Assessing the risks of SARS-CoV-2 in wildlife

Understanding zoonotic pathogens and risk factors from wildlife in Southeast Asia: a systematic literature review

The COVID-19 pandemic has demonstrated the significance of the human-animal interface in the emergence of zoonotic diseases, with wildlife serving as an important source of infection. A better understanding of the specific pathogens and mechanisms involved is vital to prepare against future outbreaks, especially in Southeast Asia, a hotspot for zoonotic diseases. This paper reviews the published literature on wildlife zoonoses in this region from 2012 to 2022. The results show a diverse range of potential zoonotic pathogens and the widespread occurrence of zoonotic diseases from wildlife. Drivers of zoonotic pathogen spillover include (i) environmental factors (e.g. animal habitat disruption, environmental conditions, exposure to contaminated water/food/soil), (ii) animal factors (e.g. movement patterns, age-related susceptibility), (iii) human factors (e.g. lack of awareness, poor hygiene practices, age, gender and income) and (iv) human-animal-environmental interface factors (e.g. close contact between humans and animals, exposure through visiting animals and presence of vectors). The diverse drivers of zoonoses in Southeast Asia put its communities at risk for infection. To mitigate these risks, global health efforts should consider adopting a One Health approach to foster collaboration across human, animal, and wildlife health sectors. This could involve educating communities on safe animal interactions and improving disease surveillance.

One Health Surveillance for SARS-CoV-2 in Non-Human Primates and Small Mammals in Minas Gerais, Brazil

Although the SARS-CoV-2 pandemic primarily affected the human population, the virus has also been detected in various animal species worldwide, raising concerns about its potential to establish new animal reservoirs. This study aimed to investigate the presence of SARS-CoV-2 in non-human primates (NHPs) and synanthropic small mammals (SSMs) in the Jequitinhonha Valley and Northern Minas Gerais, Brazil. Between October 2021 and October 2023, 119 animals were sampled, 82 NHPs and 37 SSMs, across 22 municipalities. A total of 342 biological samples-including oral and nasal swabs, lungs, livers, spleens, blood, and feces-were collected and analyzed using RT-qPCR, while 37 serum samples were submitted to neutralization tests. Despite the diversity of sampled species, habitats, and biological materials, no evidence of SARS-CoV-2 infection or specific antibodies was detected in any of the individuals tested. The results suggest that NHPs and SSMs in these regions did not act as reservoirs for SARS-CoV-2 during the study period. This finding is particularly relevant given the high synanthropy of species such as Callithrix penicillata (black-tufted marmoset) and Rattus rattus (black rat), which frequently interact with human populations. Our study underscores the importance of integrating animal, human, and environmental health perspectives under a One Health framework to monitor emerging zoonotic threats. By providing baseline data on SARS-CoV-2 dynamics in wildlife, we emphasize the need for ongoing ecological and epidemiological surveillance to assess potential spillover events and their implications for biodiversity and public health in Brazil.

Beyond the virus: ecotoxicological and reproductive impacts of SARS-CoV-2 lysate protein in C57Bl/6j female mice

Since the establishment of the COVID-19 pandemic, a range of studies have been developed to understand the pathogenesis of SARS-CoV-2 infection, vaccine development, and therapeutic testing. However, the possible impacts that these viruses can have on non-target organisms have been explored little, and our knowledge of the consequences of the COVID-19 pandemic for biota is still very limited. Thus, the current study aimed to address this knowledge gap by evaluating the possible impacts of oral exposure of C57Bl/6 J female mice to SARS-CoV-2 lysate protein (at 20 µg/L) for 30 days, using multiple methods, including behavioral assessments, biochemical analyses, and histopathological examinations. Although we did not have evidence of hematological, mutagenic, or genotoxic effects, we noted that the ingestion of SARS-CoV-2 lysate protein-induced behavioral disorders (hypoactivity, anxiety-like behavior, and short-term memory deficit), which were associated with oxidative stress and dopaminergic and cholinesterase imbalance in the animal brain. Furthermore, the elevation of bilirubin levels and lactate dehydrogenase levels in these animals suggests the occurrence of hepatic changes, and the redox imbalance, nitrosative stress, and elevated production of IFN-γ and inflammatory infiltration in the duodenum, disrupted follicular structure, and presence of vacuoles in granulosa cells, in ovarian, indicate that the SARS-CoV-2-exposed group showed significant toxicity. Principal component analysis (PCA) and cluster analysis confirmed that the groups were clearly separated and showed that the largest changes upon SARS-CoV-2 exposure were related to ROS, MDA, nitrite, IFN-γ/IL-10 levels and SOD and catalase activity in the ovary; IFN-γ/IL-10 production and SOD activity in the duodenum; BChE activity in the brain; bilirubin levels and lactate dehydrogenase activity in the serum; number of primary follicles in the ovary. In conclusion, our study provides new insights into the toxicity of SARS-CoV-2 lysate proteins in a non-target terrestrial organism of infection and, therefore, expands our understanding of the real extent of the ecological/environmental impact of the COVID-19 pandemic.

Vaccine Hesitancy and Associated Factors Amongst Health Professionals: A Scoping Review of the Published Literature

Background/Objectives: Healthcare professionals (HCPs) hold significant influence over public attitudes toward vaccinations. Studies suggest that HCPs are hesitant towards the coronavirus disease 2019 (COVID-19) vaccines. This hesitancy could lead to lower vaccination rates in the community. Therefore, this scoping review aimed to assess the extent of hesitancy towards COVID-19 booster doses among HCPs and identify the associated factors. Methods: A comprehensive search was conducted in the PubMed and Scopus databases from April to August 2024, using keywords related to COVID-19, vaccine hesitancy, HCPs, and booster vaccination. Studies that had been peer-reviewed, published in English after 2022, and focused on the hesitancy of the COVID-19 booster dose hesitancy among HCPs were included. Out of the 6703 studies screened, 24 studies were included. Results: Most of the HCPs have received their initial series of COVID-19 vaccinations. However, there is a lower rate of uptake for booster doses, with hesitancy rates ranging from 12% to 66.5%. Hesitancy rates varied significantly across continents, with Asia, Africa, and Europe ranging from 19.7% to 66.5%, 27% to 46.1%, 14% to 60.2%, respectively. Hesitancy was reported to be influenced by various factors, including concerns about vaccine safety, necessity, and effectiveness of these vaccines. In addition, the hesitancy regarding booster doses was also found to be influenced by factors like age, gender, profession, and previous COVID-19. Physicians, nurses, and pharmacists exhibited vaccine hesitancy rates ranging from 12.8% to 43.7%, 26% to 37%, and 26% to 34.6%, respectively. Conclusions: Our review underscores the hesitancy among HCPs towards receiving booster doses across countries around the world and explores the underlying factors. These findings provide valuable insights for the design of future pandemic vaccination programs.

SARS-CoV-2 surveillance in captive animals at the belo horizonte zoo, Minas Gerais, Brazil

BACKGROUND

The pandemic caused by SARS-CoV-2 has not only affected humans but also raised concerns about its transmission to wild animals, potentially creating natural reservoirs. Understanding these dynamics is critical for preventing future pandemics and developing control strategies. This study aims to investigate the presence of SARS-CoV-2 in wild mammals at the Belo Horizonte Zoo in Brazil, analyzing the virus's evolution and zoonotic potential.

METHODS

The study was conducted at the Belo Horizonte Zoo, Minas Gerais, Brazil, covering a diverse population of mammals. Oropharyngeal, rectal, and nasal swabs were collected from 47 captive animals between November 2021 and March 2023. SARS-CoV-2 presence was determined using RT-PCR, and positive samples were sequenced for phylogenetic analysis. Consensus genomes were classified using Pangolin and NextClade tools, and a maximum likelihood phylogeny was inferred using IQ-Tree.

RESULTS

Of the 47 animals tested, nine (19.1%) were positive for SARS-CoV-2. Positive samples included rectal, oropharyngeal, and nasal swabs, with the highest positivity in rectal samples. Three genomes were successfully sequenced, revealing two variants: VOC Alpha in a maned wolf (Chrysocyon brachyurus) and a fallow deer (Dama dama), and VOC Omicron in a western lowland gorilla (Gorilla gorilla gorilla). Phylogenetic analysis indicated potential human-to-animal transmission, with animal genomes clustering close to human samples from the same region.

CONCLUSIONS

This study highlights the presence of SARS-CoV-2 in various wild mammal species at the Belo Horizonte Zoo, emphasizing the virus's zoonotic potential and the complexity of interspecies transmission. The detection of different variants suggests ongoing viral evolution and adaptation in new hosts. Continuous monitoring and genomic surveillance of SARS-CoV-2 in wildlife are essential for understanding its transmission dynamics and preventing future zoonotic outbreaks. These findings underscore the need for integrated public health strategies that include wildlife monitoring to mitigate the risks posed by emerging infectious diseases.

Bison, Elk, and Other Captive Wildlife Species Humoral Immune Responses against SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, has been found to infect various domestic and wild animal species. In this study, convenience serum samples from 575 bison, 180 elk, and 147 samples from various wildlife species collected between 2020 and 2023 from several regions in the United States were analyzed for the presence of SARS-CoV-2-specific antibodies. Two commercial ELISA assays based on the inhibition of the SARS-CoV-2 receptor-binding domain (sVNT) or the nucleocapsid protein (N-ELISA) of SARS-CoV-2 were used. Positive samples from the sVNT were additionally evaluated using a conventional virus neutralization test (VNT). Our results indicated that 1.2% of bison, 2.2% of elk, and 4.1% of the other wildlife species serum samples were seropositive in the sVNT, whereas 4.2% of bison, 3.3% of elk, and 1.4% of the other captive wildlife species serum samples tested positive by the N-ELISA. Among the sVNT serum samples, two samples from bison, one sample from elk, and five serum samples from other wildlife species (one cheetah, one gorilla, two lions, and one hippopotamus) had neutralizing antibody titers in the VNT, indicating these species are susceptible to SARS-CoV-2 infection. These findings highlight the importance of broad surveillance efforts for the effective monitoring of SARS-CoV-2 in non-human hosts.

Comparative SARS-CoV-2 Omicron BA.5 variant and D614G-Wuhan strain infections in ferrets: insights into attenuation and disease progression during subclinical to mild COVID-19

Introduction

As the SARS-CoV-2 virus continues to evolve and new variants emerge, it becomes crucial to understand the comparative pathological and immunological responses elicited by different strains. This study focuses on the original Wuhan strain and the Omicron variant, which have demonstrated significant differences in clinical outcomes and immune responses.

Methods

We employed ferrets as an experimental model to assess the D614G variant (a derivative of the Wuhan strain) and the Omicron BA.5 variant. Each variant was inoculated into separate groups of ferrets to compare disease severity, viral dissemination, and immune responses.

Results

The D614G variant induced more severe disease and greater viral spread than the Omicron variant. Notably, ferrets infected with the D614G variant exhibited a robust neutralizing antibody response, whereas those infected with the Omicron variant failed to produce a detectable neutralizing antibody response. Despite the clearance of the virus from nearly all tissues by 7 days post-infection, an increase in pathological lesions was observed from 14 to 21 days, particularly in those infected with the D614G variant, suggesting a sustained immune response even after viral clearance.

Discussion

These findings underscore the adaptability of SARS-CoV-2 and illuminate how susceptibility and clinical manifestations vary across different strains and species. The results emphasize the necessity of considering both the direct effects of viral infection and the indirect, often prolonged, impacts of the immune response in evaluating the outcomes of SARS-CoV-2 infections.

Reframing wildlife disease management problems with decision analysis

Contemporary wildlife disease management is complex because managers need to respond to a wide range of stakeholders, multiple uncertainties, and difficult trade-offs that characterize the interconnected challenges of today. Despite general acknowledgment of these complexities, managing wildlife disease tends to be framed as a scientific problem, in which the major challenge is lack of knowledge. The complex and multifactorial process of decision-making is collapsed into a scientific endeavor to reduce uncertainty. As a result, contemporary decision-making may be oversimplified, rely on simple heuristics, and fail to account for the broader legal, social, and economic context in which the decisions are made. Concurrently, scientific research on wildlife disease may be distant from this decision context, resulting in information that may not be directly relevant to the pertinent management questions. We propose reframing wildlife disease management challenges as decision problems and addressing them with decision analytical tools to divide the complex problems into more cognitively manageable elements. In particular, structured decision-making has the potential to improve the quality, rigor, and transparency of decisions about wildlife disease in a variety of systems. Examples of management of severe acute respiratory syndrome coronavirus 2, white-nose syndrome, avian influenza, and chytridiomycosis illustrate the most common impediments to decision-making, including competing objectives, risks, prediction uncertainty, and limited resources.

COVID-19 in a common woolly monkey (Lagothrix lagothricha): First evidence of fatal outcome in a nonhuman primate after natural SARS-CoV-2 infection

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a pandemic by the World Health Organization in March 2020. Since then, viral spread from humans to animals has occurred worldwide. Nonhuman primates (NHPs) have been found to be susceptible to reverse-zoonosis transmission of SARS-CoV-2, but initial research suggested that platyrrhine primates are less susceptible than catarrhine primates. Here we report the natural SARS-CoV-2 infection of a common woolly monkey (Lagothrix lagothricha) from a wildlife rehabilitation center in Ecuador. The course of the disease, the eventual death of the specimen, and the pathological findings are described. Our results show the susceptibility of a new platyrrhine species to SARS-CoV-2 and provide evidence for the first time of a COVID-19-associated death in a naturally infected NHP. The putative route of transmission from humans, and implications for captive NHPs management, are also discussed. Given that common woolly monkeys are at risk of extinction in Ecuador, further understanding of the potential threat of SARS-CoV-2 to their health should be a conservation priority. A One Health approach is the best way to protect NHPs from a new virus in the same way that we would protect the human population.

Host Jump of an Exotic Fish Rhabdovirus into a New Class of Animals Poses a Disease Threat to Amphibians

Spring viremia of carp virus (SVCV) is a rhabdovirus that primarily infects cyprinid finfishes and causes a disease notifiable to the World Organization for Animal Health. Amphibians, which are sympatric with cyprinids in freshwater ecosystems, are considered non-permissive hosts of rhabdoviruses. The potential host range expansion of SVCV in an atypical host species was evaluated by testing the susceptibility of amphibians native to the Pacific Northwest. Larval long-toed salamanders Ambystoma macrodactylum and Pacific tree frog Pseudacris regilla tadpoles were exposed to SVCV strains from genotypes Ia, Ib, Ic, or Id by either intraperitoneal injection, immersion, or cohabitation with virus-infected koi Cyprinus rubrofuscus. Cumulative mortality was 100% for salamanders injected with SVCV, 98-100% for tadpoles exposed to virus via immersion, and 0-100% for tadpoles cohabited with SVCV-infected koi. Many of the animals that died exhibited clinical signs of disease and SVCV RNA was found by in situ hybridization in tissue sections of immersion-exposed tadpoles, particularly in the cells of the gastrointestinal tract and liver. SVCV was also detected by plaque assay and RT-qPCR testing in both amphibian species regardless of the virus exposure method, and viable virus was detected up to 28 days after initial exposure. Recovery of infectious virus from naïve tadpoles cohabited with SVCV-infected koi further demonstrated that SVCV transmission can occur between classes of ectothermic vertebrates. Collectively, these results indicated that SVCV, a fish rhabdovirus, can be transmitted to and cause lethal disease in two amphibian species. Therefore, members of all five of the major vertebrate groups (mammals, birds, reptiles, fish, and amphibians) appear to be vulnerable to rhabdovirus infections. Future research studying potential spillover and spillback infections of aquatic rhabdoviruses between foreign and domestic amphibian and fish species will provide insights into the stressors driving novel interclass virus transmission events.

Survey of severe acute respiratory syndrome coronavirus 2 in captive and free-ranging wildlife from Spain

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), considered a zoonotic agent of wildlife origin, can infect various animal species, including wildlife in free-range and captive environments. Detecting susceptible species and potential reservoirs is crucial for preventing the transmission, spread, genetic evolution, and further emergence of viral variants that are major threats to global health. This study aimed to detect exposure or acute infection by SARS-CoV-2 in 420 animals from 40 different wildlife species, including terrestrial and aquatic mammals, from different regions of Spain during the 2020-2023 coronavirus disease 19 (COVID-19) pandemic. In total, 8/137 animals were positive for SARS-CoV-2 antibodies against the receptor binding domain and/or viral nucleoprotein according to independent ELISAs. However, only one ELISA-positive sample of a captive bottlenose dolphin (Tursiops truncatus) tested positive for SARS-CoV-2 neutralizing antibodies with a low titre (SNT50 38.15) according to a virus neutralization test. Cetaceans are expected to have a high risk of infection with SARS-CoV-2 according to early predictive studies due to the similarity of their angiotensin converting enzyme 2 cell receptor to that of humans. Moreover, of 283 animals analysed for SARS-CoV-2 RNA using RT-qPCR, none tested positive. Our results reinforce the importance of considering cetaceans at risk for SARS-CoV-2 infection and support taking preventive biosecurity measures when interacting with them, especially in the presence of individuals with suspected or confirmed COVID-19. Although most animals in this study tested negative for acute infection or viral exposure, ongoing surveillance of wildlife species and potentially susceptible animals is important to prevent future spillover events and detect potential novel reservoirs.

DETECTION OF SARS-COV-2 IN A SQUIRREL MONKEY (SAIMIRI SCIUREUS): A ONE HEALTH INVESTIGATION AND RESPONSE

Through collaborative efforts, One Health partners have responded to outbreaks of COVID-19 among animals, including those in human care at zoos. Zoos have been faced with numerous challenges, including the susceptibility of many mammalian species, and therefore the need to heighten biosecurity measures rapidly. Robust One Health collaborations already exist in Arizona to address endemic and emerging zoonoses, but these have rarely included zoos. The pandemic shed light on this, and Arizona subsequently expanded its SARS-CoV-2 surveillance efforts to include zoo animals. Testing and epidemiologic support was provided to expedite the detection of and response to zoonotic SARS-CoV-2 infection in zoo animals, as well as to understand possible transmission events. Resulting from this program, SARS-CoV-2 was detected from a rectal swab collected from an 8-yr-old squirrel monkey (Saimiri sciureus) from a zoo in Southern Arizona. The animal had rapidly become ill with nonrespiratory symptoms and died in July 2022. Genomic sequencing from the swab revealed mutations consistent with the Omicron (BA.2) lineage. An epidemiologic investigation identified an animal caretaker in close proximity to the affected squirrel monkey who tested positive for COVID-19 the same day the squirrel monkey died. Critical One Health partners provided support to the zoo through engagement of local, state, and federal agencies. Necropsy and pathologic evaluation showed significant necrotizing colitis; the overall clinical and histopathological findings did not implicate SARS-CoV-2 infection alone as a causal or contributing factor in the squirrel monkey's illness and death. This report documents the first identification of SARS-CoV-2 in a squirrel monkey and highlights a successful and timely One Health investigation conducted through multisectoral collaboration.

Droplet Digital RT-PCR (dd RT-PCR) Detection of SARS-CoV-2 in Honey Bees and Honey Collected in Apiaries across the Campania Region

Coronaviruses (CoVs), a subfamily of Orthocoronavirinae, are viruses that sometimes present a zoonotic character. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for the recent outbreak of COVID-19, which, since its outbreak in 2019, has caused about 774,593,066 confirmed cases and 7,028,881 deaths. Aereosols are the main route of transmission among people; however, viral droplets can contaminate surfaces and fomites as well as particulate matter (PM) in suspensions of natural and human origin. Honey bees are well known bioindicators of the presence of pollutants and PMs in the environment as they can collect a great variety of substances during their foraging activities. The aim of this study was to evaluate the possible role of honey bees as bioindicators of the prevalence SARS-CoV-2. In this regard, 91 samples of honey bees and 6 of honey were collected from different apiaries of Campania region (Southern Italy) in four time periods from September 2020 to June 2022 and were analyzed with Droplet Digital RT-PCR for SARS-CoV-2 target genes Orf1b and N. The screening revealed the presence of SARS-CoV-2 in 12/91 in honey bee samples and in 2/6 honey samples. These results suggest that honey bees could also be used as indicators of outbreaks of airborne pathogens such as SARS-CoV-2.

Detection of SARS-CoV-2 Delta Variant (B.1.617.2) in Domestic Dogs and Zoo Tigers in England and Jersey during 2021

Reverse zoonotic transmission events of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been described since the start of the pandemic, and the World Organisation for Animal Health (WOAH) designated the detection of SARS-CoV-2 in animals a reportable disease. Eighteen domestic and zoo animals in Great Britain and Jersey were tested by APHA for SARS-CoV-2 during 2020-2023. One domestic cat (Felis catus), three domestic dogs (Canis lupus familiaris), and three Amur tigers (Panthera tigris altaica) from a zoo were confirmed positive during 2020-2021 and reported to the WOAH. All seven positive animals were linked with known SARS-CoV-2 positive human contacts. Characterisation of the SARS-CoV-2 variants by genome sequencing indicated that the cat was infected with an early SARS-CoV-2 lineage. The three dogs and three tigers were infected with the SARS-CoV-2 Delta variant of concern (B.1.617.2). The role of non-human species in the onward transmission and emergence of new variants of SARS-CoV-2 remain poorly defined. Continued surveillance of SARS-CoV-2 in relevant domestic and captive animal species with high levels of human contact is important to monitor transmission at the human-animal interface and to assess their role as potential animal reservoirs.

Assessment of the Risk Impact of SARS-CoV-2 Infection Prevalence between Cats and Dogs in America and Europe: A Systematic Review and Meta-Analysis

The COVID-19 pandemic represented a huge obstacle for public health and demonstrated weaknesses in surveillance and health promotion systems around the world. Its etiological agent, SARS-CoV-2, of zoonotic origin, has been the target of several studies related to the control and prevention of outbreaks and epidemics of COVID-19 not only for humans but also for animals. Domestic animals, such as dogs and cats, have extensive contact with humans and can acquire the infection both naturally and directly from humans. The objective of this article was to summarize the seroprevalence findings of SARS-CoV-2 in dogs and cats and correlate them with the strength of infection risk between each of them. This is a systematic review and meta-analysis following the recommendations of PRISMA 2020. The search and selection of papers was carried out using in vivo experimental works with animals using the descriptors (MeSH/DeCS) "Animal", "Public Health", "SARS-CoV-2" and "Pandemic" (together with AND) in English, Portuguese or Spanish for Science Direct, PUBMED, LILACS and SciELO databases. The ARRIVE checklist was used for methodological evaluation and the Comprehensive Meta-Analysis v2.2 software with the Difference Risk (RD) test to evaluate statistical inferences (with subgroups by continent). Cats showed greater susceptibility to SARS-CoV-2 compared to dogs both in a joint analysis of studies (RD = 0.017; 95% CI = 0.008-0.025; p < 0.0001) and in the American subgroup (RD = 0.053; 95% CI = 0.032-0.073; p < 0.0001), unlike the lack of significant difference on the European continent (RD = 0.009; 95% CI = -0.001-0.018; p = 0.066). Therefore, it was observed that cats have a greater interest in health surveillance due to the set of biological and ecological aspects of these animals, but also that there are a set of factors that can influence the spread and possible spillover events of the virus thanks to the anthropozoonotic context.

SARS-CoV-2 infection in brown-headed spider monkeys (Ateles fusciceps) at a wildlife rescue center on the coast of Ecuador-South America

Human populations can be affected in unpredictable ways by the emergence and spread of zoonotic diseases. The COVID-19 (coronavirus disease of 2019) pandemic was a reminder of how devastating these events can be if left unchecked. However, once they have spread globally, the impact of these diseases when entering non-exposed wildlife populations is unknown. The current study reports the infection of brown-headed spider monkeys (Ateles fusciceps) at a wildlife rescue center in Ecuador. Four monkeys were hospitalized, and all tested positive for SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) by RT-qPCR (Quantitative Reverse Transcription PCR). Fecal samples (n = 12) from monkeys at the rescue center also tested positive; three zookeepers responsible for feeding and deworming the monkeys also tested positive, suggesting human-animal transmission. Whole genome sequencing identified most samples' omicron clade 22B BA.5 lineage. These findings highlight the threat posed by an emerging zoonotic disease in wildlife species and the importance of preventing spillover and spillback events during epidemic or pandemic events.IMPORTANCEAlthough COVID-19 (coronavirus disease of 2019) has been primarily contained in humans through widespread vaccination, the impact and incidence of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus) and its transmission and epidemiology in wildlife may need to be addressed. In some natural environments, the proximity of animals to humans is difficult to control, creating perfect scenarios where susceptible wildlife can acquire the virus from humans. In these places, it is essential to understand how transmission can occur and to develop protocols to prevent infection. This study reports the infection of brown-headed spider monkeys with SARS-CoV-2, a red-listed monkey species, at a wildlife recovery center in Ecuador. This study reports the infection of brown-headed spider monkeys with SARS-CoV-2, indicating the potential for transmission between humans and wildlife primates and the importance of preventing such events in the future.

Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface

The highly conserved protease enzyme from SARS-CoV-2 (MPro) is crucial for viral replication and is an attractive target for the design of novel inhibitory compounds. MPro is known to be conformationally flexible and has been stabilized in an extended conformation in a complex with a novel nanobody (NB2B4), which inhibits the dimerization of the enzyme via binding to an allosteric site. However, the energetic contributions of the nanobody residues stabilizing the MPro/nanobody interface remain unresolved. We probed these residues using all-atom MD simulations in combination with alchemical free energy calculations by studying the physical residue-residue interactions and discovered the role of hydrophobic and electrostatic interactions in stabilizing the complex. Specifically, we found via mutational analysis that three interfacial nanobody residues (Y59, R106, and L109) contributed significantly, two residues (L107 and P110) contributed moderately, and two residues (H112 and T113) contributed minimally to the overall binding affinity of the nanobody. We also discovered that the nanobody affinity could be enhanced via a charge-reversal mutation (D62R) that alters the local interfacial electrostatic environment of this residue in the complex. These findings are potentially useful in designing novel synthetic nanobodies as allosteric inhibitors of MPro.

Possible Spreading of SARS-CoV-2 from Humans to Captive Non-Human Primates in the Peruvian Amazon

Human-to-animal transmission events of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) have been reported in both domestic and wild species worldwide. Despite the high rates of contagion and mortality during the COVID-19 (Coronavirus Diseases 2019) pandemic in Peru, no instances of natural virus infection have been documented in wild animals, particularly in the Amazonian regions where human-wildlife interactions are prevalent. In this study, we conducted a surveillance investigation using viral RNA sequencing of fecal samples collected from 76 captive and semi-captive non-human primates (NHPs) in the Loreto, Ucayali, and Madre de Dios regions between August 2022 and February 2023. We detected a segment of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 by metagenomic sequencing in a pooled fecal sample from captive white-fronted capuchins (Cebus unicolor) at a rescue center in Bello Horizonte, Ucayali. Phylogenetic analysis further confirmed that the retrieved partial sequence of the RdRp gene matched the SARS-CoV-2 genome. This study represents the first documented instance of molecular SARS-CoV-2 detection in NHPs in the Peruvian Amazon, underscoring the adverse impact of anthropic activities on the human-NHP interface and emphasizing the importance of ongoing surveillance for early detection and prediction of future emergence of new SARS-CoV-2 variants in animals.

Suburban Population of Bobcats (Lynx rufus) in Connecticut, USA, Tested Negative for SARS-CoV-2, November 2021-February 2022

A SARS-CoV-2 genomic and serologic survey was performed in a population of bobcats (Lynx rufus) inhabiting the state of Connecticut, USA. Wild animal populations are becoming established in densely populated cities with increased likelihood of direct or indirect contact with humans, as well as with household cats and dogs. Wild-caught bobcats (n=38) tested negative for SARS-CoV-2 genomic RNA by reverse-transcription quantitative PCR and for virus-neutralizing antibodies by ELISA, suggesting that either the species is not susceptible to SARS-CoV-2 or that the surveyed population has not yet been exposed to a source of infectious virus. However, this limited survey cannot rule out that human-to-bobcat or unknown reservoir-to-bobcat transmission of the virus occurs in nature.

Simian immunodeficiency virus and storage buffer: Field-friendly preservation methods for RNA viral detection in primate feces

IMPORTANCE

Simian immunodeficiency virus (SIV), which originated in African monkeys, crossed the species barrier into humans and ultimately gave rise to HIV and the global HIV/AIDS epidemic. While SIV infects over 40 primate species in sub-Saharan Africa, testing for RNA viruses in wild primate populations can be challenging. Optimizing field-friendly methods for assessing viral presence/abundance in non-invasively collected biological samples facilitates the study of viruses, including potentially zoonotic viruses, in wild primate populations. This study compares SIV RNA preservation and recovery from non-human primate feces stored in four different buffers. Our results will inform future fieldwork and facilitate improved approaches to characterizing prevalence, shedding, and transmission of RNA viruses like SIV in natural hosts including wild-living non-human primates.

Molecular surveillance of potential SARS-CoV-2 reservoir hosts in wildlife rehabilitation centers

BACKGROUND

The COVID-19 pandemic, caused by SARS-CoV-2 infection, has become the most devastating zoonotic event in recent times, with negative impacts on both human and animal welfare as well as on the global economy. Although SARS-CoV-2 is considered a human virus, it likely emerged from animals, and it can infect both domestic and wild animals. This constitutes a risk for human and animal health including wildlife with evidence of SARS-CoV-2 horizontal transmission back and forth between humans and wild animals.

AIM

Molecular surveillance in different wildlife rehabilitation centers and wildlife associated institutions in Chile, which are critical points of animal-human interaction and wildlife conservation, especially since the aim of wildlife rehabilitation centers is to reintroduce animals to their original habitat.

MATERIALS AND METHODS

The survey was conducted in six WRCs and three wildlife associated institutions. A total of 185 samples were obtained from 83 individuals belonging to 15 different species, including vulnerable and endangered species. Each specimen was sampled with two different swabs: one oropharyngeal or nasopharyngeal according to the nostril diameter, and/or a second rectal sample. RNA was extracted from the samples and two different molecular assays were performed: first, a conventional RT-PCR with pan-coronavirus primers and a second SARS-CoV-2 qPCR targeting the N and S genes.

RESULTS

All 185 samples were negative for SARS-CoV-2.

CLINICAL RELEVANCE

This study constitutes the first report on the surveillance of SARS-CoV-2 from wildlife treated in rehabilitation centers in Chile, and supports the biosafety procedures adopted in those centers.

Primate field research during a pandemic: Lessons learned from the SARS-CoV-2 outbreak

The COVID-19 pandemic abruptly halted most primate field research in early 2020. While international travel bans and regional travel restrictions made continuing primate field research impossible early on in the pandemic, ethical concerns of transmitting the virus from researchers to primates and surrounding human communities informed decisions regarding the timing of resuming research. Between June and September 2020, we surveyed field primatologists regarding the impacts of the pandemic on their research. We received 90 completed surveys from respondents residing in 21 countries, though most were from the United States and Canada. These data provide a valuable window into the perspectives and actions taken by researchers during the early stages of the pandemic as events were still unfolding. Only 2.4% of projects reported continuing research as usual, 33.7% continued with some decrease in productivity, 42.2% reported postponing research projects, and 21.7% reported canceling projects or postponing research indefinitely. Respondents most severely impacted by the pandemic were those establishing new field sites and graduate students whose projects were postponed or canceled due to pandemic-related shutdowns. Fears about increased poaching, the inability to pay local assistants, frozen research funds, declining habituation, disruptions to data collection, and delays in student projects were among the top concerns of respondents. Nearly all the projects able to continue research in any capacity during the early months of the pandemic were run by or employed primate habitat country primatologists. This finding is a major lesson learned from the pandemic; without habitat country scientists, primate research is not sustainable.

Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System

Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human-animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease management. In a previous study, we developed a straightforward mNGS procedure that greatly enhances the detection of RNA and DNA viruses in human clinical samples. In this study, we improved the mNGS protocol with transportable battery-driven equipment for the portable, non-targeted detection of RNA and DNA viruses in animals from a large zoological facility, to simulate a field setting for point-of-incidence virus detection. From the resulting metagenomic data, we detected 13 vertebrate viruses from four major virus groups: (+)ssRNA, (+)ssRNA-RT, dsDNA and (+)ssDNA, including avian leukosis virus in domestic chickens (Gallus gallus), enzootic nasal tumour virus in goats (Capra hircus) and several small, circular, Rep-encoding, ssDNA (CRESS DNA) viruses in several mammal species. More significantly, we demonstrate that the mNGS method is able to detect potentially lethal animal viruses, such as elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus) and the newly described human-associated gemykibivirus 2, a human-to-animal cross-species virus, in a Linnaeus two-toed sloth (Choloepus didactylus) and its enclosure, for the first time.

Near-complete genome of SARS-CoV-2 Delta variant of concern identified in a symptomatic dog (Canis lupus familiaris) in Botswana

We sought to investigate whether SARS-CoV-2 was present, and to perform full-length genomic sequencing, in a 5-year-old male crossbreed dog from Gaborone, Botswana that presented overt clinical signs (flu-like symptoms, dry hacking cough and mild dyspnoea). It was only sampled a posteriori, because three adult owners were diagnosed with SARS-CoV-2 infection. Next-generation sequencing based on Oxford Nanopore Technology (ONT) was performed on amplicons that were generated using a reverse transcriptase real-time polymerase chain reaction (RT-qPCR) of confirmed positive SARS-CoV-2 nasopharyngeal and buccal swabs, as well as a bronchoalveolar lavage with mean real cycle threshold (qCt) value of 36 based on the Nucleocapsid (N) gene. Descriptive comparisons to known sequences in Botswana and internationally were made using mutation profiling analysis and phylogenetic inferences. Human samples were not available. A near-full length SARS-CoV-2 genome (∼90% coverage) was successfully genotyped and classified under clade 20 O and Pango-Lineage AY.43 (Pango v.4.0.6 PLEARN-v1.3; 2022-04-21), which is a sublineage of the Delta variant of concern (VOC) (formerly called B.1.617.2, first detected in India). We did not identify novel mutations that may be used to distinguish SARS-CoV-2 isolates from the dog and humans. In addition to Spike (S) region mutation profiling, we performed phylogenetic analysis including 30 Delta sequences publicly available reference also isolated from dogs. In addition, we performed another exploratory analysis to investigate the phylogenetic relatedness of sequence isolated from dog with those from humans in Botswana (n = 1303) as of 31 March 2022 and of same sublineage. Expectedly, the sequence formed a cluster with Delta sublineages - AY.43, AY.116 and B.1.617.2 - circulating in same time frame. This is the first documented report of human-associated SARS-CoV-2 infection in a dog in Botswana. Although the direction of transmission remains unknown, this study further affirms the need for monitoring pets during different COVID-19 waves for possible clinically relevant SARS-CoV-2 transmissions between species.

SARS-CoV-2 Spillback to Wild Coatis in Sylvatic-Urban Hotspot, Brazil

We tested coatis (Nasua nasua) living in an urban park near a densely populated area of Brazil and found natural SARS-CoV-2 Zeta variant infections by using quantitative reverse transcription PCR, genomic sequencing, and serologic surveillance. We recommend a One Health strategy to improve surveillance of and response to COVID-19.

SARS-CoV-2 Affects Both Humans and Animals: What Is the Potential Transmission Risk? A Literature Review

In March 2020, the World Health Organization Department declared the coronavirus (COVID-19) outbreak a global pandemic, as a consequence of its rapid spread on all continents. The COVID-19 pandemic has been not only a health emergency but also a serious general problem as fear of contagion and severe restrictions put economic and social activity on hold in many countries. Considering the close link between human and animal health, COVID-19 might infect wild and companion animals, and spawn dangerous viral mutants that could jump back and pose an ulterior threat to us. The purpose of this review is to provide an overview of the pandemic, with a particular focus on the clinical manifestations in humans and animals, the different diagnosis methods, the potential transmission risks, and their potential direct impact on the human-animal relationship.

EFSA Panel on Animal Health and Welfare (AHAW), Nielsen SS, Alvarez J, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Velarde A, Viltrop A, Winckler C, Adlhoch C, Aznar I, Baldinelli F, Boklund A, Broglia A, Gerhards N, Mur L, Nannapaneni P, Ståhl K. SARS-CoV-2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control

The epidemiological situation of SARS-CoV-2 in humans and animals is continually evolving. To date, animal species known to transmit SARS-CoV-2 are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse and white-tailed deer. Among farmed animals, American mink have the highest likelihood to become infected from humans or animals and further transmit SARS-CoV-2. In the EU, 44 outbreaks were reported in 2021 in mink farms in seven MSs, while only six in 2022 in two MSs, thus representing a decreasing trend. The introduction of SARS-CoV-2 into mink farms is usually via infected humans; this can be controlled by systematically testing people entering farms and adequate biosecurity. The current most appropriate monitoring approach for mink is the outbreak confirmation based on suspicion, testing dead or clinically sick animals in case of increased mortality or positive farm personnel and the genomic surveillance of virus variants. The genomic analysis of SARS-CoV-2 showed mink-specific clusters with a potential to spill back into the human population. Among companion animals, cats, ferrets and hamsters are those at highest risk of SARS-CoV-2 infection, which most likely originates from an infected human, and which has no or very low impact on virus circulation in the human population. Among wild animals (including zoo animals), mostly carnivores, great apes and white-tailed deer have been reported to be naturally infected by SARS-CoV-2. In the EU, no cases of infected wildlife have been reported so far. Proper disposal of human waste is advised to reduce the risks of spill-over of SARS-CoV-2 to wildlife. Furthermore, contact with wildlife, especially if sick or dead, should be minimised. No specific monitoring for wildlife is recommended apart from testing hunter-harvested animals with clinical signs or found-dead. Bats should be monitored as a natural host of many coronaviruses.

The SARS-CoV-2 Pandemic at the Wildlife-Domestic Animal-Human Interface

Since the start of the COVID-19 pandemic, which has hitherto killed almost 7 million people worldwide-although the true mortality figures could be much higher-we have witnessed a progressively expanding number of domestic and wild mammalian species acquiring Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) infection, both spontaneously and experimentally [...].

Tissue distribution of angiotensin-converting enzyme 2 (ACE2) receptor in wild animals with a focus on artiodactyls, mustelids and phocids

Natural cases of zooanthroponotic transmission of SARS-CoV-2 to animals have been reported during the COVID-19 pandemic, including to free-ranging white-tailed deer (Odocoileus virginianus) in North America and farmed American mink (Neovison vison) on multiple continents. To understand the potential for angiotensin-converting enzyme 2 (ACE2)-mediated viral tropism we characterised the distribution of ACE2 receptors in the respiratory and intestinal tissues of a selection of wild and semi-domesticated mammals including artiodactyls (cervids, bovids, camelids, suids and hippopotamus), mustelid and phocid species using immunohistochemistry. Expression of the ACE2 receptor was detected in the bronchial or bronchiolar epithelium of several European and Asiatic deer species, Bactrian camel (Camelus bactrianus), European badger (Meles meles), stoat (Mustela erminea), hippopotamus (Hippopotamus amphibious), harbor seal (Phoca vitulina), and hooded seal (Cystophora cristata). Further receptor mapping in the nasal turbinates and trachea revealed sparse ACE2 receptor expression in the mucosal epithelial cells and occasional occurrence in the submucosal glandular epithelium of Western roe deer (Capreolus capreolus), moose (Alces alces alces), and alpaca (Vicunga pacos). Only the European badger and stoat expressed high levels of ACE2 receptor in the nasal mucosal epithelium, which could suggest high susceptibility to ACE2-mediated respiratory infection. Expression of ACE2 receptor in the intestinal cells was ubiquitous across multiple taxa examined. Our results demonstrate the potential for ACE2-mediated viral infection in a selection of wild mammals and highlight the intra-taxon variability of ACE2 receptor expression, which might influence host susceptibility and infection.

Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink

To investigate genetic signatures of adaptation to the mink host, we characterised the evolutionary rate heterogeneity in mink-associated severe acute respiratory syndrome coronaviruses (SARS-CoV-2). In 2020, the first detected anthropozoonotic spillover event of SARS-CoV-2 occurred in mink farms throughout Europe and North America. Both spill-back of mink-associated lineages into the human population and the spread into the surrounding wildlife were reported, highlighting the potential formation of a zoonotic reservoir. Our findings suggest that the evolutionary rate of SARS-CoV-2 underwent an episodic increase upon introduction into the mink host before returning to the normal range observed in humans. Furthermore, SARS-CoV-2 lineages could have circulated in the mink population for a month before detection, and during this period, evolutionary rate estimates were between 3 × 10-3 and 1.05 × 10-2 (95 per cent HPD, with a mean rate of 6.59 × 10-3) a four- to thirteen-fold increase compared to that in humans. As there is evidence for unique mutational patterns within mink-associated lineages, we explored the emergence of four mink-specific Spike protein amino acid substitutions Y453F, S1147L, F486L, and Q314K. We found that mutation Y453F emerged early in multiple mink outbreaks and that mutations F486L and Q314K may co-occur. We suggest that SARS-CoV-2 undergoes a brief, but considerable, increase in evolutionary rate in response to greater selective pressures during species jumps, which may lead to the occurrence of mink-specific mutations. These findings emphasise the necessity of ongoing surveillance of zoonotic SARS-CoV-2 infections in the future.

Contact between European bison and cattle from the cattle breeders' perspective, in the light of the risk of pathogen transmission

Pathogens transmitted between wildlife and domestic animals can pose a threat to endangered species, undermine conservation efforts in wildlife, and affect productivity and parasite control in domestic animals. There are several examples of pathogen transmission between European bison and other animals. The present study surveyed breeders from the vicinity of four large wisent populations in eastern Poland about observed contacts between wisent and cattle. Such contacts were noted by 37% of breeders, indicating a significant risk of contact between European bison and cattle in the study areas, even in the areas where the European bison live mainly in a forest complex, i.e., in the Borecka Forest. A higher potential risk of contacts between European bison and cattle was noted in the Białowieska Forest and the Bieszczady Mountains than in the Borecka and Knyszyńska Forests. In the Białowieska Forest, the risk of viral pathogen transmission resulting from contacts is higher (more direct contacts), and in the case of the Bieszczady Mountains, the probability of parasitic diseases is higher. The chance of contacts between European bison and cattle depended on the distance of cattle pastures from human settlements. Moreover, such contact was possible throughout the year, not only in spring and fall. It appears possible to minimize the risk of contacts between wisent and cattle by changing management practices for both species, such as keeping grazing areas as close as possible to settlements, and reducing the time cattle graze on pastures. However, the risk of contact is much greater if European bison populations are large and are dispersed beyond forest complexes.

Susceptibility of SARS Coronavirus-2 infection in domestic and wild animals: a systematic review

Animals and viruses have constantly been co-evolving under natural circumstances and pandemic like situations. They harbour harmful viruses which can spread easily. In the recent times we have seen pandemic like situations being created as a result of the spread of deadly and fatal viruses. Coronaviruses (CoVs) are one of the wellrecognized groups of viruses. There are four known genera of Coronavirus family namely, alpha (α), beta (β), gamma (γ), and delta (δ). Animals have been infected with CoVs belonging to all four genera. In the last few decades the world has witnessed an emergence of severe acute respiratory syndromes which had created a pandemic like situation such as SARS CoV, MERS-CoV. We are currently in another pandemic like situation created due to the uncontrolled spread of a similar coronavirus namely SARSCoV-2. These findings are based on a small number of animals and do not indicate whether animals can transmit disease to humans. Several mammals, including cats, dogs, bank voles, ferrets, fruit bats, hamsters, mink, pigs, rabbits, racoon dogs, and white-tailed deer, have been found to be infected naturally by the virus. Certain laboratory discoveries revealed that animals such as cats, ferrets, fruit bats, hamsters, racoon dogs, and white-tailed deer can spread the illness to other animals of the same species. This review article gives insights on the current knowledge about SARS-CoV-2 infection and development in animals on the farm and in domestic community and their impact on society.

Lack of SARS-CoV-2 RNA evidence in the lungs from wild European polecats (Mustela putorius) from Spain

Data on SARS-CoV-2 infection in wildlife species is limited. The high prevalences found in mustelid species such as free-ranging American minks (Neovison vison) and domestic ferrets (Mustela putorius furo) justify the study of this virus in the closely related autochthonous free-ranging European polecat (Mustela putorius). We analysed lung samples from 48 roadkilled polecats collected when the human infection reached its highest levels in Spain (2020-2021). We did not detect infections by SARS-CoV-2; however, surveillance in wild carnivores and particularly in mustelids is still warranted, due to their susceptibility to this virus.

SARS-CoV-2 and animals, a long story that doesn't have to end now: What we need to learn from the emergence of the Omicron variant

OIE, the world organization for animal health, recently released an update on the state of the art of knowledge regarding SARS-CoV-2 in animals. For farmed animals, ferrets and minks were found to be highly susceptible to the virus and develop symptomatic disease both in natural conditions and in experimental infections. Lagomorphs of the species Oryctolagus cuniculus are indicated as highly susceptible to the virus under experimental conditions, but show no symptoms of the disease and do not transmit the virus between conspecifics, unlike raccoon dogs (Nyctereutes procyonoides), which in addition to being highly susceptible to the virus under experimental conditions, can also transmit the virus between conspecifics. Among felines, the circulation of the virus has reached a level of cases such as sometimes suggests the experimental use of vaccines for human use or treatments with monoclonal antibodies. But even among wild animals, several species (White-tailed deer, Egyptian rousettes, and minks) have now been described as potential natural reservoirs of the virus. This proven circulation of SARS-CoV-2 among animals has not been accompanied by the development of an adequate surveillance system that allows following the evolution of the virus among its natural hosts. This will be all the more relevant as the surveillance system in humans inevitably drops and we move to surveillance by sentinels similar to the human flu virus. The lesson that we can draw from the emergence of Omicron and, more than likely, its animal origin must not be lost, and in this mini-review, we explain why.

Francisella tularensis PCR detection in Cape hares (Lepus capensis) and wild rabbits (Oryctolagus cuniculus) in Algeria

Tularemia is a zoonosis caused by the bacterium Francisella tularensis. Leporids are primary sources of human infections in the northern hemisphere. Africa is classically considered free of tularemia, but recent data indicate that this dogma might be wrong. We assessed the presence of this disease in wild leporids in Algeria. Between 2014 and 2018, we collected 74 leporids carcasses from spontaneously dead or hunted animals. Francisella tularensis DNA was detected by specific real-time PCR tests in 7/36 (19.44%) Cape hares (Lepus capensis) and 5/38 (13.15%) wild rabbits (Oryctolagus cuniculus). Known tularemia arthropod vectors infested half of the PCR-positive animals. At necropsy, F. tularensis-infected animals presented with an enlarged spleen (n = 12), enlarged adrenal glands (12), liver discoloration (12), hemorrhages (11), and pneumonia (11). Immunohistological examination of liver tissue from one animal was compatible with the presence of F. tularensis. Our study demonstrates the existence of tularemia in lagomorphs in Algeria. It should encourage investigations to detect this disease among the human population of this country.

Parainfluenza and corona viruses in a fallow deer (Dama dama) with fatal respiratory disease

Parainfluenza virus type 3 (PIV-3) and coronaviruses (CoV) are commonly found in respiratory tracts of ruminants and capable of causing clinical disease. Here, we investigated the cause of ill-thrift and sudden death in a five-month-old male fallow deer which occurred in December 2019. The calf was one of the five calves in a herd of 170 deer that, along with three adult hinds, died during a 2-week period. The deer calves were in a shed, sharing airspace with young cattle that had been reported to be coughing. Significant gross pathology was observed in the respiratory and alimentary tracts of the deer calf and histopathology of the lung and trachea was suggestive of likely involvement of PIV-3. Strong and specific cytoplasmic labeling of bronchiolar epithelium and terminal airway, alike those seen with PIV-3 pneumonia in cattle, was observed using a polyclonal bovine PIV-3 antibody. Metagenomic analysis detected a PIV-3 and a CoV in the lung tissue. The PIV-3 L protein gene had the highest sequence identity with those of bovine PIV-3 (83.1 to 98.4%) and phylogenetically clustered with bovine PIV-3 in the genotype C. The CoV spike protein gene shared 96.7% to 97.9% sequence identity with those of bovine CoVs, but only 53.1% identity with SARS-CoV-2 reference virus. We believe this is the first report of PIV-3 and CoV co-infection in fallow deer and their association with fatal pneumonia; major pathology caused by PIV-3.

SARS-CoV-2 variants of concerns in animals: An unmonitored rising health threat

Recent findings have highlighted the urgency for rapidly detecting and characterizing SARS-CoV-2 variants of concern in companion and wild animals. The significance of active surveillance and genomic investigation on these animals could pave the way for more understanding of the viral circulation and how the variants emerge. It enables us to predict the next viral challenges and prepare for or prevent these challenges. Horrible neglect of this issue could make the COVID-19 pandemic a continuous threat. Continuing to monitor the animal-origin SARS-CoV-2, and tailoring prevention and control measures to avoid large-scale community transmission in the future caused by the virus leaping from animals to humans, is essential. The reliance on only developing vaccines with ignoring this strategy could cost us many lives. Here, we discuss the most recent data about the transmissibility of SARS-CoV-2 variants of concern (VOCs) among animals and humans.

Wild Red Deer (Cervus elaphus) Do Not Play a Role as Vectors or Reservoirs of SARS-CoV-2 in North-Eastern Poland

Several studies reported a high prevalence of SARS-CoV-2 among white-tailed deer in North America. Monitoring cervids in all regions to better understand SARS-CoV-2 infection and circulation in other deer populations has been urged. To evaluate deer exposure and/or infection to/by SARS-CoV-2 in Poland, we sampled 90 red deer shot by hunters in five hunting districts in north-eastern Poland. Serum and nasopharyngeal swabs were collected, and then an immunofluorescent assay (IFA) to detect anti-SARS-CoV-2 antibodies was performed as well as real-time PCR with reverse transcription for direct virus detection. No positive samples were detected. There is no evidence of spillover of SARS-CoV-2 from the human to deer population in Poland.

Molecular surveillance revealed no SARS-CoV-2 spillovers to raccoons (Procyon lotor) in four German federal states

Raccoons (Procyon lotor), which are closely related to the family Mustelidae, might be susceptible to natural infection by SARS-CoV-2. This assumption is based on experimental evidence that confirmed the vulnerability of farmed fur-carnivore species, including Procyon lotor to SARS-CoV-2. To date, there are no reports of natural SARS-CoV-2 infections of raccoons in Germany. Here, we use RT-PCR to analyze 820 samples from raccoons hunted in Germany with a focus on 4 German federal states (Saxony-Anhalt, Thuringia, Hesse, North Rhine-Westphalia). Lung tissues were homogenized and processed for RNA extraction and RT-qPCR for detecting SARS-CoV-2 was performed. No viral RNA was detected in any samples (0/820). Next, we compared raccoons and human ACE-2 residues that are known to serve for binding with SARS-CoV-2 receptor binding domain (RBD). Interestingly, we found only 60% identity on amino acid level, which may have contributed to the absence of SARS-CoV-2 infections in raccoons. In conclusion, the chance of raccoons being intermediate reservoir hosts for SARS-CoV-2 seems to be very low.

Detection of SARS-CoV-2 in a free ranging leopard (Panthera pardus fusca) in India

We report 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 of Pango lineage B.1.617.2 of SARS-CoV-2. Till now, only Asiatic lions have been reported to be infected by SARS-CoV-2 in India. Infections in animals were detected during peak phase of pandemic and all the cases were captive with close contacts with humans, whereas the present case was observed when human cases were significantly low. No tangible evidence linked to widespread infection in the wild population and the incidence seems to be isolated case. High nucleotide sequence homology with prevailing viruses in humans suggested spillover infection to the animal. This report underlines the need for intensive screening of wild animals for keeping track of the virus evolution and development of carrier status of SARS-CoV-2 among wildlife species.

Risk factors for mortality among hospitalized COVID-19 patients in Northern Ethiopia: A retrospective analysis

Background

COVID-19 is a deadly pandemic caused by an RNA virus that belongs to the family of CORONA virus. To counter the COVID-19 pandemic in resource limited settings, it is essential to identify the risk factors of COVID-19 mortality. This study was conducted to identify the social and clinical determinants of mortality in COVID-19 patients hospitalized in four treatment centers of Tigray, Northern Ethiopia.

Methods

We reviewed data from 6,637 COVID-19 positive cases that were reported from May 7, 2020 to October 28, 2020. Among these, 925 were admitted to the treatment centers because of their severity and retrospectively analyzed. The data were entered into STATA 16 version for analysis. The descriptive analysis such as median, interquartile range, frequency distribution and percentage were used. Binary logistic regression model was fitted to identify the potential risk factors of mortality of COVID-19 patients. The adjusted odds ratio (AOR) with 95% confidence interval was used to determine the magnitude of the association between the outcome and predictor variables.

Results

The median age of the patients was 30 years (IQR, 25–44) and about 70% were male patients. The patients in the non-survivor group were much older than those in the survivor group (median 57.5 years versus 30 years, p-value < 0.001). The overall case fatality rate was 6.1% (95% CI: 4.5% - 7.6%) and was increased to 40.3% (95% CI: 32.2% - 48.4%) among patients with critical and severe illness. The proportions of severe and critical illness in the non-survivor group were significantly higher than those in the survivor group (19.6% versus 5.1% for severe illness and 80.4% versus 4.5% for critical illness, all p-value < 0.001). One or more pre-existing comorbidities were present in 12.5% of the patients: cardiovascular diseases (42.2%), diabetes mellitus (25.0%) and respiratory diseases (16.4%) being the most common comorbidities. The comorbidity rate in the non-survivor group (44.6%) was higher than in the survivor group (10.5%). The results from the multivariable binary regression showed that the odds of mortality was higher for patients who had cardiovascular diseases (AOR = 2.49, 95% CI: 1.03–6.03), shortness of breath (AOR = 9.71, 95% CI: 4.73–19.93) and body weakness (AOR = 3.04, 95% CI: 1.50–6.18). Moreover, the estimated odds of mortality significantly increased with patient’s age.

Conclusions

Age, cardiovascular diseases, shortness of breath and body weakness were the predictors for mortality of COVID-19 patients. Knowledge of these could lead to better identification of high risk COVID-19 patients and thus allow prioritization to prevent mortality.

No Evidence of SARS-CoV-2 Infection in Wild Mink (Mustela lutreola and Neogale vison) from Northern Spain during the First Two Years of Pandemic

Simple Summary

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causing coronavirus disease-2019 (COVID-19) is a betacoronavirus (β-CoV) closely related to Severe Acute Respiratory Syndrome (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which have also caused severe outbreaks of disease in human populations. Human-to-animal transmission events during the COVID-19 pandemic have been documented in several countries. Different animal species have been proven to be susceptible to infection with SARS-CoV-2 both naturally and by experimental infection, including mustelids such as ferrets, otters, and American mink (Neogale vison). In this sense, infected farmed American mink develop respiratory signs associated with viral pneumonia. This study evaluates the presence of SARS-CoV-2 in European mink (Mustela lutreola) and American mink from Spain, by enzyme-linked immunosorbent assay (ELISA) using the receptor binding domain (RBD) of Spike protein antigen in serum samples and/or by RT-qPCR assays in oropharyngeal and rectal swabs. From January 2020 to February 2022, a total of 162 animals (127 European mink and 35 American mink) with no evidence of SARS-CoV-2 infection were included in the study. Of the 126 serum samples analysed by serology, anti-SARS-CoV-2 antibodies were not detected in the mink included in this study. In the same way, SARS-CoV-2 RNA has not been detected in any of the 160 swabs samples analysed by RT-qPCR. This study shows the absence of the wild mink exposure to SARS-CoV-2 in a geographic area seriously affected by COVID-19. With these results, it can be considered that the probability that the virus is circulating in wild mink is low. With this, the risk of virus transmission to humans by this route is also considered improbable.

Abstract

The impact of the SARS-CoV-2 pandemic on wildlife is largely unevaluated, and extended surveillance of animal species is needed to reach a consensus on the role of animals in the emergence and maintenance of SARS-CoV-2. This infection has been detected in farmed and domestic animals and wild animals, mainly in captivity. The interactions or shared resources with wildlife could represent a potential transmission pathway for the SARS-CoV-2 spill over to other wild species and could lead to health consequences or the establishment of new reservoirs in susceptible hosts. This study evaluated the presence of SARS-CoV-2 in European mink (Mustela lutreola) and American mink (Neogale vison) in Spain by enzyme-linked immunosorbent assay (ELISA) using the receptor binding domain (RBD) of Spike antigen in serum samples and/or by RT-qPCR assays in oropharyngeal and rectal swabs. From January 2020 to February 2022, a total of 162 animals (127 European mink and 35 American mink) with no evidence of SARS-CoV-2 infection were included in the study. Antibodies against the SARS-CoV-2 were not found in the serum samples analysed (n = 126), nor was the virus amplified by RT-qPCR (n = 160 swabs). Our results suggest that the potential role of wild mink and the European mink bred in captivity and released to the wild as dispersers of SARS-CoV-2 is so far low. However, wildlife surveillance for early detection of human and animal risks should be continued. In this sense, epidemiological monitoring measures, including serology and molecular analysis, are necessary.

Chromosomal-level reference genome assembly of the North American wolverine (Gulo gulo luscus): a resource for conservation genomics

We report a chromosomal-level genome assembly of a male North American wolverine (Gulo gulo luscus) from the Kugluktuk region of Nunavut, Canada. The genome was assembled directly from long-reads, comprising: 758 contigs with a contig N50 of 36.6 Mb; contig L50 of 20; base count of 2.39 Gb; and a near complete representation (99.98%) of the BUSCO 5.2.2 set of 9,226 genes. A presumptive chromosomal-level assembly was generated by scaffolding against two chromosomal-level Mustelidae reference genomes, the ermine and the Eurasian river otter, to derive a final scaffold N50 of 144.0 Mb and a scaffold L50 of 7. We annotated a comprehensive set of genes that have been associated with models of aggressive behavior, a trait which the wolverine is purported to have in the popular literature. To support an integrated, genomics-based wildlife management strategy at a time of environmental disruption from climate change, we annotated the principal genes of the innate immune system to provide a resource to study the wolverine's susceptibility to new infectious and parasitic diseases. As a resource, we annotated genes involved in the modality of infection by the coronaviruses, an important class of viral pathogens of growing concern as shown by the recent spillover infections by severe acute respiratory syndrome coronavirus-2 to naïve wildlife. Tabulation of heterozygous single nucleotide variants in our specimen revealed a heterozygosity level of 0.065%, indicating a relatively diverse genetic pool that would serve as a baseline for the genomics-based conservation of the wolverine, a rare cold-adapted carnivore now under threat.

Transmission history of SARS-CoV-2 in humans and white-tailed deer

The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritisation of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human–animal interface.

Differential susceptibility of SARS-CoV-2 in animals: Evidence of ACE2 host receptor distribution in companion animals, livestock and wildlife by immunohistochemical characterisation

Angiotensin converting enzyme 2 (ACE2) is a host cell membrane protein (receptor) that mediates the binding of coronavirus, most notably SARS coronaviruses in the respiratory and gastrointestinal tracts. Although SARS-CoV-2 infection is mainly confined to humans, there have been numerous incidents of spillback (reverse zoonoses) to domestic and captive animals. An absence of information on the spatial distribution of ACE2 in animal tissues limits our understanding of host species susceptibility. Here, we describe the distribution of ACE2 using immunohistochemistry (IHC) on histological sections derived from carnivores, ungulates, primates and chiroptera. Comparison of mink (Neovison vison) and ferret (Mustela putorius furo) respiratory tracts showed substantial differences, demonstrating that ACE2 is present in the lower respiratory tract of mink but not ferrets. The presence of ACE2 in the respiratory tract in some species was much more restricted as indicated by limited immunolabelling in the nasal turbinate, trachea and lungs of cats (Felis catus) and only the nasal turbinate in the golden Syrian hamster (Mesocricetus auratus). In the lungs of other species, ACE2 could be detected on the bronchiolar epithelium of the sheep (Ovis aries), cattle (Bos taurus), European badger (Meles meles), cheetah (Acinonyx jubatus), tiger and lion (Panthera spp.). In addition, ACE2 was present in the nasal mucosa epithelium of the serotine bat (Eptesicus serotinus) but not in pig (Sus scrofa domestica), cattle or sheep. In the intestine, ACE2 immunolabelling was seen on the microvillus of enterocytes (surface of intestine) across various taxa. These results provide anatomical evidence of ACE2 expression in a number of species which will enable further understanding of host susceptibility and tissue tropism of ACE2 receptor-mediated viral infection.

Effects of Spike Mutations in SARS-CoV-2 Variants of Concern on Human or Animal ACE2-Mediated Virus Entry and Neutralization

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoonotic agent capable of infecting humans and a wide range of animal species. Over the duration of the pandemic, mutations in the SARS-CoV-2 spike (S) protein have arisen, culminating in the spread of several variants of concern (VOCs) with various degrees of altered virulence, transmissibility, and neutralizing antibody escape. In this study, we used pseudoviruses that express specific SARS-CoV-2 S protein substitutions and cell lines that express angiotensin-converting enzyme 2 (ACE2) from nine different animal species to gain insights into the effects of VOC mutations on viral entry and antibody neutralization capability. All animal ACE2 receptors tested, except mink, support viral cell entry for pseudoviruses expressing the ancestral prototype S at levels comparable to human ACE2. Most single S substitutions did not significantly change virus entry, although 614G and 484K resulted in a decreased efficiency. Conversely, combinatorial VOC substitutions in the S protein were associated with increased entry of pseudoviruses. Neutralizing titers in sera from various animal species were significantly reduced against pseudoviruses expressing the S proteins of Beta, Delta, or Omicron VOCs compared to the parental S protein. Especially, substitutions in the S protein of the Omicron variant significantly reduced the neutralizing titers of the sera. This study reveals important insights into the host range of SARS-CoV-2 and the effect of recently emergent S protein substitutions on viral entry, virus replication, and antibody-mediated viral neutralization. IMPORTANCE The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to have devastating impacts on global health and socioeconomics. The recent emergence of SARS-CoV-2 variants of concern, which contain mutations that can affect the virulence, transmission, and effectiveness of licensed vaccines and therapeutic antibodies, are currently becoming the common strains circulating in humans worldwide. In addition, SARS-CoV-2 has been shown to infect a wide variety of animal species, which could result in additional mutations of the SARS-CoV-2 virus. In this study, we investigate the effect of mutations present in SARS-CoV-2 variants of concern and determine the effects of these mutations on cell entry, virulence, and antibody neutralization activity in humans and a variety of animals that might be susceptible to SARS-CoV-2 infection. This information is essential to understand the effects of important SARS-CoV-2 mutations and to inform public policy to create better strategies to control the COVID-19 pandemic.

Investigating SARS-CoV-2 Susceptibility in Animal Species: A Scoping Review

In the early stages of response to the SARS-CoV-2 pandemic, it was imperative for researchers to rapidly determine what animal species may be susceptible to the virus, under low knowledge and high uncertainty conditions. In this scoping review, the animal species being evaluated for SARS-CoV-2 susceptibility, the methods used to evaluate susceptibility, and comparing the evaluations between different studies were conducted. Using the PRISMA-ScR methodology, publications and reports from peer-reviewed and gray literature sources were collected from databases, Google Scholar, the World Organization for Animal Health (OIE), snowballing, and recommendations from experts. Inclusion and relevance criteria were applied, and information was subsequently extracted, categorized, summarized, and analyzed. Ninety seven sources (publications and reports) were identified which investigated 649 animal species from eight different classes: Mammalia, Aves, Actinopterygii, Reptilia, Amphibia, Insecta, Chondrichthyes, and Coelacanthimorpha. Sources used four different methods to evaluate susceptibility, in silico, in vitro, in vivo, and epidemiological analysis. Along with the different methods, how each source described "susceptibility" and evaluated the susceptibility of different animal species to SARS-CoV-2 varied, with conflicting susceptibility evaluations evident between different sources. Early in the pandemic, in silico methods were used the most to predict animal species susceptibility to SARS-CoV-2 and helped guide more costly and intensive studies using in vivo or epidemiological analyses. However, the limitations of all methods must be recognized, and evaluations made by in silico and in vitro should be re-evaluated when more information becomes available, such as demonstrated susceptibility through in vivo and epidemiological analysis.

The One Health concept for the threat of severe acute respiratory syndrome coronavirus-2 to marine ecosystems

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health threat. This virus is the causative agent for coronavirus disease 2019 (COVID-19). Pandemic prevention is best addressed through an integrated One Health (OH) approach. Understanding zoonotic pathogen fatality and spillover from wildlife to humans are effective for controlling and preventing zoonotic outbreaks. The OH concept depends on the interface of humans, animals, and their environment. Collaboration among veterinary medicine, public health workers and clinicians, and veterinary public health is necessary for rapid response to emerging zoonotic pathogens. SARS-CoV-2 affects aquatic environments, primarily through untreated sewage. Patients with COVID-19 discharge the virus in urine and feces into residential wastewater. Thus, marine organisms may be infected with SARS-CoV-2 by the subsequent discharge of partially treated or untreated wastewater to marine waters. Viral loads can be monitored in sewage and surface waters. Furthermore, shellfish are vulnerable to SARS-CoV-2 infection. Filter-feeding organisms might be monitored to protect consumers. Finally, the stability of SARS-CoV-2 to various environmental factors aids in viral studies. This article highlights the presence and survival of SARS-CoV-2 in the marine environment and its potential to enter marine ecosystems through wastewater. Furthermore, the OH approach is discussed for improving readiness for successive outbreaks. This review analyzes information from public health and epidemiological monitoring tools to control COVID-19 transmission.

Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken

Multiple domestic and wild animal species are susceptible to SARS-CoV-2 infection. Cattle and swine are susceptible to experimental SARS-CoV-2 infection. The unchecked transmission of SARS-CoV-2 in animal hosts could lead to virus adaptation and the emergence of novel variants. In addition, the spillover and subsequent adaptation of SARS-CoV-2 in livestock could significantly impact food security as well as animal and public health. Therefore, it is essential to monitor livestock species for SARS-CoV-2 spillover. We developed and optimized species-specific indirect ELISAs (iELISAs) to detect anti-SARS-CoV-2 antibodies in cattle, swine, and chickens using the spike protein receptor-binding domain (RBD) antigen. Serum samples collected prior to the COVID-19 pandemic were used to determine the cut-off threshold. RBD hyperimmunized sera from cattle (n = 3), swine (n = 6), and chicken (n = 3) were used as the positive controls. The iELISAs were evaluated compared to a live virus neutralization test using cattle (n = 150), swine (n = 150), and chicken (n = 150) serum samples collected during the COVID-19 pandemic. The iELISAs for cattle, swine, and chicken were found to have 100% sensitivity and specificity. These tools facilitate the surveillance that is necessary to quickly identify spillovers into the three most important agricultural species worldwide.