SARS-CoV-2 in domestic and wild animals:
viral characteristics, genetics, epidemiology
and transmission
SARS-CoV-2 en animales domésticos y silvestres:
caracterÃsticas virales, genéticas, epidemiologÃa y
transmission
Roberto Darwin Coello-Peralta
1
Sandra Gabriela Parra-Guayasamin
2
Diego MartÃn Cushicóndor-Collaguazo
3
Estefania Ortega
4
Betty Pazmiño-Gómez
5
Abstract: COVID-19 is a global pandemic of zoonotic origin that has
affected more than 620 million people and is caused by a new
coronavirus called SARS-CoV-2. This is a compilation of recent
literature on the characteristics, genome, epidemiology, transmission,
interspecies transmission, interspecies barrier jumping, genetic
characteristics and evolutionary potential of this virus. Some evidence
suggests that the virus uses ACE2 to infect various wild animals such
as bats, ferrets, pangolins, monkeys, mink, snakes, tigers and lions;
and domestic animals such as cats, dogs, cows, buffaloes, goats, sheep
and pigeons. However, they can jump the species barrier and infect
humans. In addition, coronaviruses can adapt to any ecosystem,
especially in wild environments, where they can be maintained
through a transmission network in various wild and domestic animals,
but they can break paradigms at any time. SARS-CoV-2 has caused a
great impact on health systems and economies on all continents, but
it is also causing radical damage, changes in habits and common
lifestyles.
Keywords: SARS CoV-2, Zoonosis, Domestic and Wild Animals
Published
Instituto Tecnológico Superior Edwards
Deming. Quito – Ecuador
Periodicity
January-March
Vol. 2, Num. 1, 2023
http://centrosuragraria.com/index.php/revista
pp. 62-75
Dates of receipt
Received: May 11, 2022
Approved: October 15, 2022
Correspondence author
roberto.coellope@ug.edu.ec
Creative Commons License
Creative Commons License, Attribution-
NonCommercial-ShareAlike 4.0
International.https://creativecommons.org/lice
nses/by-nc-sa/4.0/deed.es
1 Magister en MicrobiologÃa-mención Biomédica,
Docente-Investigador de la FMVZ de la Universidad de
Guayaquil, Guayaquil, Ecuador,
roberto.coellope@ug.edu.ec, https://orcid.org/0000-
0001-5152-2843
2 Master's Degree in Small Animal Medicine, Professor-
Researcher of the Faculty of Veterinary Medicine,
University of Guayaquil (UG), Guayaquil, Ecuador,
sandra.parrag@ug.edu.ec, https://orcid.org/0000-0003-
2410-7999
3 Master in Poultry Production and Health, Teacher-
Researcher of the FMVZ of the University of Guayaquil,
Guayaquil, Ecuador, cdmcushicondor@outlook.com,
https://orcid.org/0000-0002-5238-673X
4 Master in Microbiology, Professor-Researcher, Faculty
of Biological Sciences, Universidad Central del Ecuador,
Quito, Ecuador, estefania1058@gmail.com,
https://orcid.org/0000-0003-3885-4186.
5 Master in Microbiology - Biomedical mention,
Professor-Researcher of the Faculty of Health Sciences,
Universidad Estatal de Milagro (UNEMI), Milagro,
Ecuador, bpazminog@unemi.edu.ec,
https://orcid.org/0000-0002-2611-2428
January - March vol. 2. Num. 1 - 2023
63
Resumen: COVID-19 es una pandemia global de origen zoonótico
que ha afectado a más de 620 millones de personas, es causada por el
nuevo coronavirus llamado SARS-CoV-2. El presente, se trata de una
recopilación de información bibliográfica reciente sobre las
caracterÃsticas, genoma, epidemiologÃa, transmisión, transmisión
entre especies, salto de barrera entre especies, caracterÃsticas
genéticas y potencial evolutivo del mencionado virus. Algunas
evidencias sugieren que el virus usa ACE2 para infectar a varios
animales salvajes como: murciélagos, hurones, pangolines, monos,
visones, serpientes, tigres y leones; y animales domésticos como:
gatos, perros, vacas, búfalos, cabras, ovejas y palomas. Sin embargo,
pueden saltar la barrera de las especies e infectar a los humanos.
Además, los coronavirus pueden adaptarse a cualquier ecosistema,
sobre todo en ambientes silvestres, donde pueden mantenerse a través
de una red de transmisión, en diversos animales salvajes y
domésticos, pero estos en cualquier momento pueden romper
paradigmas. El SARS-CoV-2 a causado un gran impacto en los
sistemas de salud y las economÃas de todos los continentes, pero
también están provocando daños radicales, cambios en los hábitos y
estilos de vida comunes.
Palabras clave: SARS CoV-2, Zoonosis, Animales domésticos y
silvestres
1. Introduction
A new coronavirus (SARS-CoV-2) that causes severe acute respiratory
syndrome in humans was determined for the first time in Wuhan in
December 2019 (Sit et al., 2020); According to the World Health
Organization (WHO) and the Pan American Health Organization
(PAHO), in 2020, reported that COVID-19 is a pandemic and an
international public health problem, with a mortality rate of up to 12%
(given in the Wuhan epicenter) (Mizumoto & Chowell, 2020). So far,
the dynamics of the new coronavirus are estimated at a transmission
rate between R0 2.2 to 2.56; also, it is important to note that person-to-
person transmission and fomite transmission have been linked to the
spread of the disease (Sohrabi et al., 2020; Zhao et al., 2020).
As of October 14, 2022, more than 250 countries and territories have
been affected by SARS-CoV-2 and 620,878,405 people infected with
more than 6,543,143 deaths, with the European continent being the
most affected with almost 258 million cases, followed by the Americas
with 179 million cases. Countries such as the United States report
95,529,652 cases, Brazil 34,736,653 cases, Argentina 9,713,594 cases,
Colombia 6,308,558 cases, Chile 4,674,373 cases and Peru 4,150,121
cases (WHO, 2022). In the world, the pandemic has caused an
SARS-CoV-2 in domestic and wild animals: viral characteristics, genetics, epidemiology and
transmission
64
unprecedented shock, where countries were forced to ban travel and
create containment policies in order to mitigate the spread of the disease
(Paul et al., 2020).
This pandemic virus can persist on surfaces such as plastic, glass or
metal for up to nine days, but can be effectively inactivated by surface
disinfection procedures using products such as 70% ethanol, 0.5%
hydrogen peroxide and 0.1% sodium hypochlorite. However, SARS-
CoV-2 can remain infective for 14 days at 4°C and 2 days at 20°C in
wastewater (OIE, 2020).
Coronaviruses (CoV) mostly infect the respiratory tract, but can also
affect the digestive tract, and few viruses can spread to the kidneys,
liver or central nervous system. Some CoVs are endemic in domestic
animals in different countries, but three are pandemic that have
produced fatal cases in humans and they are: SARS-CoV-1, MERS-
HCoV and the most recent SARS-CoV-2 (Abdel & Abdelwhab, 2020).
It is important to note that the evolutionary history of coronaviruses
defines them as circulating viruses in mammals and birds; in the case,
SARS-CoV-2 originally comes from bats, then spreads to intermediate
hosts and then infects humans, who can then infect domestic animals,
establishing a transmission network; therefore, the identity of the
animal source of SARS-CoV-2 remains a key and urgent question to
know. In addition, stopping future outbreaks of this type and preventing
the transmission of zoonotic diseases to humans should be one of the
main research priorities; therefore, it is necessary to consider
appropriate eco-sanitary measures, to reduce viral transmission (Li X,
2020).
The objective of this article is to present a comprehensive review of the
current literature on characteristics, genome, epidemiology,
transmission, interspecies transmission, interspecies barrier jumping,
genetic characteristics, and evolutionary potential of SARS-CoV-2.
2. Materials and methods
SARS-CoV-2 belongs to the order: Nidovirales, family: Coronaviridae,
subfamily: Coronavirinae, genus: Betacoronavirus, subgenus:
Sarbecovirus, lineage "B", originating from bats; it is an enveloped,
January - March vol. 2. Num. 1 - 2023
65
spherical virus, 120 nm in diameter, has a large single-stranded RNA
genome of positive polarity, with a size of 30 Kb (Leroy et al., 2020)
(Figure 1). The viral genome produces 16 non-structural proteins (nsp1
to nsp16) and four structural proteins, such as: spike (S), envelope (E),
membrane (M) and nucleocapsid (N) (Figure 2) (Abdel & Abdelwhab,
2020; Chen, 2020).
The viral envelope consists of E and M proteins on which S is anchored.
This new coronavirus enters host cells using the binding domain (RBD)
of the S protein, which binds to the cellular receptor of angiotensin-
converting enzyme 2 (ACE2). And of the co-receptor and TMPRSS2.
The proportions of cells carrying ACE2 and TMPRSS2 are high in cats,
low in pigs, very rare in dogs, and absent in chickens. Recurrent severe
coronavirus infections for humans, originating from animals in the last
two decades, this indicates that future outbreaks of related or unrelated
Coronaviruses in humans are inevitable; for such a reason, there is an
urgent need for improved universal and antiviral vaccines against CoVs
(Abdel & Abdelwhab, 2020).
Currently, seven coronaviruses have been reported to infect humans, 3
of zoonotic origin associated with severe acute respiratory syndromes
(SARS-CoV, MERS-CoV, and now SARS-CoV-2), and four are
ubiquitous with seasonal circulation and mostly cause mild colds
(HKU1, NL63, OC43, and 229E) (Leroy et al., 2020). Of these seven
human coronaviruses, five are included within the genus beta-CoV,
while the other two (NL63 and 229E) belong to the genus alpha-CoV.
(Chen et al., 2020); in the case of canine respiratory coronavirus
(CRCoV), responsible for respiratory diseases in dogs, it belongs to the
genus beta-CoV and has 97% sequence similarity (of protein S) to that
of human coronavirus (OC43), probably due to genetic recombination
(Xu et al., 2020).
The most common CoV members infecting animals are infectious
bronchitis virus (IBV; γ-CoV) in chickens; porcine transmissible
gastroenteritis coronavirus (TGEV; α-CoV), porcine hemagglutinating
encephalomyelitis coronavirus (HEV; β-CoV) and porcine epidemic
diarrhea coronavirus (PEDV; β-CoV) in pigs; bovine CoV (BCoV, β-
CoV) in cattle; canine enteric coronavirus (CECoV; α-CoV) and canine
respiratory coronavirus (CRCoV; β-CoV) in dogs; feline coronavirus
(FCoV; α-CoV) in cats; and murine hepatitis virus (MHV; β-CoV) in
mice. Interestingly, HCoV-OC43 and bovine BCoV share 95% genetic
identity, indicating possible zoonotic transmission from cattle to
humans 100 years ago. The transmission of HCoV-OC43 from bovine
SARS-CoV-2 in domestic and wild animals: viral characteristics, genetics, epidemiology and
transmission
66
to human, and not from human to bovine, is supported by the presence
of a 290 nucleotide deletion in HCoV-OC43, which was absent in
BCoV, suggesting adaptive changes after jumping the species barrier to
humans (Abdel & Abdelwhab, 2020).
Figure 1. SARS CoV 2 coronavirus virion
Available at: https://viralzone.expasy.org/30?outline=all_by_species
Figure 2. SARS CoV 2 genome
Available at: https://viralzone.expasy.org/30?outline=all_by_species
January - March vol. 2. Num. 1 - 2023
67
3. Result
In a cohort study conducted after the emergence of COVID-19 between
January and March 2020 in Wuhan, China, a seroprevalence of 14.70%
was determined in cats; three cats with higher titers were owned by
three patients, indicating possible direct human-to-cat transmission
(Zhang et al., 2020). In Hong Kong between February 12 and March
25, SAR-COV-2 RNA was determined in 2 dogs, both canines
contracted the infection in households with infected humans; the first
dog was an old animal that appeared with symptoms associated with
renal and cardiac failure problems, ultimately died; the second dog did
not develop any clinical signs (Leroy et al., 2020).
On March 27, in Belgium, virus was determined by PCR in a
symptomatic cat with the presence of diarrhea, vomiting, and difficulty
breathing; three days later, viral RNA was identified in samples
collected from the oral, nasal, and rectal cavity of an asymptomatic cat
from Hong Kong; both cats were infected in households with humans
infected with the novel coronavirus (Leroy et al., 2020; Hossain et al.,
2020).
In the United States, on April 21, 2020, the CDC and the National
Veterinary Services Laboratories (NVSL) announced two cats with
respiratory signs and confirmed with the virus in New York, one of the
owners had COVID-19 and the other did not (Zhang et al., 2020).
Between April and May, in northern Spain, one of eight cats tested
positive for SARS-CoV-2 RNA in nasal swabs; the cat had contact with
an infected patient with severe COVID-19 symptoms (Abdel &
Abdelwhab, 2020). On the other hand, on May 2, in France, the first cat
infected with the virus was described and presented clinical signs of
respiratory and digestive problems; from which two samples were taken
from the animal: one from a negative nasal swab and another from a
rectal swab that curiously tested positive for viral RNA; the cat
belonged to a person with the disease (Hossain et al., 2020).
Similarly, the U.S. National Veterinary Services Laboratories,
announced on April 5, 2020, at a New York zoo, the first report of a
tiger infected with SARS-CoV-2, showing signs of respiratory illness,
such as dry cough and decreased appetite; however, the Wildlife
SARS-CoV-2 in domestic and wild animals: viral characteristics, genetics, epidemiology and
transmission
68
Conservation Society (WCS) announced on April 22 that all lions and
tigers at the zoo tested positive for viral RNA in fecal samples by PCR.
These animals were likely infected by a zookeeper who showed no
symptoms of the disease, but was actively spreading the virus (AVMA,
2020).
On the other hand, at the end of April, Dutch authorities reported
confirmed cases of SARS-CoV-2 in a dog owned by an owner with
COVID-19; in addition, viral infection was reported in: 3 cats and mink
living together on a farm (Delong, 2020); in the Netherlands, on May
7, 2020, several cases of infections were reported, in mink from four
different farms, with presence of gastrointestinal and respiratory
disease; the mortality rate was 1.2% to 2.4% and deaths were mainly
observed in pregnant females. In both cases, farm breeders tested
positive for the new coronavirus and it is believed that they were
sources of infection for mink and then mink-to-mink transmission
occurred and then the virus spread to domestic cats (Abdel &
Abdelwhab, 2020; Hossain et al., 2020).
Mattar & Gonzalez (2018) stated that, in Brazil, by RT-PCR, canine
coronavirus strains, similar to those found in other countries and
associated with pandemic severe acute respiratory syndrome were
described in tissue samples from five puppies that died as a
consequence of severe gastroenteritis.
In Ecuador Orlando (2021), out of 47 animals (dogs and cats) from 26
households, 13 animals (12 dogs and one cat) tested positive by PCR
for SARS-CoV-2.
The virus is generally transmitted through respiratory droplets emitted
by sneezing, coughing, talking or breathing, which can enter the body
through the nose, mouth and conjunctiva. Indirect transmission can also
occur through contamination of surfaces, fomites or feces, and
asymptomatic hosts can spread the virus through respiratory droplets
(Leroy et al., 2020). Also, kissing and licking pets are presumed to be
additional risk factors that facilitate virus transmission (Hossain et al.,
2020).
The structural and biochemical properties of the SARS-CoV-2 S
antigen allow it not only to have affinity for the human ACE2 receptor
but also for that of several species of domestic animals (dogs, cats, and
January - March vol. 2. Num. 1 - 2023
69
ferrets) and farm animals (cows, sheep, pigs, orangutans, monkeys, and
horses) (Sun et al., 2020; Hossain et al., 2020; Andersen et al., 2020).
Consequently, many animals could become infected with this new
coronavirus and then act as intermediate hosts in the spread of the virus.
In the context of the COVID-19 pandemic to the present, the possibility
of cats and dogs becoming infected but not participating in the spread
of the virus must be addressed (Hossain et al., 2020).
Although there is no evidence that domestic animals can transmit the
virus to humans, Shi and collaborators (2020) describe through
experiments carried out in cats and ferrets infected with SARS-CoV-2
strains, the presence of: virus detection, specific respiratory symptoms
and viral transmission from infected cats to healthy cats through
respiratory droplets and respiratory tract. In addition, similar
experiments in dogs showed that they are less susceptible to the new
coronavirus (Fig. 3). However, pigs, chickens and ducks were not
susceptible to the virus; therefore, no viral RNA was detected and these
animals were seronegative (Shi et al., 2020; McNamara et al., 2020).
It is important to note that SARS-CoV-1 and SARS-CoV-2
coronaviruses are two closely related viruses of zoonotic origin with a
high capacity to cross species barriers. Studies of viral sequences
related to this new coronavirus in various species of Rhinolophus bats
and Malayan pangolins (Manis javanica), have led to the conclusion
that the zoonotic origin of SARS-CoV-2 is from the bat and used the
pangolin as an intermediate host (Zhou et al, 2020; Li X. et al., 2020).
Furthermore, it is of notable relevance to describe that there is a
significant difference in the binding domain of the bat virus to the
human receptor; so that, the S protein of the RaTG13 coronavirus from
the bat Rhinolophus affinis does not bind well to the human receptor
(Andersen et al.2020), whereas the S protein of the intermediate virus
binds well to ACE2 from humans, ferrets, cats and other species that
have high receptor homology (Wan et al., 2020).
The large size of the coronavirus RNA genome favors the occurrence
of point mutations, deletions or insertions, which can sometimes lead to
the appearance of different phenotypic characteristics of new viral
variants. Mutations that occur in the coronavirus genome are drift or
natural selection of mutations and by the exchange of genetic sequences
of recombinations, which can be autologous, when the exchange occurs
between viruses affecting one host species, or heterologous when the
SARS-CoV-2 in domestic and wild animals: viral characteristics, genetics, epidemiology and
transmission
70
exchange is between viruses affecting different host species (Decaro,
2010; Cui, 2019).
Coronaviruses are characterized by exceptional genetic plasticity and
evolve rapidly, changing their antigenic profile, tissue tropism or host
range through different mechanisms (Decaro & Lorusso, 2020); these,
including SARS-CoV2, encoding a viral RNA polymerase (RdRp-
nsp12) that is of low fidelity; i.e., it allows the occurrence of
spontaneous mutations (incorporates incorrect nucleotides) during virus
replication, as it has a low proofreading mechanism compared to other
RNA viruses, leading to enhanced virulence and resistance to some
antiviral drugs (Lung et al., 2020; Smith & Denison, 2013).
Recombination is an alternative mechanism that allows coronaviruses
to acquire new biological properties in terms of virulence, host range
and tissue tropism, so that CoV strains, which are non-pathogenic or
low pathogenic in the original host, can increase their pathogenicity in
the same species, or adapt to different species that disseminate in the
new host exceptionally rapidly (Decaro & Lorusso, 2020), therefore,
there is the uncertainty of the emergence of a new coronavirus with
unpredictable phenotypic characteristics in terms of transmissibility
and virulence, due to recombination of canine coronavirus and SARS-
CoV-2 infections; However, the likelihood of such a scenario is difficult
to assess (Decaro, 2013).
In a study described by Qui et al. (2020) on phylogenetic clustering and
sequence alignment, it established that the new coronavirus could use
ACE2 from various domestic animals such as cats, dogs, cows,
buffaloes, goats, sheep and pigeons. Regarding the phylogenetic tree
results, they showed that SARS-CoV-2 isolates from a cat in Wuhan
are closely related to bat and pangolin isolates from the same region;
but isolates from dogs, cats and tigers from France, the United States
and Hong Kong have been combined with human isolates. Also,
Hossain et al. (2020) describe that humans, cats, ferrets and different
types of monkeys are at high risk of contracting the virus, while dogs,
cows and goats, etc., are at moderate risk.
Birds represent the reservoir of Coronaviruses belonging to the genera
Gammacoronavirus and Deltacoronavirus, bats are the natural
reservoir of alpha and betacoronaviruses. However, several
betacoronaviruses belonging to the subgenus Embecovirus have been
January - March vol. 2. Num. 1 - 2023
71
discovered in rodents, which could represent an important source of
zoonotic disease.
There is growing evidence that all currently known HCoVs recognize
an animal origin, with bat or rodent CoVs being the most likely
ancestors. In addition, HCoV-OC43 may be neuroinvasive, and likely,
crossed species barriers to infect dogs and became established as canine
Coronavirus (Decaro & Lorusso, 2020).
Finally, the origin of the virus is described to be from bats, as
demonstrated by the evolutionary sequence of the genome; but, then it
is likely to have passed to an intermediate animal host (dogs, pangolins
and snakes are the main unknown suspects) to finally infect humans;
however, natural transmission from infected humans to domestic
animals such as: dogs, cats and mink; and wild animals such as:
monkeys, tigers and lions has been documented (Hossain et al., 2020)
(Figure 3).
4. Conclusions
SARS-CoV-2 has the proven ability to easily cross species barriers;
likewise, viral transmission from sick owners to their pets is evident;
furthermore, experimental transmission in unnatural conditions, in cats
and ferrets, has been determined. This new virus can infect several
species and different pets; therefore, further studies are needed to
establish the interaction between the virus, the environment and various
hosts.
Until now, ferrets, hamsters, cats and, to a lesser extent, bats, have been
used to assess animal-to-animal transmission. However, given the
prevalence and high genetic diversity of bat rCoV-SARS, coupled with
human habits in modern agricultural practices, urbanization, decreasing
wildlife living space, and environmental changes, could lead to the
emergence of new viral variants in the future.
Therefore, it is recommended to take measures regarding human-
wildlife contacts, also, massive genomic surveillance in wild animals
should be implemented. Mass sequencing of SARS-CoV-2 strains
detected in humans and wildlife CoV will help to further assess the
origin of this new human pandemic and plan future measures capable
of reducing the risk of occurrence of new CoV outbreak events.
SARS-CoV-2 in domestic and wild animals: viral characteristics, genetics, epidemiology and
transmission
72
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