SARS-CoV-2 Infection in Animals

Taxonomy: SARS-CoV-2 is classified to the realm Riboviria, kingdom Orthornavirae, phylum Pisuviricota, class Pisoniviricetes, order Nidovirales, suborder Cornidovirineae, family Coronaviridae, subfamily Orthocoronavirinae, genus Betacoronavirus, subgenus Sarbecovirus, and species Severe acute respiratory syndrome-related coronavirus. 

Structure and viral genome: As a coronavirus, SARS-CoV-2 is a large, roughly spherical, biomembrane-enveloped virus ~100 nm in diameter, with prominent glycoprotein projections that can reach ~20 nm in length. The virus genome is a single positive-stranded RNA molecule of ~30 kilobases, one of the largest known RNA genomes, which codes four structural, 16 nonstructural, and six accessory proteins.

Replication cycle: In brief, the viral replication cycle includes the binding of SARS-CoV-2 particles to the angiotensin-converting enzyme 2 (ACE2) cell receptor, which is a protein abundantly expressed in humans and some other mammals in cells of several tissues, including lung, nasal, and oral mucosa and nasopharynx. After binding, SARS-CoV-2 virions access the cytoplasm by fusing with the cell membrane via cleavage by the cell transmembrane serine protease 2 (TMPRSS2). Once in the cytoplasm, the viral genome is uncoated and released. Open reading frame-translated polypeptides are then processed by viral proteases to 16 nonstructural proteins. 

Rough endoplasmic reticulum (ER) is used to form the RNA replicase-transcriptase complex (RTC), which will drive synthesis of full-length (–)RNA copies that will be used as templates for full-length (+)RNA genomes. Via transcription, subgenomic RNAs including encoding structural and accessory proteins are produced. Translated structural proteins and genomic RNA are assembled into the viral nucleocapsid and envelope in the ER-Golgi intermediate complex, and then mature particles are released by exocytosis.

Origin: Phylogenetic studies reconstructing the evolutionary relationships between SARS-CoV-2 and its closest relatives suggest the ancestor of SARS-CoV-2 as an animal virus, likely in horseshoe bats (Rhinolophus spp). The virus may have emerged in the human population by way of an intermediate host. 

Spatial and genomic data suggest the two early lineages of SARS-CoV-2 were associated with the Huanan market, located in Wuhan, China. Live mammals, including raccoon dogs (Nyctereutes procyonoides), were sold at the market in late 2019, and geospatial analyses within the market show that SARS-CoV-2-positive environmental samples were strongly associated with vendors selling live animals. Together, these analyses provide evidence for the emergence of SARS-CoV-2 via the live wildlife trade and identify the Huanan market as the unambiguous epicenter of the COVID-19 pandemic.(1)

The immediate animal ancestor or progenitor virus, which was identified in civets during the SARS outbreak in 2003 and in camels during the MERS outbreak in 2012, remains elusive for SARS-CoV-2. SARS-CoV-2 was found to have the most extreme CpG dinucleotides deficiency in all known betacoronavirus genomes, similar to a virulent canine coronavirus, suggesting that canines may be an intermediate host of SARS-CoV-2.(2) 

More wildlife investigation is critical to identify intermediate species that facilitated transmission from bats to humans and to assess the extent of the diversity in the phylogeny of the related sarbecoviruses that pose high risk for future spillovers. Several coronaviruses related to SARS-CoV-2 have been retrieved from locations in Southeast Asia, some of them from bats collected as early as 2010.(3,4,5,6,7,8)  

Pathogeny: Studies of naturally infected humans and animals in additional to animal models have been useful in elucidating the pathogenesis of SARS-CoV-2 infections.(9) The virus enters the host’s respiratory tract, airway, and alveolar epithelial cells, where the vascular endothelial cells and alveolar macrophages are targets of viral entry given their relatively high expression of ACE2.(10) Detectable titers of the virus can be found in the upper respiratory tract (oropharynx and nasopharynx) even during prodromal periods, allowing for efficient respiratory transmission.

Lung injury can include diffuse alveolar damage, which can lead to a "leaky" state of the epithelium and endothelium that promotes inflammation and coagulation. Imbalance in the coagulation and fibrinolysis systems may result with immunothrombosis in severe cases.(11)

SARS-CoV-2 can also cause enteric infections, as ACE2 is abundantly expressed in mammalian intestinal tracts. Viral RNA can be found in the feces or rectal swabs of infected humans and animals; wastewater surveillance has become increasingly important in community-level surveillance for the virus.

Coronaviruses including SARS-CoV-2 have evolved mechanisms to evade the host interferon (IFN) pathways in order to survive in host cells. Patients with severe clinical disease from SARS-CoV-2 infection often have an imbalanced immune response with high concentrations of inflammatory cytokines and chemokines as well as low concentrations of circulating IFN-beta and IFN-gamma. The evasion pathway of the virus may involve evasion of IFN signaling by SARS-CoV-2 and impaired IFN production.(10)

In cases of severe lung disease, there is an elevation of serum inflammatory cytokines leading to a cytokine storm and immunopathological changes.

Incubation period: In laboratory settings, the SARS-CoV-2 incubation period in some experimentally infected nonhuman animals appears to be similar to that in humans (2–14 days). 

• Experimentally infected mink (Neogale [formerly Neovison] vison) had viral RNA in saliva from 1 to 7 days after infection.(12)

• Experimentally infected ferrets (Mustela putorius furo) transmitted SARS-CoV-2 to direct contact ferrets at 2 days after infection.(13)

• Peak oral and nasal viral shedding was recorded at 2 to 3 days after infection in experimentally infected cats and Syrian golden hamsters (Mesocricetus auratus), and viral RNA was detected in dogs’ rectal swabs 2–6 days after infection.(14,15,16)

• Nasal swab samples from two species of macaques and marmosets (Callithrix jacchus) showed peaks in the concentrations of viral genomic RNA 2 days after infection.(17)

• Infectious virus was shed from both respiratory and gastrointestinal tracts in African green monkeys (Chlorocebus sabaeus) 2–7 days after infection followed by recrudescence 14–21 days after infection.(18)

• Infectious virus was isolated from the nasal epithelium and trachea of fruit bats (Rousettus aegyptiacus), intranasally inoculated, 4 days after infection.(19)

• SARS-CoV-2 RNA was detected 2 days after infection in nasal, oral, and rectal swabs of experimentally infected white-tailed deer (Odocoileus virginianus) fawn.(20)

• Tree shrews (Tupaia belangeri) from 6–12 months old shed SARS-CoV-2 at the earlier stage of infection than adults, and genomic RNA of SARS-CoV-2 can be detected 6 days after infection in nasal, throat, and anal swabs.(21)

Morbidity: In a systematic literature review of case reports published between January 1, 2020, and June 1, 2021, 38 of 64 (59%) animals testing positive for SARS-CoV-2 by RT-PCR assay were reported to have clinical signs.(22) However, most of these data were obtained from passive surveillance, which is biased toward clinically affected cases.

Mortality and case fatality: Most cases in animals have been mild and self-limited; however, infections in farmed mink have caused respiratory disease outbreaks with death caused by interstitial pneumonia. Mortality rates varied in adult mink farms from 2.4% to 9.8% in the Netherlands, but in > 318,000 animals of different species assessed and reported to the World Organisation for Animal Health (WOAH; formerly OIE), mortality rate was 0.2% and case fatality rate 1.4%.(23)

Geographic distribution: More than 230 countries have reported human COVID-19 cases to the World Health Organization (WHO). The first case of SARS-CoV-2 infection in a nonhuman animal was officially reported to the WOAH by Hong Kong on February 29, 2021. As of April 30, 2022, 35 countries in the Americas, Africa, Asia, and Europe had reported infection in several animal species.

Transmission: Modes of SARS-CoV-2 transmission among nonhuman animals are the same as categorized for humans: inhalation and deposition of SARS-CoV-2 on exposed mucous membranes.

• Ferrets inoculated via the intranasal route and placed in direct and indirect contact with naive ferrets 2 days after infection transmitted SARS-CoV-2 by contact between animals in the same cage and by aerosol in animals from different cages. Rapid transmission occurred even prior to infected ferrets reaching their highest viral RNA copy numbers in nasal washes at 4 days after infection. Transmission also occurred prior to peak body temperature and body weight loss in infected animals, which is consistent with the infectiousness of individuals before the occurrence of clinical signs.(13)

• Experimentally infected cats shed virus both orally and nasally for up to 5 days after infection, with peak titers achieved from nasal shedding at 3 days after infection. In the same experiment, naïve cats that had contact with infected cats shed infectious virus orally by 24 hours after exposure, and the duration of viral shedding was prolonged, compared to that in the inoculated cats.

• Unlike cats, dogs did not shed virus after infection despite mounting an antiviral neutralizing antibody response.(14)

• Naive fawns of white-tailed deer that were placed in contact with experimentally infected animals shed infectious SARS-CoV-2 in oronasal samples 2 days after contact.(20)

• In an experimental study, oral swabs from at least one naive adult deer that was commingled with an infected individual had SARS-CoV-2 RNA detectable 2 to 4 days after commingling. Vertical transmission of SARS-CoV-2 was also assessed and two of three fetuses of one infected deer had detectable amounts of viral RNA in at least one of the tissues collected 4 days after infection.(24)

Public health: Confirmed transmission of SARS-CoV-2 from animals to humans remains rare. Evidence based on sequencing shows transmission to humans from mink in Europe, deer in Canada, and a cat in Thailand.(25,26,27,28)

After the outbreaks of SARS-CoV-2 on mink farms in Denmark and Poland, novel variants found in mink subsequently appeared within the local human community.(25,29,30) Experimentally infected mink transmitted SARS-CoV-2 Omicron to other individuals by contact.(12) In Utah, free-ranging mink, presumed domestic escapees, had high antibody titers to SARS-CoV-2 after the local outbreaks in mink farms, suggesting a potential transmission pathway from domestic mink farms to native wildlife.(31,32) In Spain, SARS-CoV-2 infection was detected in two feral minks caught in the wild.

A new and highly divergent lineage of SARS-CoV-2 was epidemiologically linked to a human case in Canada, suggesting transmission from white-tailed deer to a human.(27) 

A veterinarian in Thailand developed SARS-CoV-2 infection after being sneezed on by an infected, clinically affected cat with infected owners. The cat-to-human directionality of transmission was supported by analyses of viral genome sequences.

SARS-CoV-2 infection in animals is a notifiable disease to the WOAH. In the United States, the case definition and reporting criteria includes positive results of quantitative reverse transcription PCR (RT-qPCR) assay with sequencing confirmation from biological samples or from the virus isolate, or demonstrated SARS-CoV-2 neutralizing antibody. Laboratories within the United States and its territories are required to report all positive test results to the USDA Animal and Plant Health Inspection Service (APHIS).

Other coronaviruses of medical importance: In animals, various species of coronaviruses are involved in a wide spectrum of disease in several species of vertebrates. 

• Among the most common animal coronaviruses are Porcine epidemic diarrhea virus strains that have been involved in clinical infections that vary from mild respiratory signs to severe diarrhea and vomiting in pigs, and Alphacoronavirus 1, involved in diarrhea and feline infectious peritonitis in cats and enteritis in dogs.(33,34,35)

• The Betacoronavirus 1 strains of subgenus Embecovirus can cause mild respiratory signs in dogs and cattle as well as enteric disease in equines and cattle.

• A recently discovered species of Deltacoronavirus Coronavirus HKU15 has been involved in diarrhea outbreaks in swine, and it has demonstrated pathogenicity in chickens and turkeys.

• Avian coronavirus strains can cause infectious bronchitis in chickens as well as diarrhea in chickens and turkeys.

• Murine coronavirus strains can infect brain, liver, and respiratory tract and cause both acute and chronic disease in laboratory rodents.

• In dromedary camels, MERS-CoV causes primarily a benign and transient upper respiratory tract infection.

• Other coronaviruses have been identified in free-ranging rats and mice in China, but clinical infections remain unknown.

• Diverse coronaviruses have been observed in bats. More than 4,000 coronavirus sequences from 14 bat families have been identified. Whether bat species are universally tolerant of coronavirus infection remains unclear; however, experimental infections have shown mild tissue damage and no evident clinical signs of infection.

Potential for enzootic pathways of evolution of SARS-CoV-2 and other coronaviruses: Several species have demonstrated capacity to shed infectious virus in experimental infections and ultimately act as a source of infection. The biological features and level of interaction with humans and other animals make some species of particular interest.

White-tailed deer have demonstrated not only capacity to transmit horizontally SARS-CoV-2 to contact animals and humans but also to produce viral strains with amino acid substitutions in the receptor-binding domain that infrequently occur in humans. Genomic analysis of retropharyngeal lymph node samples of infected individuals revealed 12 SARS-CoV-2 lineages, suggesting multiple zooanthroponotic spillover events and deer-to-deer transmission.(36)

Genomic changes have also been found in SARS-CoV-2 strains retrieved from infected mink and are of great concern, potentially indicating different enzootic pathways for evolution.(25,37,38)

Novel highly divergent lineages of SARS-CoV-2 detected in mink and in white-tailed deer later appeared within the local human community in Denmark and Canada.(25,27) These variants could potentially present increased transmissibility and virulence, raising concern about their impact not only in humans but also nonhuman animal populations. The establishment of enzootic cycles of transmission can potentially result in spillover events to other animal species and the human population and ultimately generate recombinant strains with animal viruses resulting in strains with unknown impact for animal and public health.(39,40)

Although rare, some coronaviruses that infect animals can be transmitted to humans and then spread among them, as has been demonstrated with SARS-CoV-2. The detection of animal coronaviruses in humans has been continuously reported worldwide.

• In 2010, Alphacoronavirus 1-like strains, previously known as feline enteric coronavirus, were detected in respiratory swabs from humans with acute respiratory signs who tested negative for influenza in Arkansas. Analysis of partial sequences revealed Betacoronavirus 1-like strains, previously known as human coronavirus OC43, suggestive of Alphacoronavirus 1 and Betacoronavirus 1 coinfection, or potential recombination.(41)

• From 192 human swabs collected from hospitalized pneumonia patients in Malaysia between 2017 and 2018, four tested positive by RT-PCR assay for a virus genetically similar to Alphacoronavirus 1, previously known as canine coronavirus.(42)

• A novel Alphacoronavirus recombinant of previously known as canine and feline coronaviruses was recently isolated from respiratory samples of a group of children with pneumonia in Malaysia.(43)

• Another study found a Deltacoronavirus, which causes diarrhea in swine, chickens, and turkeys, in plasma samples of three Haitian children with acute undifferentiated febrile illness.(44)

The discovery of animal and potentially recombinant coronaviruses in humans underscores the public health threat of animal coronaviruses and the urgent need to strengthen animal virus surveillance. Despite the self-limiting aspect of interspecies transmission, the possibility of adaptation and generation of recombinant viruses may pose a threat for epidemics or pandemics.

SARS-CoV-2 clinical infection is mostly manifested in humans as a respiratory tract infection; however, cells of multiple other systems where ACE2 receptors abound, including digestive, muscular, urinary, nervous, and cardiovascular systems, can be infected. For that reason, a wide spectrum of clinical signs and symptoms have been reported in humans infected by different variants of SARS-CoV-2, including shortness of breath, cough, chills, fever, fatigue, muscle ache, chest distress, headache, diarrhea, anorexia, nausea, vomiting, loss of smell, and loss of taste.

Similar clinical signs have occurred in nonhuman vertebrates. Clinical features in animals may include elevation of body temperature, coughing, sneezing, respiratory distress, nasal discharge, ocular discharge, vomiting or diarrhea, fever, inappetence, and lethargy.

• Mink experimentally infected with the SARS-CoV-2 variant Omicron developed lethargy, anorexia, diarrhea, nasal and lacrimal discharge, and sneezing.(12) Disease indicators of farmed mink naturally infected by SARS-CoV-2 in Utah included, most notably, sudden death, anorexia, and increased respiratory effort.(31)

• Experimentally infected ferrets developed elevated body temperatures, loss of appetite, decreased activity, and occasional coughing.(13,16,45)

• Increases in body temperature were observed in two macaque species (Macaca fascicularis and Macaca mulatta) and a marmoset, and loss of body weight was noticed at 10 days after experimental infection in the macaques.(17)

• Clinical disease was mild in African green monkeys, and respiratory function revealed a transient decrease in the volume of air inhaled, or tidal volume, at 7 days after infection.(18)

• After oronasal inoculation of pigs with SARS-CoV-2, one individual developed mild, nonspecific clinical signs, including coughing and lethargy.(46)

• When infected by SARS-CoV-2, tree shrews (Tupaia belangeri), a mammal of the order Scandentia that possesses a closer genetic relationship to primates than to rodents, developed only increased body temperature, particularly in females.(21)

• Ocular and nasal discharge were noted in experimentally infected white-tailed deer from 5 to 10 days after infection, and a slight elevation in body temperature was observed from 0 to 3 days after infection.(24)

As in humans, inapparent infections can occur in animals. In a study of cats and dogs from households with COVID-19 cases in Texas, pet owners reported mild clinical signs of disease, including vomiting, diarrhea, lethargy, and sneezing, in 37 of 169 (22%) infected animals. The percentage of uninfected animals with these clinical signs also reported was not significantly different (63/356 [18%]), suggesting in part that these signs may not be attributable to SARS-CoV-2 infection (personal communication).(47)

Histopathologic and postmortem findings:In naturally infected mink, acute interstitial pneumonia was found in nearly all mink that died at the height of the outbreaks and were examined after death. Acute alveolar damage was a consistent histopathologic finding in mink that died with pneumonia.(23)

On histologic examination of a naturally infected cat that was euthanized, bronchointerstitial pneumonia, acute myocardial degeneration and necrosis, and mild hypertrophic cardiomyopathy were observed.(48)

Many other species that were experimentally infected by SARS-CoV-2 developed pathological changes, mainly in the respiratory tract.

• Necropsy of experimentally infected macaques and baboons found that lungs were the most affected organ. Multifocal minimal to mild interstitial mononuclear inflammation was evident, generally composed of macrophages and lymphocytes that expanded the alveolar septa with variable neutrophil infiltrates or fibrosis. In the same study, interstitial and alveolar pneumonitis was observed in marmosets, although not as prevalent as in macaques or baboons. Pathological changes were moderate to severe in baboons, moderate in macaques, and mild in aged marmosets.(49)

• In transgenic mice expressing the human ACE2 receptor, the typical histopathologic diagnosis was interstitial pneumonia with prominent inflammatory cell infiltration around the bronchioles and blood vessels.(50)

• Some experimentally infected rabbits developed enlarged tracheobronchial lymph nodes consistent with mild lymphoid hyperplasia.(51)

• In the respiratory tract of infected pregnant white-tailed deer, mild to moderate multifocal lymphohistiocytic and neutrophilic rhinitis, erosive to suppurative tracheitis, and erosive bronchitis with mixed peribronchiolitis was noted. Bronchioles and blood vessels were delineated by perivascular and peribronchiolar lymphocytes, histiocytes, and few neutrophils; mild erosive tonsillitis was also noted. Fetal lungs occasionally contained intrabronchial and intrabronchiolar foci of squamous cells; however, no viral antigen was detected in fetal lungs or within the placenta.(24)

• Pathological studies in experimentally infected ferrets revealed severe lymphoplasmacytic perivasculitis and vasculitis as well as mild peribronchitis in the lungs.(16)

• In the necropsies of raccoon dogs (Nyctereutes procyonoides), mild rhinitis affecting the respiratory and olfactory regions was identified in all experimentally infected animals. Histopathologic lesions indicative of SARS-CoV-2 replication were found in the nasal conchae.(52)

• Gross lesions were not observed in any of the experimentally infected cats or dogs. Histologically, moderate ulcerative, suppurative lymphoplasmacytic rhinitis was observed in the nasal turbinates along with mild lymphoplasmacytic tracheitis in cats.(14)

Natural infections: Several species of wild and domestic mammals have been naturally infected with SARS-CoV-2 worldwide. Most commonly, disease in these animals has been mostly inapparent or mild. In rare circumstances, some species may develop moderate to severe clinical signs of infection.(45) Of 19 vertebrate species reported infected by SARS-CoV-2 worldwide by March 2022 (OIE, 2022b), severe clinical infection has been mostly restricted to mink, and on rare occasions, individuals with underlying medical conditions.

Most wild species reportedly infected are captive zoo animals believed to have been exposed to infected zoo workers or visitors. Zoo animals reportedly infected by SARS-CoV-2 include big cats such as the Malayan tiger (Panthera tigris jacksoni), lion (Panthera leo), snow leopard (Panthera uncia), fishing cat (Prionailurus viverrinus), Eurasian lynx (Lynx lynx), Canadian lynx (Lynx canadensis), and puma (Puma concolor) as well as other groups such as the gorilla, spotted hyena, coatimundi, binturong, otter, and hippopotamus.

Natural infection of captive big cats has caused clinical signs of lethargy, anorexia, and abnormal respiratory signs. Further, exposed zoo gorillas have developed mild respiratory signs such as coughing and congestion.(53)  In March 2020, four tigers and three lions at the Bronx Zoo in New York developed mild, abnormal respiratory signs caused by SARS-CoV-2 infection. Virus isolation was positive in tracheal wash fluid from one tiger and in fecal samples of one tiger and one lion.

In companion animals, naturally exposed individuals were reported to have mild clinical signs. In an active surveillance study conducted in Texas, of 17 dogs and cats confirmed positive for SARS-CoV-2 infection, 14 developed no clinical signs, with the others reported to have lethargy or sneezing.(54) In the same surveillance, repeated sampling of SARS-CoV-2-positive dogs and cats showed persistence of viral RNA for at least 25 days after initial test, and infectious SARS-CoV-2 was successfully isolated from the respiratory swabs of two naturally infected cats.(54,55) The isolation of infectious SARS-CoV-2 has also been reported in dogs.(56)

Exceptional events involving more severe disease have been reported mainly in captive mink (N. vison), and in rare circumstances also in domestic cats and dogs. Outbreaks of SARS-CoV-2 have occurred on mink farms and have been associated with high mortality rates in mink:

• In Utah, infection was transmitted rapidly between independently housed animals and farms, causing severe respiratory disease and death.

• In the Netherlands, SARS-CoV-2 caused respiratory disease outbreaks with increased mortality rates in mink farms. Acute alveolar damage was a consistent histopathologic finding in mink that died with pneumonia.

• In Denmark, SARS-CoV-2 was transmitted rapidly among farmed mink, resulting in respiratory disease.

• SARS-CoV-2 infection was linked to myocarditis in the United Kingdom and France.

Another species that has demonstrated high susceptibility to SARS-CoV-2 infection and confirmed capacity to transmit SARS-CoV-2 to other animals is the white-tailed deer (Odocoileus virginianus). A high seroprevalence of SARS-CoV-2 infection has been found in free-ranging white-tailed deer, which have also shown to be susceptible to several lineages of SARS-CoV-2. A series of studies demonstrated that virtually all captive white-tailed deer at a deer facility harbored SARS-CoV-2 neutralizing antibodies, and retrospective analysis of samples showed that all the deer seroconverted at the same time point and maintained neutralizing antibodies for at least 13 months.

In rare circumstances, SARS-CoV-2 can cause severe disease or contribute to death in animals. In the US, SARS-CoV-2 was suspected to have contributed to the severity of clinical signs leading to euthanasia in one dog, and to be the primary reason for death in one cat.

Experimental infection studies: Experimental infection studies have defined the ability of several nonhuman vertebrate taxa to become infected and shed infectious virus. They have also been critical for identifying species that are not susceptible to infections under experimental conditions.

Several mammalian orders, including Primates, Carnivora, Rodentia, Lagomorpha, and Chiroptera, are susceptible to natural or experimental infection with SARS-CoV-2. As of March 31, 2022, 669 SARS-CoV-2 outbreaks in 20 animal species had been reported by 35 countries in the Americas, Africa, Asia, and Europe to the World Organisation for Animal Health. Nonhuman species with demonstrated capacity to shed infectious SARS-CoV-2 based on experimental and natural infections, as of March 2022, include the following:

• Bushy-tailed woodrats (Neotoma cinerea)

• Cat (Felis catus domesticus)

• Deer mice (Peromyscus maniculatus)

• Dog (Canis familiaris)

• Egyptian fruit bats (Rousettus aegyptiacus)

• Ferret (Mustela putorius)

• Golden Syrian hamster (Mesocricetus auratus)

• Lion (Panthera leo)

• Mink (Neogale vison)

• Pig (Sus scrofa)

• Rabbit (Oryctolagus c. domesticus)

• Raccoon dogs (Nyctereutes procyonoides)

• Red fox (Vulpes vulpes)

• Striped skunks (Mephitis mephitis)

• Tiger (Panthera tigris)

• White-tailed deer (Odocoileus virginianus)

Species groups with the capacity to shed infectious SARS-CoV-2 are those that have been shown to transmit the virus by contact or have had virus isolated from natural or experimental infections.

Nonhuman species without demonstrated capacity to shed infectious SARS-CoV-2 based on experimental and natural infections, as of March 2022, include the following:

• Black-tailed prairie dogs (Cynomys ludovicianus)

• Chicken (Gallus domesticus)

• Cottontail rabbits (Sylvilagus floridanus)

• Coyote (Canis latrans)

• Duck (Anas platyrhynchos domesticus)

• Fox squirrels (Sciurus niger)

• House mice (Mus musculus)

• Raccoon (Procyon lotor)

• Wyoming ground squirrels (Urocitellus elegans)

Despite being unlikely to develop clinical disease, experimentally infected cats have been shown to be highly susceptible to infection with SARS-CoV-2 and able to transmit the virus to other cats under laboratory conditions via both direct and indirect contact.

Mink experimentally infected with the SARS-CoV-2 variant Omicron developed clinical signs and transmitted the virus to uninfected recipients.(12)

The role of domestic production animals and associated risks for humans in close contact with food production animals have also been investigated for SARS-CoV-2. When infected with SARS-CoV-2, rabbits excreted infectious virus from the nose and throat.(51) In pigs, results of experimental infection studies have varied, and the difference in outcomes is believed to be related to infectious dose, viral isolate, age, and breed or colony of swine used in each experiment.

In one study, after oronasal inoculation with 106 plaque-forming units (PFU) of SARS-CoV-2 in 16 pigs, viral RNA was detected in oral fluids and nasal wash of two pigs; infectious virus was isolated from one pig; two animals seroconverted as determined on the basis of 70% plaque reduction neutralization titer (PRNT70); and one pig developed mild, nonspecific clinical signs, including coughing and lethargy.(46) In two other studies, however, experimentally infected pigs showed no evidence of viral RNA or neutralizing antibodies.(16,19) In dairy calves, experimental infection demonstrated viral replication, albeit absence of infection among in-contact animals.(57)

In a study conducted in China, no viral RNA in oropharyngeal swabs was detected in dogs, chickens, or ducks, and only half of the dogs seroconverted.(16) In other experimental studies, chickens and ducks were not susceptible to SARS-CoV-2 infection. Despite evidence of SARS-CoV-2 isolation from natural infections, in experimental infections, apparently dogs do not support viral replication and do not shed virus to the same degree as cats.

For wildlife, several species have been infected experimentally. An experimental infection study in white-tailed deer showed that SARS-CoV-2 can be transmitted via direct contact as well as vertically from doe to fetus. Infectious virus could be isolated from nasal and rectal swabs up to a week after infection, and viral RNA could be detected until 22 days after infection.(24,58)

Efficient SARS-CoV-2 replication with virus isolation and transmission to all animals in direct contact was also observed in ferrets (Mustela putorius furo). Virus isolation was successful from nasal washes collected on days 2 and 4 after infection, and virus RNA was detected until 21 days after infection. In the same study, experimentally infected Egyptian fruit bats (Rousettus aegyptiacus) transmitted SARS-CoV-2 to animals in direct contact and had infectious virus isolated from nasal conchae and trachea at day 2 after infection.(19)

Among nonhuman primates, macaques (Macaca mulatta), baboons (Papio hamadryas), and marmosets (Callithrix jacchus) were infected by multiple routes (ocular, intratracheal, and intranasal) with a target dose of ~10₆ PFU of SARS-CoV-2. Viral RNA was detected early in all species at 3 days after infection and decreased thereafter at variable rates.

Macaques had clinical signs of viral infection, mild to moderate pneumonitis, and extrapulmonary disease. Baboons had prolonged viral RNA shedding and substantially more lung inflammation, compared with macaques. Marmosets had a mild infection.

Acute respiratory distress in macaques and baboons recapitulates the progression of COVID-19 in humans. No SARS-CoV-2 subgenomic RNA was detected in lung samples of macaques and baboons.(49)

Raccoon dogs (Nyctereutes procyonoides) have been demonstrated to be susceptible to SARS-CoV-2 infection; they developed no clinical signs of illness and transmitted the virus to direct in-contact animals,(52) which corroborates the hypothesis that raccoon dogs could have been the intermediate hosts of SARS-CoV-2.(1)

Ferrets have upper respiratory tracts infected by SARS-CoV-2 that resembled a subclinical infection in humans with different results for efficient transmission.(16,19)

Experimentally inoculated red foxes (Vulpes vulpes) become infected and shed virus in oral and respiratory secretions.(59)

Several common peridomestic species of North America, including deer mice (Peromyscus maniculatus), bushy-tailed woodrats (Neotoma cinerea), and striped skunks (Mephitis mephitis), are also susceptible to SARS-CoV-2 experimental infection and can shed the virus in respiratory secretions. None of the animals developed clinical signs of disease at any time during the study. No elevation of temperature or behavior change was observed in all animals included in the study.(60)

Deer mice shed virus orally for up to 4 days after infection, and virus was isolated from lungs and trachea of animals tested at 3 days after infection. Bushy-tailed woodrats shed virus orally for < 5 days after infection and had virus isolated from turbinates, trachea, and lung 3 days after infection. Striped skunks shed virus orally, nasally, or both, and of the three skunks that underwent necropsy 3 days after infection, two had infectious virus in the turbinates.(60)

In contrast, cottontail rabbits (Sylvilagus floridanus), fox squirrels (Sciurus niger), Wyoming ground squirrels (Urocitellus elegans), black-tailed prairie dogs (Cynomys ludovicianus), house mice (Mus musculus), raccoons (Procyon lotor), and coyotes (Canis latrans) were not susceptible to SARS-CoV-2 infection.(59,60)

• Direct: swab samples

• Indirect: neutralization testings

The diagnostic tools and protocols used to detect SARS-CoV-2 infection in animals are similar to the algorithm used to detect current and past infection in humans. Laboratory testing is based on the direct diagnosis of acute infection, mainly through the detection of SARS-CoV-2 RNA or virus isolation from swab samples of respiratory tract or rectal swabs, and based on the indirect diagnosis of convalescent infection via the detection of specific antibodies on serum samples. Biological samples of the respiratory tract include nasopharyngeal or oropharyngeal swabs, sputum, lower respiratory tract aspirates, bronchoalveolar lavage, and nasopharyngeal wash or aspirate or nasal aspirate. 

The gold standard for serologic diagnosis of coronavirus is neutralization testing, which includes virus neutralization (VNT), plaque reduction neutralization testing (PRNT), and microneutralization. The neutralization tests are highly specific and are used to confirm the presence of neutralizing antibodies to SARS-CoV-2. Serum or plasma samples are heat-inactivated and tested for their ability to neutralize CPE (VNT) or lysis plaque (PRNT) formation by infectious SARS-CoV-2.

Tests are designed to mimic the virus-host cell interaction in cell culture plates. These approaches typically require a biosafety level 3 (BSL-3) containment facility and highly trained personnel. Because the potential circulation of animal coronaviruses could generate cross-reacting neutralizing antibodies, a conservative threshold for detection of neutralizing antibodies of at least 90% for PRNT is preferred.

An alternative to the VNT and PRNT is a test that uses viruses such as lentiviruses and vesiculoviruses expressing the viral protein of interest. Whereas a pseudovirus-based virus neutralization test (pVNT) does not use infectious SARS-CoV-2, its main advantage is that it can be performed in BSL-2 facilities. These cell culture–based techniques are species-independent and can be used to investigate neutralizing antibodies in diverse animal taxa.

During the COVID-19 pandemic, commercial SARS-CoV-2 surrogate virus neutralization test (sVNT) kits were developed. These kits detect neutralizing antibodies without the need to use infectious or active virus or cells via the use of purified receptor binding domain (RBD) from the SARS-CoV-2 viral spike (S) protein and the host cell receptor ACE2. Because they do not use infectious viruses, these tests can be conducted at BSL-2 facilities.

Alternative serologic tests have been used to investigate humoral response of animals to SARS-CoV-2 infection. They include in-house or commercial ELISA approaches, which are designed to be specific for certain species and are typically used as screening tests to detect antibodies to the most conserved proteins of SARS-CoV-2.

Preventing SARS-CoV-2 transmission from humans to animals involves biosecurity and hygiene measures. Humans suspected or confirmed to be infected with SARS-CoV-2 should restrict contact with animals, including pets, as they would with humans during their illness. This includes wearing a mask in the presence of an animal. Animals suspected or confirmed to be infected with SARS-CoV-2 should remain separated from other animals and humans while infected.

After the identification in September 2020 of a novel mink-originated variant of SARS-CoV-2 in a human community, 17 million mink were culled in Denmark. This measure was implemented by the Denmark Government for fear that novel and perhaps more virulent variants of SARS-CoV-2 could emerge and be transmitted worldwide.

Due to their susceptibility, some animal species are being used as models to test vaccines for use in humans, and some animal vaccines are already being administered. SARS-CoV-2 vaccines for use in mink and other susceptible animal species have been administered by several countries in farms and zoos (OIE, 2022a). The first animal vaccine developed for animals was designed by the Russian Federal Service for Veterinary and Phytosanitary Surveillance for carnivores. Based on the reported clinical trial findings, it was suggested that the vaccine, which is an inactivated virus vaccine, was safe and was capable of producing immunity in all animals enrolled in the study.

In July 2021, a commercial veterinary pharmaceutical company announced the donation of thousands of doses of an experimental vaccine against SARS-CoV-2.

Captive orangutans and bonobos at the San Diego Zoo in the US became the first nonhuman primates to receive an experimental COVID-19 vaccine. The USDA and state veterinarians authorized the vaccine for experimental use on a case-by-case basis.

A nonhuman animal vaccine candidate is being developed for use in cats. The vaccine received regulatory approval from the USDA to advance to clinical trials for evaluating the safety and immunogenicity of the vaccine in domestic cats. The vaccine has been administered on some mink farms to generate data on safety and efficacy necessary for conditional approval by the USDA.

Vaccinated zoo animals have subsequently tested positive for SARS-CoV-2.

SARS-CoV-2 and other human and animal coronaviruses have remarkably short persistence on copper, latex, and surfaces with low porosity, compared to stainless steel, plastics, glass, and highly porous fabrics. Depending on the initial viral load and environmental conditions, SARS-CoV-2 can persist on surfaces such as plastic, stainless steel, or glass for 3–7 days; human coronaviruses such as SARS, MERS, and endemic human coronaviruses can persist for up to 9 days. Under experimental conditions, SARS-CoV-2 remained viable in the environment after aerosolization for at least 3 hours. Certain coronaviruses persist in human excrement, sewage, and water for several days.

Coronaviruses remain active longer in the environment at lower temperatures and lower relative humidity. SARS-CoV-2 was found to remain infectious for 14 days at 4°C, but for only 2 days at 20°C in sewage water. Higher temperatures (eg, 30° or 40°C) decrease the duration of persistence of MERS and veterinary coronaviruses such as alphacoronaviruses and betacoronaviruses, previously known as transmissible gastroenteritis virus and mouse hepatitis virus.

Experimentally, ethanol solutions at concentrations of 62%–75% decreased SARS-CoV-2, SARS-CoV, and MERS-CoV infectivity within 1 minute of exposure; however, a 70% solution took > 10 minutes to decrease the titer of alphacoronaviruses and betacoronaviruses. Solutions of 0.1%–0.5% sodium hypochlorite and 2% glutardialdehyde were also quite effective for decrease in viral titer.

SARS-CoV-2 is less effectively inactivated by 0.05%–0.2% benzalkonium chloride or 0.02% chlorhexidine digluconate.

The FDA has not approved any drugs for treatment of SARS-CoV-2 infection in animals. The USDA APHIS Veterinary Services Center for Veterinary Biologics regulates veterinary biologics, including vaccines, diagnostic kits, and other products of biological origin. In special circumstances, zoo animals have been experimentally treated with monoclonal antibodies, similar to treatments administered to humans. However, the FDA's recommendation is prevention of SARS-CoV-2 transmission from humans to animals via biosecurity and hygiene measures.

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