Cats and SARS-CoV-2: A Scoping Review

Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source

We conducted an in silico analysis to better understand the potential factors impacting host adaptation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in white-tailed deer, humans, and mink due to the strong evidence of sustained transmission within these hosts. Classification models trained on single nucleotide and amino acid differences between samples effectively identified white-tailed deer-, human-, and mink-derived SARS-CoV-2. For example, the balanced accuracy score of Extremely Randomized Trees classifiers was 0.984 ± 0.006. Eighty-eight commonly identified predictive mutations are found at sites under strong positive and negative selective pressure. A large fraction of sites under selection (86.9%) or identified by machine learning (87.1%) are found in genes other than the spike. Some locations encoded by these gene regions are predicted to be B- and T-cell epitopes or are implicated in modulating the immune response suggesting that host adaptation may involve the evasion of the host immune system, modulation of the class-I major-histocompatibility complex, and the diminished recognition of immune epitopes by CD8+ T cells. Our selection and machine learning analysis also identified that silent mutations, such as C7303T and C9430T, play an important role in discriminating deer-derived samples across multiple clades. Finally, our investigation into the origin of the B.1.641 lineage from white-tailed deer in Canada discovered an additional human sequence from Michigan related to the B.1.641 lineage sampled near the emergence of this lineage. These findings demonstrate that machine-learning approaches can be used in combination with evolutionary genomics to identify factors possibly involved in the cross-species transmission of viruses and the emergence of novel viral lineages.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible virus capable of infecting and establishing itself in human and wildlife populations, such as white-tailed deer. This fact highlights the importance of developing novel ways to identify genetic factors that contribute to its spread and adaptation to new host species. This is especially important since these populations can serve as reservoirs that potentially facilitate the re-introduction of new variants into human populations. In this study, we apply machine learning and phylogenetic methods to uncover biomarkers of SARS-CoV-2 adaptation in mink and white-tailed deer. We find evidence demonstrating that both non-synonymous and silent mutations can be used to differentiate animal-derived sequences from human-derived ones and each other. This evidence also suggests that host adaptation involves the evasion of the immune system and the suppression of antigen presentation. Finally, the methods developed here are general and can be used to investigate host adaptation in viruses other than SARS-CoV-2.

Seroprevalence of Anti-SARS-CoV-2 Antibodies in Cats during Five Waves of COVID-19 Epidemic in Thailand and Correlation with Human Outbreaks

Human-to-animal SARS-CoV-2 transmission was observed, including a veterinarian contracting COVID-19 through close contact with an infected cat, suggesting an atypical zoonotic transmission. This study investigated the prevalence of SARS-CoV-2 antibodies in cats during human outbreaks and elucidated the correlation between cat infections and human epidemics. A total of 1107 cat serum samples were collected and screened for SARS-CoV-2 antibodies using a modified indirect ELISA human SARS-CoV-2 antibody detection kit. The samples were confirmed using a cPass™ neutralization test. The SARS-CoV-2 seropositivity rate was 22.67% (199/878), mirroring the trend observed in concomitant human case numbers. The waves of the epidemic and the provinces did not significantly impact ELISA-positive cats. Notably, Chon Buri exhibited a strong positive correlation (r = 0.99, p = 0.009) between positive cat sera and reported human case numbers. Additionally, the cPass™ neutralization test revealed a 3.99% (35/878) seropositivity rate. There were significant differences in numbers and proportions of positive cat sera between epidemic waves. In Samut Sakhon, a positive correlation (r = 1, p = 0.042) was noted between the proportion of positive cat sera and human prevalence. The findings emphasize the need for ongoing surveillance to comprehend SARS-CoV-2 dynamics in both human and feline populations.

An overview of SARS-CoV2 natural infections in companion animals: A systematic review of the current evidence

This systematic review provides a comprehensive overview of natural SARS-CoV-2 infections in companion animals. The findings show that these infections are relatively rare. Among the examined dogs, only 1.32% tested positive for SARS-CoV-2, while for cats, the rate was 1.55%. Infections in rabbits and ferrets were even less common, at less than 1%. These results support previous research indicating the infrequency of natural infections in companion animals. The review also includes updated studies that involved various pets, such as cats, dogs, ferrets, and rabbits. The majority of the studies analyzed were primarily concerned with screening pets that visited veterinary clinics, regardless of whether they showed any specific signs of SARS-CoV-2 infection. Only a limited number of studies investigated infections in animals suspected of being in contact with owners or other animals that had COVID-19 or were exhibiting symptoms. The most common variant identified among the SARS-CoV-2 variants in the reviewed studies was B.1.1.7 (alpha), followed by B.1.617.2 (delta), B.1.526 (Iota), and others. The emergence of these variants raises concerns about their potential for increased transmissibility and virulence, highlighting the importance of ongoing monitoring of SARS-CoV-2 infections in both humans and animals. Furthermore, most of the reviewed studies indicated that infected pets either showed no symptoms or experienced mild symptoms. This aligns with previous reports suggesting that animals infected with SARS-CoV-2 generally have less severe illness compared to humans. However, it is essential to recognize the possibility of severe illness or death in animals, particularly those with underlying health conditions. Continuous surveillance of SARS-CoV-2 infections in companion animals is crucial for better understanding the virus's epidemiology in animals and developing effective strategies to protect both animal and human health.

Evolution of SARS-CoV-2 Spikes shapes their binding affinities to animal ACE2 orthologs

IMPORTANCE

Spike-receptor interaction is a critical determinant for the host range of coronaviruses. In this study, we investigated the SARS-CoV-2 WHU01 strain and five WHO-designated SARS-CoV-2 variants of concern (VOCs), including Alpha, Beta, Gamma, Delta, and the early Omicron variant, for their Spike interactions with ACE2 proteins of 18 animal species. First, the receptor-binding domains (RBDs) of Alpha, Beta, Gamma, and Omicron were found to display progressive gain of affinity to mouse ACE2. More interestingly, these RBDs were also found with progressive loss of affinities to multiple ACE2 orthologs. The Omicron RBD showed decreased or complete loss of affinity to eight tested animal ACE2 orthologs, including that of some livestock animals (horse, donkey, and pig), pet animals (dog and cat), and wild animals (pangolin, American pika, and Rhinolophus sinicus bat). These findings shed light on potential host range shift of SARS-CoV-2 VOCs, especially that of the Omicron variant.

Transmission of severe acute respiratory syndrome coronavirus 2 from humans to animals: is there a risk of novel reservoirs?

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoonotic virus able to infect humans and multiple nonhuman animal species. Most natural infections in companion, captive zoo, livestock, and wildlife species have been related to a reverse transmission, raising concern about potential generation of animal reservoirs due to human-animal interactions. To date, American mink and white-tailed deer are the only species that led to extensive intraspecies transmission of SARS-CoV-2 after reverse zoonosis, leading to an efficient spread of the virus and subsequent animal-to-human transmission. Viral host adaptations increase the probability of new SARS-CoV-2 variants' emergence that could cause a major global health impact. Therefore, applying the One Health approach is crucial to prevent and overcome future threats for human, animal, and environmental fields.

Development of a Multispecies Double-Antigen Sandwich ELISA Using N and RBD Proteins to Detect Antibodies against SARS-CoV-2

SARS-CoV-2 infects humans and a broad spectrum of animal species, such as pets, zoo animals, and nondomestic animals. Monitoring infection in animals is important in terms of the risk of interspecies transmission and the emergence of new viral variants. Economical, fast, efficient, and sensitive diagnostic tests are needed to analyze animal infection. Double-antigen sandwich ELISA has the advantage of being multispecies and can be used for detecting infections caused by pathogens that infect several animal hosts. This study aimed to develop a double-antigen sandwich ELISA using two SARS-CoV-2 proteins, N and RBD. We compared its performance, when using these proteins separately, with an indirect ELISA and with a surrogate virus neutralization test. Positive and negative controls from a cat population (n = 31) were evaluated to compare all of the tests. After confirming that double-antigen sandwich ELISA with both RBD and N proteins had the best performance (AUC= 88%), the cutoff was adjusted using positive and negative samples from cats, humans (n = 32) and guinea pigs (n = 3). The use of samples from tigers (n = 2) and rats (n = 51) showed good agreement with the results previously obtained using the microneutralization test. Additionally, a cohort of samples from dogs with unknown infection status was evaluated. These results show that using two SARS-CoV-2 proteins in the double-antigen sandwich ELISA increases its performance and turns it into a valuable assay with which to monitor previous infection caused by SARS-CoV-2 in different animal species.

SARS-CoV-2 Prevalence and Variant Surveillance among Cats in Pittsburgh, Pennsylvania, USA

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infects many mammals, and SARS-CoV-2 circulation in nonhuman animals may increase the risk of novel variant emergence. Cats are highly susceptible to SARS-CoV-2 infection, and there were cases of virus transmission between cats and humans. The objective of this study was to assess the prevalence of SARS-CoV-2 variant infection of cats in an urban setting. We investigated the prevalence of SARS-CoV-2 variant infections in domestic and community cats in the city of Pittsburgh (n = 272). While no cats tested positive for SARS-CoV-2 viral RNA, 35 cats (12.86%) tested SARS-CoV-2-antibody-positive. Further, we compared a cat-specific experimental lateral flow assay (eLFA) and species-agnostic surrogate virus neutralization assay (sVNT) for SARS-CoV-2 antibody detection in cats (n = 71). The eLFA demonstrated 100% specificity compared to sVNT. The eLFA also showed 100% sensitivity for sera with >90% inhibition and 63.63% sensitivity for sera with 40-89% inhibition in sVNT. Using a variant-specific pseudovirus neutralization assay (pVNT) and antigen cartography, we found the presence of antibodies to pre-Omicron and Omicron SARS-CoV-2 variants. Hence, this approach proves valuable in identifying cat exposure to different SARS-CoV-2 variants. Our results highlight the continued exposure of cats to SARS-CoV-2 and warrant coordinated surveillance efforts.

Serological screening of SARS-CoV-2 infection in companion animals of Buenos Aires suburbs

The Coronavirus Disease 2019 (COVID-19) is a zoonotic disease caused by the pandemic virus SARS-CoV-2. Domestic and wild animals are susceptible to infection and are potential reservoirs for virus variants. To date, there is no information about the exposure of companion animals in Buenos Aires Suburbs, the area with the largest population in Argentina where the highest number of COVID-19 human cases occurred during the first infection wave. Here we developed a multi-species indirect ELISA to measure antibodies reactive to the SARS-CoV-2 receptor-binding domain (RBD) from several vertebrates constituting the class Mammalia, making it a valuable tool for field serosurveillance. The ELISA cut-off value was estimated by sera from dogs, cats, cattle, and pigs sampled before 2019 (n = 170), considering a 98% percentile and a grey zone to completely exclude any false positive result. Specificity was confirmed by measuring levels of neutralizing antibodies against canine coronavirus, the avidity of specific antibodies, and their capacity to impede the binding of a recombinant RBD protein to VERO cells in an In-Cell ELISA. Sera from 464 cats and dogs sampled in 2020 and 2021 ("pandemic" samples) were assessed using the RBD-ELISA. Information on COVID-19 disease in the household and the animals' lifestyles was collected. In Buenos Aires Suburbs cats were infected at a higher proportion than dogs, seroprevalence was 7.1 and 1.68%, respectively. Confirmed COVID-19 in the caregivers and outdoor lifestyle were statistically associated with seropositivity in cats. The risk of cats getting infected living indoors in COVID-19-negative households was null. The susceptibility of mammals to SARS-CoV-2, the possibility of transmission between animals themselves and humans, together with the free-roaming lifestyle typical of Buenos Aires suburban companion animals, urge pursuing responsible animal care and avoiding human interaction with animals during the disease course. The multi-species RBD-ELISA we developed can be used as a tool for serosurveillance of SARS-CoV-2 infection in mammalians (domestic and wild), guiding further targeted virological analyses to encounter susceptible species, interspecies transmission, and potential virus reservoirs in our region.

Immune Responses and Pathogenesis following Experimental SARS-CoV-2 Infection in Domestic Cats

Several reports demonstrated the susceptibility of domestic cats to SARS-CoV-2 infection. Here, we describe a thorough investigation of the immune responses in cats after experimental SARS-CoV-2 inoculation, along with the characterization of infection kinetics and pathological lesions. Specific pathogen-free domestic cats (n = 12) were intranasally inoculated with SARS-CoV-2 and subsequently sacrificed on DPI (days post-inoculation) 2, 4, 7 and 14. None of the infected cats developed clinical signs. Only mild histopathologic lung changes associated with virus antigen expression were observed mainly on DPI 4 and 7. Viral RNA was present until DPI 7, predominantly in nasal and throat swabs. The infectious virus could be isolated from the nose, trachea and lungs until DPI 7. In the swab samples, no biologically relevant SARS-CoV-2 mutations were observed over time. From DPI 7 onwards, all cats developed a humoral immune response. The cellular immune responses were limited to DPI 7. Cats showed an increase in CD8+ cells, and the subsequent RNA sequence analysis of CD4+ and CD8+ subsets revealed a prominent upregulation of antiviral and inflammatory genes on DPI 2. In conclusion, infected domestic cats developed a strong antiviral response and cleared the virus within the first week after infection without overt clinical signs and relevant virus mutations.

Do pathogens always evolve to be less virulent? The virulence–transmission trade-off in light of the COVID-19 pandemic

The direction the evolution of virulence takes in connection with any pathogen is a long-standing question. Formerly, it was theorized that pathogens should always evolve to be less virulent. As observations were not in line with this theoretical outcome, new theories emerged, chief among them the transmission–virulence trade-off hypotheses, which predicts an intermediate level of virulence as the endpoint of evolution. At the moment, we are very much interested in the future evolution of COVID-19’s virulence. Here, we show that the disease does not fulfill all the assumptions of the hypothesis. In the case of COVID-19, a higher viral load does not mean a higher risk of death; immunity is not long-lasting; other hosts can act as reservoirs for the virus; and death as a consequence of viral infection does not shorten the infectious period. Consequently, we cannot predict the short- or long-term evolution of the virulence of COVID-19.

Serological Investigation on the Presence of Feline Coronavirus (FCoV) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Domestic Cats Living with COVID-19 Positive Owners in the UAE, 2022

Feline coronavirus (FCoV) is widely circulating among domestic cats (Felis catus). The zoonotic origin of the emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and the biological characteristics of CoVs, including the ability to cross interspecies barriers, facilitate its emergence in different animals, including cats' populations. The current study is the first to report the serological investigation on the presence of FCoV and SARS-CoV-2 in domestic cats living with COVID-19-positive owners in the UAE. A total of 83 sera were collected from domestic cats living with COVID-19-positive owners (by RT-qPCR). The cats were sampled during the period between February and May 2022 in Al-Ain and Abu Dhabi Cities, UAE. Detection of FCoV and SARS-CoV-2 was carried out by enzyme-linked immunosorbent assay (ELISA). FCoV antibodies were detected in 54 samples (65%). The frequencies of FCoV were significantly higher in purebred cats (48%; 40/83) and in the cat group with outdoor access (49.4%; 41/83). SARS-CoV-2 seroprevalence in collected sera revealed 8 samples (9.6%) with positive results. Four samples (4.8%) showed positive results for both FCoV and SARS-CoV-2 antibodies. In conclusion, FCoV is widely circulating within cats' populations involved in the study. The antibodies for SARS-CoV-2 were detected in cats' populations but at a low prevalence rate. COVID-19-positive people should avoid close contact with their cats. Future serological testing of large cats' populations is crucial for providing a good understanding of COVID-19 dynamics in cats.

A Retrospective Study of Viral Molecular Prevalences in Cats in Southern Italy (Campania Region)

From 2019 to 2021, a retrospective molecular study was conducted in the Campania region (southern Italy) to determine the prevalence of viral diseases in domestic cats. A total of 328 dead animals were analyzed by Real-Time PCR for the presence of feline panleukopenia virus (FPV), feline leukemia virus (FeLV), feline enteric coronavirus (FCoV), rotavirus (RVA), feline herpesvirus type 1 (FHV-1), and feline calicivirus (FCV). The possible presence of SARS-CoV-2 was also investigated by Real-Time PCR. The cats included in this study were specifically sourced and referred by local veterinarians and local authorities to the Zooprofilactic Experimental Institute of Southern Italy (IZSM) for pathological evaluation. The samples consisted of owners, catteries, and stray cats. Results revealed: 73.5% positive cats for FPV (189/257), 23.6% for FeLV (21/89), 21.5% for FCoV (56/266), 11.4% for RVA (16/140), 9.05% for FeHV-1 (21/232), and 7.04 for FCV (15/213). In contrast, SARS-CoV-2 was never detected. FPV was more prevalent in winter (p = 0.0027). FCoV FHV-1, FCV, and RVA predominated in autumn, whereas FeLV predominated in summer. As expected, viral infections were found more frequently in outdoor and shelter cats than in indoor ones, although no statistical association was found between animal lifestyle and viral presence. The study showed a high prevalence of FPV, FeLV, and FCoV and a moderate prevalence of RVA, FHV-1, and FCV. Moreover, the prevalence of these pathogens varied among the cat populations investigated.

Structural basis for the broad and potent cross-reactivity of an N501Y-centric antibody against sarbecoviruses

More than 80% of SARS-CoV-2 variants, including Alpha and Omicron, contain an N501Y mutation in the receptor-binding domain (RBD) of the spike protein. The N501Y change is an adaptive mutation enabling tighter interaction with the human ACE2 receptor. We have developed a broadly neutralizing antibody (nAb), D27LEY, whose binding affinity was intentionally optimized for Y501. This N501Y-centric antibody not only interacts with the Y501-containing RBDs of SARS-CoV-2 variants, including Omicron, with pico- or subnanomolar binding affinity, but also binds tightly to the RBDs with a different amino acid at residue 501. The crystal structure of the Fab fragment of D27LEY bound to the RBD of the Alpha variant reveals that the Y501-containing loop adopts a ribbon-like topology and serves as a small but major epitope in which Y501 is a part of extensive intermolecular interactions. A hydrophobic cleft on the most conserved surface of the RBD core serves as another major binding epitope. These data explain the broad and potent cross-reactivity of this N501Y-centric antibody, and suggest that a vaccine antigenic component composed of the RBD core and a part of receptor-binding motif (RBM) containing tyrosine at residue 501 might elicit broad and potent humoral responses across sarbecoviruses.

SARS-CoV-2 as a Zooanthroponotic Infection: Spillbacks, Secondary Spillovers, and Their Importance

In the midst of a persistent pandemic of a probable zoonotic origin, one needs to constantly evaluate the interplay of SARS-CoV-2 (severe acute respiratory syndrome-related coronavirus-2) with animal populations. Animals can get infected from humans, and certain species, including mink and white-tailed deer, exhibit considerable animal-to-animal transmission resulting in potential endemicity, mutation pressure, and possible secondary spillover to humans. We attempt a comprehensive review of the available data on animal species infected by SARS-CoV-2, as presented in the scientific literature and official reports of relevant organizations. We further evaluate the lessons humans should learn from mink outbreaks, white-tailed deer endemicity, zoo outbreaks, the threat for certain species conservation, the possible implication of rodents in the evolution of novel variants such as Omicron, and the potential role of pets as animal reservoirs of the virus. Finally, we outline the need for a broader approach to the pandemic and epidemics, in general, incorporating the principles of One Health and Planetary Health.

Companion animal adoption and relinquishment during the COVID-19 pandemic: Peri-pandemic pets at greatest risk of relinquishment

The COVID-19 pandemic has created a situation globally where companion animals may be at increased risk of relinquishment and abandonment due to multiple interrelated factors. The aims of this study were to establish the prevalence of self-reported adoption and relinquishment of cats and dogs during the pandemic, and to identify characteristics associated with relinquishment. A survey was distributed to 4,000 participants across several countries including the UK, USA, Canada, Italy, Spain and France. N = 3,945 responses were available for analysis. Three groups of participants were identified; Those that never considered relinquishment (NCR), those that have considered relinquishment (CR) and those that have already relinquished a cat or dog (R). Two follow-up surveys were sent to CR and R participants. Considering data from the three surveys, 4.06% of participants considered giving up their pet, 0.74% relinquished their pet, and 0.2% considered and then later give up their pet. Compared to pets given as a gift, there was a 38.7% decreased likelihood of relinquishment in pets sourced from a shelter (P < 0.001), 31.2% decrease in those sourced from a breeder, and a 24.4% decrease in those acquired directly from someone that needed to find a new home for their cat or dog. Compared to owners who acquired their pet > 6 months before COVID-19 was declared a pandemic, those acquired < 6 months before COVID-19 was declared a pandemic were three times more likely to be considered for, or be, given up (P < 0.001) and those acquired after COVID-19 was declared a pandemic were two times more likely to be considered for, or be, given up (P < 0.001). There was a trend for greater likelihood of CR or R of pets acquired online (P = 0.074). Of those that had already given up their pet, 14.3% relinquished to a shelter, 66.7% gave their pet to a new owner and 19% obtained temporary care from someone else. A total of 65.0% of CR participants were male, increasing to 72.2% of R participants. There was no effect of species (cat or dog) on risk of relinquishment. Financial constraints were the most mentioned reason for both giving up a pet and considering giving up a pet, followed by health concerns specific to COVID-19, and behavioral problems. The findings from this study should be used to inform interventions aimed at reducing companion animal relinquishment.