Animal Health

SARS-CoV-2 in animals situation update

6 December 2022, 17:00 hours; Rome

Overview

Situation: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2): A virus that is spreading globally through human-to-human transmission, but has also demonstrated ability to infect multiple animal species (from Bovidae, Canidae, Cebidae, Cercopithecidae, Cervidae, Cricetidae, Felidae, Hominidae, Hyaenidae, Mustelidae, Procionidae, Viverridae, Hippopotamidae, Myrmecophagidae families) with spillover potential from one animal species to another. In rare occasions, spill-back from animals to humans has been evidenced (mink-to-human in the Netherlands [reference] and in Denmark [reference]; hamster-to-human in Hong Kong Special Administrative Region (China) [reference]).

Reported human cases: As of 5 December 2022, there have been 641 435 884 confirmed cases of COVID-19 including 6 621 060 deaths reported to WHO. In the last seven days, 2 716 294 new human cases and 6 629 deaths were reported worldwide. Since the beginning of the pandemic in March 2020, 233 countries, states, and territories reported COVID-19 human cases across five geographic regions including Africa (57), the Americas (57), Asia (46), Europe (50), and Oceania (23). [reference]. Cumulative COVID-19 cases reported in humans globally are presented Map 1. For detailed information on human cases, please refer to WHO COVID-19 Dashboard and WHO COVID-19 Weekly Updates.

Countries and territories with reported findings in animals (virological findings)1:France, Switzerland, Hong Kong SAR (China), Belgium, Netherlands, Germany, Russia, United States of America, Denmark, Japan, United Kingdom of Great Britain and Northern Ireland, Chile, Canada, Brazil, Sweden, Italy, Spain, South Africa, Greece, Argentina, Lithuania, Mexico, Slovenia, Estonia, Bosnia and Herzegovina, Latvia, Poland, Portugal, Puerto Rico, Croatia, Thailand, Uruguay, Myanmar, Indonesia, Singapore, Colombia, Finland, India, Ecuador.
1 in order of first reported occurrence.

Situation in animals

Map 1 shows SARS-CoV-2 events2 in animals up to 6 December 2022 at national level, over an estimated cumulative COVID-19 human cases distribution map. Circles indicate countries reporting positive events in animals; circle size is proportional to the number of events reported in each country (see legend). The background layer map includes cumulative number of COVID-19 human cases according to WHO, 2022.
2 Events include animal cases officially reported by national authorities and the WOAH, or positive findings referred to in scientific publications.

Map. Results of published SARS-CoV-2 events in animals up to 6 December 2022 at national level, over a cumulative COVID-19 human cases background map

Results of published SARS-CoV-2 events in animals up to 6 September 2022 at national level, over a cumulative COVID-19 human cases background map

Table 1Animal species naturally infected (RNA detection) by SARS-CoV-2

Animal species Scientific name Country/Territory Site Year reported & number of epidemiological units affected (individual animal cases) or [production or marketing units such as farms or markets]

Domestic cat

Felis catus

Argentina, Belgium, Brazil, Canada, Chile, Croatia, Ecuador, Estonia, France, Finland, Germany, Greece, Hong Kong SAR., Irana, Italy, Japan, Latvia, Mexico, Netherlands, Portugal, Republic of Korea, Russia, Spain, Switzerland, Thailand, United Kingdom of Great Britain and Northern Ireland, United States of America, and Uruguay

Household

2020 (56)
2021 (63)
2022 (10)

Domestic Dog

Canis lupus familiaris

Argentina, Bosnia and Herzegovina, Brazil, Canada, Colombia, Croatia, Denmark, Ecuador, Finland, France, Hong Kong SAR, India, Italy, Japan, Jersey, Mexico, Myanmar, Netherlands, Portugal, Republic of Korea, Spain, Switzerland, Thailand, the United Kingdom of Great Britain and Northern Ireland, United States of America, and Uruguay

Household

2020 (70)
2021 (61)
2022 (83)b

Domestic American Mink

Neovison vison

Canada, Denmark, France, Greece, Italy, Latvia, Lithuania, Netherland, Poland, Spain, Sweden

Farm

2020 [349]
2021 [32]
2022 [2]

Domestic Ferret

Mustela furo

United States of America
Slovenia

Household

2020 (1)
2021 (1)

Wild American Mink

Neovison vison

United States of America
Spain

Free range

2020 (no data)
2021 (2)

Western lowland Gorilla

Gorilla gorilla gorilla

United States of America
Spain

Zoo

2021 (7)
2022 (4)

White-tailed deer

Odocoileus virginianus

United States of America
Canada

Natural Park
Wild habitat (hunted)

2021 (31)

Binturong

Arctictis binturong

United States of America

Zoo

2021 (1)

Coatimundi

Nasua nasua

United States of America
Brazil

Zoo
Urban Park

2021 (3)

Fishing cat

Prionailurus viverrinus

United States of America

Zoo

2021 (1)

Tiger

Panthera tigris

Argentina
United States of America
Denmark
Indonesia
Sweden
United Kingdom of Great Britain and Northern Ireland

Animal sanctuary
Zoo
Wild animal exhibitor facility

2020 (1)
2021 (24)
2022 (4)

Lion

Panthera leo

United States of America, Croatia, Colombia, Estonia, Puerto Rico, Singapore, South Africa, Spain, Sweden

Zoo

2020 (2)
2021 (24)
2022 (1)

Puma

Puma concolor

United States of America
Argentina
South Africa

Wild animal exhibitor facility
Rescue center

2020 (2)
2021 (1)

Snow Leopard

Panthera uncia

United States of America

Zoo

2020 (3)
2021 (2)

Indian Leopard

Panthera pardus fusca

India

Free range

2021 (1)

Canada Lynx

Lynx canadensis

United States of America

Zoo

2021 (1)c

Spotted hyenas

Crocuta crocuta

United States of America

Zoo

2021 (2)d

Asian small-clawed otters

Aonyx cinereus

United States of America

Aquarium
Zoo

2021 (9)

Hamster

Unspecified

Hong Kong, SAR

Pet shop
Warehouse of pets

2022 (2)

Wild Eurasian River Otter

Lutra lutra

Spain

Free range

2021 (1)*

Hippopotamus

Unspecified

Belgium

Zoo

2022 (2)

Black-Tailed Marmoset

Mico melanurus

Brazil

Free range

2022 (1)*

Mule deer

Odocoileus hemionus

United States of America

Natural Park

2021 (1)

Antillean manatees

Trichechus manatus manatus

Brazil

Captive

2020 (2)*

Giant anteater

Myrmecophaga tridactyla

Brazil

Free range

2022 (1)

Mandrill

Mandrillus sphinx

United States of America

Zoo

2022 (1)

Monkey Squirrel

Saimiri sciureus

United States of America

Zoo

2022 (1)

Red fox

Vulpes vulpes

Switzerland

Zoo

2022 (1)

Cattle

Unspecified

India

Animal-rearing pockets

2021/2022 (15)

Buffalo

Unspecified

India

Animal-rearing pockets

2021/2022 (13)

Source: WOAH WAHIS, country reports and peer-reviewed journals3.
3 Information from preprints is not included in this table

a https://www.sciencedirect.com/science/article/abs/pii/S0168170222000016
b https://www.mdpi.com/1660-4601/19/21/14391
c APHIS/USDA
d APHIS/USDA
* Please see the respective articles under section “recent publications”.

Table 2. Animal species susceptibility to SARS-CoV-2 based on experimental infection studies

Animal species Scientific name (wild animals) Susceptibility Transmission to co-housed animals of same species

Raccoon dogs (reference)

Nyctereutes procyonoides

Yes

Yes

Red Fox (reference)

Vulpes vulpes

Yes

Not specified

Coyotes
(reference)

Canis latrans

No

-

Deer mice (reference)

Peromyscus maniculatus

Yes

Yes

Bank voles (reference)

Myodes glareolus

Yes

No

Bushy-tailed woodrats (reference)

Neotoma cinerea

Yes

Not specified

Laboratory BALB/c mice (reference)

 

Yes

Yes

White-tailed deer (reference)

Odocoileus virginianus

Yes

Yes

Ferret (reference)

Mustela furo

Yes

Yes

Egyptian fruit bat

Rousettus aegyptiacus

Yes

Yes

Striped skunks (reference)

Mephitis mephitis

Yes

Not specified

Zebra fish (reference)

Danio rerio

Yes

Not specified

Zebra mussel (reference1) (reference2)

Dreissena polymorpha

Yes

Not specified

Syrian hamsters

Mesocricetus auratus

Yes

Yes

Tree shrews (reference1) (reference2)

Tupaia belangeri chinensis

Yes

Not specified

Rhesus macaques (reference)

Macaca mulatta

Yes

Not specified

The crab-eating macaque (reference)

Macaca fascicularis

Yes

Not specified

Baboons (reference)

Papio hamadryas

Yes

Not specified

Common marmosets (reference)

Callithrix jacchus

Yes

Not specified

Cynomolgus macaques (reference)

Macaca fascicularis

Yes

Not specified

African green monkeys (reference)

Chlorocebus aethiops

Not susceptible

Not specified

Mosquitoes (reference1) (reference2

Aedes aegypti, Aedes. albopictus, Culex tarsalis and Culex quinquefasciatus

Not susceptible

-

Midge (reference)

Culicoides sonorensis

Not susceptible

-

Chicken – Duck – Geese – Turkey – Quail and Pigeon (reference)

-

Not susceptible

-

Pig (reference1) (reference2) (reference3)

-

Yes (Low susceptibility)

No

Cattle (reference1) (reference2)

-

Yes (Low susceptibility)

No

Horse (reference)

-

No

-

Sheep (reference)

-

Yes (Low susceptibility)

No2

Goat (reference1) (reference2)

-

Yes (Low susceptibility)

Not specified

Alpaca (reference)

-

No

-

Rabbit (reference)

-

Yes

Not specified

Cat (reference) - Yes Yes

Dog (reference)

-

Yes (Low susceptibility)

No

Sprague Dawley rats (reference)

Rattus norvegicus

Yes

Not specified

2 Though RNA detected in some in-contact animals but none of them seroconverted.

Vaccination in animals

  • The Toronto Zoo, Canada, has administered Zoetis vaccine to nearly 150 animals including primates, big cats, swine, bats and Mustelidae. Other zoos in Canada such as the Assiniboine Park Zoo in Winnipeg, Manitoba Province have also carried out vaccination in susceptible animals. [reference 1; reference 2]
  • An experimental vaccination study was performed in juvenile cats using a spike protein-based subunit SARS-CoV-2 vaccine. The two adjuvanted vaccine formulations protected juvenile cats against virus shedding from the upper respiratory tract and viral replication in the lower respiratory tract and hearts. [reference]
  • The Finnish Fur Breeders’ Association (FIFUR) and the University of Helsinki developed the Furcovac vaccine to allow for a vaccination roll out in mink farms, targeting about 50 000 animals. The Finnish Food Safety Authority provided a conditional license for the vaccine. [reference]
  • A COVID-19 vaccine for animals is being developed jointly by Applied DNA Sciences and Evvivax. [reference]
  • The United States based veterinary pharmaceutical company Zoetis has developed a COVID-19 inactivated vaccine uniquely formulated for animal species. The vaccine has already been used in multiple zoos in -United States since 2021 targeting multiple animal species including great apes, tigers, cheetahs, snow leopards, mountain lions, ferrets, black bears, and grizzly bears, among others. [reference 1; reference 2]
  • Zoetis published a study assessing vaccine efficacy in cats and dogs [reference]. Vaccines were efficacious in mounting an immune response as judged by the generation of serum neutralizing antibodies in-vitro
  • Zoetis has started the process of donating around 26,000 doses of its COVID-19 vaccine for animals to zoos and animal sanctuaries in 13 countries, including the United States and Canada [reference]
  • The Federal Center for Animal Health (FGBI ARRIAH) in the Russian Federation developed an inactivated vaccine named Carnivac-Cov that targets cats, dogs, minks, and foxes [reference]. Several countries worldwide have already held negotiations with the manufacturer for the registration and supply of the drug to their countries [reference 1; reference 2; reference 3].

Recent publications

Arteaga, F. L., Jodar, M. N., Mondino, M., Portu, A., Boeris, M., Joly, […] & Bratanich, A. (2022). An outbreak of SARS-COV-2 in big hairy armadillos (chaetophractus villosus) associated with gamma variant in Argentina three months after being undetectable in humans. bioRxiv 2022.08.23.503528. [reference]. SARS-CoV-2 Gamma variant infection confirmed by RT-PCR in four specimens of Chaetophractus villosus (big hairy armadillo/armadillo peludo) in Argentina three months after its last detection in humans, raising the question of potential unidentified viral reservoirs. The sequencing data from three animals clearly points to a single transmission event to the animals. The nonsynonymous mutations identified in Chaetophractus villosus have not been reported previously in other animals infected naturally or experimentally with SARS-CoV-2 Gamma variant.

Bae, D. Y., Tark, D., Moon, S. H., Oem, J. K., Kim, W. I., […] & Cho, H. S. (2022). Evidence of Exposure to SARS-CoV-2 in Dogs and Cats from Households and Animal Shelters in KoreaAnimals: an open access journal from MDPI12(20), 2786. [reference]. SARS-CoV-2 viral RNA was detected in 2 cats out of 1018 pets (672 dogs and 346 cats). A total of 16 dogs (2.38%) and 18 cats (5.20%) tested positive using ELISA, and 14 dogs (2.08%) and 17 cats (4.91%) tested positive using PRNT. Antigens of- and/or antibodies to SARS-CoV-2 were detected in the animals regardless of whether the companion family was infected; this was the case in animal shelters, which have been regarded as relatively safe from transmission.

Caserta, L., Martins, M., Butt, S., Hollingshead, N., Covaleda, L., […] & Diel, D. (2022). White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern. bioRxiv 2022.09.02.506368. [reference]. A total of 5,462 retropharyngeal lymph node samples collected from free-ranging hunter-harvested White-tailed deer during the hunting seasons of 2020 and 2021 and tested for SARS-CoV-2 detection by real-time RT-PCR. The virus RNA was detected in 17 samples (0.6%) from 2020 and in 583 (21.1%) samples from 2021, the gene sequence analysis from 164 samples demonstrated the presence multiple SARS-CoV-2 lineages as well as the co-circulation of three variants of concern (Alpha, Gamma, and Delta). The analyzed data suggested the occurrence of multiple spillover events (human-to-deer) of the Alpha and Delta variants with subsequent deer-to-deer transmission of the viruses. Detection of Alpha and Gamma variants in white tailed deer long after their broad circulation in humans in suggests that this animal species may serve as a wildlife reservoir for variants of concern no longer circulating in humans.

Choga, W., Letsholo, S., Marobela-Raborokgwe, C., Mazwiduma, M., Maruapula, D. […] & Moyo, S. (2022). Near-complete genome of SARS-CoV-2 Delta variant of concern identified in a symptomatic dog (Canis lupus familiaris) in BotswanaAuthorea preprint. [reference]. This gene sequencing study reports on the detection of SARS-CoV-2 lineage AY.43 of the Delta variant of concern in sample collected from a symptomatic dog in Botswana.

Fernández-Bastit, L., Roca, N., Romero-Durana, M., Rodon, J., Cantero, G., […] & Lorca-Oró, C. (2022). Susceptibility of Domestic Goat (Capra aegagrus hircus) to Experimental Infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) B.1.351/Beta VariantViruses14(9). [reference]. This experimental infection study demonstrated low susceptibility of goats to SARS-CoV-2 Beta variant, the virus RNA was detected in nasal swabs and tissues by RT-qPCR and/or immunohistochemistry, and seroneutralisation was confirmed via ELISA and live virus neutralisation assays. However, the viral amount and tissue distribution suggest a low susceptibility of goats.

Goldberg, A., Langwig, K., Marano, J., Sharp, A., Brown, K., Ceci, A. […] & Hoyt J. (2022). Wildlife exposure to SARS-CoV-2 across a human use gradient. bioRxiv 2022.11.04.515237. [reference]. 18 different wildlife species in the Eastern U.S. were samples for the detection of exposure to SARS-CoV-2. Using quantitative reverse transcription polymerase chain reaction and whole genome sequencing, SARS-CoV-2 RNA detected in the Virginia opossum and had equivocal detections in six additional species. Species considered human commensals like squirrels, and raccoons had high seroprevalence, ranging between 62%-71%. The whole genome sequence of the SARS-CoV-2 variant infecting the opossum revealed several mutations shared within the Omicron clade as well as unique amino acid substitutions not previously identified in other human-infected SARS-CoV-2 virus at the time of collection

Hoppe, J. M., Füeßl, L. U., Hartmann, K., Hofmann-Lehmann, R., Graf, A., […] & Muenchhoff, M. (2022). Secondary zoonotic dog-to-human transmission of SARS-CoV-2 suggested by timeline but refuted by viral genome sequencingInfection, 1–7. Advance online publication. [reference]. This study report on a 44-year-old COVID-19 human patient, who reported that his dog displayed respiratory signs shortly prior to his infection. The dog tested real-time-PCR positive for SARS-CoV-2 RNA and the timeline of events suggested a transmission from the dog to the patient.

Kaczorek-Łukowska, E., Wernike, K., Beer, M., Wróbel, M., Małaczewska, J., […] & Siwicki, A. K. (2022). High Seroprevalence against SARS-CoV-2 among Dogs and Cats, Poland, 2021/2022Animals: an open access journal from MDPI12(16), 2016. [reference]. Serum samples were collected from a total of 388 dogs and 243 cats from three veterinary clinics in Poland between October 2021 and February 2022, when the country was during the fourth wave of viral spread. 18.9% of the feline sera and 16.0% of the canine sera tested positive for SARS-CoV-2 antibodies using ELISA and immunofluorescence assay. This relatively high seroprevalence among randomly selected animals is most likely related to the high case numbers in the human population and indicates a continuous occurrence of trans-species virus transmissions from infected owners to their pets.

Krupińska, M., Borkowski, J., Goll, A., Nowicka, J., Baranowicz, K., […] & Grzybek, M. (2022). Wild Red Deer (Cervus elaphus) Do Not Play a Role as Vectors or Reservoirs of SARS-CoV-2 in North-Eastern PolandViruses, 14(10), 2290. [reference]. In this study serum and nasopharyngeal swabs were collected from 90 red deer shot by hunters in five hunting districts in Poland. None of the collected samples tested positive for anti-SARS-CoV-2 antibodies or SARS-CoV-2 RNA using immunofluorescent and real-time PCR with reverse transcription, respectively.

Lawton, K., Keller, S. M., Barnum, S., Arredondo-Lopez, C., Spann, K., Pusterla, N. (2022). Seroprevalence of SARS-CoV-2 in 1186 Equids Presented to a Veterinary Medical Teaching Hospital in California from 2020 to 2022Viruses, 14(11), 2497. [reference]. The aim of this study was to determine the seroprevalence of SARS-CoV-2 and selected prevalence factors in equids presented to a Veterinary Medical Teaching Hospital over a two-year period using ELISA targeting the receptor binding domain of the SARS-CoV-2 spike protein. 42/1186 (3.5%) horses had detectable SARS-CoV-2 antibodies. Amongst the prevalence factors investigated, only seasonality (spring) was associated with a greater frequency of seropositivity. Horses with medical and surgical complaints were more likely to test seropositive to SARS-CoV-2.

Liew, A., Carpenter, A., Moore, T., Wallace, R., Hamer, S., [...]& Behravesh,C. (2022) Clinical and epidemiologic features of SARS-CoV-2 in dogs and cats compiled through national surveillance in the United States. Researchsquare preprints. [reference]. This study aimed to characterizing the clinical and epidemiologic features of SARS-CoV-2 in companion animals detected in the U.S. Data on 204 companion animals (109 cats, 95 dogs) with confirmed SARS-CoV-2 infections between March 2020 and December 2021 were analyzed. Among dogs and cats identified through passive surveillance, 94% (n=87) had reported exposure to a person with COVID-19 before infection. Clinical signs of illness were present in 74% of pets identified through passive surveillance and 27% of pets identified through active surveillance. Duration of illness averaged 15 days in cats and 12 days in dogs. The average time between human and pet onset of illness was 10 days. Viral nucleic acid was first detected at 3 days post exposure in both cats and dogs. Antibodies were detected starting 5 days post exposure and titers were highest at 9 days in cats and 14 days in dogs.

Mahajan, S., Karikalan, M., Chander, V., Pawde, A. M., Saikumar, G., […] & Sharma, G. K. (2022). Detection of SARS-CoV-2 in a free ranging leopard (Panthera pardus fusca) in IndiaEuropean journal of wildlife research68(5), 59. [reference]. This study reports an incidence of natural infection of SARS-CoV-2 in free-ranging Indian leopard (Panthera pardus fusca). The case was detected during routine screening. Post-mortem and laboratory examination suggested virus-induced interstitial pneumonia. Viral genome could be detected in various organs including brain, lung, spleen, and lymph nodes by real-time PCR. Whole-genome sequence analysis confirmed infection with Delta variant.

Marques, A. D., Sherrill-Mix, S., Everett, J. K., Adhikari, H., Reddy, S., […] & Anis, E. (2022). Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in PennsylvaniamBio13(5), e0210122. [reference]. 123 nasal swab samples were collected during 2021 from hunter-harvested deer and injured deer within hours of death. 20 (16.3%) samples were positive for SARS-CoV-2 by RT-qPCR. Seven whole genome sequences were obtained, together with six more partial spike gene sequences. These annotated as alpha and delta variants, the first reported observations of these lineages in deer, documenting multiple new jumps from humans to deer. The alpha lineage persisted in deer after its displacement by delta in humans, and deer-derived alpha variants diverged significantly from those in humans, consistent with a distinctive evolutionary trajectory in deer.

Montagutelli, X., Decaudin, B., Beretta, M., Mouquet, H., Simon-Lorière, E. (2022). SARS-CoV-2 infection in domestic rats after transmission from their infected owner. bioRxiv 2022.10.13.512053. [reference]. This study reports serological evidence of SARS-CoV-2 transmission from a COVID-19 symptomatic individual to two domestic rats which tested IgG and IgM ELISA positive against Wuhan and Omicron spike antigens.

Moreno, A., Lelli, D., Trogu, T., Lavazza, A., Barbieri, I., […] & Giorgi, M. (2022). SARS-CoV-2 in a Mink Farm in Italy: Case Description, Molecular and Serological Diagnosis by Comparing Different TestsViruses14(8), 1738. [reference]. This study describes SARS-CoV-2 infection in minks on an Italian farm after one of the farm workers tested positive by RT-PCR. Diagnostic tests detected only four weak PCR-positive mink samples out of 1909 samples tested, but 100% (n=74) of sera were positive for SARS-CoV-2 antibodies. The phylogenetic analysis of two SARS-CoV-2 sequences from two minks and the sequence of the worker showed that they belonged to different clades.

Padilla-Blanco, M., Vega, S., Enjuanes, L., Morey, A., Lorenzo, T., […] & Rubio-Guerri, C. (2022). Detection of SARS-CoV-2 in a dog with hemorrhagic diarrheaBMC veterinary research18(1), 370. [reference]. This study detected SARS-CoV-2 Alpha variant of concern in a fecal sample from a dog presenting hemorrhagic diarrhea with negative tests for candidate microbial pathogens.

Panei, C. J., Bravi, M. E., Moré, G., De Felice, L., Unzaga, J. M., […] & Fuentealba, N. A. (2022). Serological evidence of SARS-CoV-2 infection in pets naturally exposed during the COVID-19 outbreak in ArgentinaVeterinary immunology and immunopathology254, 110519. Advance online publication. [reference]. The present study aimed to detect SARS-CoV-2 antibodies by ELISA and virus neutralization test in pets owned by previously confirmed as COVID-19 human cases in Argentina. Three out of the seven cats and 14 out of the 31 dogs were positive for SARS-CoV-2 by ELISA, and one cat and six dogs showed the presence of neutralizing antibodies.

Pickering, B., Lung, O., Maguire, F., Kruczkiewicz, P., Kotwa, J. […] & Bowman, J.  (2022). Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission. Nat Microbiol 7, 2011–2024. [reference]. This study conducted in Ontario, Canada during November and December 2021 (n = 300 deer) and identified a highly divergent lineage of SARS-CoV-2 (B.1.641) in white-tailed deer. This lineage is one of the most divergent SARS-CoV-2 lineages identified so far, with 76 mutations (including 37 previously associated with non-human mammalian hosts). From a set of five complete and two partial deer-derived viral genomes the phylogenomic, recombination, selection and mutation spectrum analyses provided evidence for evolution and transmission in deer and a shared ancestry with mink-derived virus. The analysis also revealed an epidemiologically linked human infection.

Robinson, SJ., Kotwa, JD., Jeeves, S., Himsworth, C., Pearl, D., […] & Jardine C. 2022. Surveillance for SARS-CoV-2 in Norway rats (Rattus norvegicus) from southern Ontario. Authorea Preprints; PPR539706. [reference]. 224 rats were submitted by collaborating pest control companies from October 2019 to June 2021, of them 202 samples were collected prior to the emergence of VOCs, and 22 were collected while the Alpha variant was the predominant circulating VOC in humans. Nasal turbinate and small intestinal tissue samples were analyzed for SARS-CoV-2 RNA by RT-PCR. Thoracic cavity fluid samples were tested for neutralizing antibodies using a surrogate virus neutralization test (sVNT), the plaque reduction neutralization test (PRNT) was conducted on presumptive positive samples. SARS-CoV-2 RNA was not detected in any samples tested while two out of eleven samples positive by sVNT had neutralizing antibodies by PRNT.

Solís-Hernández, M., Freddy, D., Roxana, P., Nadia, C., Liljehult-Fuentes, F., […] & Hernández, J. (2022). Neutralizing antibodies against the SARS-CoV-2 ancestral strain and Omicron BA.1 subvariant in dogs and cats in Mexico. Authorea. August 19. [reference]. A total of 1111 samples from dogs (n=1052) and cats (n=59) were collected in different regions of Mexico, and the presence of neutralizing antibodies was evaluated by a plaque reduction neutralization test (PRNT90) and microneutralization. The results showed that 15.25% (9 of 59) of cats and 2.85% (30 of 1052) of dogs are seropositive against the ancestral strain of SARS-CoV-2. However, the analysis of neutralizing antibodies against Omicron BA.1 in cats showed the same percentage of positive animals but a reduction in the titer while in the case of dogs, 2.09% (22 of 1052) showed neutralizing antibodies against Omicron BA.1.

Villanueva-Saz, S., Giner, J., Palomar, A. M., Gómez, M. A., Põdra, M., […] & Fernández, A. (2022). No Evidence of SARS-CoV-2 Infection in Wild Mink (Mustela lutreola and Neogale vison) from Northern Spain during the First Two Years of PandemicAnimals: an open access journal from MDPI12(15), 1971. [reference].  From January 2020 to February 2022, a total of 162 animals (127 European mink and 35 American mink) were sampled to evaluate the presence of SARS-CoV-2. Antibodies against the SARS-CoV-2 were not found in the serum samples (n = 126) analysed by ELISA nor was the virus amplified by RT-qPCR (n = 160 swabs).

Villanueva-Saz, S., Martínez, M., Giner, J., González, A., Tobajas, A. P., […] & Fernández, A. (2022). A cross-sectional serosurvey of SARS-CoV-2 and co-infections in stray cats from the second wave to the sixth wave of COVID-19 outbreaks in SpainVeterinary research communications, 1–15. [reference]. This study analyzed the seroprevalence variation of SARS-CoV-2 in stray cats from different waves of outbreaks using ELISA followed by confirmation by serum virus neutralization assay. A seropositivity of 1.57% (n=3) was observed.

Wang, Y., Lenoch, J., Kohler, D., DeLiberto, T. J., Tang, C., […] & Wan, X. F. (2022). SARS-CoV-2 exposure in Norwegian rats (Rattus norvegicus) from New York CitybioRxiv, 2022.11.18.517156. [reference]. This field and experimental infection study evaluated SARS-CoV-2 exposure among 79 rats captured from New York City during the fall of 2021. The results showed that 13 (16.5%) rats tested IgG or IgM positive by ELISA however, none of them tested positive by microneutralization assays against the B.1 lineage and the Alpha and Delta variant. Four (5%) of the tissue samples were positive by qRT-PCR. To investigate whether Alpha, Delta, or Omicron variants are capable of infecting rats, these variants were intranasally inoculated in 6-week-old wild-type Sprague Dawley rats, the results showed that Alpha, Delta, and Omicron variants can cause robust infections in the inoculated rats, including high level replications in the upper and lower respiratory tracts and induction of both innate and adaptive immune responses. Additionally, the Delta variant resulted in the highest infectivity.

FAO publications

Global level
  • FAO takes part in regular WHO virus evolution group meetings to discuss latest findings on SARS-CoV-2 variants of interest and variants of concern.
  • FAO is in the process of designating Reference Centres for Zoonotic Coronaviruses. To date, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe) and Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise Giuseppe Caporale (IZSAM), Italy (joint center), the Federal State-Financed Institution “The Federal Center for Animal Health” (FSVPS-FGBI ARRIAH), Russian Federation , CSIRO Australian Centre for Diseases Preparedness (ACDP), Australia, and Ohio State University Infectious Diseases Institute (OSU-IDI), USA have been appointed. Furthermore,  Friedrich-Loeffler-Institut (FLI),Germany designated as Reference Centre for Emerging Zoonotic Pathogens and High Biosecurity/ Biocontainment Facilities. On 7 March 2022, the Tripartite Organization (FAO/ WHO/WOAH) issued a joint statement on the prioritization of monitoring SARS-CoV-2 infection in wildlife and preventing the formation of animal reservoirs. [reference]
  • FAO presented the SARS-CoV-2 guidance in animals during the One Health event organized by the University of Nanjing, China on 9 December 2021.
  • FAO attended the WHO virtual global workshop on enhancing sequencing for SARS-CoV-2 held on 19 March 2021.
  • The FAO/WOAH advisory group on SARS-CoV-2 evolution group meets regularly to discuss latest information available regarding disease situation updates and SARS-CoV-2 evolution in animal populations.
  • FAO established a Letter of Agreement with Hong Kong University for MERS-CoV and SARS-CoV-2 testing and capacity building for project countries.
  • FAO HQ supported the elaboration of Letters of Agreement between FAO SNG and veterinary authorities in United Arab Emirates to implement the FAO recommendations to investigate SARS-COV-2 transmission to in-contact farmed and companion animals.
  • The Joint FAO/IAEA Centre (Nuclear Techniques in Food and Agriculture) (CJN) is working, through its veterinary laboratory network in 69 countries, to support diagnosis of SARS-CoV-2 in animals and monitoring of virus contamination in the environment.
Regional and national level

Within FAO’s COVID-19 Recovery and Response Programme, several projects are already in place as part of Preventing the Next Zoonotic Pandemic (PNP), that help countries to better prevent and mitigate risks related to SARS-CoV-2 at the animal-human interface and build national capacities in pandemic preparedness (see below for details).

Regional level

  • FAO Regional Office for Asian and the Pacific (RAP):
    • Strengthening regional capacities to address COVID-19 impacts on animal health sector in East and Southeast Asia [April 2020 – September 2022]
  • FAO Regional Office for Africa (RAF):
    • Strengthening regional capacities to address negative impacts of COVID-19 on the animal health sector in Africa [June 2020 - June 2022].
    • Support project for COVID-19 case detection and emergency response along livestock value chains in Cameroon [July 2020 - March 2021].

Through these projects and others, FAO is supporting countries in West and Central Africa since the beginning of the pandemic in mitigating negative impacts of COVID-19 by:

    • Strengthening national animal disease surveillance systems through joint risk assessments at the animal-human-environment interface and trainings on field investigation, sample collection, shipment and transportation [since October 2020].
    • Improving COVID-19 testing and reinforcing veterinary laboratories as effective tools for the detection of animal diseases. For instance, in Ghana, national veterinary laboratories actively supported public health laboratories in COVID-19 testing. FAO ECTAD Ghana also supported the installation of a Laboratory Information Management System (SILAB/LIMS) One Health module at the Accra Veterinary Laboratory to improve management of COVID-19 samples [since October 2020].
    • Assisting the Governments such as in Cameroon to secure a Technical Cooperation Programme project to support COVID-19 detection and emergency response along the livestock value chain in Cameroon [since July 2020].

National level

  • Cameroon:
    • COVID-19 cases detection and reporting in livestock value chain actors in North-West and South-West regions, Cameroon [February – April 2021]
    • Support project for COVID-19 cases detection and emergency response along livestock value chain in Cameroon [July 2020 – March 2021].
    • Risk communication and community engagement plan for COVID-19 control, was developed and validated [March 2021].
  • Cote d’Ivoire:
    • As part of the surveillance for COVID-19, FAO supported the Department of Veterinary Services (DVS) in the detection, investigation, and follow-up testing of SARS-CoV-2 in domestic animals in contact with COVID-19 patients. Four veterinary clinics were involved in sample collection from animals received in care. A total of 52 samples were collected in four veterinary clinics and all were tested negative at Pasteur Institute of Cote d'Ivoire (IPCI) [September 2021].
    • In collaboration with the national One Health Platform FAO conducted a joint risk assessment using a One Health approach (MoL , MoH and MoE) on COVID-19 and Highly Pathogenic Avian Influenza [October 2021].
  • Ghana:
    • A training was held for staff of the Accra Veterinary Laboratory on dissemination of existing biosecurity and biosafety guidelines and standard operating procedures for SARS-CoV-2 testing in Veterinary Laboratories [May 2021].
    • Provision of 11 000 units of filtering face piece (FFP3) respirators on 3 December 2020 to the Ministry of Health in response to a request from the Government of Ghana, which aimed to protect health workers in the Ghana Health Service from COVID-19. This donation came at a time when the country was facing a second wave of the COVID-19 pandemic [December 2020].
    • A two-day advocacy awareness training was held for 30 multi-disciplinary stakeholders in the food value chains on the impacts of the COVID 19 pandemic on food security/nutrition and livelihoods [March 2021].
    • A three-day training workshop “Training of bushmeat traders, hunters and wildlife exporters in Kumasi and Accra to create awareness on COVID-19 and other related Priority Zoonotic Diseases (PZDs) of wildlife with potential to spill over to humans from bush meat traders and consumers” was held in collaboration with the Veterinary Service Directorate (VSD) of the Ministry of Food and Agriculture (MOFA), Wildlife Division of the Forestry Commission, Food and Drugs Authority (FDA), Environmental Health Department (EHD), Ghana Health Service, and Ghana Police Service (GPS) [April 2021]
    • Improving COVID-19 testing by reinforcing veterinary laboratories (see under ‘Regional level’).
  • Guinea: A total of 1 116 biological samples from 244 animals of various species (bat, rodent, swine and small ruminants) in 13 human-animal-environment interfaces were collected and all tested negative for Ebola and Marburg virus as well as for SARS-CoV-2 [May - June 2021].
  • Liberia: Training and mentorship of staff on Biosafety and Biosecurity including COVID-19 bio-risk management [March 2022].
  • Nigeria:
    • A study was conducted to evaluate COVID-19-related risk communication; results indicated no COVID-19 related risk communication messaging was conducted with animal health professionals, even though there are efforts for other zoonoses. A suggestion was made to engage the One Health Risk Communication pillar to address this deficiency [June - July 2021].
    • A workshop was held to discuss biosecurity and biosafety; guidelines and SOPs for COVID-19 were disseminated and discussed to establish a unified set of national guidelines [July 2021].
  • Senegal:
    • In collaboration with the national One Health Platform FAO conducted a joint risk assessment using a One Health approach (MoL , MoH and MoE) on Covid-19 and Highly Pathogenic Avian Influenza [February - April 2021].
    • Surveillance and research activities at human-wildlife-livestock-ecosystem interface and their results were mapped and shared during a workshop with the OH platform to enhance multisectoral collaboration [June 2020 - July 2021].
    • Guidelines elaborated by the National Park Direction were updated and disseminated, including Information, Education and Communication (IEC) materials for various audiences and stakeholders [February - April 2021].
    • National Veterinary Laboratory readiness for SARS-COV-2 testing was assessed using the FAO Laboratory Mapping tools (LMT-Core, LMT-safety modules and LMT-COVID) and a Biorisk assessment was conducted, ensuring that capacities of laboratories are built to handle (collect, transport, store) samples with appropriate levels of biosecurity and biosafety of SARS-COV-2 testing [February - April 2021].
  • Mali, Mauritania, Niger, and Senegal: IESA - Mitigating the effects of Covid-19 on pastoral communities in West Africa [October 2020 – October 2022].
  • Papua New Guinea: Emergency support to prevent and mitigate the impact of COVID-19 along the agricultural value chain [April 2021 – March 2022].
  • Rwanda: TCPF: Support to Fostering the One Health Operationalization in Rwanda [May 2021 – April 2023].
  • China: Emergency response to mitigate the impact of coronavirus (COVID-19) on the most vulnerable persons in rural areas in China [March 2020 – December 2022]
  • Sultanate of Oman: Understanding and mitigating the risks of SARS-CoV-2 transmission from COVID-19 human patients to in-contact farmed and companion animals [June 2021 – December 2022].
    • Collection of serum samples from 617 animals including camels, cattle, sheep and goats has been completed in June 2022, and the sera were submitted to the virology laboratory of Hong Kong University for testing using surrogate virus neutralization test; positive results (if any) will be confirmed by another assay.
    • The laboratory testing was completed in August 2022 at the virology laboratory of the Hong Kong University. Sera of six animals, representing four species (cattle, camel, sheep, and goat), tested positive by both surrogate virus neutralization test and the plague reduction neutralization test 50.
  • United Arab Emirates:
    • Detection of potential recombination of MERS-CoV with SARS-CoV-2 or other Coronaviruses in dromedary camels [October 2021 – April 2022].
    • Understanding and mitigating the risks of SARS-CoV-2 transmission from COVID-19 human patients to in-contact farmed and companion animals [December 2021 - December 2022].
    • The laboratory testing was completed in September 2022 at the animal health laboratory of the Abu Dhabi Agriculture and Food Safety Authority (ADAFSA). Sera of 13 animals, representing three species (sheep, goats, and captive gazelles), had positive ELISA results, however, none of them tested positive by the surrogate virus neutralization test. All collected nasal swab samples tested negative for SARS-CoV-2 RNA by RT-PCR. However, all collected sera of camels, tested for MERS CoV-Ab using ELISA, revealed that 164 of the 181 samples were positive (90.6%).
Next issue: 7 March 2023
The disease situation updates are produced by the FAO Emergency Prevention System for Animal Health (EMPRES-AH) as part of its mission to increase global disease intelligence.
Disclaimer

Information provided herein is current as of the date of issue. Information added or changed since the last SARS-COV-2 animal situation update appears in orange. Human cases are depicted in the geographic location of their report. For some cases, exposure may have occurred in one geographic location but reported in another. For cases with unknown onset date, reporting date was used instead. FAO compiles information drawn from multiple national (Ministries of Agriculture or Livestock, Ministries of Health; Centers for Disease Prevention and Control [CDC]) and international sources (World Health Organization [WHO], World Organisation for Animal Health [WOAH]) as well as peer-reviewed scientific articles and preprints. FAO makes every effort to ensure, but does not guarantee, accuracy, completeness or authenticity of the information. The boundaries and names shown and the designations used on these map(s) do not imply the expression of any opinion whatsoever on the part of FAO concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers and boundaries. Dashed lines on maps represent approximate border lines for which there may not yet be full agreement.

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