Interventions to Reduce Risk for Pathogen Spillover and Early Disease Spread to Prevent Outbreaks, Epidemics, and Pandemics.

The pathogens that cause most emerging infectious diseases in humans originate in animals, particularly wildlife, and then spill over into humans. The accelerating frequency with which humans and domestic animals encounter wildlife because of activities such as land-use change, animal husbandry, and markets and trade in live wildlife has created growing opportunities for pathogen spillover. The risk of pathogen spillover and early disease spread among domestic animals and humans, however, can be reduced by stopping the clearing and degradation of tropical and subtropical forests, improving health and economic security of communities living in emerging infectious disease hotspots, enhancing biosecurity in animal husbandry, shutting down or strictly regulating wildlife markets and trade, and expanding pathogen surveillance. We summarize expert opinions on how to implement these goals to prevent outbreaks, epidemics, and pandemics.

Presence of ß-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals.

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum ß-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant ß-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-ß-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

Helminths of urban rats in developed countries: a systematic review to identify research gaps.

Although black (Rattus rattus) and brown (Rattus norvegicus) rats are among the most widespread synanthropic wild rodents, there is a surprising scarcity of knowledge about their ecology in the urban ecosystem. In particular, relatively few studies have investigated their helminth species diversity in such habitat. We followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guideline to synthesize the existing published literature regarding the helminth fauna of urban rats in developed countries (North America, Europe, Australia, New Zealand and Japan). We aimed at describing the species diversity and richness of urban rat helminths, the species prevalence and associations, the methods of investigation, the pathological changes observed in the hosts, the risk factors of infection and the public health significance of rat-borne helminthiases. Twenty-three scientific papers published between 1946 and 2019 were reviewed, half of them were conducted in Europe. Twenty-five helminth species and eight genera were described from the liver, digestive tract, lungs and muscles of urban rats. The most commonly reported parasite was Calodium hepaticum. Prevalence and risk factors of helminth infection in urban rats varied greatly between studies. Observed pathological findings in the rat host were generally minor, except for C. hepaticum. Several rat helminths can parasitize humans and are therefore of public health significance. The lack of references to identification keys and the rare use of molecular tools for species confirmation represent the main limitation of these studies. Knowledge gap on this topic and the needs for future research are discussed.

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary.

Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species' range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the "restocking from the wild" hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.

Urban brown rats (Rattus norvegicus) as possible source of multidrug-resistant Enterobacteriaceae and meticillin-resistant Staphylococcus spp., Vienna, Austria, 2016 and 2017.

BackgroundBrown rats (Rattus norvegicus) are an important wildlife species in cities, where they live in close proximity to humans. However, few studies have investigated their role as reservoir of antimicrobial-resistant bacteria.AimWe intended to determine whether urban rats at two highly frequented sites in Vienna, Austria, carry extended-spectrum ß-lactamase-producing Enterobacteriaceae, fluoroquinolone-resistant Enterobacteriaceae and meticillin-resistant (MR) Staphylococcus spp. (MRS).MethodsWe surveyed the presence of antimicrobial resistance in 62 urban brown rats captured in 2016 and 2017 in Vienna, Austria. Intestinal and nasopharyngeal samples were cultured on selective media. We characterised the isolates and their antimicrobial properties using microbiological and genetic methods including disk diffusion, microarray analysis, sequencing, and detection and characterisation of plasmids.ResultsEight multidrug-resistant Escherichia coli and two extensively drug-resistant New Delhi metallo-ß-lactamases-1 (NDM-1)-producing Enterobacter xiangfangensis ST114 (En. cloacae complex) were isolated from nine of 62 rats. Nine Enterobacteriaceae isolates harboured the bla CTX-M gene and one carried a plasmid-encoded ampC gene (bla CMY-2). Forty-four MRS were isolated from 37 rats; they belonged to seven different staphylococcal species: S. fleurettii, S. sciuri, S. aureus, S. pseudintermedius, S. epidermidis, S. haemolyticus (all mecA-positive) and mecC-positive S. xylosus.ConclusionOur findings suggest that brown rats in cities are a potential source of multidrug-resistant bacteria, including carbapenem-resistant En. xiangfangensis ST114. Considering the increasing worldwide urbanisation, rodent control remains an important priority for health in modern cities.

Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum).

The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR) was common during much of the twentieth century, declining rapidly since the 1970s, and now only two post-reproductive individuals remain. Despite this species's conservation status, it lacks a genetic assessment of its demographic history. We therefore sampled 232 individuals from extant and museum sources and analysed ten microsatellite loci and the mtDNA control region. Both marker types reliably partitioned the species into SWR and NWR, with moderate nuclear genetic diversity and only three mtDNA haplotypes for the species, including historical samples. We detected ancient interglacial demographic declines in both populations. Both populations may also have been affected by recent declines associated with the colonial expansion for the SWR, and with the much earlier Bantu migrations for the NWR. Finally, we detected post-divergence secondary contact between NWR and SWR, possibly occurring as recently as the last glacial maximum. These results suggest the species was subjected to regular periods of fragmentation and low genetic diversity, which may have been replenished upon secondary contact during glacial periods. The species's current situation thus reflects prehistoric declines that were exacerbated by anthropogenic pressure associated with the rise of late Holocene technological advancement in Africa. Importantly, secondary contact suggests a potentially positive outcome for a hybrid rescue conservation strategy, although further genome-wide data are desirable to corroborate these results.

Equine behavioral enrichment toys as tools for non-invasive recovery of viral and host DNA.

Direct collection of samples from wildlife can be difficult and sometimes impossible. Non-invasive remote sampling for the purpose of DNA extraction is a potential tool for monitoring the presence of wildlife at the individual level, and for identifying the pathogens shed by wildlife. Equine herpesviruses (EHV) are common pathogens of equids that can be fatal if transmitted to other mammals. Transmission usually occurs by nasal aerosol discharge from virus-shedding individuals. The aim of this study was to validate a simple, non-invasive method to track EHV shedding in zebras and to establish an efficient protocol for genotyping individual zebras from environmental DNA (eDNA). A commercially available horse enrichment toy was deployed in captive Grévy's, mountain, and plains zebra enclosures and swabbed after 4-24 hr. Using eDNA extracted from these swabs four EHV strains (EHV-1, EHV-7, wild ass herpesvirus and zebra herpesvirus) were detected by PCR and confirmed by sequencing, and 12 of 16 zebras present in the enclosures were identified as having interacted with the enrichment toy by mitochondrial DNA amplification and sequencing. We conclude that, when direct sampling is difficult or prohibited, non-invasive sampling of eDNA can be a useful tool to determine the genetics of individuals or populations and for detecting pathogen shedding in captive wildlife.

RADIOGRAPHY IN THE FIELD: ASSESSING A LIGHTWEIGHT, HANDHELD, BATTERY-POWERED DENTISTRY UNIT FOR FIELD DIAGNOSTIC APPLICATIONS.

Radiography units are not used commonly in wildlife medicine field settings, primarily because of their weight and requirement for a power supply. In this study, a portable, battery-powered, and lightweight radiography unit, originally developed for dentistry, was assessed for its potential field applications. Radiographs of various animal species (ranging in weight from 14 g to 1,000 kg) were imaged using varying source image distance (SID) and exposure time. The quality of these images was evaluated for their resolution, image noise, and motion blur. When required, image resolutions were further enhanced using computed radiography postprocessing. Other parameters evaluated were the freehand use of the device, its battery durability, the maximum obtainable image size, and multiple use of a single computed radiography cassette. Using an SID of 60 cm, radiographs delivered adequate image quality. The quality, however, was found deteriorated in images of larger animals (>50 kg) or thicker tissues (>15 cm). The use of a tripod proved unnecessary in most cases, and its exclusion greatly facilitated equipment handling. Under field conditions, the battery was depleted after a total running time of 1.6 hr or 36 radiographs. The maximum size of a radiographic image reached a diameter of 40 cm, and radiation shielding allowed the multiple use of a single computed radiography cassette. Taken together, the radiography unit evaluated in this study presented a balanced compromise between portability and radiograph quality for field use. However, the unit image resolution cannot replace those of the fixed standard radiography units commonly used in veterinary medicine.

Two methods to adapt the human haemoglobin-oxygen dissociation algorithm to the blood of white rhinoceros (Ceratotherium simum) and to determine the accuracy of pulse oximetry.

OBJECTIVES: To adapt the algorithm for the calculation of oxygen saturation to the blood characteristics of the white rhinoceros by two different methods and to determine the accuracy of conventional pulse oximetry measurements. STUDY DESIGN: Adaptation of two mathematical models of the oxygen dissociation curve (ODC). ANIMALS: Twenty-five captive white rhinoceros (Ceratotherium simum), including 12 males and 13 females, aged 6-32 years. METHODS: During 33 anaesthetic events, 94 arterial blood gas samples with 72 simultaneous pulse oximetry measurements were analysed. The calculation of oxygen saturation was adapted to the characteristics of rhinoceros blood using two different methods. Firstly, a mathematical model developed in 1984 and, secondly, an oxygen status algorithm (OSA) produced by the same developer in 2005 were tested for their applicability for clinical use. RESULTS: When arterial partial pressure of oxygen is >7.98 kPa (60 mmHg), oxygen saturation exceeds 95%. At partial pressures of 6.12-6.52 kPa (46-49 mmHg) Method 1 determined oxygen saturations of 92.5-95.3% and Method 2 oxygen saturations of 90.2-91.6%. Both methods resulted in similar ODCs and accounted for the low p50 value of rhinoceros blood. Method 1 provided better adaptation in respect to the physiological parameters of the rhinoceros, especially with regard to the Bohr effect, than Method 2. Pulse oximetry was an unreliable method of monitoring arterial oxygen saturation during general anaesthesia in this species. CONCLUSION: Adapting the oxygen saturation algorithm to consider the left shift of the ODC provides a useful tool for monitoring oxygen status, especially as pulse oximetry is insufficiently accurate. Experimental determination of the complete Hill curve is required to further validate and optimize the algorithm for use in the white rhinoceros. CLINICAL RELEVANCE: The method will facilitate the accurate interpretation of oxygen saturation calculated by blood gas analysis in white rhinoceros.

NEPHROPATHIES IN THE EUROPEAN CAPTIVE CHEETAH (ACINONYX JUBATUS) POPULATION.

According to previous studies in captive cheetah ( Acinonyx jubatus ) populations, one of the most threatening diseases besides amyloidosis, myelopathy, veno occlusive disease, and gastritis, is renal failure. Contrary to captive cheetahs in North America and South Africa, morphological data concerning renal lesions in the cheetah European Endangered Species Program (EEP) are lacking. This study details the histological characterization as well as immunohistochemical and morphometrical analysis of nephropathies in 35 captive cheetahs from the EEP, which were necropsied between 1985 and 2003. Examination of paraffin- and glycolmethacrylate-methylmethacrylate (GMA-MMA) embedded kidney samples by light microscopy revealed glomerulonephritis in 91%, with a high prevalence for glomerulosclerosis and glomerulonephritis with the histologic pattern of membranous glomerulonephritis (77%). Besides these predominating glomerulopathies, a wide range of other renal lesions, like acute tubular necrosis, interstitial nephritis, calcinosis, and amyloidosis, were present. Pathological expression of collagen type IV, complement C3, fibronectin, and IgG was demonstrated in the glomeruli of the cheetah kidneys with the use of the avidin-biotin complex method. Morphometrical analysis was performed on GMA-MMA embedded kidney samples to obtain glomerulosclerosis index and glomerulosclerosis incidence.

Red deer as maintenance host for bovine tuberculosis, Alpine region.

To estimate the prevalence of bovine tuberculosis in the Alpine region, we studied the epidemiology of Mycobacterium caprae in wildlife during the 2009-2012 hunting seasons. Free-ranging red deer (Cervus elaphus) were a maintenance host in a hot-spot area, mainly located in Austria.

Space and habitat use by wild Bactrian camels in the Transaltai Gobi of southern Mongolia.

Wild Bactrian camels (Camela ferus) are listed as Critically Endangered by the International Union for Conservation of Nature (IUCN) and only persist in some of the most remote locations in northern China and southern Mongolia. Although the species has been recognized as an umbrella species for the fragile central Asian desert ecosystem and has been high on the conservation agenda, little is known about the species' habitat requirements, with most information coming from anecdotal sightings and descriptive studies. We compiled the only available telemetry data from wild camels worldwide. Seven wild camels, which were followed for 11-378 monitoring days, covered a total range of 28,410 km2, with individual annual ranges being >12,000 km2 for three animals followed over a year. Camels reacted strongly to capture events, moving up to 64 km from the capture site within a day, whereas normal average daily straight line distances were 3.0-6.4 km/day. Camels showed a preference for intermediate productivity values (NDVI, habitat type) and landscape parameters (distance to water, elevation) and an avoidance of steep slopes. Our telemetry results suggest that wild camels still range throughout the entire Great Gobi A Strictly Protected Area (SPA), are highly mobile, and very sensitive to human disturbance. Their habitat preference may be a trade-off between dietary and safety requirements. Small sample size did not allow the development of a full habitat model testing all variables simultaneously and we urgently call for more data from additional wild camels as a foundation for evidence driven conservation actions.

Characterization of methicillin-resistant Staphylococcus spp. carrying the mecC gene, isolated from wildlife.

OBJECTIVES: A recently identified mecA homologue, mecC, in methicillin-resistant Staphylococcus aureus (MRSA) has been isolated from humans and different animal hosts. The aim of this study was to determine antimicrobial resistance and provide molecular characterization of MRSA and methicillin-resistant non-Staphylococcus aureus staphylococci (MRnSA) isolated from wildlife that carried the gene mecC. METHODS: Five S. aureus and one coagulase-negative Staphylococcus isolate displaying phenotypic oxacillin resistance, but not recognized with conventional PCR for mecA, were further characterized by a polyphasic approach. The presence of mecC in all isolates was determined using specific PCR. PCR targeting Panton-Valentine leucocidin (PVL) genes of MRSA was performed. MRSA isolates were genotyped by spa typing and multilocus sequence typing. All isolates were genotyped by staphylococcal cassette chromosome mec (SCCmec) typing. 16S rDNA sequence analysis for MRnSA identification was performed. Antimicrobial susceptibility testing was performed for all isolates. RESULTS: All five MRSA isolates contained the mecC gene, were PVL negative, carried SCCmec type XI and belonged to ST130 (where ST stands for sequence type), with spa types t843, t10513 or t3256, or to ST2620, with spa type t4335. The MRnSA isolate, most closely related to Staphylococcus stepanovicii, carried mecA and blaZ genes related to SCCmec XI. MRSA isolates exhibited resistance to the ß-lactams only. CONCLUSIONS: The MRSA isolates described in this study represent the first detection of mecC-positive MRSA in a European otter (Lutra lutra) and a European brown hare (Lepus europaeus). The MRnSA isolate represents the first isolation of MRnSA from a Eurasian lynx (Lynx lynx).

The continuum of care as a unifying framework for intergenerational and interspecies health equity.

Introduction: Unlocking the full potential of different people and organizations to address existential health threats requires shared goals and frameworks that allow people to see themselves contributing to a common and shared continuum of care. A new narrative to help people implement collective action for collective problems is needed. Methods: This paper is draw from the co-authors experience working from the local to international level on planetary health problems. Results: The proposed conceptual framework expands the socioecological model of health to help formulate multilevel approaches that foster healthier circumstances for all by revealing the mutual benefits that emerge from pooling expertise, funding, and political will to solve multiple problems with coordinated investment of resources and effort. It is intended to support program planning and communication. This framework is a response to the absence of systematic attempts to concurrently counteract the social and environmental conditions leading to disease, dysfunction and deficits which is increasingly seen as being problematic, especially as the root causes of health problems and solutions converge across species, sectors, and generations. The framework is embedded in the idea of interspecies and intergenerational health equity. Discussion: Ensuring interspecies and intergenerational health equity requires each actor to fulfill their roles along the continuum while supporting the needs of others. A socio-ecological continuum of care provides bundled options that combine knowledge from different sectors, disciplines and perspectives to guide interventions over time across a comprehensive array of services and support spanning all levels of needs, species and generations.

Data on SARS-CoV-2 events in animals: Mind the gap!

Current research on SARS-CoV-2 has largely focused on the pandemic's impact on humans, with insufficient attention paid to monitoring, sharing, and communicating information about viral circulation and evolution in animal hosts. The objective of this study was to estimate and characterise the data gap between the number of SARS-CoV-2 cases and related deaths in animals officially notified to the World Organisation for Animal Health (WOAH) via its World Animal Health Information System (WAHIS) and known cases reported through two other data sources: ProMED-mail and scientific papers. We used the previously published dataset SARS-ANI to retrieve SARS-CoV-2 events in animals published through WAHIS and ProMED-mail. Additionally, we generated SARS-ANI SciLit v1.0, a novel structured dataset of SARS-CoV-2 events in animals published through scientific literature retrieved from PubMed. We evidenced that at least 52.8% of the SARS-CoV-2 animal cases and 65.8% of the deaths were not reported to WAHIS during 29/02/2020-16/08/2022. Combining information from three different data sources, we compiled a new comprehensive list of 35 animal species reported as susceptible to SARS-CoV-2 under natural conditions, representing a significant advance from the figures reported by the WOAH and the Food and Agriculture Organization of the United Nations. Furthermore, we identified animal species that were underreported to the WAHIS and found that dogs and cats garnered the most attention in research studies. We also showed that, compared to the official WAHIS reports, scientific papers generally experienced longer publication lags and demonstrated that national strategies regarding reporting/publishing of SARS-CoV-2 events in animals greatly differed among countries. This analysis provides valuable insights into the patterns of reporting animal infections with SARS-CoV-2. The study emphasises the need for improvements in data sharing regarding SARS-CoV-2 events in animals, as this is crucial for effective One Health surveillance, prevention, and control of emerging diseases of zoonotic origin.

One Health Surveillance Highlights Circulation of Viruses with Zoonotic Potential in Bats, Pigs, and Humans in Viet Nam.

A One Health cross-sectoral surveillance approach was implemented to screen biological samples from bats, pigs, and humans at high-risk interfaces for zoonotic viral spillover for five viral families with zoonotic potential in Viet Nam. Over 1600 animal and human samples from bat guano harvesting sites, natural bat roosts, and pig farming operations were tested for coronaviruses (CoVs), paramyxoviruses, influenza viruses, filoviruses and flaviviruses using consensus PCR assays. Human samples were also tested using immunoassays to detect antibodies against eight virus groups. Significant viral diversity, including CoVs closely related to ancestors of pig pathogens, was detected in bats roosting at the human-animal interfaces, illustrating the high risk for CoV spillover from bats to pigs in Viet Nam, where pig density is very high. Season and reproductive period were significantly associated with the detection of bat CoVs, with site-specific effects. Phylogeographic analysis indicated localized viral transmission among pig farms. Our limited human sampling did not detect any known zoonotic bat viruses in human communities living close to the bat cave and harvesting bat guano, but our serological assays showed possible previous exposure to Marburg virus-like (Filoviridae), Crimean-Congo hemorrhagic fever virus-like (Bunyaviridae) viruses and flaviviruses. Targeted and coordinated One Health surveillance helped uncover this viral pathogen emergence hotspot.

Comparison of S(+)-ketamine and ketamine, with medetomidine, for field anaesthesia in the European brown hare (Lepus europaeus).

OBJECTIVE: To compare anaesthesia and recovery parameters of racemic ketamine or S(+)-ketamine in combination with medetomidine for intramuscular (IM) field anaesthesia in the European brown hare (EBH) (Lepus europaeus). STUDY DESIGN: Randomized, prospective, blinded clinical trial. ANIMALS: 20 adult EBH (eight male, 12 female), mean ± SD weight 3360 341). METHODS: Medetomidine (0.2 mg kg(-1) ) and ketamine (30 mg kg(-1) ) (K-M group) or S(+)-ketamine (15 mg kg(-1) ) (S-M group) were administered by IM injection. Time until first effect and loss of righting reflex were recorded. During sedation and anaesthesia heart rate, saturation of arterial haemoglobin, respiratory rate, side stream end tidal CO(2) (Pe'CO(2) ), non invasive blood pressure, body temperature, cardiorespiratory parameters, palpebral reflex, jaw tone and nociception were recorded every 5 minutes. Medetomidine was antagonized with IM atipamezole (1 mg kg(-1) ) 45 minutes after treatment injection. Time until first head lift, standing and total recovery time (T-Recov) were recorded. Incidences of falling and involuntary movements during recovery were counted. Recovery quality was scored by visual analogue scale. Descriptive statistics were used to visualize maintenance data. All other data were included in multiple linear regression models. RESULTS: Surgical anesthesia was not produced reliably with either protocol. Hypoxaemia occurred in both groups (SpO(2) < 90%). During recovery, falling was noted significantly less often (p < 0.001) in the S-M group (13 ± 7) versus the K-M group (27 ± 13). T-Recov was long, lasting for more than 3 hours in individuals with no significant differences between groups. CONCLUSION AND CLINICAL RELEVANCE: S(+)-ketamine showed only minor advantages over racemic ketamine. Surgical anaesthesia was not achieved reliably with either protocol. Oxygen supplementation should be considered to prevent hypoxaemia. Further research is needed to develop an injectable field protocol adequate for surgical procedures, but with a rapid smooth recovery.

Monitoring Urban Zoonotic Virus Activity: Are City Rats a Promising Surveillance Tool for Emerging Viruses?

Urban environments represent unique ecosystems where dense human populations may come into contact with wildlife species, some of which are established or potential reservoirs for zoonotic pathogens that cause human diseases. Finding practical ways to monitor the presence and/or abundance of zoonotic pathogens is important to estimate the risk of spillover to humans in cities. As brown rats (Rattus norvegicus) are ubiquitous in urban habitats, and are hosts of several zoonotic viruses, we conducted longitudinal sampling of brown rats in Vienna, Austria, a large population center in Central Europe. We investigated rat tissues for the presence of several zoonotic viruses, including flaviviruses, hantaviruses, coronaviruses, poxviruses, hepatitis E virus, encephalomyocarditis virus, and influenza A virus. Although we found no evidence of active infections (all were negative for viral nucleic acids) among 96 rats captured between 2016 and 2018, our study supports the findings of others, suggesting that monitoring urban rats may be an efficient way to estimate the activity of zoonotic viruses in urban environments.

SARS-ANI: a global open access dataset of reported SARS-CoV-2 events in animals.

The zoonotic origin of SARS-CoV-2, the etiological agent of COVID-19, is not yet fully resolved. Although natural infections in animals are reported in a wide range of species, large knowledge and data gaps remain regarding SARS-CoV-2 in animal hosts. We used two major health databases to extract unstructured data and generated a global dataset of SARS-CoV-2 events in animals. The dataset presents harmonized host names, integrates relevant epidemiological and clinical data on each event, and is readily usable for analytical purposes. We also share the code for technical and visual validation of the data and created a user-friendly dashboard for data exploration. Data on SARS-CoV-2 occurrence in animals is critical to adapting monitoring strategies, preventing the formation of animal reservoirs, and tailoring future human and animal vaccination programs. The FAIRness and analytical flexibility of the data will support research efforts on SARS-CoV-2 at the human-animal-environment interface. We intend to update this dataset weekly for at least one year and, through collaborations, to develop it further and expand its use.

Evidence of SARS-CoV-2 Related Coronaviruses Circulating in Sunda pangolins (Manis javanica) Confiscated From the Illegal Wildlife Trade in Viet Nam.

Despite the discovery of several closely related viruses in bats, the direct evolutionary progenitor of SARS-CoV-2 has not yet been identified. In this study, we investigated potential animal sources of SARS-related coronaviruses using archived specimens from Sunda pangolins (Manis javanica) and Chinese pangolins (Manis pentadactyla) confiscated from the illegal wildlife trade, and from common palm civets (Paradoxurus hermaphroditus) raised on wildlife farms in Viet Nam. A total of 696 pangolin and civet specimens were screened for the presence of viral RNA from five zoonotic viral families and from Sarbecoviruses using primers specifically designed for pangolin coronaviruses. We also performed a curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, to illustrate the global pangolin supply chain in the context of Viet Nam where the trade confiscated pangolins were sampled for this study. All specimens from pangolins and civets sampled along the wildlife supply chains between February 2017 and July 2018, in Viet Nam and tested with conventional PCR assays designed to detect flavivirus, paramyxovirus, filovirus, coronavirus, and orthomyxovirus RNA were negative. Civet samples were also negative for Sarbecoviruses, but 12 specimens from seven live pangolins confiscated in Hung Yen province, northern Viet Nam, in 2018 were positive for Sarbecoviruses. Our phylogenetic trees based on two fragments of the RdRp gene revealed that the Sarbecoviruses identified in these pangolins were closely related to pangolin coronaviruses detected in pangolins confiscated from the illegal wildlife trade in Yunnan and Guangxi provinces, China. Our curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, reflected what is known about pangolin trafficking globally. Pangolins confiscated in Viet Nam were largely in transit, moving toward downstream consumers in China. Confiscations included pangolin scales sourced originally from Africa (and African species of pangolins), or pangolin carcasses and live pangolins native to Southeast Asia (predominately the Sunda pangolin) sourced from neighboring range countries and moving through Viet Nam toward provinces bordering China.