaccinia virus 

Ankara vector

S 

(membrane 

anchored, 

pre-fusion 

stabilized)

not specified748 intramuscular Yes Yes Yes

mRNA

S mRNA-1273716 intramuscular Yes Yes Yes

S BNT162b2749 intramuscular Yes N/A Yes
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Protein

RBD not specified750 intramuscular Yes Yes Yes

S, trimer S-Trimer751 intramuscular Yes N/A Yes

VSV vector S not specified752 intramuscular; 

intranasal

Yes (both 

routes)

Yes 

(intramuscular 

only)

Yes 

(intramuscular 

only)

Macaca 

nemestrina

SARSCoV-2

mRNA S repRNACoV2S753 intramuscular Yes Yes N/A

nanoparticle + 

mRNA S LION/repRNACoV2S754 intramuscular Yes Yes N/A

Mesocricetus 

auratus

SARSCoV-2

inactivated 

rabies viral DNA 

vector plus 

MPLA-AddaVax 

(TRL4 agonist)

S1 CORAVAX755 intramuscular Yes N/A Yes

mRNA

S Moderna 

vaccine756 intramuscular N/A N/A Yes

S (prefusion 

stabilization 

mutation 

and furin 

cleavage 

site 

mutation)

MRT5500732 intramuscular Yes N/A Yes

VSV vector S not specified757 intramuscular; 

intranasal N/A N/A Yes
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Mus 

musculus

SARSCoV-1

adenovirus 

vector N, S not specified758 intramuscular; 

intranasal Yes Yes Yes

protein (RBDFc); AAV (RBD) RBD RBD-Fc; RBDrAAV759

intramuscular; 

intramuscular 

or intranasal

Yes Yes N/A

Venezualan

equine 

encephalitis 

virus replicon 

particles 

S VRP-S760 not specified Yes N/A Yes

virus like 

particles

whole virus not specified761 intramuscular; 

intranasal Yes N/A Yes

whole virus not specified762 subcutaneous Yes Yes N/A

whole killed 

virus whole virus not specified758 subcutaneous Yes Yes Yes

Mus 

musculus

(adapted 

SARS-CoV-2 

virus)

SARSCoV-2

virus-like 

nanoparticle 

(contains 120 

RBD copies)

RBD VLP-RBD763 intramuscular Yes N/A Yes

Mustela 

putorius furo

SARSCoV-1

adenovirus 

vector N, S not specified764 intramuscular Yes N/A Yes, 

incomplete

human 

adenovirus 

vector (prime); 

chimpanzee 

adenovirus 

vector (boost)

S not specified740 intramuscular Yes Yes Yes

modified 

vaccinia Ankara 

vector

N, S not specified765 subcutaneous Yes (spike 

only) No

No, caused 

inflammatory 

response
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whole killed 

virus whole virus not specified764 intramuscular Yes N/A Yes, 

incomplete

SARSCoV-2 

adenovirus 

vector S Ad5-nCoV766 intramuscular; 

oral + intranasal Yes N/A Yes

DNA S INO-48002 intramuscular Yes N/A N/A

Oryctolagus 

cuniculus

SARSCoV-2 inactivated 

virus whole virus BBIBP-CorV726 intramuscular Yes N/A N/A

Papio anubis SARSCoV-2 Protein S NVXCoV2373767 intramuscular Yes Yes N/A

Therapeutics

Similar to vaccines, some data on therapeutic efficacy against animal coronaviruses come from 

studies in animal model conducted for human drugs. Wherever wildtype animals are employed 

in these studies, they can provide helpful information relevant to controlling coronavirus in 

animal species, with implications not only for treating animal infection but also for reducing risk 

of subsequent transmission. This summary surveys the mechanisms of action and impacts of 

the predominant drug classes of antivirals and biologics, as well as of a broader class of FDAapproved agents includes microbicides, polyphenols, anti-inflammatory, and other agents with 

varying degrees of efficacy across animal species.

FDA-Approved Antivirals

Antivirals Targeting RNA-Dependent RNA Polymerase 

Rhesus macaques

Remdesivir is an FDA-approved antiviral that, as an adenosine nucleoside triphosphate analog, 

is incorporated during replication by RdRp, which results in chain termination and halting of 

replication in SARS-CoV-1, MERS-CoV, and SARS-CoV-2.768–771 A novel subcutaneous formulation 

was studied using SARS-CoV-2-infected M. mulatta. M. mulatta treated with 10 milligrams per 

kilogram (mg/kg) of remdesivir for 6 days showed no signs of interstitial pneumonia starting at 

12 hours post-infection.772 Additionally, there were reduced signs of respiratory disease and 

virus replication in the lower respiratory tract compared to untreated animals.772 
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Mice

Remdesivir in mice has relatively poor plasma stability. However, GS-441524, the parent 

nucleoside and metabolite of remdesivir, inhibits SARS-CoV-2 with a mechanism similar to 

remdesivir in vivo.

773 An intraperitoneal dose of 25 mg/kg GS-441524 24 hours prior to infection 

resulted in significant viral clearance in the lungs at 2 dpi and no weight loss in M. musculus.

2

An additional study tested molnupiravir, which is an analogue that increases the frequency of 

mutations resistant to the proofreading exoribonuclease encoded by coronavirus. Severe 

combined immunodeficient (SCID) mice infected with the beta variant of SARS-CoV-2 were 

treated with 200 mg/kg of molnupiravir orally and experienced reduced viral RNA loads. Fifty 

percent of the treated animals showed no infectious viral titers and demonstrated improved 

lung histology scores.774 

Ferrets

GS-621762 is an oral prodrug of parent nucleoside GS-441525 and is effective at controlling 

SARS-CoV-2 infection in ferrets that received treatment twice daily for 4 dpi.

775 Compared to 

the vehicle control group, virus was undetectable in nasal turbinates and RNA copy numbers 

were lower in treated ferrets.

775 Molnupiravir has also been tested in ferrets.776 Ferrets treated 

with molnupiravir twice daily demonstrated reduced viral load in the upper respiratory tract, 

which subsequently prevented spread to other animals.

776 

Syrian Hamsters

Early treatment of SARS-CoV-2 with galidesivir, molnupiravir, or favipiravir reduced weight loss, 

viral titers, and viral burden in Syrian hamsters.

774,777,778 Molnupiravir may be particularly 

advantageous in the treatment of animals because it can be administered orally. Combination 

treatment with molnupiravir and favipiravir for early treatment of SARS-CoV-2 in hamsters

resulted in higher overall potency, with undetectable virus titers in the lungs of greater than 60

percent of animals.

779 This effect was lessened when treatment was delayed by 1 day.779

Favipiravir increases antiviral activity because it increases the number of mutations in the SARSCoV-2 genome, ultimately decreasing viral infectivity.

778,779

Hamsters treated with remdesivir and methylprednisolone demonstrated reduced weight loss 

and inflammation.

780 The combinatorial effect reduced viral protein expression and viral loads. 

In the presence of remdesivir, methylprednisolone suppressed antibody activity.

780

Reverse Transcriptase Inhibitor

Ferrets

Emtricitabine-tenofovir is used for the treatment of HIV and has been tested for the treatment 

of SARS-CoV-2.306 Emtricitabine-tenofovir-treated ferrets had reduced virus titers compared to 

untreated animals, but this effect was eliminated when the immune system was compromised 

with exposure to azathioprine.

306
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Protease Inhibitors

BALB/cAJcl and K18-hACE2 mice

Ensitrelvir, which targets the 3C-like protease (3cLpro) of SARS-CoV-2, was shown to be 

effective against the SARS-CoV-2 gamma strain in mice treated twice daily for 5 dpi. Ensitrelvir 

reduced viral loads and body weight loss in mice compared to the vehicle control group.

781

Post-infection treatment of SARS-CoV-2 with GC376 (i.e., 3cLpro inhibitor) increased survival 

and decreased lung viral titers in mice.

17 

Syrian Golden Hamsters

Nirmatrelvir, an orally administered inhibitor of viral 3cLpro, has antiviral activity against four 

SARS-CoV-2 variants of concern in vitro.

782 PF-332 administered orally twice daily to hamsters 

conferred complete protection against SARS-CoV-2 beta and delta variants and prevented 

transmission.

782 

Ferrets

Although lopinavir-ritonavir treatment has shown efficacy against SARS-CoV-1, MERS-CoV, and 

SARS-CoV-2 in vitro, those results have not translated to in vivo effectiveness. The antiviral 

efficacy of lopinavir-ritonavir was assessed in a ferret infection immunosuppressive model, in 

which ferrets were administered 16 mg/kg daily post-infection via oral gavage for 14 days. The 

lopinavir-ritonavir-treated group demonstrated clinical symptoms (cough, rhinorrhea, and 

reduced activity) comparable to the placebo group.306

Biologics

Antibodies

Marmosets

Two human neutralizing MERS-CoV antibodies, REGN3051 and REGN3048, have shown 

prophylactic and therapeutic efficacy in a murine MERS model. MERS-infected marmosets 

treated with either one or both antibodies also had less severe respiratory disease and lung 

lesions and reduced viral loads in the lungs compared to untreated animals.783 de Wit et al. 

demonstrated that the combination antibody treatment was most effective in MERS-CoVinfected marmosets, with reduced virus replication when the combination was administered 

prophylactically 24 h before infection compared to a single neutralizing antibody.783 

Hamster

NIH-CoVnb-112, a neutralizing nanobody, binds to SARS-CoV-2 RBD in the spike trimer in the 

“up” conformation.

784 SARS-CoV-2-infected hamsters treated with NIH-CoVnb-112 

demonstrated a reduction in viral lung burden and weight loss compared to untreated 

animals.784 The ZRC3308 monoclonal antibody cocktail contains two humanized monoclonal 
Report Page 97

antibodies (mAbs), ZRC3308-A7 and ZRC3308-B10, that bind to SARS-CoV-2 RBD. Hamsters 

treated with this antibody cocktail prophylactically did not develop pneumonia and had 

reduced viral loads compared to untreated controls.785 Polyclonal immune sera from previously 

challenged rhesus macaques were also used to treat SARS-CoV-2 infected hamsters, resulting in 

protection against the virus.786 Hamsters had reduced weight loss and macrophage infiltrates in 

the lungs, but the number of innate and adaptive immune cells present was not affected by 

immune sera treatment.786 

Cas Proteins

Hamsters

Certain bacteria use Cas13a as part of an immune system to degrade foreign RNAs. Blanchard 

et al. designed clustered regularly interspaced short palindromic repeats (CRISPR) RNA with 

conserved regions for influenza virus and replicase and nucleocapsid genes of SARS-CoV-2 as 

targets to create a polymer-formulated Cas13a mRNA.787 SARS-CoV-2-infected hamsters were 

treated pre- and post- infection using a nebulizer, and Cas13a degraded influenza RNA in lung 

tissue and reduced viral load.

787

Other FDA-Approved Drugs

Anti-virals 

Rhesus macaques

IFNs are antiviral factors secreted from infected cells that induce cytokine production. The 

combined treatment effect of IFN and ribavirin was assessed in MERS-CoV-infected rhesus 

macaques. The antiviral effect of IFN-a2b against MERS-CoV was enhanced by the concomitant 

use of ribavirin 8 h post infection. Interestingly, elevated levels of IL-6, IFN-γ, and MCP-1 in 

homogenates of lung tissue three dpi indicated a tissue-specific host response to infection that 

can be moderated by treatment.788

Microbicides

Mice

Astodrimer sodium is a polyanionic, polysulfonate compound that is currently used to treat 

bacterial vaginosis. It effectively prevents the formation of biofilms and its polyanionic surface 

attaches to targets on viruses, thereby blocking viral entry into host cells. Some evidence 

suggests that astodrimer sodium can prevent SARS-CoV-2 infection and reduce the severity of 

COVID-19.

789 SARS-CoV-2-infected mice treated with astrodrimer sodium 1% nasal spray 

exhibited reduced viral genome copies and virus in the lung, trachea, and nasal cavity.

789

Astodrimer sodium 1% also reduces pro-inflammatory cytokines interleukin (IL)-6, IL-1β, IL-1α, 

tumor necrosis factor alpha (TNFα), transforming growth factor beta (TGFβ), and MCP-1 in the 

serum, lung, and trachea.

789 
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Antidepressants

K18-hACE2 Mice

Fluoxetine has potential as a SARS-CoV-2 treatment due to its inhibitory effect on acid 

sphingomyelinase/ceramidase.790 Acid ceramidase, which is considered a host factor, is an 

essential component involved in viral replication, and inhibiting acid ceramidase increases the 

ceramide content in SARS-CoV-2-infected cells. Fluoxetine treatment demonstrated antiviral 

properties in mice infected with different SARS-CoV-2 variants (i.e., delta, omicron, alpha, and 

gamma).

790 Fluoxetine significantly reduced both lung tissue viral titers and pro-inflammatory 

expression markers in serum, such as IL-6, TNFα, chemokine ligand 2 (CCL2), and C-X-C motif 

chemokine ligand 10 (CXCL10).790

Polyphenols

C57BL/6 Mice

Catechin is a phenolic compound found in green tea polyphenols that helps protect cells against 

damage from free radicals. This potent antioxidant molecule is also abundant in cocoa and 

berries.791 A previous study demonstrated that epigallocatechin gallate (EGCG), a green tea 

polyphenol, inhibited coronavirus replication in vitro.792 Park et al (2021) demonstrated that

EGCG incorporated into regular drinking water for two weeks post infection in mice infected 

with human coronavirus OC43 reduced coronavirus RNA and protein levels in mouse lungs.792

Aldehyde dehydrogenase inhibitors

Golden Hamsters

Disulfiram is an FDA-approved drug for the treatment of alcohol use disorder, and its ability to 

block gasdermin D-dependent neutrophil extracellular trap (NET) formation in macrophages 

suggests it may be useful as a SARS-CoV-2 treatment. Upon lung injury caused by SARS-CoV-2 

and other insults, neutrophil infiltrates form NETs that trigger additional damage and an 

increased immune response. Adrover et al. demonstrated that disulfiram’s ability to inhibit NET 

formation provided protection against SARS-CoV-2 in hamsters. SARS-CoV-2-infected hamsters 

that were treated with 50 mg/kg of disulfiram had reduced NETs and less perivascular fibrosis in

their lungs. Additionally, disulfiram treatment downregulated innate immune and 

complement/coagulation pathways.793

Non-structural protein targets

Syrian hamsters

Ranitidine bismuth citrate is a metal compound previously used as an effective treatment for 

Helicobacter pylori infection.

794 Ranitidine bismuth citrate targets helicase, which inhibits DNA 

unwinding activity, and quantitative reverse transcriptase PCR experiments indicated that the 

compound inhibits a late-stage process in the SARS coronavirus replication cycle.

795 Yuan et al. 
Report Page 99

investigated whether this antimicrobial drug also impedes viral helicase in Syrian hamsters

infected with SARS-CoV-2. Hamsters treated with ranitidine bismuth citrate had decreased viral 

loads in the upper and lower respiratory tracts and no lung damage or cell infiltration in the 

alveolar space.794

Fatty Acid Synthesis

Mice

Chu et al. demonstrated that SARS-CoV-2 requires fatty acid synthesis to establish and maintain 

infection in the lungs.

796 Mice treated with orlistat (fatty acid synthase inhibitor) pre- and postinfection exhibited lower SARS-CoV-2 viral levels in the lung, reduced lung pathology, and 

increased survival.

796 

Statins

Mice

Simvastatin reduces physiological inflammatory response triggered by SARS-CoV-2.797 Mice 

treated orally with simvastatin (20 mg/kg) 24 hours prior to infection demonstrated reduced 

virus replication and lung damage, as well as increased survival time compared to vehicletreated groups.

797 Interestingly, there was no difference in mortality between treated mice and 

the vehicle control group.797 Teixeira et al. demonstrated that simvastatin disrupts SARS-CoV-2 

cell entry by shifting host ACE2 on cell membrane rafts.

797 

Anti-inflammatory

Rhesus macaques

The duration and severity of inflammation influences the burden of disease associated with 

SARS-CoV-2 infection. Baricitinib is a janus kinase (JAK) inhibitor and anti-inflammatory drug 

used to treat moderate to severe rheumatoid arthritis that has also shown potential against 

SARS-CoV-2-related inflammation.

798 SARS-CoV-2-infected Rhesus macaques that were orally 

administered 4 mg of baricitinib demonstrated reduced neutrophil degranulation in BALs.798

Further analyses showed that baricitinib treatment inhibited inflammatory cytokines and 

neutrophil chemoattractant expression in BALs. Barcitinib treatment also decreased T cell 

proliferation and activation.

798

Rodents

Loratidine (antihistamine) stabilizes mast cells and prevents the influx of pro-inflammatory 

cytokines. Hamsters that received a combination dose of loratidine and remdesivir 

demonstrated a reduction in not only SARS-CoV-2 replication but also inflammation, which 

protected against lung injury.

799 
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Glucocorticoids (steroid hormones), such as dexamethasone, are also used to treat 

inflammation, as well as autoimmune disorders, asthma, and organ transplant. Dexamethasone 

has been evaluated against a particular type of pulmonary inflammation observed in SARS-CoV1, in which the nucleocapsid protein (N-protein) triggers a poorly regulated influx of proinflammatory and anti-inflammatory cytokines. The effect of dexamethasone was evaluated in 

a rat model of SARS-CoV with pulmonary inflammatory reaction induced by .2 mg/kg of Nprotein of SARS-CoV. Levels of IL-6, IL-10, and TGF-beta1 were significantly lower in rats 

administered dexamethasone compared to the untreated group. This result suggests that 

glucocorticoids can be used to mitigate the pulmonary inflammatory reaction induced by the Nprotein of SARS-COV.800

Anti-parasitic

Rhesus macaques

Hydroxychloroquine (HCQ) and chloroquine are antimalarial drugs that are also used as 

immunosuppressives and DMARDs (disease-modifying antirheumatic drugs). Both drugs 

demonstrated an inhibitory effect on SARS-CoV-2 replication in vitro both alone and in 

combination with macrolide antibiotic azithromycin. However, these results did not translate to 

an in vivo context. A SARS-CoV-2 Rhesus macaques model was administered 6.5 mg/kg of HCQ 

prophylactically (weekly) and as a treatment (daily). There was no effect on replication and no

impact on viral shedding or signs of disease progression.801

Hamsters

The administration of HCQ alone was not beneficial either as a treatment (50 mg/kg daily) or 

prophylactically (50 mg/weekly). Therefore, Cochin et al tested the combination of 

azithromycin (20 mg/ml) and (200 mg/ml) HCQ and (200 mg/ml) HCQ alone in a SARS-CoV-2 

hamster model at the time of infection. Neither course of treatment inhibited SARS-CoV-2 

replication, or impeded lung impairments in the hamster model. Hydroxychloroquine and 

chloroquine are not effective treatments for SARS-CoV-2.802 

Biosecurity

Although this review focuses on coronaviruses in animal populations, humans play a necessary 

role in implementing biosecurity measures. Because humans are a primary reservoir of 

coronaviruses, with the potential for zoonosis (i.e., animal to human transmission) and 

subsequent reverse zoonosis (i.e., human to animal transmission),803,804 human infection 

prevention must be considered part of animal biosecurity. In addition, many species-specific 

coronaviruses, such as Bov-CoV, cause respiratory disease and are transmitted through droplets 

and/or aerosol, similar to SARS-CoV-1, MERS-CoV, and SARS-CoV-2.805 Therefore, animal 

biosecurity measures implemented for these species-specific coronaviruses should be 

considered as relevant strategies for SARS-CoV-1, MERS-CoV, and SARS-CoV-2. Outlined below 

are considerations for areas of biosecurity measures against coronaviruses, accounting for the 

protection of animals and humans, to prevent viral transmission to animals.
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Vaccines

Vaccines are one of the most effective methods for controlling the spread of infectious diseases 

such as SARS-CoV-1, MERS-CoV, and SARS-CoV-2. Furthermore, vaccinating animals that are 

susceptible to these coronaviruses can substantially reduce animal-to-animal and animal-tohuman transmission, which in turn reduces the emergence of novel variants.806 Viral 

transmission is reduced from vaccination through population immunity (i.e., herd immunity), in 

which an entire population is protected from viral infection once a specified percentage of the 

population produces sufficient immune responses from vaccination. In veterinary medicine, 

population immunity has been successfully reached to completely eradicate animal diseases.805

Therefore, vaccination of susceptible animal populations should be a top measure of 

biosecurity (see “Biosecurity”). However, with vaccines only being approved for use in 

humans807 and tested on a limited quantity of species, such as companion and zoo animals,1–4

other biosecurity measures should also be considered.

Surveillance

During the 2003 SARS-CoV-1 pandemic, non-specific symptoms of SARS-CoV-1 infection 

prevented accurate clinical diagnosis, and thus enhanced disease transmission to local 

communities through delayed implementation of biosecurity measures. Surveillance of 

coronaviruses within animal populations is necessary for early viral detection and diagnosis, 

which can facilitate implementation of biosecurity measures, such as quarantine of infected 

animals.808 Under a One Health approach that aims to “balance and optimize the health of 

people, animals, and ecosystems,”809 coordinated surveillance should be established for 

wildlife, farmed wildlife, domestic animals, and individuals who have frequent contact with 

animals.810 When animals test positive, diagnostic and clinical factors should be evaluated to 

determine potential viral sources and other animals that were potentially exposed.804 To rapidly 

identify potential viral sources, the Norwegian BRSV [bovine respiratory syncytial virus] and 

Bov-CoV Control Program implemented a hotline through which farmers can report potential 

respiratory disease outbreaks.811 In addition, samples from known wildlife viral reservoirs can 

be collected for genome sequencing, which can identify novel variants that can potentially 

evade coronavirus immune responses from vaccines or prior infections (see “Surveillance” for 

more details).614,810

Disinfection, Decontamination, and Personal Protective Equipment

USDA APHIS provides guidance for N. vison and O. virginianus farmers on proper disinfection, 

decontamination, and personal protective equipment (PPE) usage in “One Health: Keeping 

Animal and People Safe from SARS-CoV-2.” When working around healthy animals, workers 

should wear a cloth face covering and wash or sanitize their hands regularly. However, when 

working around animals that are suspected of having illness, workers should use appropriate 

PPE, such as gloves, face masks, and goggles or face shields. In addition, workers should 

immediately wash their hands for at least 20 seconds after coming in direct contact with sick 

animals, their food, water supply, or waste.812 Takahashi et al. (2020) also found that when 

workers exchanged boots and used footbaths at the entrance of calf sheds on bovine farms, 

detection of Bov-CoV and calf mortality rates were significantly reduced.813
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According to the USDA APHIS guidance, surfaces frequently used by workers or animals should 

be cleaned and disinfected regularly.812 Some conventional disinfection measures include liquid 

spray, ultraviolet light, and heat treatment.814 Workers should avoid using disinfection methods 

that could spray infectious material into the air, such as compressed air or pressurized water.812

Air filtration or treatment systems are another effective means of removing infectious material 

from animal housing areas, especially when negative-pressure ventilation is implemented, 

which effectively reduces viral load.805

Lastly, animal carcasses that are positive, or suspected to be positive, for a coronavirus should 

be properly disposed to prevent contamination and viral transmission. Carcasses should be 

carefully transported to an approved disposal site or disposed of using onsite composting, 

burial, incineration, landfill, and/or rendering. During any carcass transport, measures should 

be implemented to prevent the escape of contaminated material and vehicles should be 

disinfected after each use.812 In addition, farmers should use caution when handling products 

(e.g., dairy and meat products) from animals that are positive, or suspected to be positive, for a 

coronavirus. Although heat treatment can reduce or eliminate viral detection of SARS-CoV-2,

815

MERS-CoV can survive in milk for prolonged periods of time.

816 Thus, farmers should consider 

appropriately disposing of any raw animal products from positive animals to prevent further 

contamination and viral transmission.

Reducing Animal Contact

Reducing contact between animals and humans and other animals as a biosecurity measure 

should be highly prioritized because physical separation and distancing substantially reduces 

exposures to coronaviruses. CDC provides guidance on reducing wildlife animal contact in 

“Reducing the Risk of SARS-CoV-2 Spreading between People and Wildlife,” stating that wildlife 

researchers should substitute animal capture with remote monitoring methods, which can 

reduce human contact and animal transport to other locations where virus can spread. When 

onsite field research is necessary, the minimum number of personnel should be deployed to 

safely complete tasks. Wildlife rehabilitation facilities should also consider suspending 

rehabilitation of wildlife species that are highly susceptible to SARS-CoV-2 infection.817

USDA APHIS also provides guidance on reducing animal contact on N. vison and O. virginianus

farms in “One Health: Keeping Animals and People Safe from SARS-CoV-2.” Workers should 

stagger work hours, maintain social distancing between each other, and implement physical 

partitions between each other and animals when possible.812 Similar methods are used when 

controlling Bov-CoV transmission on bovine farms, in which farmers have separate pastures and 

use separate transport vehicles for sero-positive and -negative herds.811 In addition, to reduce 

the risk of externally introducing virus to a farm, access to animal housing facilities should be 

restricted, and workers should stay home if they feel sick.811,812

According to CDC’s guidance on reducing the risk of viral transmission among pets in “What You 

Should Know about COVID-19 and Pets,” pet owners should avoid contact with pets that test 

positive for SARS-CoV-2, and depending on veterinarian recommendation, should isolate their 

infected pets. In addition, pet owners should not allow pets that test positive to roam outside, 
Report Page 103

in order to reduce viral transmission to other pets and wildlife.818 Omrani et al. (2015) provides 

similar recommendations for reducing the transmission of MERS-CoV from camels, such as 

strict regulation of camel movements and isolation of camels that test positive for MERSCoV.819

Land Use Changes

Land use changes, such as logging, mining, and railroad building, can alter the movement of 

wildlife and create new habitats for species, allowing for contact between previously isolated 

species, and thus increasing the risk of recombinant viral mutations.810 Reducing land use 

changes can help keep ecosystems with high species diversity intact, which enhances the 

ecological conditions that maintain and strengthen wildlife immune function and prevents 

conditions that lead to high viral prevalence and transmission.820 In accordance with a One 

Health approach,809 wildlife conservation and distancing measures are needed to maintain 

these optimal ecological conditions and reduce viral transmission among wildlife.

820

Policy on Markets and Trade

The origins of SARS-CoV-2 can be traced back to a live animal market in Wuhan, China,168 in 

which intermediate animal hosts may have contributed to the eventual outbreak of the COVID19 pandemic.808 Due to the nature of live animal markets in the United States and worldwide, 

where multiple species that are otherwise isolated from each are in close proximity, there is 

high likelihood of viral transmission and the emergence of novel recombinant viruses.821 Thus, 

biosecurity measures should be enforced in live animal markets and the trade of livestock. 

However, policies should aim to modify market and trade practices rather than ban them 

because these practices are often culturally rooted.810 As a result of placing bans on live animal 

markets, illegal trade that completely lacks biosecurity may increase, as exemplified through 

bans enacted by the Chinese government.808 In contrast, policy changes that can increase 

biosecurity within live animal markets and livestock trade include behavior change programs, 

risk education, effective communication, enforcement of regulations, incentives for more 

sustainable food production, and market rest days to allow for disinfection.810,822

Depopulation and Culling

Because of the susceptibility of minks to SARS-CoV-2 and the rapid transmission rates of the 

virus among minks, both from human-to-mink and mink-to-mink transmission, mink farms have 

been highly affected by the COVID-19 pandemic. Many farmers have resorted to depopulation 

(i.e., culling) of animals, which can quickly eliminate viral transmission within infected farm 

populations. However, depopulation raises ethical concerns for animal rights and welfare.814

Therefore, other biosecurity measures should be prioritized to reduce virus transmission, 

especially as more coronavirus vaccinations become available for highly susceptible farm 

animal populations.
Appendix A: References Page 104

Appendix A: References

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1252 (2021).

2. Riddell, S. et al. Live Virus Neutralisation of the 501Y.V1 and 501Y.V2 SARS-CoV-2 Variants 

following INO-4800 Vaccination of Ferrets. Front. Immunol. 12, 694857 (2021).

3. Hoyte, A. et al. Experimental veterinary SARS-CoV-2 vaccine cross neutralization of the 

Delta (B.1.617.2) variant virus in cats. Vet. Microbiol. 268, 109395 (2022).

4. Ga, E. et al. A COVID-19 Vaccine for Dogs Prevents Reverse Zoonosis. Vaccines 10, 676 

(2022).

5. Li, W. et al. Bats are natural reservoirs of SARS-like coronaviruses. Science 310, 676–679 

(2005).

6. Cui, J., Li, F. & Shi, Z.-L. Origin and evolution of pathogenic coronaviruses. Nat. Rev. 

Microbiol. 17, 181–192 (2019).

7. Schountz, T., Baker, M. L., Butler, J. & Munster, V. Immunological Control of Viral 

Infections in Bats and the Emergence of Viruses Highly Pathogenic to Humans. Front. 

Immunol. 8, 1098 (2017).

8. Plowright, R. K. et al. Transmission or Within-Host Dynamics Driving Pulses of Zoonotic 

Viruses in Reservoir-Host Populations. PLoS Negl. Trop. Dis. 10, (2016).

9. Ng, M. et al. Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus 

susceptibility in bats. eLife 4, e11785 (2015).
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10. Takadate, Y. et al. Niemann-Pick C1 Heterogeneity of Bat Cells Controls Filovirus Tropism. 

Cell Rep. 30, 308-319.e5 (2020).

11. Zhou, P. et al. Contraction of the type I IFN locus and unusual constitutive expression of 

IFN-α in bats. Proc. Natl. Acad. Sci. U. S. A. 113, 2696–2701 (2016).

12. Subudhi, S., Rapin, N. & Misra, V. Immune System Modulation and Viral Persistence in 

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