Possibility for reverse zoonotic transmission of SARS-CoV-2 to free-ranging wildlife: A case study of bats

Origin and diversification of Dicrocoeliidae (Neodermata, Trematoda) with the description of a new species of Euparadistomum, a parasite of Tropidurus torquatus (Squamata, Tropiduridae) in South America

A new digenean trematode species, Euparadistomum cisalpinai sp. n., is described parasitizing the gallbladder of Tropidurus torquatus from Brazil. A set of morphological features, including ovary shape, the oral/ventral sucker ratio, and the presence of cuticular papillae, distinguish the new species from other Euparadistomum species. Phylogenetic inferences using 28S rDNA sequences confirmed its placement within the family Dicrocoeliidae. Although some morphological variability was observed, COI sequences support conspecificity among the specimens. The origin of Dicrocoeliidae is estimated to date back to the Late Jurassic, a period marked by the fragmentation of Pangaea, the greatest radiation of insects, and the emergence of modern birds. These paleogeographic events, combined with the ecological traits of the hosts, likely served as key drivers of dicrocoeliid diversification. Additionaly, the opening of the North Atlantic, the dispersal of yangochiropteran bats, and the spread of Turdus birds significantly influenced the evolution of genera such as Lyperosomum, Anenterotrema, Metadelphis, and Lutztrema. This research provides key insights into the evolutionary and biogeographic history of Dicrocoeliidae, highlighting the pivotal role of host-parasite interactions and geographic events in shaping the diversification of these trematodes.

Cross-Species Surveillance of Respiratory Viruses in Domestic and Wild Mammals of an Urban Atlantic Forest from Brazil

Our aim was to investigate respiratory viruses circulating in animals from the urban Atlantic Forest, which is located in the most densely populated area near Rio de Janeiro in Brazil. This study focused on the detection of Influenza A viruses and diverse coronaviruses, including SARS-CoV-2, in domestic and wild animals, including bats, nonhuman primates, rodents, and marsupials. From August 2020 to September 2022, biological samples were collected from a total of 72 pets, 66 primates, 20 rodents, 36 marsupials, and 390 bats. Samples were tested using RT-PCR for Influenza A and coronaviruses, and positive samples were sequenced. When blood samples were available, they were tested for SARS-CoV-2 antibodies. All terrestrial animals were negative for evidence of infection with SARS-CoV-2 and Influenza A viruses. However, samples from 17 phyllostomid bats, including Great fruit-eating bat (Artibeus lituratus), Silky short-tailed bat (Carollia brevicauda), Seba's short-tailed bat (Carollia perspicillata), Common big-eared bat (Micronycteris microtis), Greater spear-nosed bat (Phyllostomus hastatus), White-lined broad-nosed bat (Platyrrhinus lineatus), Little yellow-shouldered bat (Sturnira lilium), Greater round-eared bat (Tonatia bidens), and Common vampire bat (Desmodus rotundus), were positive for bat coronaviruses classified as Alphacoronavirus. Our study adds new information on the occurrence of coronaviruses in bats and contributes to a long-term program of Influenza surveillance. Developing active surveillance for viruses in wildlife species, as implemented in this study, is crucial for understanding zoonotic risks and preventing future global pandemics.

WITHDRAWN: MHC-B Diversity and Signs of Respiratory Illness in Wild, East African Chimpanzees ( Pan troglodytes schweinfurthii )

bioRxiv has withdrawn this preprint following a formal investigation by the University of New Mexico Office of Research Integrity and Compliance.

A computationally designed antigen eliciting broad humoral responses against SARS-CoV-2 and related sarbecoviruses

The threat of spillovers of coronaviruses associated with the severe acute respiratory syndrome (SARS) from animals to humans necessitates vaccines that offer broader protection from sarbecoviruses. By leveraging a viral-genome-informed computational method for selecting immune-optimized and structurally engineered antigens, here we show that a single antigen based on the receptor binding domain of the spike protein of sarbecoviruses elicits broad humoral responses against SARS-CoV-1, SARS-CoV-2, WIV16 and RaTG13 in mice, rabbits and guinea pigs. When administered as a DNA immunogen or by a vector based on a modified vaccinia virus Ankara, the optimized antigen induced vaccine protection from the Delta variant of SARS-CoV-2 in mice genetically engineered to express angiotensin-converting enzyme 2 and primed by a viral-vector vaccine (AZD1222) against SARS-CoV-2. A vaccine formulation incorporating mRNA coding for the optimized antigen further validated its broad immunogenicity. Vaccines that elicit broad immune responses across subgroups of coronaviruses may counteract the threat of zoonotic spillovers of betacoronaviruses.

Alpha and Betacoronavirus Detection in Neotropical Bats from Northeast Brazil Suggests Wide Geographical Distribution and Persistence in Natural Populations

The emergence of zoonotic viral diseases, notably exemplified by the recent coronavirus disease pandemic in 2019 (COVID-19), underscores the critical need to understand the dynamics of viruses circulating in wildlife populations. This study aimed to investigate the diversity of coronaviruses in bat populations from northeastern Brazil, particularly in the state of Ceará, where little research on bat pathogens has been conducted previously. Bat sampling was performed between March 2021 and March 2022 across three municipalities, resulting in the collection of oral and rectal swabs from 298 captured individuals. Molecular analyses revealed alphacoronaviruses in multiple bat species. Additionally, a novel Betacoronavirus was identified in Artibeus planirostris, which did not fall within an established subgenus. Phylogenetic placement of these new coronavirus sequences suggests that closely related coronavirus lineages can infect a wide range of bat species sampled in distantly related Brazilian states and biomes. No SARS-CoV-2 and influenza A viruses were found in the sampled bats. These findings expand our understanding of coronavirus diversity in Brazilian bats. The detection of coronaviruses in various bat species underscores the importance of bats as reservoirs for these viruses. The absence of SARS-CoV-2 in the sampled bats indicates a lack of spillback events from human or environmental sources. However, the potential for future transmission events underscores the importance of ongoing surveillance and transmission mitigation protocols in wildlife management practices.

Nipah virus outbreak trends in Bangladesh during the period 2001 to 2024: a brief review

Nipah virus (NiV) is a zoonotic threat that has caused recurrent outbreaks in Bangladesh since 2001, raising significant public health concerns. This study provides a descriptive analysis of NiV outbreaks from 2001 to 2024, examining trends in infection and death rates and their correlation with climatic factors such as temperature, humidity, and rainfall. The findings highlight significant spikes in NiV cases during specific years, with environmental factors, particularly temperature and precipitation, showing solid correlations with outbreak patterns. The study also explores the impact of population dynamics on transmission risks, including urbanization and density. By focusing on these factors, this research supports the development of targeted public health interventions in high-risk areas, particularly in Bangladesh's northwestern and central districts, where recurrent outbreaks have been observed. These insights improve surveillance and preventive strategies for mitigating future NiV outbreaks.

Detection and Prevalence of Coronaviruses in European Bats: A Systematic Review

Bats are known hosts for a wide range of coronaviruses (CoVs), including those that cause severe acute respiratory syndrome (SARS-CoV-1) and Middle East respiratory syndrome (MERS-CoV). With the emergence of the COVID-19 pandemic caused by the SARS-CoV-2 virus, it has become increasingly important to understand the diversity and prevalence of CoVs in bat populations. This systematic review aimed to compile studies that have sampled CoVs from bats across Europe and assessed various aspects related to the testing of bat samples, including the country where the bats were collected, the CoV genomic region studied, the CoV genera that were detected, and the identification of bat species that were found to be carrying CoV. We identified 30 studies that assessed CoVs presence in bats across multiple countries including Italy, Germany, and various other nations with one or two studies each, which tested them for CoVs using a variety of matrices. CoVs were found in nine genera of bats, and the genomic regions included RdRp, ORF1a gene, as well as full genome, detecting α- and/or β-CoVs, with most of them being detectable only in faeces. This review provides a comprehensive overview of the CoVs detected in bats across Europe and highlights the importance of continued surveillance and monitoring of bat populations for potential emerging zoonotic CoVs.

Antiviral Effects of Avian Interferon-Stimulated Genes

Interferons (IFNs) stimulate the expression of numerous IFN-stimulating genes via the Janus kinase-signal transducers and activators of the transcription (JAK-STAT) signaling pathway, which plays an important role in the host defense against viral infections. In mammals, including humans and mice, a substantial number of IFN-stimulated genes (ISGs) have been identified, and their molecular mechanisms have been elucidated. It is important to note that avian species are phylogenetically distant from mammals, resulting in distinct IFN-induced ISGs that may have different functions. At present, only a limited number of avian ISGs have been identified. In this review, we summarized the identified avian ISGs and their antiviral activities. As gene-editing technology is widely used in avian breeding, the identification of avian ISGs and the elucidation of their molecular mechanism may provide important support for the breeding of avians for disease resistance.

Strategic vaccine stockpiles for regional epidemics of emerging viruses: A geospatial modeling framework

Multinational epidemics of emerging infectious diseases are increasingly common, due to anthropogenic pressure on ecosystems and the growing connectivity of human populations. Early and efficient vaccination can contain outbreaks and prevent mass mortality, but optimal vaccine stockpiling strategies are dependent on pathogen characteristics, reservoir ecology, and epidemic dynamics. Here, we model major regional outbreaks of Nipah virus and Middle East respiratory syndrome, and use these to develop a generalized framework for estimating vaccine stockpile needs based on spillover geography, spatially-heterogeneous healthcare capacity and spatially-distributed human mobility networks. Because outbreak sizes were highly skewed, we found that most outbreaks were readily contained (median stockpile estimate for MERS-CoV: 2,089 doses; Nipah: 1,882 doses), but the maximum estimated stockpile need in a highly unlikely large outbreak scenario was 2-3 orders of magnitude higher (MERS-CoV: ∼87,000 doses; Nipah ∼ 1.1 million doses). Sensitivity analysis revealed that stockpile needs were more dependent on basic epidemiological parameters (i.e., death and recovery rate) and healthcare availability than any uncertainty related to vaccine efficacy or deployment strategy. Our results highlight the value of descriptive epidemiology for real-world modeling applications, and suggest that stockpile allocation should consider ecological, epidemiological, and social dimensions of risk.

One Health Ethics and the Ethics of Zoonoses: A Silent Call for Global Action

This paper presents a critical review of key issues related to the emergence of new networks for the spread of zoonotic diseases amid the mass extinction of species. Zoonotic and infectious diseases account for approximately 70% of new and existing diseases affecting humans and animals. The initial section argues that the term "zoonoses" should not be confined to single-cause events within veterinary medicine. Instead, zoonoses should be viewed as complex, systemic phenomena shaped by interrelated factors, including environmental, sociocultural, and economic elements, influenced by anthropogenic climate change. The second section presents bioethical principles and potential strategies for those engaged in zoonotic disease prevention. The third section uses the slaughter of animals in disaster settings as a case study to illustrate the need for further clarification of normative and interspecies justice conflicts in One Health ethics. This section concludes with an outlook on "zoonoethics". Section four develops the analysis of the interlinked elements that trigger zoonoses and examines antimicrobial resistance (AMR) from an ethical and political standpoint, concluding with policy recommendations for addressing AMR. Section five offers a critical reflection, integrating contributions from zoonoethics, human ecology, and the ecotheological turn. Finally, section six concludes with a call to action and policy recommendations for an inclusive, intercultural, and gender-sensitive One Health approach.

Reverse Zoonotic Transmission of SARS-CoV-2 and Monkeypox Virus: A Comprehensive Review

Reverse zoonosis reveals the process of transmission of a pathogen through the human-animal interface and the spillback of the zoonotic pathogen. In this article, we methodically demonstrate various aspects of reverse zoonosis, with a comprehensive discussion of SARS-CoV-2 and MPXV reverse zoonosis. First, different components of reverse zoonosis, such as humans, different pathogens, and numerous animals (poultry, livestock, pets, wild animals, and zoo animals), have been demonstrated. Second, it explains the present status of reverse zoonosis with different pathogens during previous occurrences of various outbreaks, epidemics, and pandemics. Here, we present 25 examples from literature. Third, using several examples, we comprehensively illustrate the present status of the reverse zoonosis of SARS-CoV-2 and MPXV. Here, we have provided 17 examples of SARS-CoV-2 reverse zoonosis and two examples of MPXV reverse zoonosis. Fourth, we have described two significant aspects of reverse zoonosis: understanding the fundamental aspects of spillback and awareness. These two aspects are required to prevent reverse zoonosis from the current infection with two significant viruses. Finally, the One Health approach was discussed vividly, where we urge scientists from different areas to work collaboratively to solve the issue of reverse zoonosis.

Advances in understanding bat infection dynamics across biological scales

Over the past two decades, research on bat-associated microbes such as viruses, bacteria and fungi has dramatically increased. Here, we synthesize themes from a conference symposium focused on advances in the research of bats and their microbes, including physiological, immunological, ecological and epidemiological research that has improved our understanding of bat infection dynamics at multiple biological scales. We first present metrics for measuring individual bat responses to infection and challenges associated with using these metrics. We next discuss infection dynamics within bat populations of the same species, before introducing complexities that arise in multi-species communities of bats, humans and/or livestock. Finally, we outline critical gaps and opportunities for future interdisciplinary work on topics involving bats and their microbes.

Potential zoonotic spillover at the human-animal interface: A mini-review

Wildlife markets and wet wildlife markets, a type of human-animal interface, are commonly trading centers for wild-caught and captive-exotic animals as well as their products. These markets provide an ideal environment for spillovers of zoonotic and emerging infectious diseases (EIDs). These conditions may raise serious concerns, particularly in relation to wildlife species that frequently interact with humans and domestic animals. EIDs pose a significant risk to humans, ecosystems, and public health, as demonstrated by the current COVID-19 pandemic, and other previous outbreaks, including the highly pathogenic avian influenza H5N1. Even though it seems appears impossible to eliminate EIDs, we may still be able to minimalize the risks and take several measures to prevent new EIDs originated from animals. The aim of this study was to review several types of human-animal interfaces with a high risk of zoonotic spillover, infectious agents, and animal hosts or reservoirs. Identifying those factors will support the development of interventions and effective disease control in human-animal interface settings.

The panzootic potential of SARS-CoV-2

Each year, SARS-CoV-2 is infecting an increasingly unprecedented number of species. In the present article, we combine mammalian phylogeny with the genetic characteristics of isolates found in mammals to elaborate on the host-range potential of SARS-CoV-2. Infections in nonhuman mammals mirror those of contemporary viral strains circulating in humans, although, in certain species, extensive viral circulation has led to unique genetic signatures. As in other recent studies, we found that the conservation of the ACE2 receptor cannot be considered the sole major determinant of susceptibility. However, we are able to identify major clades and families as candidates for increased surveillance. On the basis of our findings, we argue that the use of the term panzootic could be a more appropriate term than pandemic to describe the ongoing scenario. This term better captures the magnitude of the SARS-CoV-2 host range and would hopefully inspire inclusive policy actions, including systematic screenings, that could better support the management of this worldwide event.

Structural basis of white-tailed deer, Odocoileus virginianus, ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity

SARS-CoV-2 has been expanding its host range, among which the white-tailed deer (WTD), Odocoileus virginianus, became the first wildlife species infected on a large scale and might serve as a host reservoir for variants of concern (VOCs) in case no longer circulating in humans. In this study, we comprehensively assessed the binding of the WTD angiotensin-converting enzyme 2 (ACE2) receptor to the spike (S) receptor-binding domains (RBDs) from the SARS-CoV-2 prototype (PT) strain and multiple variants. We found that WTD ACE2 could be broadly recognized by all of the tested RBDs. We further determined the complex structures of WTD ACE2 with PT, Omicron BA.1, and BA.4/5 S trimer. Detailed structural comparison revealed the important roles of RBD residues on 486, 498, and 501 sites for WTD ACE2 binding. This study deepens our understanding of the interspecies transmission mechanisms of SARS-CoV-2 and further addresses the importance of constant monitoring on SARS-CoV-2 infections in wild animals. IMPORTANCE Even if we manage to eliminate the virus among humans, it will still circulate among wildlife and continuously be transmitted back to humans. A recent study indicated that WTD may serve as reservoir for nearly extinct SARS-CoV-2 strains. Therefore, it is critical to evaluate the binding abilities of SARS-CoV-2 variants to the WTD ACE2 receptor and elucidate the molecular mechanisms of binding of the RBDs to assess the risk of spillback events.

Roost selection by synanthropic bats in rural Kenya: implications for human-wildlife conflict and zoonotic pathogen spillover

Many wildlife species are synanthropic and use structures built by humans, creating a high-risk interface for human-wildlife conflict and zoonotic pathogen spillover. However, studies that investigate features of urbanizing areas that attract or repel wildlife are currently lacking. We surveyed 85 buildings used by bats and 172 neighbouring buildings unused by bats (controls) in southeastern Kenya during 2021 and 2022 and evaluated the role of microclimate and structural attributes in building selection. We identified eight bat species using buildings, with over 25% of building roosts used concurrently by multiple species. Bats selected taller cement-walled buildings with higher water vapour pressure and lower presence of permanent human occupants. However, roost selection criteria differed across the most common bat species: molossids selected structures like those identified by our main dataset whereas Cardioderma cor selected buildings with lower presence of permanent human occupants. Our results show that roost selection of synanthropic bat species is based on specific buildings attributes. Further, selection criteria that facilitate bat use of buildings are not homogeneous across species. These results provide information on the general mechanisms of bat-human contact in rural settings, as well as specific information on roost selection for synanthropic bats in urbanizing Africa.

Development of monoclonal antibody-based blocking ELISA for detecting SARS-CoV-2 exposure in animals

The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a significant threat to public health. Besides humans, SARS-CoV-2 can infect several animal species. Highly sensitive and specific diagnostic reagents and assays are urgently needed for rapid detection and implementation of strategies for prevention and control of the infection in animals. In this study, we initially developed a panel of monoclonal antibodies (mAbs) against SARS-CoV-2 nucleocapsid protein. To detect SARS-CoV-2 antibodies in a broad spectrum of animal species, an mAb-based blocking enzyme-linked immunosorbent assay (bELISA) was developed. Test validation using a set of animal serum samples with known infection status obtained an optimal percentage of inhibition cut-off value of 17.6% with diagnostic sensitivity of 97.8% and diagnostic specificity of 98.9%. The assay demonstrates high repeatability as determined by a low coefficient of variation (7.23%, 4.89%, and 3.16%) between-runs, within-run, and within-plate, respectively. Testing of samples collected over time from experimentally infected cats showed that the bELISA was able to detect seroconversion as early as 7 days post-infection. Subsequently, the bELISA was applied for testing pet animals with coronavirus disease 2019 (COVID-19)-like symptoms and specific antibody responses were detected in two dogs. The panel of mAbs generated in this study provides a valuable tool for SARS-CoV-2 diagnostics and research. The mAb-based bELISA provides a serological test in aid of COVID-19 surveillance in animals. IMPORTANCE Antibody tests are commonly used as a diagnostic tool for detecting host immune response following infection. Serology (antibody) tests complement nucleic acid assays by providing a history of virus exposure, no matter symptoms developed from infection or the infection was asymptomatic. Serology tests for COVID-19 are in high demand, especially when the vaccines become available. They are important to determine the prevalence of the viral infection in a population and identify individuals who have been infected or vaccinated. ELISA is a simple and practically reliable serological test, which allows high-throughput implementation in surveillance studies. Several COVID-19 ELISA kits are available. However, they are mostly designed for human samples and species-specific secondary antibody is required for indirect ELISA format. This paper describes the development of an all species applicable monoclonal antibody (mAb)-based blocking ELISA to facilitate the detection and surveillance of COVID-19 in animals.

Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV

The main protease (Mpro) of SARS-CoV-2 is essential for viral replication, which suggests that the Mpro is a critical target in the development of small molecules to treat COVID-19. This study used an in-silico prediction approach to investigate the complex structure of SARS-CoV-2 Mpro in compounds from the United States National Cancer Institute (NCI) database, then validate potential inhibitory compounds against the SARS-CoV-2 Mpro in cis- and trans-cleavage proteolytic assays. Virtual screening of ∼280,000 compounds from the NCI database identified 10 compounds with highest site-moiety map scores. Compound NSC89640 (coded C1) showed marked inhibitory activity against the SARS-CoV-2 Mpro in cis-/trans-cleavage assays. C1 strongly inhibited SARS-CoV-2 Mpro enzymatic activity, with a half maximal inhibitory concentration (IC50) of 2.69 μM and a selectivity index (SI) of >74.35. The C1 structure served as a template to identify structural analogs based on AtomPair fingerprints to refine and verify structure-function associations. Mpro-mediated cis-/trans-cleavage assays conducted with the structural analogs revealed that compound NSC89641 (coded D2) exhibited the highest inhibitory potency against SARS-CoV-2 Mpro enzymatic activity, with an IC50 of 3.05 μM and a SI of >65.57. Compounds C1 and D2 also displayed inhibitory activity against MERS-CoV-2 with an IC50 of <3.5 μM. Thus, C1 shows potential as an effective Mpro inhibitor of SARS-CoV-2 and MERS-CoV. Our rigorous study framework efficiently identified lead compounds targeting the SARS-CoV-2 Mpro and MERS-CoV Mpro.

Human interactions with bats and bat coronaviruses in rural Côte d'Ivoire

Bats are presumed reservoirs of diverse α- and β- coronaviruses (CoVs) and understanding the diversity of bat-CoVs and the role bats play in CoV transmission is highly relevant in the context of the current COVID pandemic. We sampled bats in Côte d'Ivoire (2016-2018) living at ecotones between anthropogenic and wild habitats in the Marahoué National Park, a recently encroached protected area, to detect and characterize the CoVs circulating in bats and humans. A total of 314 bats were captured, mostly during the rainy season (78%), and CoV RNA was detected in three of the bats (0.96%). A CoV RNA sequence similar to Chaerephon bat coronavirus/Kenya/KY22/2006 (BtKY22) was found in a Chaerephon cf. pumilus and a Mops sp. fecal swab, while a CoV RNA sequence similar to the two almost identical Kenya bat coronaviruses BtKY55 and BtKY56 (BtKY55/56) was detected in an Epomops buettikoferi oral swab. Phylogenetic analyses indicated differences in the degree of evolutionary host-virus co-speciation for BtKY22 and BtKY55/56. To assess potential for human exposure to these viruses, we conducted human syndromic and community-based surveillance in clinics and high-risk communities. We collected data on participant characteristics, livelihoods, animal contact, and high-risk behaviors that may be associated with exposure to zoonotic diseases. We then collected biological samples for viral testing from 401 people. PCR testing of these biological samples revealed no evidence of CoV infection among the enrolled individuals. We identified higher levels of exposure to bats in people working in crop production and in hunting, trapping and fishing. Finally, we used the 'Spillover' risk-ranking tool to assess the potential for viral spillover and concluded that, while there is no evidence to suggest imminent risk of spillover for these CoVs, their host range and other traits suggest caution and vigilance are warranted in people with high exposure risk.

Little Brown Bats (Myotis lucifugus) Support the Binding of SARS-CoV-2 Spike and Are Likely Susceptible to SARS-CoV-2 Infection

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), believed to have originated from a bat species, can infect a wide range of non-human hosts. Bats are known to harbor hundreds of coronaviruses capable of spillover into human populations. Recent studies have shown a significant variation in the susceptibility among bat species to SARS-CoV-2 infection. We show that little brown bats (LBB) express angiotensin-converting enzyme 2 receptor and the transmembrane serine protease 2, which are accessible to and support SARS-CoV-2 binding. All-atom molecular dynamics (MD) simulations revealed that LBB ACE2 formed strong electrostatic interactions with the RBD similar to human and cat ACE2 proteins. In summary, LBBs, a widely distributed North American bat species, could be at risk of SARS-CoV-2 infection and potentially serve as a natural reservoir. Finally, our framework, combining in vitro and in silico methods, is a useful tool to assess the SARS-CoV-2 susceptibility of bats and other animal species.

Discovery of a coronavirus in the Eurasian badger (Meles meles) belonging to a putative new genus

In the aftermath of COVID-19, coronaviruses gained renewed attention by the scientific community. The study reports the identification and genetic characterization of a novel coronavirus in the European badger (Meles meles) obtained in the framework of passive surveillance implemented in Italian wildlife in response to the pandemic. Positive samples were characterized using next generation sequencing as well as genetic and phylogenetic analyses, aiming for taxonomic placement under ICTV guidelines of the viruses contained in each sample. Results obtained for six conserved domains within the polyprotein showed that the virus clustered as outgroup and shared <46% amino acid identity with other coronaviruses, supporting the assumption that it belongs to a new putative genus Epsiloncoronavirus. This finding highlights that mammals still hide diverse coronaviruses whose zoonotic and epizootic potential remains unknown.

The presence of COVID-19 face masks in the largest hypersaline lagoon of South America is predicted by urbanization level

The inadequate disposal of face masks has caused a widespread presence of COVID-19 litter in the environment. We monitored 10 beach arcs along approximately 15 km of the largest hypersaline lagoon of South America looking for face masks during the lockdown (2021) and in the "new normal" (2022) period. Our working hypothesis is that the probability of finding face masks increases with higher urbanization levels, which was estimated by the Human Modification Metric. Approximately 3 × 10-3 face masks m-2 were found on nine of 10 beaches (90 %) during the lockdown. However, this reduced to 1 × 10-4 face masks m-2 found in eight beaches (80 %) after the lockdown. The probability of finding a face mask was significantly higher as urbanization increased (z = 2.799; p = 0.005). This situation imposes the need for a better waste management and environmental education actions, targeting the reduction of direct littering on coastal ecosystem.

Development of monoclonal antibody-based blocking ELISA for detecting SARS-CoV-2 exposure in animals

The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a significant threat to public health. Besides humans, SARS-CoV-2 can infect several animal species. Highly sensitive and specific diagnostic reagents and assays are urgently needed for rapid detection and implementation of strategies for prevention and control of the infection in animals. In this study, we initially developed a panel of monoclonal antibodies (mAbs) against SARS-CoV-2 nucleocapsid (N) protein. To detect SARS-CoV-2 antibodies in a broad spectrum of animal species, a mAb-based bELISA was developed. Test validation using a set of animal serum samples with known infection status obtained an optimal percentage of inhibition (PI) cut-off value of 17.6% with diagnostic sensitivity of 97.8% and diagnostic specificity of 98.9%. The assay demonstrates high repeatability as determined by a low coefficient of variation (7.23%, 6.95%, and 5.15%) between-runs, within-run, and within-plate, respectively. Testing of samples collected over time from experimentally infected cats showed that the bELISA was able to detect seroconversion as early as 7 days post-infection. Subsequently, the bELISA was applied for testing pet animals with COVID-19-like symptoms and specific antibody responses were detected in two dogs. The panel of mAbs generated in this study provides a valuable tool for SARS-CoV-2 diagnostics and research. The mAb-based bELISA provides a serological test in aid of COVID-19 surveillance in animals.

IMPORTANCE

Antibody tests are commonly used as a diagnostic tool for detecting host immune response following infection. Serology (antibody) tests complement nucleic acid assays by providing a history of virus exposure, no matter symptoms developed from infection or the infection was asymptomatic. Serology tests for COVID-19 are in high demand, especially when the vaccines become available. They are important to determine the prevalence of the viral infection in a population and identify individuals who have been infected or vaccinated. ELISA is a simple and practically reliable serological test, which allows high-throughput implementation in surveillance studies. Several COVID-19 ELISA kits are available. However, they are mostly designed for human samples and species-specific secondary antibody is required for indirect ELISA format. This paper describes the development of an all species applicable monoclonal antibody (mAb)-based blocking ELISA to facilitate the detection and surveillance of COVID-19 in animals.

The need and challenges for development of vaccines against emerging infectious diseases

OBJECTIVE

To identify and describe learnings from past pandemics and to suggest a framework for vaccine development as part of epi/pandemic readiness.

SOURCE OF DATA

Articles/ reviews/letters on pandemic preparedness/ vaccines published between 2005 and 2022 in PubMed, MEDLINE, MedRxiv, BioRxiv, Research Square, Gates Open Research; who.int, cepi.net, visualcapitalist.com, airfinity.com, ted.com websites; press releases.

SUMMARY OF FINDINGS

Disease pandemics caused by emerging pathogens impacted the social development, health and wealth of most societies in human history. In an outbreak, the first months determine its course. To block an exponential spread and the development of an epi/ pandemic early, vaccine availability in sufficient quantities is of paramount importance. It is inevitable that new human viruses will emerge. Any future pandemic will come likely from RNA viruses through zoonotic or vector transmission, but we cannot predict when or where "Disease X" will strike. Public health, scientific and societal readiness plans need to include: continuous identification of new viruses in common mammalian reservoir hosts; continuous epidemiological surveillance, including wastewater sampling; establishment of prototype vaccine libraries against various virus families sharing functional and structural properties; testing of various and innovative vaccine platforms including mRNA, vector, nasal or oral vaccines for suitability by virus family; functional clinical trial sites and laboratory networks in various geographies; more efficient phasing of preclinical and clinical activities; global harmonization and streamlining of regulatory requirements including pre-established protocols; and societal preparedness including combating any pandemic of misinformation.

CONCLUSIONS

"Outbreaks are unavoidable, pandemics are optional".

Oral Sampling of Little Brown Bat (Myotis lucifugus) Maternity Colonies for SARS-CoV-2 in the Northeast and Mid-Atlantic, USA

The potential introduction of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, into North American bat populations is of interest to wildlife managers due to recent disease-mediated declines of several species. Populations of little brown bats (Myotis lucifugus) have collapsed due to white-nose syndrome (WNS), a disease caused by the introduction and spread of the fungal pathogen Pseudogymnoascus destructans (Pd). Throughout much of the United States and southern Canada, large colonies of the species routinely established diurnal roosts in anthropogenic structures, thereby creating the potential for direct human contact and cross-species disease transmission. Given recent declines and the potential for further disease impacts, we collected oral swabs from eight little brown bat maternity colonies to assess the presence and prevalence of SARS-CoV-2 by RT-qPCR analysis. Little brown bat colonies in Maryland (n = 1), New Hampshire (n = 1), New Jersey (n = 2), New York (n = 1), Rhode Island (n = 2), and Virginia (n = 1) were taken during May-August, 2022. From 235 assayed individuals, no bat tested positive for SARS-CoV-2. Our results indicate that little brown bats may not contract SARS-CoV-2 or that the virus persists at undetectable levels in populations of the Mid-Atlantic and Northeast during summer months. Nonetheless, continued monitoring and future work addressing other seasons may still be warranted to conclusively determine infection status.

SURVEILLANCE OF BATS IN THE UNITED STATES FOR SARS-COV-2 AND OTHER CORONAVIRUSES

Bat coronaviruses (CoVs) are extremely prevalent throughout the globe and exhibit a wide range of genetic diversity. Currently, little is known about the susceptibility of New World bats to severe acute respiratory syndrome-2 (SARS-CoV-2), the causative agent of COVID-19. Also, there is limited information about the genetic diversity of other CoVs in the New World bats. The determination of genetic diversity of bat CoVs through continuous surveillance is essential to predict and mitigate the emergence of new CoVs and their impacts on the health of both humans and animals. In this study, 491 guano specimens collected from New World bats and 37 specimens collected from Old World bats during July 2020 to July 2021 were tested for SARS-COV-2 and other CoVs using a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) panel and pan-coronavirus PCR that target a highly conserved region of CoVs. No evidence of SARS-CoV-2 was found in the tested specimens. An alpha CoV was detected in a single specimen from a big brown bat (Eptesicus fuscus). This information was used by wildlife agencies and rehabilitation facilities to permit the release of bats during the pandemic while mitigating the risk of spreading SARS-CoV-2 among North American bats and other wild animal populations.

Lessons from the pandemic: Responding to emerging zoonotic viral diseases-a Keystone Symposia report

The COVID-19 pandemic caught the world largely unprepared, including scientific and policy communities. On April 10-13, 2022, researchers across academia, industry, government, and nonprofit organizations met at the Keystone symposium "Lessons from the Pandemic: Responding to Emerging Zoonotic Viral Diseases" to discuss the successes and challenges of the COVID-19 pandemic and what lessons can be applied moving forward. Speakers focused on experiences not only from the COVID-19 pandemic but also from outbreaks of other pathogens, including the Ebola virus, Lassa virus, and Nipah virus. A general consensus was that investments made during the COVID-19 pandemic in infrastructure, collaborations, laboratory and manufacturing capacity, diagnostics, clinical trial networks, and regulatory enhancements-notably, in low-to-middle income countries-must be maintained and strengthened to enable quick, concerted responses to future threats, especially to zoonotic pathogens.

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.

GPS Tracking of Free-Roaming Cats (Felis catus) on SARS-CoV-2-Infected Mink Farms in Utah

Zoonotic transmission of SARS-CoV-2 from infected humans to other animals has been documented around the world, most notably in mink farming operations in Europe and the United States. Outbreaks of SARS-CoV-2 on Utah mink farms began in late July 2020 and resulted in high mink mortality. An investigation of these outbreaks revealed active and past SARS-CoV-2 infections in free-roaming and in feral cats living on or near several mink farms. Cats were captured using live traps, were sampled, fitted with GPS collars, and released on the farms. GPS tracking of these cats show they made frequent visits to mink sheds, moved freely around the affected farms, and visited surrounding residential properties and neighborhoods on multiple occasions, making them potential low risk vectors of additional SARS-CoV-2 spread in local communities.

An ACE2-dependent Sarbecovirus in Russian bats is resistant to SARS-CoV-2 vaccines

Spillover of sarbecoviruses from animals to humans has resulted in outbreaks of severe acute respiratory syndrome SARS-CoVs and the ongoing COVID-19 pandemic. Efforts to identify the origins of SARS-CoV-1 and -2 has resulted in the discovery of numerous animal sarbecoviruses–the majority of which are only distantly related to known human pathogens and do not infect human cells. The receptor binding domain (RBD) on sarbecoviruses engages receptor molecules on the host cell and mediates cell invasion. Here, we tested the receptor tropism and serological cross reactivity for RBDs from two sarbecoviruses found in Russian horseshoe bats. While these two viruses are in a viral lineage distinct from SARS-CoV-1 and -2, the RBD from one virus, Khosta 2, was capable of using human ACE2 to facilitate cell entry. Viral pseudotypes with a recombinant, SARS-CoV-2 spike encoding for the Khosta 2 RBD were resistant to both SARS-CoV-2 monoclonal antibodies and serum from individuals vaccinated for SARS-CoV-2. Our findings further demonstrate that sarbecoviruses circulating in wildlife outside of Asia also pose a threat to global health and ongoing vaccine campaigns against SARS-CoV-2

SARS-CoV-2, the sarbecovirus behind COVID-19, emerged in the human population after cross-species transmission from an animal source. While hundreds of sarbecoviruses have been discovered, predominantly in bats in Asia, the majority are not capable of infecting human cells. Khosta-2, a sarbecovirus discovered in Russia, has been shown to interact with the same entry receptor as SARS-CoV-2. In this study, we tested how well the spike proteins from these bat viruses infect human cells under different conditions. We found that the spike from virus, Khosta-2, could infect cells similar to human pathogens using the same entry mechanisms, but was resistant to neutralization by serum from individuals who had been vaccinated for SARS-CoV-2.

Transmission dynamics and susceptibility patterns of SARS-CoV-2 in domestic, farmed and wild animals: Sustainable One Health surveillance for conservation and public health to prevent future epidemics and pandemics

The exact origin of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and source of introduction into humans has not been established yet, though it might be originated from animals. Therefore, we conducted a study to understand the putative reservoirs, transmission dynamics, and susceptibility patterns of SARS-CoV-2 in animals. Rhinolophus bats are presumed to be natural progenitors of SARS-CoV-2-related viruses. Initially, pangolin was thought to be the source of spillover to humans, but they might be infected by human or other animal species. So, the virus spillover pathways to humans remain unknown. Human-to-animal transmission has been testified in pet, farmed, zoo and free-ranging wild animals. Infected animals can transmit the virus to other animals in natural settings like mink-to-mink and mink-to-cat transmission. Animal-to-human transmission is not a persistent pathway, while mink-to-human transmission continues to be illuminated. Multiple companions and captive wild animals were infected by an emerging alpha variant of concern (B.1.1.7 lineage) whereas Asiatic lions were infected by delta variant, (B.1.617.2). To date, multiple animal species - cat, ferrets, non-human primates, hamsters and bats - showed high susceptibility to SARS-CoV-2 in the experimental condition, while swine, poultry, cattle showed no susceptibility. The founding of SARS-CoV-2 in wild animal reservoirs can confront the control of the virus in humans and might carry a risk to the welfare and conservation of wildlife as well. We suggest vaccinating pets and captive animals to stop spillovers and spillback events. We recommend sustainable One Health surveillance at the animal-human-environmental interface to detect and prevent future epidemics and pandemics by Disease X.

Experimental Infection of Brazilian Free-Tailed Bats (Tadarida brasiliensis) with Two Strains of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is presumed to have originated from wildlife and shares homology with other bat coronaviruses. Determining the susceptibility of North American bat species to SARS-CoV-2 is of utmost importance for making decisions regarding wildlife management, public health, and conservation. In this study, Brazilian free-tailed bats (Tadarida brasiliensis) were experimentally infected with two strains of SARS-CoV-2 (parental WA01 and Delta variant), evaluated for clinical disease, sampled for viral shedding and antibody production, and analyzed for pathology. None of the bats (n = 18) developed clinical disease associated with infection, shed infectious virus, or developed histopathological lesions associated with SARS-CoV-2 infection. All bats had low levels of viral RNA in oral swabs, six bats had low levels of viral RNA present in the lungs during acute infection, and one of the four bats that were maintained until 28 days post-infection developed a neutralizing antibody response. These findings suggest that Brazilian free-tailed bats are permissive to infection by SARS-CoV-2, but they are unlikely to contribute to environmental maintenance or transmission.

A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia

Emerging diseases caused by coronaviruses of likely bat origin (e.g., SARS, MERS, SADS, COVID-19) have disrupted global health and economies for two decades. Evidence suggests that some bat SARS-related coronaviruses (SARSr-CoVs) could infect people directly, and that their spillover is more frequent than previously recognized. Each zoonotic spillover of a novel virus represents an opportunity for evolutionary adaptation and further spread; therefore, quantifying the extent of this spillover may help target prevention programs. We derive current range distributions for known bat SARSr-CoV hosts and quantify their overlap with human populations. We then use probabilistic risk assessment and data on human-bat contact, human viral seroprevalence, and antibody duration to estimate that a median of 66,280 people (95% CI: 65,351-67,131) are infected with SARSr-CoVs annually in Southeast Asia. These data on the geography and scale of spillover can be used to target surveillance and prevention programs for potential future bat-CoV emergence.

Optimising predictive models to prioritise viral discovery in zoonotic reservoirs

Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guide sampling target prioritisation, but the predictions from any given model might be highly uncertain; moreover, systematic model validation is rare, and the drivers of model performance are consequently under-documented. Here, we use the bat hosts of betacoronaviruses as a case study for the data-driven process of comparing and validating predictive models of probable reservoir hosts. In early 2020, we generated an ensemble of eight statistical models that predicted host-virus associations and developed priority sampling recommendations for potential bat reservoirs of betacoronaviruses and bridge hosts for SARS-CoV-2. During a time frame of more than a year, we tracked the discovery of 47 new bat hosts of betacoronaviruses, validated the initial predictions, and dynamically updated our analytical pipeline. We found that ecological trait-based models performed well at predicting these novel hosts, whereas network methods consistently performed approximately as well or worse than expected at random. These findings illustrate the importance of ensemble modelling as a buffer against mixed-model quality and highlight the value of including host ecology in predictive models. Our revised models showed an improved performance compared with the initial ensemble, and predicted more than 400 bat species globally that could be undetected betacoronavirus hosts. We show, through systematic validation, that machine learning models can help to optimise wildlife sampling for undiscovered viruses and illustrates how such approaches are best implemented through a dynamic process of prediction, data collection, validation, and updating.

Species-Specific Molecular Barriers to SARS-CoV-2 Replication in Bat Cells

Bats are natural reservoirs of numerous coronaviruses, including the potential ancestor of SARS-CoV-2. Knowledge concerning the interaction between coronaviruses and bat cells is sparse. We investigated the ability of primary cells from Rhinolophus and Myotis species, as well as of established and novel cell lines from Myotis myotis, Eptesicus serotinus, Tadarida brasiliensis, and Nyctalus noctula, to support SARS-CoV-2 replication. None of these cells were permissive to infection, not even the ones expressing detectable levels of angiotensin-converting enzyme 2 (ACE2), which serves as the viral receptor in many mammalian species. The resistance to infection was overcome by expression of human ACE2 (hACE2) in three cell lines, suggesting that the restriction to viral replication was due to a low expression of bat ACE2 (bACE2) or the absence of bACE2 binding in these cells. Infectious virions were produced but not released from hACE2-transduced M. myotis brain cells. E. serotinus brain cells and M. myotis nasal epithelial cells expressing hACE2 efficiently controlled viral replication, which correlated with a potent interferon response. Our data highlight the existence of species-specific and cell-specific molecular barriers to viral replication in bat cells. These novel chiropteran cellular models are valuable tools to investigate the evolutionary relationships between bats and coronaviruses. IMPORTANCE Bats are host ancestors of several viruses that cause serious disease in humans, as illustrated by the ongoing SARS-CoV-2 pandemic. Progress in investigating bat-virus interactions has been hampered by a limited number of available bat cellular models. We have generated primary cells and cell lines from several bat species that are relevant for coronavirus research. The various permissivities of the cells to SARS-CoV-2 infection offered the opportunity to uncover some species-specific molecular restrictions to viral replication. All bat cells exhibited a potent entry-dependent restriction. Once this block was overcome by overexpression of human ACE2, which serves at the viral receptor, two bat cell lines controlled well viral replication, which correlated with the inability of the virus to counteract antiviral responses. Other cells potently inhibited viral release. Our novel bat cellular models contribute to a better understanding of the molecular interplays between bat cells and viruses.

Major bat-borne zoonotic viral epidemics in Asia and Africa: A systematic review and meta-analysis

Bats are the natural reservoir host for many pathogenic and non-pathogenic viruses, potentially spilling over to humans and domestic animals directly or via an intermediate host. The ongoing COVID-19 pandemic is the continuation of virus spillover events that have taken place over the last few decades, particularly in Asia and Africa. Therefore, these bat-associated epidemics provide a significant number of hints, including respiratory cellular tropism, more intense susceptibility to these cell types, and overall likely to become a pandemic for the next spillover. In this systematic review, we analysed data to insight, through bat-originated spillover in Asia and Africa. We used STATA/IC-13 software for descriptive statistics and meta-analysis. The random effect of meta-analysis showed that the pooled estimates of case fatality rates of bat-originated viral zoonotic diseases were higher in Africa (61.06%, 95%CI: 50.26 to 71.85, l2 % = 97.3, p < 0.001). Moreover, estimates of case fatality rates were higher in Ebola (61.06%; 95%CI: 50.26 to 71.85, l2 % = 97.3, p < 0.001) followed by Nipah (55.19%; 95%CI: 39.29 to 71.09, l2 % = 94.2, p < 0.001), MERS (18.49%; 95%CI: 8.19 to 28.76, l2 % = 95.4, p < 0.001) and SARS (10.86%; 95%CI: 6.02 to 15.71, l2 % = 85.7, p < 0.001) with the overall case fatality rates of 29.86 (95%CI: 29.97 to 48.58, l2 % = 99.0, p < 0.001). Bat-originated viruses have caused several outbreaks of deadly diseases, including Nipah, Ebola, SARS and MERS in Asia and Africa in a sequential fashion. Nipah virus emerged first in Malaysia, but later, periodic outbreaks were noticed in Bangladesh and India. Similarly, the Ebola virus was detected in the African continent with neurological disorders in humans, like Nipah, seen in the Asian region. Two important coronaviruses, MERS and SARS, were introduced, both with the potential to infect respiratory passages. This paper explores the dimension of spillover events within and/or between bat-human and the epidemiological risk factors, which may lead to another pandemic occurring. Further, these processes enhance the bat-originated virus, which utilises an intermediate host to jump into human species.

A SARS-CoV-2 nanobody that can bind to the RBD region may be used for treatment in COVID-19 in animals

Coronavirus disease 2019 (COVID-19) caused by an infectious virus, severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), poses a threat to the world. The suitable treatments must be identified for this disease in animals. Nanobody have therapeutic potential in the COVID-19. In this study, SARS-CoV-2 Spike RBD protein was used to make the nanobody. Nanobodies binding to the SARS-CoV-2 Spike RBD protein was obtained. Interestingly, the nanobody could bind to SARS-CoV-2 Spike S protein and RBD protein at the same time. Nanobodies were validated with a neutralizing antibody detection kit. The use of pseudoviruses confirmed that nanobodies could prevent pseudoviruses from infecting cells. We believe the nanobody are very valuable and could be used in the treatment of COVID-19. SARS-CoV-2 nanobodies can be rapidly mass-produced from microorganisms to block SARS-CoV-2 infection in vitro and in vivo with preventive and therapeutic effects.

Assessing the risk of human-to-wildlife pathogen transmission for conservation and public health

The SARS-CoV-2 pandemic has led to increased concern over transmission of pathogens from humans to animals, and its potential to threaten conservation and public health. To assess this threat, we reviewed published evidence of human-to-wildlife transmission events, with a focus on how such events could threaten animal and human health. We identified 97 verified examples, involving a wide range of pathogens; however, reported hosts were mostly non-human primates or large, long-lived captive animals. Relatively few documented examples resulted in morbidity and mortality, and very few led to maintenance of a human pathogen in a new reservoir or subsequent "secondary spillover" back into humans. We discuss limitations in the literature surrounding these phenomena, including strong evidence of sampling bias towards non-human primates and human-proximate mammals and the possibility of systematic bias against reporting human parasites in wildlife, both of which limit our ability to assess the risk of human-to-wildlife pathogen transmission. We outline how researchers can collect experimental and observational evidence that will expand our capacity for risk assessment for human-to-wildlife pathogen transmission.

Possible Cross-Reactivity of Feline and White-Tailed Deer Antibodies against the SARS-CoV-2 Receptor Binding Domain

In late 2019, a novel coronavirus began circulating within humans in central China. It was designated SARS-CoV-2 because of its genetic similarities to the 2003 SARS coronavirus (SARS-CoV). Now that SARS-CoV-2 has spread worldwide, there is a risk of it establishing new animal reservoirs and recombination with native circulating coronaviruses. To screen local animal populations in the United States for exposure to SARS-like coronaviruses, we developed a serological assay using the receptor binding domain (RBD) from SARS-CoV-2. SARS-CoV-2's RBD is antigenically distinct from common human and animal coronaviruses, allowing us to identify animals previously infected with SARS-CoV or SARS-CoV-2. Using an indirect enzyme-linked immunosorbent assay (ELISA) for SARS-CoV-2's RBD, we screened serum from wild and domestic animals for the presence of antibodies against SARS-CoV-2's RBD. Surprisingly prepandemic feline serum samples submitted to the University of Tennessee Veterinary Hospital were ∼50% positive for anti-SARS RBD antibodies. Some of these samples were serologically negative for feline coronavirus (FCoV), raising the question of the etiological agent generating anti-SARS-CoV-2 RBD cross-reactivity. We also identified several white-tailed deer from South Carolina with anti-SARS-CoV-2 antibodies. These results are intriguing, as cross-reactive antibodies toward SARS-CoV-2 RBD have not been reported to date. The etiological agent responsible for seropositivity was not readily apparent, but finding seropositive cats prior to the current SARS-CoV-2 pandemic highlights our lack of information about circulating coronaviruses in other species. IMPORTANCE We report cross-reactive antibodies from prepandemic cats and postpandemic South Carolina white-tailed deer that are specific for that SARS-CoV RBD. There are several potential explanations for this cross-reactivity, each with important implications to coronavirus disease surveillance. Perhaps the most intriguing possibility is the existence and transmission of an etiological agent (such as another coronavirus) with similarity to SARS-CoV-2's RBD region. However, we lack conclusive evidence of prepandemic transmission of a SARS-like virus. Our findings provide impetus for the adoption of a One Health Initiative focusing on infectious disease surveillance of multiple animal species to predict the next zoonotic transmission to humans and future pandemics.

Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses

BACKGROUND

Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife.

RESULTS

Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident).

CONCLUSIONS

The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstract.

The risk from SARS-CoV-2 to bat species in england and mitigation options for conservation field workers

The newly evolved coronavirus, SARS-CoV-2, which has precipitated a global COVID-19 pandemic among the human population, has been shown to be associated with disease in captive wild animals. Bats (Chiroptera) have been shown to be susceptible to experimental infection and therefore may be at risk from disease when in contact with infected people. Numerous conservation fieldwork activities are undertaken across the United Kingdom bringing potentially infected people into close proximity with bats. In this study, we analysed the risks of disease from SARS-CoV-2 to free-living bat species in England through fieldworkers undertaking conservation activities and ecological survey work, using a qualitative, transparent method devised for assessing threats of disease to free-living wild animals. The probability of exposure of bats to SARS-CoV-2 through fieldwork activities was estimated to range from negligible to high, depending on the proximity between bats and people during the activity. The likelihood of infection after exposure was estimated to be high and the probability of dissemination of the virus through bat populations medium. The likelihood of clinical disease occurring in infected bats was low, and therefore, the ecological, economic and environmental consequences were predicted to be low. The overall risk estimation was low, and therefore, mitigation measures are advisable. There is uncertainty in the pathogenicity of SARS-CoV-2 in bats and therefore in the risk estimation. Disease risk management measures are suggested, including the use of personal protective equipment, good hand hygiene and following the existing government advice. The disease risk analysis should be updated as information on the epidemiology of SARS-CoV-2 and related viruses in bats improves. The re-analysis may be informed by health surveillance of free-living bats.

The urgency of wider adoption of one health approach for the prevention of a future pandemic

Recurring outbreaks of emerging and re-emerging zoonoses serve as a reminder that the health of humans, animals, and the environment are interconnected. Therefore, multisectoral, transdisciplinary, and collaborative approaches are required at local, regional, and global levels to tackle the ever-increasing zoonotic threat. The ongoing pandemic of COVID-19 zoonosis has been posing tremendous threats to global human health and economies. The devastation caused by the COVID-19 pandemic teaches us to adopt a "One Health Approach (OHA)" to tackle a possible future pandemic through a concerted effort of the global scientific community, human health professionals, public health experts, veterinarians and policymakers through open science and open data sharing practices. The OHA is an integrated, holistic, collaborative, multisectoral, and transdisciplinary approach to tackle potential pandemic zoonotic diseases. It includes expanding scientific inquiry into zoonotic infections; monitoring, and regulating traditional food markets, transforming existing food systems, and incentivizing animal husbandry and legal wildlife trade to adopt effective zoonotic control measures. To adopt an OHA globally, research and academic institutions, governments and non-government sectors at the local, regional, and international levels must work together. This review aimed to provide an overview of the major pandemics in human history including the COVID-19, anthropogenic drivers of zoonoses, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) reverse zoonoses, the concept of OHA and how an OHA could be utilized to prevent future pandemic threats to the human-animal-ecosystem interfaces. In addition, this review article discusses the strategic framework of OHA and possible challenges to implement OHA in practice to prevent any future pandemics. The practices of open data sharing, open science, and international collaboration should be included in the OHA to prevent and/or rapidly tackle any health emergencies in the future.

Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade

Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent ancestral sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.

Live animal markets: Identifying the origins of emerging infectious diseases

Emerging infectious diseases (EIDs) of zoonotic origin appear, affect a population and can spread rapidly. At the beginning of 2020, the World Health Organization pronounced an emergency public health advisory because of the SARS-CoV-2 coronavirus outbreak, and declared that COVID-19 had reached the level of a pandemic, rapidly spreading around the world. In order to identify one of the origins of EIDs, and propose some control alternatives, an extensive review was conducted of the available literature. The problem can originate in live animal markets, where animal species of all kinds, from different origins, ecosystems, and taxonomic groups are caged and crowded together, sharing the same unsanitary and unnatural space, food, water, and also the ecto- and endoparasitic vectors of disease. They defecate on each other, leading to the exchange of pathogenic and parasitic microorganisms, forcing interactions among species that should never happen. This is the ideal scenario for causing zoonoses and outbreaks of EIDs. We must start by stopping the illegal collection and sale of wild animals in markets. The destruction of ecosystems and forests also promote zoonoses and outbreaks of EIDs. Science and knowledge should be the basis of the decisions and policies for the development of management strategies. Wildlife belongs in its natural habitat, which must be defended, conserved, and restored at all costs.

Experimental Susceptibility of North American Raccoons (Procyon lotor) and Striped Skunks (Mephitis mephitis) to SARS-CoV-2

Recent spillback events of SARS-CoV-2 from humans to animals has raised concerns about it becoming endemic in wildlife. A sylvatic cycle of SARS-CoV-2 could present multiple opportunities for repeated spillback into human populations and other susceptible wildlife. Based on their taxonomy and natural history, two native North American wildlife species -the striped skunk (Mephitis mephitis) and the raccoon (Procyon lotor) -represent a high likelihood of susceptibility and ecological opportunity of becoming infected with SARS-CoV-2. Eight skunks and raccoons were each intranasally inoculated with one of two doses of the virus (103 PFU and 105 PFU) and housed in pairs. To evaluate direct transmission, a naïve animal was added to each inoculated pair 48 h post-inoculation. Four control animals of each species were handled like the experimental groups. At predetermined intervals, we collected nasal and rectal swabs to quantify virus shed via virus isolation and detect viral RNA via rRT-PCR and blood for serum neutralization. Lastly, animals were euthanized at staggered intervals to describe disease progression through histopathology and immunohistochemistry. No animals developed clinical disease. All intranasally inoculated animals seroconverted, suggesting both species are susceptible to SARS-CoV-2 infection. The highest titers in skunks and raccoons were 1:128 and 1:64, respectively. Low quantities of virus were isolated from 2/8 inoculated skunks for up to day 5 post-inoculation, however no virus was isolated from inoculated raccoons or direct contacts of either species. Neither species had gross lesions, but recovering mild chronic pneumonia consistent with viral insult was recorded histologically in 5/8 inoculated skunks. Unlike another SARS-CoV-2 infection trial in these species, we detected neutralizing antibodies in inoculated raccoons; thus, future wildlife serologic surveillance results must be interpreted with caution. Due to the inability to isolate virus from raccoons, the lack of evidence of direct transmission between both species, and low amount of virus shed by skunks, it seems unlikely for SARS-CoV-2 to become established in raccoon and skunk populations and for virus to spillback into humans. Continued outbreaks in non-domestic species, wild and captive, highlight that additional research on the susceptibility of SARS-CoV-2 in wildlife, especially musteloidea, and of conservation concern, is needed.

The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes

Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and nonhomologous recombination, because such events may affect the emergence of novel CoV strains, alter their host range, infection rate, tissue tropism pathogenicity, and their ability to escape vaccination programs. Intratypic recombination among closely related CoVs of the same subgenus has often been reported; however, the patterns and limits of genomic exchange between more distantly related CoV lineages (intertypic recombination) need further investigation. Here, we report computational/evolutionary analyses that clearly demonstrate a substantial ability for CoVs of different subgenera to recombine. Furthermore, we show that CoVs can obtain-through nonhomologous recombination-accessory ORFs from core ORFs, exchange accessory ORFs with different CoV genera, with other viruses (i.e., toroviruses, influenza C/D, reoviruses, rotaviruses, astroviruses) and even with hosts. Intriguingly, most of these radical events result from double crossovers surrounding the Spike ORF, thus highlighting both the instability and mobile nature of this genomic region. Although many such events have often occurred during the evolution of various CoVs, the genomic architecture of the relatively young SARS-CoV/SARS-CoV-2 lineage so far appears to be stable.

The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2

Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense single-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as well as many previous epidemics in humans that were of zoonotic origin, highlights the importance of studying the evolution of the entire CoV subfamily in order to understand how novel strains emerge and which molecular processes affect their adaptation, transmissibility, host/tissue tropism, and patho non-homologous genicity. In this review, we focus on studies over the last two years that reveal the impact of point mutations, insertions/deletions, and intratypic/intertypic homologous and non-homologous recombination events on the evolution of CoVs. We discuss whether the next generations of CoV vaccines should be directed against other CoV proteins in addition to or instead of spike. Based on the observed patterns of molecular evolution for the entire subfamily, we discuss five scenarios for the future evolutionary path of SARS-CoV-2 and the COVID-19 pandemic. Finally, within this evolutionary context, we discuss the recently emerged Omicron (B.1.1.529) VoC.

Infectious disease in an era of global change

The twenty-first century has witnessed a wave of severe infectious disease outbreaks, not least the COVID-19 pandemic, which has had a devastating impact on lives and livelihoods around the globe. The 2003 severe acute respiratory syndrome coronavirus outbreak, the 2009 swine flu pandemic, the 2012 Middle East respiratory syndrome coronavirus outbreak, the 2013-2016 Ebola virus disease epidemic in West Africa and the 2015 Zika virus disease epidemic all resulted in substantial morbidity and mortality while spreading across borders to infect people in multiple countries. At the same time, the past few decades have ushered in an unprecedented era of technological, demographic and climatic change: airline flights have doubled since 2000, since 2007 more people live in urban areas than rural areas, population numbers continue to climb and climate change presents an escalating threat to society. In this Review, we consider the extent to which these recent global changes have increased the risk of infectious disease outbreaks, even as improved sanitation and access to health care have resulted in considerable progress worldwide.