Virus–Host Coevolution with a Focus on Animal and Human DNA Viruses

Abstract: Viruses have been infecting their host cells since the dawn of life, and this extremely long-term coevolution gave rise to some surprising consequences for the entire tree of life. It is hypothesised that viruses might have contributed to the formation of the first cellular life form, or that even the eukaryotic cell nucleus originates from an infection by a coated virus. The continuous struggle between viruses and their hosts to maintain at least a constant fitness level led to the development of an unceasing arms race, where weapons are often shuttled between the participants. In this literature review we try to give a short insight into some general consequences or traits of virus–host coevolution, and after this we zoom in to the viral clades of adenoviruses, herpesviruses, nucleo-cytoplasmic large DNA viruses, polyomaviruses and, finally, circoviruses.


Origins of MERS-CoV, and lessons for 2019-nCoV


The Origin and Evolution of Viruses

Abstract: The lecture covers three main topics: (i) Viruses: properties, place in the living world, and possible origin; (ii) Molecular basis of viral variability and evolution; and (iii) Evolution of viral pathogenicity and emerging viral infections.


Diversity of Coronaviruses in Bats: Insights Into Origin of SARS Coronavirus


Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans.

Abstract: The Chinese rufous horseshoe bat (Rhinolophus sinicus) has been suggested to carry the direct ancestor of severe acute respiratory syndrome (SARS) coronavirus (SCoV), and the diversity of SARS-like CoVs (SLCoV) within this Rhinolophus species is therefore worth investigating. Here, we demonstrate the remarkable diversity of SLCoVs in R. sinicus and identify a strain with the same pattern of phylogenetic incongruence (i.e. an indication of recombination) as reported previously in another SLCoV strain. Moreover, this strain possesses a distinctive 579 nt deletion in the nsp3 region that was also found in a human SCoV from the late-phase epidemic. Phylogenetic analysis of the Orf1 region suggested that the human SCoVs are phylogenetically closer to SLCoVs in R. sinicus than to SLCoVs in other Rhinolophus species. These findings reveal a closer evolutionary linkage between SCoV in humans and SLCoVs in R. sinicus, defining the scope of surveillance to search for the direct ancestor of human SCoVs.


Evidence for an Ancestral Association of Human Coronavirus 229E with Bats.

Abstract: UNLABELLED We previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in the RNA-dependent RNA polymerase (RdRp) and spike genes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3' end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E. IMPORTANCE The ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a large sample of African bats and characterizing several bat viruses on a full-genome level. Our evolutionary analyses show that animal and human viruses are genetically closely related, can exchange genetic material, and form a single viral species. We show that the putative host switches leading to the formation of HCoV-229E were accompanied by major genomic changes, including deletions in the viral spike glycoprotein gene and loss of an open reading frame. We reanalyze a previously described genetically related alpaca virus and discuss the role of camelids as potential intermediate hosts between bat and human viruses. The evolutionary history of HCoV-229E likely shares important characteristics with that of the recently emerged highly pathogenic Middle East respiratory syndrome (MERS) coronavirus.


Animal source of the coronavirus continues to elude scientists.


Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination.

Abstract: UNLABELLED Despite the identification of horseshoe bats as the reservoir of severe acute respiratory syndrome (SARS)-related coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nucleotide signature deletion among human strains, remains obscure. Although two SARS-related Rhinolophus sinicus bat CoVs (SARSr-Rs-BatCoVs) previously detected in Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, RsSHC014 and Rs3367, possessed 95% genome identities to human and civet SARSr-CoVs, their ORF8 protein exhibited only 32.2 to 33% amino acid identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nucleotide identities to human/civet SARSr-CoV genomes. Although these two betacoronaviruses displayed lower similarities than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein to civet SARSr-CoVs, their ORF8 proteins demonstrated exceptionally high (80.4 to 81.3%) amino acid identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2 to 37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that the ORF8 protein may be functional in SARSr-Rf-BatCoVs. The high Ka/Ks ratio among human SARS-CoVs compared to that among SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal-to-human transmission. Molecular clock analysis using ORF1ab showed that SARSr-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs in approximately 1990. SARS-CoV ORF8 originated from SARSr-CoVs of greater horseshoe bats through recombination, which may be important for animal-to-human transmission. IMPORTANCE Although horseshoe bats are the primary reservoir of SARS-related coronaviruses (SARSr-CoVs), it is still unclear how these bat viruses have evolved to cross the species barrier to infect civets and humans. Most human SARS-CoV epidemic strains contain a signature 29-nucleotide deletion in ORF8, compared to civet SARSr-CoVs, suggesting that ORF8 may be important for interspecies transmission. However, the origin of SARS-CoV ORF8 remains obscure. In particular, SARSr-Rs-BatCoVs from Chinese horseshoe bats (Rhinolophus sinicus) exhibited <40% amino acid identities to human/civet SARS-CoV in the ORF8 protein. We detected diverse alphacoronaviruses and betacoronaviruses among various bat species in Yunnan, China, including two SARSr-Rf-BatCoVs from greater horseshoe bats that possessed ORF8 proteins with exceptionally high amino acid identities to that of human/civet SARSr-CoVs. We demonstrated recombination events around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. Our findings offer insight into the evolutionary origin of SARS-CoV ORF8 protein, which was likely acquired from SARSr-CoVs of greater horseshoe bats through recombination.


COVID-19-A Novel Zoonotic Disease: A Review of the Disease, the Virus, and Public Health Measures.

Abstract: A cluster of cases of pneumonia of unknown etiology emerged in Wuhan, China, at the end of December 2019. The cluster was largely associated with a seafood and animal market. A novel Betacoronavirus was quickly identified as the causative agent, and it is shown to be related genetically to SARS-CoV and other bat-borne SARS-related Betacoronaviruses. The number of cases increased rapidly and spread to other provinces in China, as well as to another 4 countries. To help control the spread of the virus, a "cordon sanitaire" was instituted for Wuhan on January 23, 2020, and subsequently extended to other cities in Hubei Province, and the outbreak declared a Public Health Emergency of International Concern by the Director General of the World Health Organization on January 30, 2020. The virus was named SARS-CoV-2 by the International Committee for the Taxonomy of Viruses, and the disease it causes was named COVID-19 by the World Health Organization. This article described the evolution of the outbreak, and the known properties of the novel virus, SARS-CoV-2 and the clinical disease it causes, and the major public health measures being used to help control it's spread. These measures include social distancing, intensive surveillance and quarantining of cases, contact tracing and isolation, cancellation of mass gatherings, and community containment. The virus is the third zoonotic coronavirus, after SARS-CoV and MERS-CoV, but appears to be the only one with pandemic potential. However, a number of important properties of the virus are still not well understood, and there is an urgent need to learn more about its transmission dynamics, its spectrum of clinical severity, its wildlife origin, and its genetic stability. In addition, more research is needed on possible interventions, particularly therapeutic and vaccines.


COVID-19: animals, veterinary and zoonotic links.

Abstract: Coronavirus disease 2019 (COVID-19), has spread over 210 countries and territories beyond China shortly. On February 29, 2020, the World Health Organization (WHO) denoted it in a high-risk category, and on March 11, 2020, this virus was designated pandemic, after its declaration being a Public Health International Emergency on January 30, 2020. World over high efforts are being made to counter and contain this virus. The COVID-19 outbreak once again proves the potential of the animal-human interface to act as the primary source of emerging zoonotic diseases. Even though the circumstantial evidence suggests the possibility of an initial zoonotic emergence, it is too early to confirm the role of intermediate hosts such as snakes, pangolins, turtles, and other wild animals in the origin of SARS-CoV-2, in addition to bats, the natural hosts of multiple coronaviruses such as SARS-CoV and MERS-CoV. The lessons learned from past episodes of MERS-CoV and SARS-CoV are being exploited to retort this virus. Best efforts are being taken up by worldwide nations to implement effective diagnosis, strict vigilance, heightened surveillance, and monitoring, along with adopting appropriate preventive and control strategies. Identifying the possible zoonotic emergence and the exact mechanism responsible for its initial transmission will help us to design and implement appropriate preventive barriers against the further transmission of SARS-CoV-2. This review discusses in brief about the COVID-19/SARS-CoV-2 with a particular focus on the role of animals, the veterinary and associated zoonotic links along with prevention and control strategies based on One-health approaches.


Global genetic patterns reveal host tropism versus cross-taxon transmission of bat Betacoronaviruses

Abstract: Emerging infectious diseases due to coronavirus (CoV) infections have received significant global attention in the past decade and have been linked to bats as the original source. The diversity, distribution, and host associations of bat CoVs were investigated to assess their potential for zoonotic transmission. Phylogenetic, network, and principal coordinate analysis confirmed the classification of betacoronaviruses (BetaCoVs) into five groups (2A to 2E) and a potentially novel group, with further division of 2D into five subgroups. The genetic co-clustering of BetaCoVs among closely related bats reflects host taxon-specificity with each bat family as the host for a specific BetaCoV group, potentially a natural barrier against random transmission. The divergent pathway of BetaCoV and host evolution suggests that the viruses were introduced just prior to bat dispersal and speciation. As such, deviant patterns were observed such as for 2D-IV, wherein cross-taxon transmission due to overlap in bat habitats and geographic range among genetically divergent African bat hosts could have played a strong role on their shared CoV lineages. In fact, a few bat taxa especially the subfamily Pteropodinae were shown to host diverse groups of BetaCoVs. Therefore, ecological imbalances that disturb bat distribution may lead to loss of host specificity through cross-taxon transmission and multi-CoV infection. Hence, initiatives that minimize the destruction of wildlife habitats and limit wildlife-livestock-human interfaces are encouraged to help maintain the natural state of bat BetaCoVs in the wild. Importance Bat Betacoronaviruses (BetaCoVs) pose a significant threat to global public health and have been implicated in several epidemics such as the recent pandemic by severe acute respiratory syndrome coronavirus 2. Here, we show that bat BetaCoVs are predominantly host-specific, which could be a natural barrier against infection of other host types. However, a strong overlap in bat habitat and geographic range may facilitate viral transmission to unrelated hosts, and a few bat families have already been shown to host multi-CoV variants. We predict that continued disturbances on the ecological balance may eventually lead to loss of host specificity. When combined with enhanced wildlife-livestock-human interfaces, spillover to humans may be further facilitated. We should therefore start to define the ecological mechanisms surrounding zoonotic events. Global surveillance should be expanded and strengthened to assess the complete picture of bat coronavirus diversity and distribution and their potential to cause spillover infections.


2019 Novel Coronavirus Disease Outbreak and Molecular Genetic Characteristics of Severe Acute Respiratory Syndrome-coronavirus-2

Abstract: The 2019 novel coronavirus disease (COVID-19) outbreaks that emerged in Wuhan city, Hubei province, have led to a formidable number of confirmed cases that resulted in >5,700 deaths globally, including 143 countries in all 6 continents. The World Health Organization declared a Public Health Emergency of International Concern with a very high level of global risk assessment. Severe acute respiratory syndrome (SARS)-coronavirus-2 (SARS-CoV-2), the agent of COVID-19, has >79% nucleotide sequence homology to SARS-CoV; therefore, both belong to the genus betacoronavirus and subgenus sarbecovirus. The S1 domains of the two appeared to share the cellular receptor ACE2, but revealed a much higher S1-ACE2 binding affinity. As seen in many other human coronaviruses, SARS-CoV-2 also shows respiratory infection, but the basic reproductive number (R0) in transmission and the clinical latency are quite dissimilar from those of SARS-or MERS-CoVs. Many scientists infer that the time point of cross-barrier transfer from bats to mediate animals or to humans should be a rather recent event based on the full-length genome analyses obtained from the very first patients. Copy-choice polymerization, which often leads to a significant genome recombination rate in most coronaviruses, predicts the continued emergence of novel coronaviruses.


Predicting wildlife hosts of betacoronaviruses for SARS-CoV-2 sampling prioritization

Abstract: Despite massive investment in research on reservoirs of emerging pathogens, it remains difficult to rapidly identify the wildlife origins of novel zoonotic viruses. Viral surveillance is costly but rarely optimized using model-guided prioritization strategies, and predictions from a single model may be highly uncertain. Here, we generate an ensemble of eight network- and trait-based statistical models that predict mammal-virus associations, and we use model predictions to develop a set of priority recommendations for sampling potential bat reservoirs and intermediate hosts for SARS-CoV-2 and related betacoronaviruses. We find over 200 bat species globally could be undetected hosts of betacoronaviruses. Although over a dozen species of Asian horseshoe bats (Rhinolophus spp.) are known to harbor SARS-like coronaviruses, we find at least two thirds of betacoronavirus reservoirs in this bat genus might still be undetected. Although identification of other probable mammal reservoirs is likely beyond existing predictive capacity, some of our findings are surprisingly plausible; for example, several civet and pangolin species were highlighted as high-priority species for viral sampling. Our results should not be over-interpreted as novel information about the plausibility or likelihood of SARS-CoV-2’s ultimate origin, but rather these predictions could help guide sampling for novel potentially zoonotic viruses; immunological research to characterize key receptors (e.g., ACE2) and identify mechanisms of viral tolerance; and experimental infections to quantify competence of suspected host species.


The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey

Abstract: OBJECTIVE: Turkey is one of the latest countries that COVID-19 disease was reported, with the first case on March 11, 2020, and since then, Istanbul became the epicenter of the pandemic in Turkey Here, we reveal sequences of the virus isolated from three different patients with various clinical presentations METHODS: Nasopharyngeal swab specimens of the patients were tested positive for the COVID-19 by qRT-PCR Viral RNA extraction was performed from the same swab samples Amplicon based libraries were prepared and sequenced using the Illumina NextSeq platform Raw sequencing data were processed for variant calling and generating near-complete genome sequences All three genomes were evaluated and compared with other worldwide isolates RESULTS: The patients showed various clinics (an asymptomatic patient, patient with mild disease, and with severe pulmonary infiltration) Amplicon-based next-generation sequencing approach successfully applied to generate near-complete genomes with an average depth of 2 616 All three viral genomes carried the D614G variant (G clade according to GISAID classification) with implications for the origin of a spread first through China to Europe then to Istanbul CONCLUSION: Here, we report the viral genomes circulating in Istanbul for the first time Further sequencing of the virus isolates may enable us to understand variations in disease presentation and association with viral factors if there is any In addition, the sequencing of more viral genomes will delineate the spread of disease and will guide and ease the necessary measures taken to stem the spread of the novel coronavirus


Animal origins of SARS coronavirus: possible links with the international trade in small carnivores.

Abstract: The search for animal host origins of severe acute respiratory syndrome (SARS) coronavirus has so far remained focused on wildlife markets, restaurants and farms within China. A significant proportion of this wildlife enters China through an expanding regional network of illegal, international wildlife trade. We present the case for extending the search for ancestral coronaviruses and their hosts across international borders into countries such as Vietnam and Lao People's Democratic Republic, where the same guilds of species are found on sale in similar wildlife markets or food outlets. The three species that have so far been implicated, a viverrid, a mustelid and a canid, are part of a large suite of small carnivores distributed across this region currently overexploited by this international wildlife trade. A major lesson from SARS is that the underlying roots of newly emergent zoonotic diseases may lie in the parallel biodiversity crisis of massive species loss as a result of overexploitation of wild animal populations and the destruction of their natural habitats by increasing human populations. To address these dual threats to the long-term future of biodiversity, including man, requires a less anthropocentric and more interdisciplinary approach to problems that require the combined research expertise of ecologists, conservation biologists, veterinarians, epidemiologists, virologists, as well as human health professionals.


Mosaic evolution of the severe acute respiratory syndrome coronavirus.

Abstract: Severe acute respiratory syndrome (SARS) is a deadly form of pneumonia caused by a novel coronavirus, a viral family responsible for mild respiratory tract infections in a wide variety of animals including humans, pigs, cows, mice, cats, and birds. Analyses to date have been unable to identify the precise origin of the SARS coronavirus. We used Bayesian, neighbor-joining, and split decomposition phylogenetic techniques on the SARS virus replicase, surface spike, matrix, and nucleocapsid proteins to reveal the evolutionary origin of this recently emerging infectious agent. The analyses support a mammalian-like origin for the replicase protein, an avian-like origin for the matrix and nucleocapsid proteins, and a mammalian-avian mosaic origin for the host-determining spike protein. A bootscan recombination analysis of the spike gene revealed high nucleotide identity between the SARS virus and a feline infectious peritonitis virus throughout the gene, except for a 200- base-pair region of high identity to an avian sequence. These data support the phylogenetic analyses and suggest a possible past recombination event between mammalian-like and avian-like parent viruses. This event occurred near a region that has been implicated to be the human receptor binding site and may have been directly responsible for the switch of host of the SARS coronavirus from animals to humans.


Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus.

Abstract: Bats have been identified as the natural reservoir of severe acute respiratory syndrome (SARS)-like and SARS coronaviruses (SLCoV and SCoV). However, previous studies suggested that none of the currently sampled bat SLCoVs is the descendant of the direct ancestor of SCoV, based on their relatively distant phylogenetic relationship. In this study, evidence of the recombinant origin of the genome of a bat SLCoV is demonstrated. We identified a potential recombination breakpoint immediately after the consensus intergenic sequence between open reading frame 1 and the S coding region, suggesting the replication intermediates may participate in the recombination event, as previously speculated for other CoVs. Phylogenetic analysis of its parental regions suggests the presence of an uncharacterized SLCoV lineage that is phylogenetically closer to SCoVs than any of the currently sampled bat SLCoVs. Using various Bayesian molecular-clock models, interspecies transfer of this SLCoV lineage from bats to the amplifying host (e.g., civets) was estimated to have happened a median of 4.08 years before the SARS outbreak. Based on this relatively short window period, we speculate that this uncharacterized SLCoV lineage may contain the direct ancestor of SCoV. This study sheds light on the possible host bat species of the direct ancestor of SCoV, providing valuable information on the scope and focus of surveillance for the origin of SCoV.


SARS coronavirus without reservoir originated from an unnatural evolution, experienced the reverse evolution, and finally disappeared in the world.


[Source of the COVID-19 pandemic: ecology and genetics of coronaviruses (Betacoronavirus: Coronaviridae) SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS-CoV (subgenus Merbecovirus).]

Abstract: Since the early 2000s, three novel zooanthroponous coronaviruses (Betacoronavirus) have emerged. The first outbreak of infection (SARS) caused by SARS-CoV virus occurred in the fall of 2002 in China (Guangdong Province). A second outbreak (MERS) associated with the new MERS-CoV virus appeared in Saudi Arabia in autumn 2012. The third epidemic, which turned into a COVID-19 pandemic caused by SARS-CoV-2 virus, emerged in China (Hubei Province) in the autumn 2019. This review focuses on ecological and genetic aspects that lead to the emergence of new human zoanthroponous coronaviruses. The main mechanism of adaptation of zoonotic betacoronaviruses to humans is to changes in the receptor-binding domain of surface protein (S), as a result of which it gains the ability to bind human cellular receptors of epithelial cells in respiratory and gastrointestinal tract. This process is caused by the high genetic diversity and variability combined with frequent recombination, during virus circulation in their natural reservoir - bats (Microchiroptera, Chiroptera). Appearance of SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS (subgenus Merbecovirus) viruses is a result of evolutionary events occurring in bat populations with further transfer of viruses to the human directly or through the intermediate vertebrate hosts, ecologically connected with bats. This review is based on the report at the meeting «Coronavirus - a global challenge to science¼ of the Scientific Council «Life Science¼ of the Russian Academy of Science: Lvov D.K., Alkhovsky S.V., Burtseva E.I. COVID-19 pandemic sources: origin, biology and genetics of coronaviruses of SARS-CoV, SARS-CoV-2, MERS-CoV (Conference hall of Presidium of RAS, 14 Leninsky Prospect, Moscow, Russia. April 16, 2020).


Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses

Abstract: The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2.


COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives

Abstract: The recent outbreak of COVID-19 in Wuhan turned into a public health emergency of international concern. With no antiviral drugs nor vaccines, and the presence of carriers without obvious symptoms, traditional public health intervention measures are significantly less effective. Here, we report the epidemiological and virological characteristics of the COVID-19 outbreak. Originated in bats, 2019-nCoV/ severe acute respiratory syndrome coronavirus (SARS-CoV)-2 likely experienced adaptive evolution in intermediate hosts before transfer to humans at a concentrated source of transmission. Similarities of receptor sequence binding to 2019-nCoV between humans and animals suggest a low species barrier for transmission of the virus to farm animals. We propose, based on the One Health model, that veterinarians and animal specialists should be involved in a cross-disciplinary collaboration in the fight against this epidemic.


Cross-species transmission of the newly identified coronavirus 2019-nCoV

Abstract: The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many initial patients were exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019-nCoV sequence. Results obtained from our analyses suggest that the 2019-nCoV may appear to be a recombinant virus between the bat coronavirus and an origin-unknown coronavirus. The recombination may occurred within the viral spike glycoprotein, which recognizes a cell surface receptor. Additionally, our findings suggest that 2019-nCoV has most similar genetic information with bat coronovirus and most similar codon usage bias with snake. Taken together, our results suggest that homologous recombination may occur and contribute to the 2019-nCoV cross-species transmission.


2019_nCoV/SARS-CoV-2: rapid classification of betacoronaviruses and identification of Traditional Chinese Medicine as potential origin of zoonotic coronaviruses

Abstract: The current outbreak of a novel severe acute respiratory syndrome-like coronavirus, 2019_nCoV (now named SARS-CoV-2), illustrated difficulties in identifying a novel coronavirus and its natural host, as the coding sequences of various Betacoronavirus species can be highly diverse. By means of whole-genome sequence comparisons, we demonstrate that the noncoding flanks of the viral genome can be used to correctly separate the recognized four betacoronavirus subspecies. The conservation would be sufficient to define target sequences that could, in theory, classify novel virus species into their subspecies. Only 253 upstream noncoding sequences of Sarbecovirus are sufficient to identify genetic similarities between species of this subgenus. Furthermore, it was investigated which bat species have commercial value in China, and would thus likely be handled for trading purposes. A number of coronavirus genomes have been published that were obtained from such bat species. These bats are used in Traditional Chinese Medicine, and their handling poses a potential risk to cause zoonotic coronavirus epidemics. SIGNIFICANCE AND IMPACT OF THE STUDY: The noncoding upstream and downstream flanks of coronavirus genomes allow for rapid classification of novel Betacoronavirus species and correct identification of genetic relationships. Although bats are the likely natural host of 2019_nCoV, the exact bat species that serves as the natural host of the virus remains as yet unknown. Chinese bat species with commercial value were identified as natural reservoirs of coronaviruses and are used in Traditional Chinese Medicine. Since their trading provides a potential risk for spreading zoonoses, a change in these practices is highly recommended.


Spillover of SARS-CoV-2 into novel wild hosts in North America: A conceptual model for perpetuation of the pathogen

Abstract: There is evidence that the current outbreak of the novel coronavirus SARS-CoV-2, which causes COVID-19, is of animal origin. As with a number of zoonotic pathogens, there is a risk of spillover into novel hosts. Here, we propose a hypothesized conceptual model that illustrates the mechanism whereby the SARS-CoV-2 could spillover from infected humans to naive wildlife hosts in North America. This proposed model is premised on transmission of SARS-CoV-2 from human feces through municipal waste water treatment plants into the natural aquatic environment where potential wildlife hosts become infected. We use the existing literature on human coronaviruses, including SARS CoV, to support the potential pathways and mechanisms in the conceptual model. Although we focus on North America, our conceptual model could apply to other parts of the globe as well.


Origin and evolution of the 2019 novel coronavirus


Response to "Comments on "Homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human" and "Codon bias analysis alone is uninformative for identifying host(s) of new virus"

Abstract: We have recently reported for the first time that SARS-CoV-2 maybe a bat-originated coronavirus with a recombination occurred within the spike (S) protein gene based on phylogenetic and simplot analyses1 . These two conclusions are supported by findings recently reported by others and are well accepted in the field of SARS-CoV-2 research2-4 . This article is protected by copyright. All rights reserved.


Mystery deepens over animal source of coronavirus


A pneumonia outbreak associated with a new coronavirus of probable bat origin

Abstract: Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats1-4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans5-7. Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor-angiotensin converting enzyme II (ACE2)-as SARS-CoV.


COVID-19 and veterinarians for one health, zoonotic- and reverse-zoonotic transmissions

Abstract: A novel coronavirus emerged in human populations and spread rapidly to cause the global coronavirus disease 2019 pandemic. Although the origin of the associated virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) remains unclear, genetic evidence suggests that bats are a reservoir host of the virus, and pangolins are a probable intermediate. SARS-CoV-2 has crossed the species barrier to infect humans and other animal species, and infected humans can facilitate reverse-zoonotic transmission to animals. Considering the rapidly changing interconnections among people, animals, and ecosystems, traditional roles of veterinarians should evolve to include transdisciplinary roles.


Genomic variance of the 2019-nCoV coronavirus

Abstract: There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by the worldwide scientific community in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and severe acute respiratory syndrome. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hypervariable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.


Zoonotic origins of human coronaviruses

Abstract: Mutation and adaptation have driven the co-evolution of coronaviruses (CoVs) and their hosts, including human beings, for thousands of years. Before 2003, two human CoVs (HCoVs) were known to cause mild illness, such as common cold. The outbreaks of severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) have flipped the coin to reveal how devastating and life-threatening an HCoV infection could be. The emergence of SARS-CoV-2 in central China at the end of 2019 has thrusted CoVs into the spotlight again and surprised us with its high transmissibility but reduced pathogenicity compared to its sister SARS-CoV. HCoV infection is a zoonosis and understanding the zoonotic origins of HCoVs would serve us well. Most HCoVs originated from bats where they are non-pathogenic. The intermediate reservoir hosts of some HCoVs are also known. Identifying the animal hosts has direct implications in the prevention of human diseases. Investigating CoV-host interactions in animals might also derive important insight on CoV pathogenesis in humans. In this review, we present an overview of the existing knowledge about the seven HCoVs, with a focus on the history of their discovery as well as their zoonotic origins and interspecies transmission. Importantly, we compare and contrast the different HCoVs from a perspective of virus evolution and genome recombination. The current CoV disease 2019 (COVID-19) epidemic is discussed in this context. In addition, the requirements for successful host switches and the implications of virus evolution on disease severity are also highlighted.


Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study

Abstract: BACKGROUND: Human infections with zoonotic coronaviruses (CoVs), including severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV, have raised great public health concern globally. Here, we report a novel bat-origin CoV causing severe and fatal pneumonia in humans. METHODS: We collected clinical data and bronchoalveolar lavage (BAL) specimens from five patients with severe pneumonia from Wuhan Jinyintan Hospital, Hubei province, China. Nucleic acids of the BAL were extracted and subjected to next-generation sequencing. Virus isolation was carried out, and maximum-likelihood phylogenetic trees were constructed. RESULTS: Five patients hospitalized from December 18 to December 29, 2019 presented with fever, cough, and dyspnea accompanied by complications of acute respiratory distress syndrome. Chest radiography revealed diffuse opacities and consolidation. One of these patients died. Sequence results revealed the presence of a previously unknown ß-CoV strain in all five patients, with 99.8% to 99.9% nucleotide identities among the isolates. These isolates showed 79.0% nucleotide identity with the sequence of SARS-CoV (GenBank NC_004718) and 51.8% identity with the sequence of MERS-CoV (GenBank NC_019843). The virus is phylogenetically closest to a bat SARS-like CoV (SL-ZC45, GenBank MG772933) with 87.6% to 87.7% nucleotide identity, but is in a separate clade. Moreover, these viruses have a single intact open reading frame gene 8, as a further indicator of bat-origin CoVs. However, the amino acid sequence of the tentative receptor-binding domain resembles that of SARS-CoV, indicating that these viruses might use the same receptor. CONCLUSION: A novel bat-borne CoV was identified that is associated with severe and fatal respiratory disease in humans.


Detection of novel coronaviruses in bats in Myanmar

Abstract: The recent emergence of bat-borne zoonotic viruses warrants vigilant surveillance in their natural hosts. Of particular concern is the family of coronaviruses, which includes the causative agents of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and most recently, Coronavirus Disease 2019 (COVID-19), an epidemic of acute respiratory illness originating from Wuhan, China in December 2019. Viral detection, discovery, and surveillance activities were undertaken in Myanmar to identify viruses in animals at high risk contact interfaces with people. Free-ranging bats were captured, and rectal and oral swabs and guano samples collected for coronaviral screening using broadly reactive consensus conventional polymerase chain reaction. Sequences from positives were compared to known coronaviruses. Three novel alphacoronaviruses, three novel betacoronaviruses, and one known alphacoronavirus previously identified in other southeast Asian countries were detected for the first time in bats in Myanmar. Ongoing land use change remains a prominent driver of zoonotic disease emergence in Myanmar, bringing humans into ever closer contact with wildlife, and justifying continued surveillance and vigilance at broad scales.


Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2

Abstract: We showed that severe acute respiratory syndrome coronavirus 2 is probably a novel recombinant virus. Its genome is closest to that of severe acute respiratory syndrome-related coronaviruses from horseshoe bats, and its receptor-binding domain is closest to that of pangolin viruses. Its origin and direct ancestral viruses have not been identified.


Zoonotic origins of human coronavirus 2019 (HCoV-19 / SARS-CoV-2): why is this work important?

Abstract: The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by infection with human coronavirus 2019 (HCoV-19 / SARS-CoV-2 / 2019-nCoV), is a global threat to the human population. Here, we briefly summarize the available data for the zoonotic origins of HCoV-19, with reference to the other two epidemics of highly virulent coronaviruses, SARS-CoV and MERS-CoV, which cause severe pneumonia in humans. We propose to intensify future efforts for tracing the origins of HCoV-19, which is a very important scientific question for the control and prevention of the pandemic.


Master Regulator Analysis of the SARS-CoV-2/Human Interactome

Abstract: The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. In this paper, we set out to shed light on the SARS-CoV-2/host receptor recognition, a crucial factor for successful virus infection. Based on the current knowledge of the interactome between SARS-CoV-2 and host cell proteins, we performed Master Regulator Analysis to detect which parts of the human interactome are most affected by the infection. We detected, amongst others, affected apoptotic and mitochondrial mechanisms, and a downregulation of the ACE2 protein receptor, notions that can be used to develop specific therapies against this new virus.


Coronaviruses: origin and evolution


Mapping the genomic landscape & diversity of COVID-19 based on >3950 clinical isolates of SARS-CoV-2: Likely origin & transmission dynamics of isolates sequenced in India


Pangolins Harbor SARS-CoV-2-Related Coronaviruses

Abstract: The pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has posed a severe threat to global public health. Yet, the origin of SARS-CoV-2 remains mysterious. Several recent studies (e.g., Lam et al.,Xiao et al.) identified SARS-CoV-2-related viruses in pangolins, providing novel insights into the evolution and diversity of SARS-CoV-2-related viruses.


Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats

Abstract: SARS coronavirus (SARS-CoV), the causative agent of the large SARS outbreak in 2003, originated in bats. Many SARS-like coronaviruses (SL-CoVs) have been detected in bats, particularly those that reside in China, Europe, and Africa. To further understand the evolutionary relationship between SARS-CoV and its reservoirs, 334 bats were collected from Zhoushan city, Zhejiang province, China, between 2015 and 2017. PCR amplification of the conserved coronaviral protein RdRp detected coronaviruses in 26.65% of bats belonging to this region, and this number was influenced by seasonal changes. Full genomic analyses of the two new SL-CoVs from Zhoushan (ZXC21 and ZC45) showed that their genomes were 29,732 nucleotides (nt) and 29,802 nt in length, respectively, with 13 open reading frames (ORFs). These results revealed 81% shared nucleotide identity with human/civet SARS CoVs, which was more distant than that observed previously for bat SL-CoVs in China. Importantly, using pathogenic tests, we found that the virus can reproduce and cause disease in suckling rats, and further studies showed that the virus-like particles can be observed in the brains of suckling rats by electron microscopy. Thus, this study increased our understanding of the genetic diversity of the SL-CoVs carried by bats and also provided a new perspective to study the possibility of cross-species transmission of SL-CoVs using suckling rats as an animal model.


The virus whose family expanded

Abstract: The discovery of many new species of hepaciviruses and pegiviruses, which exhibit enormous genetic diversity, in wild rodent and bat populations might help us to understand the origins of the hepatitis C virus.


Comments to the predecessor of human SARS coronavirus in 2003–2004 epidemic


2019-nCoV in context: lessons learned?


Host-related nucleotide composition and codon usage as driving forces in the recent evolution of the Astroviridae

Abstract: Abstract The evolutionary history of the Astroviridae comprises the ancient separation between avian and mammalian astrovirus lineages followed by diversification among mammalian astroviruses. The latter process included several cross-species transmissions. We found that the recent, but not the ancient, evolution of astroviruses was associated with a switch in nucleotide composition and codon usage among non-human mammalian versus human/avian astroviruses. Virus and hosts phylogenies based on codon usage agreed with each other and matched the hosts' evolutionary emergence order. This recent switch in driving forces acting at the synonymous level points to the adaptation of codon usage by viruses to that of their hosts after cross-species transmissions. This is the first demonstration of nucleotide composition and codon usage being active driving forces during the recent evolutionary history of a virus group in the host–parasite system.


Exceptional diversity and selection pressure on SARS-CoV and SARS-CoV-2 host receptor in bats compared to other mammals

Abstract: Pandemics originating from pathogen transmission between animals and humans highlight the broader need to understand how natural hosts have evolved in response to emerging human pathogens and which groups may be susceptible to infection. Here, we investigate angiotensin-converting enzyme 2 (ACE2), the host protein bound by SARS-CoV and SARS-CoV-2. We find that the ACE2 gene is under strong selection pressure in bats, the group in which the progenitors of SARS-CoV and SARS-CoV-2 are hypothesized to have evolved, particularly in residues that contact SARS-CoV and SARS-CoV-2. We detect positive selection in non-bat mammals in ACE2 but in a smaller proportion of branches than in bats, without enrichment of selection in residues that contact SARS-CoV or SARS-CoV-2. Additionally, we evaluate similarity between humans and other species in residues that contact SARS-CoV or SARS-CoV-2, revealing potential susceptible species but also highlighting the difficulties of predicting spillover events. This work increases our understanding of the relationship between mammals, particularly bats, and coronaviruses, and provides data that can be used in functional studies of how host proteins are bound by SARS-CoV and SARS-CoV-2 strains.


Newly identified viral genomes in pangolins with fatal disease

Abstract: Epizootic pathogens pose a major threat to many wildlife species, particularly in the context of rapidly changing environments. Pangolins (order Pholidota) are highly threatened mammals, in large part due to the trade in illegal wildlife. During July to August 2018 four sick wild pangolins (three Manis javanica and one Manis pentadactyla) exhibiting a variety of clinical symptoms were rescued by the Jinhua Wildlife Protection Station in Zhejiang province, China. Although three of these animals died, fortunately one recovered after 2 weeks of symptomatic treatment. Using meta-transcriptomics combined with reverse transcription polymerase chain reaction (RT-PCR), we identified two novel RNA viruses in two of the dead pangolins. Genomic analysis revealed that these viruses were most closely related to pestiviruses and coltiviruses, although still highly genetically distinct, with more than 48 and 25 per cent sequence divergence at the amino acid level, respectively. We named these Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV) based on the sampling site and hosts. Although coltiviruses (LSPV) are known to be transmitted by ticks, we found no evidence of LSPV in ticks sampled close to where the pangolins were collected. In addition, although DYPV was present in nymph ticks (Amblyomma javanense) collected from a diseased pangolin, they were not found in the local tick population. Epidemiological investigation revealed that both novel viruses might have been imported following the illegal international trade of pangolins. Hence, these data indicate that illegal wildlife trafficking not only threatens the status of pangolin populations, but may also spread epizootic pathogens.


Origins of major human infectious diseases

Abstract: Many of the major human infectious diseases, including some now confined to humans and absent from animals, are ‘new’ ones that arose only after the origins of agriculture. Where did they come from? Why are they overwhelmingly of Old World origins? Here we show that answers to these questions are different for tropical and temperate diseases; for instance, in the relative importance of domestic animals and wild primates as sources. We identify five intermediate stages through which a pathogen exclusively infecting animals may become transformed into a pathogen exclusively infecting humans. We propose an initiative to resolve disputed origins of major diseases, and a global early warning system to monitor pathogens infecting individuals exposed to wild animals. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature05775) contains supplementary material, which is available to authorized users.


A Mathematical Model of the Evolution and Spread of Pathogenic Coronaviruses from Natural Host to Human Host

Abstract: Coronaviruses are highly transmissible and are pathogenic viruses of the 21(st) century worldwide. In general, these viruses are originated in bats or rodents. At the same time, the transmission of the infection to the human host is caused by domestic animals that represent in the habitat the intermediate host. In this study, we review the currently collected information about coronaviruses and establish a model of differential equations with piecewise constant arguments to discuss the spread of the infection from the natural host to the intermediate, and from them to the human host, while we focus on the potential spillover of bat-borne coronaviruses. The local stability of the positive equilibrium point of the model is considered via the Linearized Stability Theorem. Besides, we discuss global stability by employing an appropriate Lyapunov function. To analyze the outbreak in early detection, we incorporate the Allee effect at time t and obtain stability conditions for the dynamical behavior. Furthermore, it is shown that the model demonstrates the Neimark-Sacker Bifurcation. Finally, we conduct numerical simulations to support the theoretical findings.


Common RNA replication signals exist among group 2 coronaviruses: evidence for in vivo recombination between animal and human coronavius molecules

Abstract: Abstract 5′ and 3′ UTR sequences on the coronavirus genome are known to carry cis-acting elements for DI RNA replication and presumably also virus genome replication. 5′ UTR-adjacent coding sequences are also thought to harbor cis-acting elements. Here we have determined the 5′ UTR and adjacent 289-nt sequences, and 3′ UTR sequences, for six group 2 coronaviruses and have compared them to each other and to three previously reported group 2 members. Extensive regions of highly similar UTR sequences were found but small regions of divergence were also found indicating group 2 coronaviruses could be subdivided into those that are bovine coronavirus (BCoV)-like (BCoV, human respiratory coronavirus-OC43, human enteric coronavirus, porcine hemagglutinating encephalomyelitis virus, and equine coronavirus) and those that are murine hepatitis virus (MHV)-like (A59, 2, and JHM strains of MHV, puffinosis virus, and rat sialodacryoadenitis virus). The 3′ UTRs of BCoV and MHV have been previously shown to be interchangeable. Here, a reporter-containing BCoV DI RNA was shown to be replicated by all five BCoV-like helper viruses and by MHV-H2 (a human cell-adapted MHV strain), a representative of the MHV-like subgroup, demonstrating group 2 common 5′ and 3′ replication signaling elements. BCoV DI RNA, furthermore, acquired the leader of HCoV-OC43 by leader switching, demonstrating for the first time in vivo recombination between animal and human coronavirus molecules. These results indicate that common replication signaling elements exist among group 2 coronaviruses despite a two-cluster pattern within the group and imply there could exist a high potential for recombination among group members.


Isolation and Characterization of 2019-nCoV-like Coronavirus from Malayan Pangolins

Abstract: The outbreak of 2019-nCoV in the central Chinese city of Wuhan at the end of 2019 poses unprecedent public health challenges to both China and the rest world1. The new coronavirus shares high sequence identity to SARS-CoV and a newly identified bat coronavirus2. While bats may be the reservoir host for various coronaviruses, whether 2019-nCoV has other hosts is still ambiguous. In this study, one coronavirus isolated from Malayan pangolins showed 100%, 98.2%, 96.7% and 90.4% amino acid identity with 2019-nCoV in the E, M, N and S genes, respectively. In particular, the receptor-binding domain of the S protein of the Pangolin-CoV is virtually identical to that of 2019-nCoV, with one amino acid difference. Comparison of available genomes suggests 2019-nCoV might have originated from the recombination of a Pangolin-CoV-like virus with a Bat-CoV-RaTG13-like virus. Infected pangolins showed clinical signs and histopathological changes, and the circulating antibodies reacted with the S protein of 2019-nCoV. The isolation of a coronavirus that is highly related to 2019-nCoV in the pangolins suggests that these animals have the potential to act as the intermediate host of 2019-nCoV. The newly identified coronavirus in the most-trafficked mammal could represent a continuous threat to public health if wildlife trade is not effectively controlled.


Effect modification of environmental factors on influenza-associated mortality: a time-series study in two Chinese cities

Abstract: BACKGROUND: Environmental factors have been associated with transmission and survival of influenza viruses but no studies have ever explored the role of environmental factors on severity of influenza infection. METHODS: We applied a Poisson regression model to the mortality data of two Chinese metropolitan cities located within the subtropical zone, to calculate the influenza associated excess mortality risks during the periods with different levels of temperature and humidity. RESULTS: The results showed that high absolute humidity (measured by vapor pressure) was significantly (p < 0.05) associated with increased risks of all-cause and cardiorespiratory deaths, but not with increased risks of pneumonia and influenza deaths. The association between absolute humidity and mortality risks was found consistent among the two cities. An increasing pattern of influenza associated mortality risks was also found across the strata of low to high relative humidity, but the results were less consistent for temperature. CONCLUSIONS: These findings highlight the need for people with chronic cardiovascular and respiratory diseases to take extra caution against influenza during hot and humid days in the subtropics and tropics.


Nature of transmission of Covid19 in India

Abstract: We examine available data on the number of individuals infected by the Covid-19 virus, across several different states in India, over the period January 30, 2020 to April 10, 2020. It is found that the growth of the number of infected individuals $N(t)$ can be modeled across different states with a simple linear function $N(t)=\gamma+\alpha t$ beyond the date when reasonable number of individuals were tested (and when a countrywide lockdown was imposed). The slope $\alpha$ is different for different states. Following recent work by Notari (arxiv:2003.12417), we then consider the dependency of the $\alpha$ for different states on the average maximum and minimum temperatures, the average relative humidity and the population density in each state. It turns out that like other countries, the parameter $\alpha$, which determines the rate of rise of the number of infected individuals, seems to have a weak correlation with the average maximum temperature of the state. In contrast, any significant variation of $\alpha$ with humidity or minimum temperature seems absent with almost no meaningful correlation. Expectedly, $\alpha$ increases (slightly) with increase in the population density of the states; however, the degree of correlation here too is negligible. These results seem to barely suggest that a natural cause like a hot summer (larger maximum temperatures) may contribute towards reducing the transmission of the virus, though the role of minimum temperature, humidity and population density remains somewhat obscure from the inferences which may be drawn from presently available data.


Any contribution of the season change to the spread of covid-19 caused by sars-cov-2?

Abstract: Background: Most people raise a similar concern during this tough time of the COVID-19 pandemic caused by SARS-CoV-2 infection regarding when this outbreak will come to end. A recent thorough-general study on the success of China dealing with COVID-19 outbreak has concluded to recommend the need for a multi-sectoral approach to prevent future outbreaks of emerging infectious diseases including for the still-occurring COVID-19 outbreak with the initiative for the highest interest of the health of mankind Discussion: The prevalence of SARS-CoV as the predecessor of SARS-CoV-2 has been concluded to be more suitable in spring than autumn and winter, with nothing prevalence in summer. No coincidence that SARS-CoV-2 infection has outbreak around the world from January 2020 to the present, April 2020, as ever predicted to reoccur based on its predecessor, SARS-CoV, that have prevalence been high since January, February, March, April, until early May 2003. As opposed to other seasons, summer has low atmospheric pressure as its exemption that provenly causes virus inactivation. Conclusions: The denotative nature of SARS-CoV-2 seems to reflect its predecessor, SARS-CoV, which begins nearing the end of the year and reaches its optimum hence in spring, thereafter, finally ends in summer. Low atmospheric pressure in the summer impresses that it is the potential cause of ending the outbreak by deactivating SARS-CoV-2, apart from the hot temperature of weather. The knowledge to be gained here is further closely correlated to the fact that coronavirus is able to have genetic recombination that may bring about new genotypes and, consequently, outbreaks later occurring.


An environmental determinant of viral respiratory disease

Abstract: The evident seasonality of influenza suggests a significant role for weather and climate as one of several determinants of viral respiratory disease (VRD), including social determinants which play a major role in shaping these phenomena. Based on the current mechanistic understanding of how VRDs are transmitted by small droplets, we identify an environmental variable, Air Drying Capacity (ADC), as an atmospheric state-variable with significant and direct relevance to the transmission of VRD. ADC dictates the evolution and fate of droplets under given temperature and humidity conditions. The definition of this variable is rooted in the Maxwell theory of droplet evolution via coupled heat and mass transfer between droplets and the surrounding environment. We present the climatology of ADC, and compare its observed distribution in space and time to the observed prevalence of influenza and COVID-19 from extensive global data sets. Globally, large ADC values appear to significantly constrain the observed transmission and spread of VRD, consistent with the significant coherency of the observed seasonal cycles of ADC and influenza. Our results introduce a new environmental determinant, rooted in the mechanism of VRD transmission, with potential implications for explaining seasonality of influenza, and for describing how environmental conditions may impact to some degree the evolution of similar VRDs, such as COVID-19.


Impact Of Temperature and Sunshine Duration on Daily New Cases and Death due to COVID-19

Abstract: Background: The coronavirus pandemic (COVID-19) control has now become a critical issue for public health. Many ecological factors are proven to influence the transmission and survival of the virus. In this study, we aim to determine the association of different climate factors with the spread and mortality due to COVID-19. Methods: The climate indicators included in the study were duration of sunshine, average minimum temperature and average maximum temperature, with cumulative confirmed cases, deceased and recovered cases. The data was performed for 138 different countries of the world, between January 2020 to May 2020. Both univariate and multivariate was performed for cumulative and month-wise analysis using SPSS software. Results: The average maximum temperature, and sunshine duration was significantly associated with COVID-19 confirmed cases, deceased and recovered. For every one degree increase in mean average temperature, the confirmed, deceased and recovered cases decreased by 2047(p=0.03), 157(p=0.016), 743 (p=0.005) individuals. The association remained significant even after adjusting for environmental such as sunshine duration as well as non-environmental variables. Average sunshine duration was inversely correlated with increase in daily new cases ({rho}= -2261) and deaths ({rho}= -0.2985). Conclusion: Higher average temperature and longer sunshine duration was strongly associated with COVID-19 cases and deaths in 138 countries. Hence the temperature is an important factor in SARS CoV-2 survival and this study will help in formulating better preventive measures to combat COVID-19 based on their climatic conditions.


Impact of Daily Weather on COVID-19 outbreak in India

Abstract: The COVID-19 pandemic has outspread obstreperously in India. As of June 04, 2020, more than 2 lakh cases have been confirmed with a death rate of 2.81%. It has been noticed that, out of each 1000 tests, 53 result positively infected. In order to investigate the impact of weather conditions on daily transmission occurring in India, daily data of Maximum (TMax), Minimum (TMin), Mean (TMean) and Dew Point Temperature (TDew), Diurnal Temperature range (TRange), Average Relative Humidity, Range in Relative Humidity, and Wind Speed (WS) over 9 most affected cities are analysed in several time frames: weather of that day, 7, 10, 12, 14, 16 days before transmission. Spearman rank correlation (r) shows significant but low correlation with most of the weather parameters, however, comparatively better association exists on 14 days lag. Diurnal range in Temperature and Relative Humidity shows non-significant correlation. Analysis shows, COVID-19 cases likely to be increased with increasing air temperature, however role of humidity is not clear. Among weather parameters, Minimum Temperature was relatively better correlate than other. 80% of the total confirmed cases were registered when TMax, TMean, TMin, TRange, TDew, and WS on 12-16 days ago vary within a range of 33.6-41.3 deg C, 29.8-36.5 deg C, 24.8-30.4 deg C, 7.5-15.2 deg C, 18.7-23.6 deg C, and 4.2-5.75 m/s respectively, hence, it gives an idea of susceptible weather conditions for such transmission in India. Using Support Vector Machine based regression, the daily cases are profoundly estimated with more than 80% accuracy, which indicate that coronavirus transmission cannot be well linearly correlated with any single weather parameters, rather multivariate non-linear approach must be employed. Accounting lag of 12-16 days, the association found to be excellent, thus depict that there is an incubation period of 12-16 days for coronavirus transmission in Indian scenario.


Effect of Temperature on the Transmission of COVID-19: A Machine Learning Case Study in Spain

Abstract: The novel coronavirus (COVID-19) has already spread to almost every country in the world and has infected over 3 million people. To understand the transmission mechanism of this highly contagious virus, it is necessary to study the potential factors, including meteorological conditions. Here, we present a machine learning approach to study the effect of temperature, humidity and wind speed on the number of infected people in the three most populous autonomous communities in Spain. We find that there is a moderate inverse correlation between temperature and the daily number of infections. This correlation manifests for temperatures recorded up to 6 days before the onset, which corresponds well to the known mean incubation period of COVID-19. We also show that the correlation for humidity and wind speed is not significant.


Associations of ambient air pollutants and meteorological factors with COVID-19 transmission in 31 Chinese provinces: A time-series study

Abstract: Background: Evidence regarding the effects of ambient air pollutants and meteorological factors on COVID-19 transmission is limited. Objectives: To explore the associations of air pollutants and meteorological factors with COVID-19 confirmed cases across 31 Chinese provinces during the outbreak period. Methods: The number of COVID-19 confirmed cases, air pollutant concentrations and meteorological factors in 31 Chinese provinces from January 25 to February 29, 2020 were extracted from authoritative electronic databases. The associations were estimated for a single-day lag (lag0-lag6) as well as moving averages lag (lag01-lag05) using generalized additive mixed models (GAMMs), adjusted for time trends, day of the week, holidays and meteorological variables. Region-specific analyses and meta-analysis were conducted in five selected regions with diverse air pollution levels and weather conditions. Nonlinear exposure-response analyses were performed. Results: We examined 77,578 COVID-19 confirmed cases across 31 Chinese provinces during the study period. An increase of each interquartile range in PM2.5, PM10, SO2, NO2, O3 and CO at lag4 corresponded to 1.40 (1.37-1.43), 1.35 (1.32-1.37), 1.01 (1.00-1.02), 1.08 (1.07-1.10), 1.28 (1.27-1.29) and 1.26 (1.24-1.28) odds ratios (ORs) of daily COVID-19 confirmed new cases, respectively. For 1 oc, 1% and 1 m/s increase in temperature, relative humidity and wind velocity, the ORs were 0.97 (0.97-0.98), 0.96 (0.96-0.97), and 0.94 (0.92-0.95), respectively. The estimates of PM2.5, PM10, NO2 and all meteorological factors remained statistically significant after meta-analysis for the five selected regions. The exposure-response relationships showed that higher concentrations of air pollutants and lower meteorological factors were associated with daily COVID-19 confirmed new cases increasing. Conclusions: Higher air pollutant concentrations and lower temperature, relative humidity and wind velocity may favor COVID-19 transmission. As summer months are arriving in the Northern Hemisphere, the environmental factors and implementation of public health control measures may play an optimistic role in controlling COVID-19 epidemic.


The Association of Social Distancing, Population Density, and Temperature with the SARS-CoV-2 Instantaneous Reproduction Number in Counties Across the United States

Abstract: Importance: The Covid-19 pandemic has been marked by considerable heterogeneity in outbreaks across the United States. Local factors that may be associated with variation in SARS-CoV-2 transmission have not been well studied. Objective: To examine the association of county-level factors with variation in the SARS-CoV-2 reproduction number over time. Design: Observational study Setting: 211 counties in 46 states and the District of Columbia between February 25, 2020 and April 23, 2020. Participants: Residents within the counties (55% of the US population) Exposures: Social distancing as measured by percent change in visits to non-essential businesses, population density, lagged daily wet bulb temperatures. Main Outcomes and Measures: The instantaneous reproduction number (Rt) which is the estimated number of cases generated by one case at a given time during the pandemic. Results: Median case incidence was 1185 cases and fatality rate was 43.7 deaths per 100,000 people for the top decile of 21 counties, nearly ten times the incidence and fatality rate in the lowest density quartile. Average Rt in the first two weeks was 5.7 (SD 2.5) in the top decile, compared to 3.1 (SD 1.2) in the lowest quartile. In multivariable analysis, a 50% decrease in visits to non-essential businesses was associated with a 57% decrease in Rt (95% confidence interval, 56% to 58%). Cumulative temperature effects over 4 to 10 days prior to case incidence were nonlinear; relative Rt decreased as temperatures warmed above 32F to 53F, which was the point of minimum Rt, then increased between 53F and 66F, at which point Rt began to decrease. At 55F, and with a 70% reduction in visits to non-essential business, 96% of counties were estimated to fall below a threshold Rt of 1.0, including 86% of counties among the top density decile and 98% of counties in the lowest density quartile. Conclusions and Relevance: Social distancing, lower population density, and temperate weather change were associated with a decreased SARS-Co-V-2 Rt in counties across the United States. These relationships can inform selective public policy planning in communities during the SARS-CoV-2 pandemic.


Diverse local epidemics reveal the distinct effects of population density, demographics, climate, depletion of susceptibles, and intervention in the first wave of COVID-19 in the United States

Abstract: The SARS-CoV-2 pandemic has caused significant mortality and morbidity worldwide, sparing almost no community. As the disease will likely remain a threat for years to come, an understanding of the precise influences of human demographics and settlement, as well as the dynamic factors of climate, susceptible depletion, and intervention, on the spread of localized epidemics will be vital for mounting an effective response. We consider the entire set of local epidemics in the United States; a broad selection of demographic, population density, and climate factors; and local mobility data, tracking social distancing interventions, to determine the key factors driving the spread and containment of the virus. Assuming first a linear model for the rate of exponential growth (or decay) in cases/mortality, we find that population-weighted density, humidity, and median age dominate the dynamics of growth and decline, once interventions are accounted for. A focus on distinct metropolitan areas suggests that some locales benefited from the timing of a nearly simultaneous nationwide shutdown, and/or the regional climate conditions in mid-March; while others suffered significant outbreaks prior to intervention. Using a first-principles model of the infection spread, we then develop predictions for the impact of the relaxation of social distancing and local climate conditions. A few regions, where a significant fraction of the population was infected, show evidence that the epidemic has partially resolved via depletion of the susceptible population (i.e., "herd immunity"), while most regions in the United States remain overwhelmingly susceptible. These results will be important for optimal management of intervention strategies, which can be facilitated using our online dashboard.


Correlation of the global spread of coronavirus disease-19 with atmospheric air temperature

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus that may be sensitive to heat. We assessed whether the spread of coronavirus disease 2019 (COVID-19) correlates with air temperature. We also studied whether additional climate, geographical, and population variables were correlated. The total number of confirmed COVID-19 cases and mortality rates reported in each country between 1st Jan and 31st Mar 2020 were compared with the country's three-month average atmospheric air temperature, precipitation and latitude. Spearman's correlation coefficient (rs) was used to identify significant correlations. Our analysis included a total of 748,555 confirmed COVID-19 cases worldwide. The total number of patients with COVID-19 decreased with increasing atmospheric air temperature (rs = -0.54, 95%CI: [-0.64, -0.42]; P <0.001) and increased with an increasing latitude (rs =0.60, 95%CI: [0.48, 0.70]; P <0.001). Our findings justify further studies to examine the effect of air temperature on infectivity of SAR-CoV-2.


Temperature and Humidity Do Not Influence Global COVID-19 Incidence as Inferred from Causal Models

Abstract: The relationship between meteorological factors such as temperature and humidity with COVID-19 incidence is still unclear after 6 months of the beginning of the pandemic. Some literature confirms the association of temperature with disease transmission while some oppose the same. This work intends to determine whether there is a causal association between temperature, humidity and Covid-19 cases. Three different causal models were used to capture stochastic, chaotic and symbolic natured time-series data and to provide a robust & unbiased analysis by constructing networks of causal relationships between the variables. Granger-Causality method, Transfer Entropy method & Convergent Cross-Mapping (CCM) was done on data from regions with different temperatures and cases greater than 50,000 as of 13th May 2020. From the Granger-Causality test we found that in only Canada, the United Kingdom, temperature and daily new infections are causally linked. The same results were obtained from Convergent Cross Mapping for India. Again using Granger-Causality test, we found that in Russia only, relative humidity is causally linked to daily new cases. Thus, a Generalized Additive Model with a smoothing spline function was fitted for these countries to understand the directionality. Using the combined results of the said models, we were able to conclude that there is no evidence of a causal association between temperature, humidity and Covid-19 cases.


Temperature and relative humidity are not major contributing factor on the occurrence of COVID-19 pandemic: An observational study in 57 countries

Abstract: The world searching for hope has already experienced a huge loss of lives due to COVID-19 caused by SARS-CoV-2 started in Wuhan, China. There are speculations that climatic conditions can slowdown the transmission of COVID-19.Findings from the early outbreak indicated the possible association of air temperature and relative humidity in COVID-19 occurrence in China. Current study focused on whether climatic conditions(temperature and relative humidity)are having any influence in the occurrence of COVID-19 when the outbreak has been classified as pandemic. To determine the effect of daily average temperature and average relative humidity on log-transformed total daily cases of COVID-19, polynomial regression as a quadratic term and linear regression were done. Linear regression analysis was also carried out to explore the same effect on selected countries. Present study observed no correlation between the climatic conditions (the daily average temperature and relative humidity) and the number of cases of COVID-19. Similar result was found in relation between daily average temperature and average number of cases per day in country-wise analysis. However, about 93.5% cases of COVID-19 occurred between 10C to 160C and the average number of cases per day was lower in high temperature country than low temperature country with exceptions. The minimum effect of summer temperature may not be effective to control the pandemic rather need to apply the control measures of COVID-19.


Impacts of regional climate on the COVID-19 pandemic

Abstract: The COVID-19 pandemic has led to six million confirmed cases by May 31, 2020. Impacts of regional weather and climate on epidemics have been investigated but need further study with new methods. We combined the number of monthly confirmed new cases and death with month, latitude, temperature, humidity, rainfall, and sunshine ultraviolet (UV) to explore the climate impact on epidemics in 116 countries and territories with at least 1000 confirmed cases. Correlation and regression analyses were performed with Stata. Humid subtropical climate regions had the most confirmed COVID-19 cases (24.4%). The case mortality in temperate marine regions was the highest (11.6%). Case-weighted means of the latitude, monthly maximum temperature, relative humidity, rainfall, and sunshine UV were 36.7 degrees, 20.5, 63%, 63mm, and 53.5, respectively. The case mortality was 7.44% in cold regions but only 4.68% in hot regions, 7.14% in rainy regions but only 3.86% in rainless regions, and 7.40% in cloudy regions but only 4.64% in sunny regions. Monthly confirmed cases increase as the temperature, rainfall, and sunshine UV rise in cold regions (r=0.34, 0.26, 0.26, respectively), but no correlation in hot regions. Every 1 increase in monthly maximum temperature leads to an increase in the natural logarithm of monthly confirmed new cases by 2.4% in cold regions. Monthly confirmed cases increase as the temperature, rainfall, and sunshine UV rise in arid regions (r=0.29, 0.28, 0.26, respectively), but no correlation in humid regions. Monthly confirmed new cases increase as the temperature and sunshine UV rise in rainy regions (r=0.30, 0.29), but no correlation in rainless regions. Monthly confirmed new deaths increase as the temperature and sunshine UV rise in cloudy regions (r=0.30, 0.30), but no correlation in sunny regions. It is wise to escape from an epicenter full of miasma to a hot sunny place in dry season without pollution. As peaking in the spring depends on the climate, the peak will go in the summer.


Climatic influence on the magnitude of COVID-19 outbreak: a stochastic model-based global analysis

Abstract: This study examines the association between community transmission of COVID-19 cases and climatic predictors, considering travel information and annual parasite index across the three climatic zones, i.e., tropical, subtropical, and temperate. A Boosted Regression Tree model has been employed to understand the association between the COVID-19 cases. The results show that average temperature and average relative humidity are the major contributors in explaining the differentials of COVID-19 transmission in temperate and subtropical regions whereas the mean diurnal temperature range and temperature seasonality are the most significant determinants in tropical regions. The average temperature is the most influential factor affecting the number of COVID-19 cases in France, Turkey, the US, the UK, and Germany, and the cases decrease sharply above 10oC. Among the tropical countries, India found to be most affected by mean diurnal temperature, and Brazil fazed by temperature seasonality. Most of the temperate countries like France, USA, Turkey, UK, and Germany with an average temperature between 5-12oC had high number of COVID-19 cases. The findings are expected to add to the ongoing debates on the influence of climatic factors influencing the number of COVID-19 cases and could help researchers and policymakers to make appropriate decisions for preventing the spread.


Early transmission of COVID-19 has an optimal temperature but late transmission decreases in warm climate

Abstract: The COVID-19 novel virus, as an emerging highly pathogenic agent, has caused a pandemic. Revealing the influencing factors affecting transmission of COVID-19 is essential to take effective control measures. Several previous studies suggested that the spread of COVID-19 was likely associated with temperature and/or humidity. But, a recent extensive review indicated that conclusions on associations between climate and COVID-19 were elusive with high uncertainty due to caveats in most previous studies, such as limitations in time and space, data quality and confounding factors. In this study, by using a more extensive global dataset covering 578 time series from China, USA, Europe and the rest of the world, we show that climate show distinct impacts on early and late transmission of COVID-19 in the world after excluding the confounding factors. The early transmission ability of COVID-19 peaked around 6.3{degrees}C without or with little human intervention, but the later transmission ability was reduced in high temperature conditions under human intervention, probably driven by increased control efficiency of COVID-19. The transmission ability was positively associated with the founding population size of early reported cases and population size of a location. Our study suggested that with the coming summer seasons, the transmission risk of COVID-19 would increase in the high-latitude or high-altitude regions but decrease in low-latitude or low-altitude regions; human intervention is essential in containing the spread of COVID-19 around the world.


Meteorological Conditions and Covid-19 in Large U.S. Cities

Abstract: To determine whether prevalence of Coronavirus disease 2019 (Covid-19) is modulated by meteorological conditions, we herein conducted meta-regression of data in large U.S. cities. We selected 33 large U.S. cities with a population of >500,000. The integrated numbers of confirmed Covid-19 cases in the country to which the city belongs on 14 May 2020, the estimated population in 2019 in the country, and monthly meteorological conditions at the city for 4 months (from January to April 2020) were obtained. Meteorological conditions consisted of mean temperature (F), total precipitation (inch), mean wind speed (MPH), mean sky cover, and mean relative humidity (%). Monthly data for 4 months were averaged or integrated. The Covid-19 prevalence was defined as the integrated number of Covid-19 cases divided by the population. Random-effects meta-regression was performed by means of OpenMetaAnalyst. In a meta-regression graph, Covid-19 prevalence (plotted as the logarithm transformed prevalence on the y-axis) was depicted as a function of a given factor (plotted as a meteorological datum on the x-axis). A slope of the meta-regression line was significantly negative (coefficient, -0.069; P < 0.001) for the mean temperature and significantly positive for the mean wind speed (coefficient, 0.174; P = 0.027) and the sky cover (coefficient, 2.220; P = 0.023). In conclusion, lower temperature and higher wind speed/sky cover may be associated with higher Covid-19 prevalence, which should be confirmed by further epidemiological researches adjusting for various risk and protective factors (in addition to meteorological conditions) of Covid-19.


Study of the Dependence of Effective Reproduction Number of COVID-19 on the Temperature and Humidity: A Case Study with the Indian States

Abstract: Corona Virus Disease 2019 (COVID-19) started in Wuhan province of China in November 2019 and within a short time, it was declared as a worldwide pandemic by World Health Organisation due to very fast worldwide spread of the virus. In the absence of any vaccine, various mitigation measures were used. In the past, the effect of temperature and humidity on the spread of the virus was studied for a very early phase of the data with mixed results. We are studying the impact of COVID-19 on the maximum temperature and relative humidity of a place using Indian states as test cases for SIR, SIRD, and SEIR models. We used a linear regression method to look for any dependency between effective reproduction number with maximum temperature and relative humidity. Most of the states show a correlation with the negative slope between the effective reproduction number with the maximum temperature and the relative humidity. It indicates that the effective reproduction number goes down as maximum temperature or relative humidity rise. But, the regression coefficient R2 is low for these correlations which means that the correlation is not strong.


UV light influences covid-19 activity through big data: trade offs between northern subtropical, tropical, and southern subtropical countries

Abstract: UV (ultraviolet) light is an important factor should be considered to predict coronavirus epidemic growth pace. UV is different from weather temperature since UV is electromagnetic wavelength from 10 nm to 400 nm in size, shorter than of visible lights. For some people, UV light can lead to cancer from unprotected sun exposure, however, for tropical people, which have been used to live in such condition, have resisted from negative effect high UV index. Moreover, UV has the capability to inactivate virus. This conclusion has been discussed deeply with biological experts. Although UV light has the ability to inactivate viruses, it may be meaningless in areas with high air pollution where UV light turns into heat.


Warmer weather and global trends in the coronavirus COVID-19

Abstract: Predicting COVID-19 epidemic development in the upcoming warm season has attracted much attention in the hope of providing helps to fight the epidemic. It requires weather (environmental) factors to be included in prediction models, but there are few models to achieve it successfully. In this study, we proposed a new concept of environmental infection rate (RE), based on floating time of respiratory droplets in the air and inactivation rate of virus to solve the problem. More than half of the particles in the droplets can float in the atmosphere for 1-2 hours. The prediction results showed that high RE values (>3.5) are scattered around 30N in winter (Dec.-Feb.). As the weather warms, its distribution area expands and extends to higher latitudes of northern hemisphere, reaching its maximum in April, and then shrinking northward. These indicated that the spread of COVID-19 in most parts of the northern hemisphere is expected to decline after Apr., but the risks in high latitudes will remain high in May. In the south of southern hemisphere, the RE values tend to subside from Apr. to July. The high modeled RE values up to July, however, suggested that warmer weather will not stop COVID-19 from spreading. Public health intervention is needed to overcome the outbreak.


REGIONAL DETERMINANTS OF THE EXPANSION OF COVID-19 IN BRAZIL

Abstract: Objective: This study investigates the regional differences in the occurrence of COVID-19 in Brazil and its relationship with climatic and demographic factors, for this, using data about identified cases of COVID-19 on Brazil from February 26 to April 04, 2020. Methods: A model using the Polynomial Regression with cubic adjustments of the number of days of contagion, demographic density, city population and climatic factors was designed to explain the spread of COVID-19 in Brazil. Main results: It was evidenced that temperature variation maintains a relationship with the reduction in the number of cases of COVID-19, but on a very small scale. With a simulation of 30 days of contagion, a variation of -0.9% was found for each increase of 1 C. Conclusion: Temperature, despite being an intervening factor in the variation in the number of COVID-19 cases, has a reduced magnitude effect. Cities with higher temperatures do not necessarily it is more protected from the SARS-CoV-2 than those with lower temperatures, however, strong statistical significance was found, this relationship deserves to be investigated in other tests with longer time series, wide and with especially non-linear data adjustments.


No Evidence for Temperature-Dependence of the COVID-19 Epidemic

Abstract: The pandemic of the COVID-19 disease extended from China across the north-temperate zone, and more recently to the tropics and southern hemisphere. We find no evidence that spread rates decline with temperatures above 20 oC, suggesting that the COVID-19 disease is unlikely to behave as a seasonal respiratory virus.


ICU admissions and in-hospital deaths linked to covid-19 in the Paris region are correlated with previously observed ambient temperature

Abstract: OBJECTIVE To study the effect of weather on severity indicators of coronavirus disease 2019 (covid-19). DESIGN Ecological study. SETTING Paris region. POPULATION Severely ill patients with covid-19. MAIN OUTCOME MEASURES Daily covid-19-related intensive care unit (ICU) admission and in-hospital deaths in the Paris region, and the daily weather characteristics of Paris midtown. RESULTS Daily ICU admissions and in-hospital deaths were strongly and negatively correlated to ambient temperatures, with a time lag. The highest Pearson correlation coefficients and statistically significant P values were found 8 days before occurrence of ICU admissions and 15 days before deaths. CONCLUSIONS The study findings show a strong effect of previously observed ambient temperature that has an effect on severity indicators of covid-19.


Temperature dependence of COVID-19 transmission

Abstract: The recent coronavirus pandemic follows in its early stages an almost exponential expansion, with the number of cases N reasonably well fit by N eαt, in many countries. We analyze the rate α in different countries, choosing as a starting point in each country the first day with 30 cases and fitting for the following 12 days, capturing thus the early exponential growth in a rather homogeneous way. We look for a link between the rate α and the average temperature T of each country, in the month of the epidemic growth. We analyze a {\it base} set of 42 countries, which developed the epidemic at an earlier stage, an {\it intermediate} set of 88 countries and an {\it extended} set of 125 countries, which developed the epidemic more recently. Fitting with a linear behavior α(T), we find increasing evidence in the three datasets for a decreasing growth rate as a function of T, at $99.66\%$C.L., $99.86\%$C.L. and $99.99995 \%$ C.L. ($p$-value $5 \cdot 10^{-7}$, or 5$\sigma$ detection) in the {\it base}, {\it intermediate} and {\it extended} dataset, respectively. The doubling time is expected to increase by $40\%\sim 50\%$, going from $5^\circ$ C to $25^\circ$ C. In the {\it base} set, going beyond a linear model, a peak at about $(7.7\pm 3.6)^\circ C$ seems to be present in the data, but such evidence disappears for the larger datasets. Moreover we have analyzed the possible existence of a bias: poor countries, typically located in warm regions, might have less intense testing. By excluding countries below a given GDP per capita from the dataset, we find that this affects our conclusions only slightly and only for the {\it extended} dataset. The significance always remains high, with a $p$-value of about $10^{-3}-10^{-4}$ or less. Our findings give hope that, for northern hemisphere countries, the growth rate should significantly decrease as a result of both warmer weather and lockdown policies. In general the propagation should be hopefully stopped by strong lockdown, testing and tracking policies, before the arrival of the next cold season.


Higher Air Temperature, Pressure, and Ultraviolet Are Associated with Less Covid-19 Incidence

Abstract: A recent study from China suggests that high temperature and ultraviolet (UV) radiation cannot decrease the epidemics of Coronavirus disease 2019 (Covid-19). To determine whether COVID-19 incidence is modulated by meteorological factors, meta-regression of Japanese prefectural data was herein conducted. We extracted 1) cumulative numbers of confirmed Covid-19 patients in each Japanese prefecture from January to April 2020; 2) populations per 1-km2 inhabitable area in each prefecture in 2020; and 3) meteorological factors at each prefectural capital city from January to April 2020. Meteorological factors included monthly mean air temperature (degree Celsius), wind speed (m/s), sea level air pressure (hPa), relative humidity (%), and percentage of possible sunshine (%); monthly total of sunshine duration (h) and precipitation (mm); and monthly mean daily maximum ultraviolet (UV) index. To adjust for prefectural population density, we defined the incidence of Covid-19 as the cumulative number of Covid-19 patients divided by the population per 100-km2 inhabitable area. Random-effects meta-regression was performed, and its graph depicted Covid-19 incidence (plotted as the logarithm transformed incidence on the y-axis) as a function of a given meteorological factor (plotted on the x-axis). A slope of the meta-regression line was significantly negative as a function of the mean air temperature (coefficient, -0.127; P = 0.023), the mean sea level air pressure (coefficient, -0.351; P < 0.001), and the mean daily maximum UV index (coefficient, -0.001; P = 0.012) which indicated that Covid-19 incidence decreased significantly as air temperature, air pressure, and UV increased. In conclusion, higher air temperature, air pressure, and UV may be associated with less Covid-19 incidence.


Weather variables impact on COVID-19 incidence

Abstract: We test the hypothesis of COVID-19 contagion being influenced by meteorological parameters such as temperature or humidity. We analysed data at high spatial resolution (regions in Italy and counties in the USA) and found that while at low resolution this might seem the case, at higher resolution no correlation is found. Our results are consistent with a poor outdoors transmission of the disease. However, a possible indirect correlation between good weather and a decrease in disease spread may occur, as people spend longer time outdoors.


Impact of weather on COVID-19 pandemic in Turkey

Abstract: The coronavirus pandemic, which has numerous global implications, has led people to believe that nothing will be the same as before. The present day is dominated by studies on determining the factors that affect, taking preventive actions, and trying to find an effective treatment on top priority. Meteorological parameters are among the crucial factors affecting infectious diseases. The present study examines the correlation between weather and coronavirus disease 2019 (COVID-19) by considering nine cities in Turkey. In this regard, temperature (°C), dew point (°C), humidity (%), and wind speed (mph) are considered as parameters of weather. Research states that the incubation period of COVID-19 varies from 1â¯day to 14â¯days. Therefore, the effects of each parameter within 1, 3, 7, and 14â¯days are examined. In addition, the population is included as an effective parameter for evaluation. The analyses are conducted based on Spearman's correlation coefficients. The results showed that the highest correlations were observed for population, wind speed 14â¯days ago, and temperature on the day, respectively. The study results may guide authorities and decision-makers on taking specific measures for the cities.


Investigation of effective climatology parameters on COVID-19 outbreak in Iran

Abstract: SARS CoV-2 (COVID-19) Coronavirus cases are confirmed throughout the world and millions of people are being put into quarantine. A better understanding of the effective parameters in infection spreading can bring about a logical measurement toward COVID-19. The effect of climatic factors on spreading of COVID-19 can play an important role in the new Coronavirus outbreak. In this study, the main parameters, including the number of infected people with COVID-19, population density, intra-provincial movement, and infection days to end of the study period, average temperature, average precipitation, humidity, wind speed, and average solar radiation investigated to understand how can these parameters effects on COVID-19 spreading in Iran? The Partial correlation coefficient (PCC) and Sobol'-Jansen methods are used for analyzing the effect and correlation of variables with the COVID-19 spreading rate. The result of sensitivity analysis shows that the population density, intra-provincial movement have a direct relationship with the infection outbreak. Conversely, areas with low values of wind speed, humidity, and solar radiation exposure to a high rate of infection that support the virus's survival. The provinces such as Tehran, Mazandaran, Alborz, Gilan, and Qom are more susceptible to infection because of high population density, intra-provincial movements and high humidity rate in comparison with Southern provinces.