Case Definition for SARS-CoV-2 as of 6/11/2021

SARS-CoV-2

Case Definition – June 11, 2021

Subject to change as situation evolves

(Notifiable Emerging Disease)

1. General Disease/Pathogen Information

1.1 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes 

the disease known as COVID-19 in humans, is an enveloped, positive sense, singlestranded RNA virus that belongs to the family Coronaviridae. Based on phylogenetic 

analyses, SARS-CoV-2 is currently believed to have originated from an animal host;

however, investigations into the origins of SARS-CoV-2 are ongoing. Since the

introduction of SARS-CoV-2 into human populations, the COVID-19 pandemic has 

been driven by person-to-person spread. Based on the information available, the 

risk of animals spreading the virus to people is considered to be low; however, SARSCoV-2 spread from an infected person to several animal species has been 

documented.

1

1.2 Clinical Signs: The clinical spectrum of illness in animals infected with SARS-CoV-2 is 

still being defined. Some infected animals may show signs of illness, while others 

may not. When present, clinical signs may include a combination of the following:

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• Fever

• Coughing

• Difficulty breathing or 

shortness of breath

• Lethargy

• Sneezing

• Nasal discharge

• Ocular discharge

• Vomiting

• Diarrhea

2. Laboratory criteria: The decision to test any animal for the SARS-CoV-2 virus will be 

made collaboratively between local, state, or federal public health and animal health 

officials3, and/or between federal agencies4, using a One Health approach. SARS-CoV-2 

is an OIE reportable disease in animals. The USDA APHIS VS National Veterinary Services 

Laboratories (NVSL) performs confirmatory testing of SARS-CoV-2 infection in animals5.

2.1 PCR: Detection of genetic material of SARS-CoV-2 on a quantitative PCR assay using 

manufacturer’s standards for identifying a cutoff cycle threshold (Ct) value. Nasal, 

1

For more information see the OIE COVID-19 Q&A

2

For more information see CDC COVID-19 and Animals

3

For more information see FAQ for State Animal and Public Health Officials on Animal Coronavirus Testing

4

Federal officials will consult on decisions concerning animals maintained in federal facilities or on federal lands.

5

For more information see USDA One Health

Animal and Plant 

Health Inspection 

Service

Veterinary Services

June 2021
Case Definition for SARS-CoV-2 as of 6/11/2021

oral, and rectal/fecal swabs are recommended per OIE. Store nasal, oral, and rectal

swabs in separate vials of viral transport media and maintain the cold chain at 2-8°C. 

2.2 Serology: Detection of antibodies against SARS-CoV-2 in an unvaccinated animal. 

Blood samples may be collected; remove from clot prior to storage. Serum may be 

frozen at -20°C.

2.3 Virus characterization: Genomic sequence generated either directly from diagnostic 

sample or from virus isolate.

3. Case definition and reporting criteria*

3.1 Suspect case: Animal determined to have an epidemiologic link with a confirmed 

human COVID-19 patient, SARS-CoV-2 infected animal, or other exposure of public 

and animal health concern OR the detection of SARS-CoV-2 antibody by a test 

intended for use in that species. If the animal is clinically ill, with the above 

exposures, other potential causes of illness should be ruled out by a veterinarian.

3.2 Presumptive positive case: Nasal, oral, or rectal swabs, tissues, or fecal samples from 

an animal tests positive by a real-time RT-PCR assay developed specifically for SARSCoV-2.

3.3 Confirmed positive case6: A suspect or presumptive positive case as above with:

sequence confirmation of virus either a) direct from nasal, oral, or rectal swabs,

tissues, or fecal samples from an animal with SARS-CoV-2 or b) from virus isolate or 

from SARS-CoV-2 virus recovered from the animal,

OR 

an animal with demonstrated SARS-CoV-2 neutralizing antibody.

3.3.1 An animal may be excluded as a confirmed case after review of all available 

case information if any of the following applies:

• An alternative diagnosis can explain the illness fully.

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• Antibody to SARS-CoV-2 is undetectable in a serum specimen obtained at 

least 14 days after initial test or onset of illness.

• Test result(s) are poorly or not repeatable and resampling is either not 

possible or testing from resampling is negative.

*Additionally, given the emerging nature of SARS-CoV-2 and the speed at which tests 

have been developed, laboratories should select test(s) appropriate for the sample type 

and interpret results in the context of all available information for each case. Collection 

of additional sample(s) from the animal and testing for virus neutralizing antibody is 

6 All confirmatory testing is currently conducted at NVSL

7

Factors that may be considered when assigning alternate diagnoses include the strength of the epidemiologic 

evidence for SARS-CoV-2 exposure, the specificity of the alternate diagnostic test, and the compatibility of the 

clinical presentation and course of illness for the alternative diagnosis.
Case Definition for SARS-CoV-2 as of 6/11/2021

recommended where test result(s) are poorly repeatable and/or approach the limit of 

detection for an assay.