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New Zealand’s endemic reptile fauna is highly threatened and pathogens causing infectious diseases may be a significant risk to already endangered species. Here, we investigate Cryptosporidium infection in captive endemic New Zealand reptiles. We found two mammal-related Cryptosporidium species (C. hominis and C. parvum) and six subtypes from three gp60 families (Ib, Ig and IIa) in 12 individuals of captive endemic Tuatara, Otago and Grand skinks, and Jewelled and Rough geckos. Cryptosporidium serpentis was identified in two Jewelled geckos using 18S. In New Zealand, C. hominis and C. parvum are associated with infections in humans and introduced domestic animals but have also been recently found in wildlife. Our finding of Cryptosporidium infection in endemic reptiles can help inform strategies to monitor the conservation of species and manage potential introductions of pathogens to in-situ and ex-situ populations.

The emergence of SARS-like coronaviruses is a multi-stage process from wildlife reservoirs to people. Here we characterize multivariate indicators associated with the risk of zoonotic spillover of SARS-like coronaviruses in different areas to help inform surveillance and mitigation activities. We consider direct and indirect transmission pathways by modeling four scenarios with livestock and mammalian wildlife as potential and known reservoirs, before examining how access to healthcare varies within areas. We found 19 multivariate clusters that had differing risk factor contributions. High-risk areas were mostly close (11-20%) rather than far (TeaserMultivariate clusters of stressors associated with SARS-like coronavirus spillover risk.

ObjectiveAvoiding duodenal biopsy in adults for coeliac disease (CD) diagnosis is controversial. Some retrospective and prospective studies have shown that CD can be reliably diagnosed in adults with serology rather than duodenal biopsies. This study aimed to check the accuracy of a cut-off value of ≥10 upper limit of normal of anti-tissue transglutaminase antibody (anti-TTG IgA) titres for CD diagnosis in adult patients.MethodWe retrospectively analysed adult patients (≥16 years) who underwent gastroscopy from 2013 to 2018 for positive coeliac serology. The relationship between titres and disease was determined by using linear models, whereas sensitivity and specificity were assessed by receiver operator curve.ResultsWe analysed 144 newly anti-TTG antibody-positive adult patients with a median age of 48.5 years (IQR 32–62); among them, 86 (60%) patients had CD (Marsh III: n=68 and Marsh II and I: n=18) with a higher prevalence in females (n=59 (69%)) and Europeans (n=60 (70%)). Fifty (58%) patients with CD had colonoscopy and five (6%) had imaging; only six patients were diagnosed with additional conditions. An anti-TTG IgA titre cut-off value of 150 U/L was 100% specific for CD in our dataset, with 70% (95% CI: 60% to 88%) sensitivity for this patient group.ConclusionCoeliac serology using anti-TTG IgA with titres ≥10× normal value is an excellent predictor of CD, irrespective of age, gender and ethnicity. Duodenal biopsy may not be necessary in selected adult patients with CD, especially younger than 50 years of age without additional gastrointestinal red-flag signs and symptoms.

Coronavirus disease-2019 (Covid-19) nonpharmaceutical interventions have proven effective control measures for a range of respiratory illnesses throughout the world. These measures, which include isolation, stringent border controls, physical distancing and improved hygiene also have effects on other human pathogens, including parasitic enteric diseases such as cryptosporidiosis. Cryptosporidium infections in humans are almost entirely caused by two species: C. hominis, which is primarily transmitted from human to human, and Cryptosporidium parvum, which is mainly zoonotic. By monitoring Cryptosporidium species and subtype families in human cases of cryptosporidiosis before and after the introduction of Covid-19 control measures in New Zealand, we found C. hominis was completely absent after the first months of 2020 and has remained so until the beginning of 2021. Nevertheless, C. parvum has followed its typical transmission pattern and continues to be widely reported. We conclude that ~7 weeks of isolation during level 3 and 4 lockdown period interrupted the human to human transmission of C. hominis leaving only the primarily zoonotic transmission pathway used by C. parvum. Secondary anthroponotic transmission of C. parvum remains possible among close contacts of zoonotic cases. Ongoing 14-day quarantine measures for new arrivals to New Zealand have likely suppressed new incursions of C. hominis from overseas. Our findings suggest that C. hominis may be controlled or even eradicated through nonpharmaceutical interventions.

In multihost disease systems, differences in mortality between species may reflect variation in host physiology, morphology, and behavior. In systems where the pathogen can persist in the environment, microclimate conditions, and the adaptation of the host to these conditions, may also impact mortality. White‐nose syndrome (WNS) is an emerging disease of hibernating bats caused by an environmentally persistent fungus, Pseudogymnoascus destructans. We assessed the effects of body mass, torpid metabolic rate, evaporative water loss, and hibernaculum temperature and water vapor deficit on predicted overwinter survival of bats infected by P. destructans. We used a hibernation energetics model in an individual‐based model framework to predict the probability of survival of nine bat species at eight sampling sites across North America. The model predicts time until fat exhaustion as a function of species‐specific host characteristics, hibernaculum microclimate, and fungal growth. We fit a linear model to determine relationships with each variable and predicted survival and semipartial correlation coefficients to determine the major drivers in variation in bat survival. We found host body mass and hibernaculum water vapor deficit explained over half of the variation in survival with WNS across species. As previous work on the interplay between host and pathogen physiology and the environment has focused on species with narrow microclimate preferences, our view on this relationship is limited. Our results highlight some key predictors of interspecific survival among western bat species and provide a framework to assess impacts of WNS as the fungus continues to spread into western North America., White‐nose syndrome is an emerging disease of hibernating bats caused by an environmentally persistent fungus, Pseudogymnoascus destructans. We used a hibernation energetics model in an individual‐based model framework to predict the probability of survival of nine bat species at eight sampling sites across North America. These results indicate that heavier bats that roost in drier conditions, which are unsuitable for the fungus that causes white‐nose syndrome, are less susceptible to the disease. Our results highlight some key predictors of interspecific survival among western bat species and provide a framework to assess impacts of white‐nose syndrome as the fungus continues to spread into western North America.

Background: Histological changes induced by gluten in the duodenal mucosa of patients with non-coeliac gluten sensitivity (NCGS) are poorly defined. \ud \ud \ud \ud Objectives: To evaluate the structural and inflammatory features of NCGS compared to controls and coeliac disease (CeD) with milder enteropathy (Marsh I-II). \ud \ud \ud \ud Methods: Well-oriented biopsies of 262 control cases with normal gastroscopy and histologic findings, 261 CeD, and 175 NCGS biopsies from 9 contributing countries were examined. Villus height (VH, in μm), crypt depth (CrD, in μm), villus-to-crypt ratios (VCR), IELs (intraepithelial lymphocytes/100 enterocytes), and other relevant histological, serologic, and demographic parameters were quantified. \ud \ud \ud \ud Results: The median VH in NCGS was significantly shorter (600, IQR: 400–705) than controls (900, IQR: 667–1112) (p < 0.001). NCGS patients with Marsh I-II had similar VH and VCR to CeD [465 µm (IQR: 390–620) vs. 427 µm (IQR: 348–569, p = 0·176)]. The VCR in NCGS with Marsh 0 was lower than controls (p < 0.001). The median IEL in NCGS with Marsh 0 was higher than controls (23.0 vs. 13.7, p < 0.001). To distinguish Marsh 0 NCGS from controls, an IEL cut-off of 14 showed 79% sensitivity and 55% specificity. IEL densities in Marsh I-II NCGS and CeD groups were similar. \ud \ud \ud \ud Conclusion: NCGS duodenal mucosa exhibits distinctive changes consistent with an intestinal response to luminal antigens, even at the Marsh 0 stage of villus architecture.

Environmental DNA (eDNA) offers a new avenue for investigating changes in the water microbial community associated with faecal contamination. Faeces in drinking water might include pathogens, which...

Parasites sometimes expand their host range and cause new disease aetiologies. Genetic changes can then occur due to host-specific adaptive alterations, particularly when parasites cross between evolutionarily distant hosts. Characterizing genetic variation inCryptosporidiumfrom humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multipleCryptosporidiumspecies reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans ofCryptosporidium meleagridis, Cryptosporidium cuniculus, Cryptosporidium hominisandCryptosporidium parvum. A deviation of expected values of neutrality using Tajima'sDwas observed inC. cuniculusandC. meleagridis. The high genetic diversity inC. meleagridisandC. cuniculusdid not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event.Cryptosporidium hominiswas also found with a significant Tajima's D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.

Aim The aim of our study was to assess the presence and risk of waterborne pathogens in the drinking water of outdoor facilities in New Zealand and track potential sources of microbial contamination in water sources. Methods and results A serial cross-sectional study with a risk-based sample collection strategy was conducted at 15 public campgrounds over two summer seasons (2011-2012 and 2012-2013). Drinking water supplied to these campgrounds was not compliant with national standards, based on Escherichia coli as an indicator organism, in more than half of the sampling occasions. Campylobacter contamination of drinking water at the campgrounds was likely to be of wild bird origin. Faecal samples from rails (pukeko and weka) were 35 times more likely to return a Campylobacter-positive result compared to passerines. Water treatment using ultraviolet (UV) irradiation or a combination of filtration and UV irradiation or chemicals was more likely to result in water that was compliant with the national standards than water from a tap without any treatment. The use of filters alone was not associated with the likelihood of compliance. Conclusions Providing microbiologically safe drinking water at outdoor recreational facilities is imperative to avoid gastroenteritis outbreaks. This requires an in-depth understanding of potential sources of contamination in drinking water sources and the installation of adequate water treatment facilities. Significance and impact of the study Our study provides evidence that drinking water without treatment or filter-only treatment in public campgrounds is unlikely to comply with national standards for human consumption and extra water treatment measures such as UV irradiation or chemical treatment are needed.

BackgroundGiardia is one of the most common causes of diarrhoea in the world and is a notifiable disease in New Zealand. Recent advances in molecular techniques, such as PCR and Sanger sequencing, have greatly improved our understanding of the taxonomic classification and epidemiology of this parasite. However, there has been an inability to identify shared subtypes between samples from the same epidemiologically linked cases, due to samples showing multiple dominant subtypes within the same outbreak when characterised using Sanger sequencing. MethodsHere, NGS was employed to uncover the genetic diversity within samples from sporadic and outbreak cases of giardiasis that occurred in New Zealand between 2010 and 2018. ResultsThis strategy exposed the significant diversity of subtypes of Giardia present in each sample. The utilisation of NGS and metabarcoding at the glutamate dehydrogenase (gdh) locus enabled the identification of shared subtypes between samples from shared outbreaks, providing a better understanding of the epidemiology of outbreaks of giardiasis in New Zealand.ConclusionsNext-generation sequencing technologies provides a superior tool, when compared to consensus sequencing technologies, for capturing the genetic diversity of Giardia within hosts. This study showed that infections in humans are frequently mixed, with multiple subtypes present in each host.

Global changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of viral spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecological niche modelling pipeline for bat hosts of SARS-like viruses (subgenus Sarbecovirus ), given that several closely related viruses have been discovered and sarbecovirus–host interactions have gained attention since SARS-CoV-2 emergence. We assessed sampling biases and modelled current distributions of bats based on climate and landscape relationships and project future scenarios for host hotspots. The most important predictors of species distributions were temperature seasonality and cave availability. We identified concentrated host hotspots in Myanmar and projected range contractions for most species by 2100. Our projections indicate hotspots will shift east in Southeast Asia in locations greater than 2°C hotter in a fossil-fuelled development future. Hotspot shifts have implications for conservation and public health, as loss of population connectivity can lead to local extinctions, and remaining hotspots may concentrate near human populations.

Hypervirulent Klebsiella pneumoniae infection causes significant mortality of endangered New Zealand sea lion pups at Enderby Island, Auckland Islands. Gross necropsy and histopathology findings are well reported, but little is known about the clinical course of disease in affected pups. To determine factors feasible as clinical screening tools for hypervirulent K. pneumoniae in live pups, 150 pups over two field seasons (2016–18) were recruited shortly after birth for a prospective cohort study. A randomised controlled clinical treatment trial with the anthelmintic ivermectin was conducted concurrently and risk factor data and biological samples were collected approximately fortnightly. Treatment with ivermectin has been demonstrated to reduce the risk of hypervirulent K. pneumoniae mortality in pups, so effects on clinical parameters between the treated and control cohorts were also investigated. A broader sample of pups were monitored for clinical signs to investigate the course of disease in affected pups. Clinical signs, haematology and oral and rectal swabs to detect gastrointestinal carriage of hypervirulent K. pneumoniae were not useful for detection of disease prior to death. Of those pups that died due to hypervirulent K. pneumoniae, only 26.1% (18/69) had any clinical signs prior, likely a reflection of the peracute course of disease. On comparison of haematological parameters between ivermectin-treated and control pups, significantly lower total plasma protein and higher eosinophil counts were seen in control versus treated pups, however standard length as a surrogate for age was a more important influence on parameters overall than ivermectin treatment. This study also highlighted a cohort of pups with severe clinical signs suggestive of hypervirulent K. pneumoniae infection were lost to follow up at the end of the monitored season, which could be contributing to cryptic juvenile mortality.

Salmonella enterica serovar Typhimurium DT160 was the predominant cause of notified human salmonellosis cases in New Zealand from 2000 to 2010, before it was superseded by another S. Typhimurium strain, DT56 variant (DT56v). Whole genome sequencing and phenotypic testing were used to compare 109 DT160 isolates with eight DT56v isolates from New Zealand animal and human sources. Phylogenetic analysis provided evidence that DT160 and DT56v strains were distantly related with an estimated date of common ancestor between 1769 and 1821. The strains replicated at different rates but had similar antimicrobial susceptibility profiles. Both strains were resistant to the phage expressed from the chromosome of the other strain, which may have contributed to the emergence of DT56v. DT160 contained the pSLT virulence plasmid, and the sseJ and sseK2 genes that may have contributed to the higher reported prevalence compared to DT56v. A linear pBSSB1-family plasmid was also found in one of the DT56v isolates, but there was no evidence that this plasmid affected bacterial replication or antimicrobial susceptibility. One of the DT56v isolates was also sequenced using long-read technology and found to contain an uncommon chromosome arrangement for a Typhimurium isolate. This study demonstrates how comparative genomics and phenotypic testing can help identify strain-specific elements and factors that may have influenced the emergence and supersession of bacterial strains of public health importance.

Septicaemia due to hypervirulent (HV) Klebsiella pneumoniae is the leading cause of neonatal pup mortality in endangered New Zealand sea lions (Phocarctos hookeri) at Enderby Island, in the New Zealand sub-Antarctic. Accounting for approximately 60% of annual pup mortality at this site following an epizootic event in 2001–02, HV K. pneumoniae is also emerging worldwide as a significant community-acquired human pathogen. To facilitate efficient direct mitigation to reduce pup mortality, a case-control study and prospective cohort study were conducted to identify risk factors amenable to active management. Additionally, to investigate impacts of hookworm (Uncinaria spp.), a nested treatment trial with the anthelmintic ivermectin was undertaken concurrently. During two austral summer field seasons (2016–2018), 698 pups were captured for treatment trial recruitment and the collection of morphometric measurements, biological samples and risk factor data. Gastrointestinal carriage of the virulent phenotype of K. pneumoniae was a consistent risk factor, while ivermectin treatment and higher body condition index consistently reduced risk of HV K. pneumoniae mortality. Significantly fewer ivermectin-treated pups were found dead (24.1% control, 11.1% treatment), with a trend towards a higher proportion of HV K. pneumoniae deaths amongst the control group. This study provides evidence to support ivermectin treatment as a pup mortality mitigation strategy in New Zealand sea lions at Enderby Island. If applied to larger colonies where HV K. pneumoniae and hookworm impact pup survival, this intervention could have population-scale benefits for this endangered species. Further work is required to understand how ivermectin prevents HV K. pneumoniae septicaemia, but removal of hookworms before intestinal mucosal damage occurs could limit systemic spread of virulent bacteria from the gastrointestinal tract.

Many species use stored energy to hibernate through periods of resource limitation. Hibernation, a physiological state characterized by depressed metabolism and body temperature, is critical to winter survival and reproduction, and therefore has been extensively quantified and modeled. Hibernation consists of alternating phases of extended periods of torpor (low body temperature, low metabolic rate), and energetically costly periodic arousals to normal body temperature. Arousals consist of multiple phases: warming, euthermia, and cooling. Warming and euthermic costs are regularly included in energetic models, but although cooling to torpid body temperature is an important phase of the torpor-arousal cycle, it is often overlooked in energetic models. When included, cooling cost is assumed to be 67% of warming cost, an assumption originally derived from a single study that measured cooling cost in ground squirrels. Since this study, the same proportional value has been assumed across a variety of hibernating species. However, no additional values have been derived. We derived a model of cooling cost from first principles and validated the model with empirical energetic measurements. We compared the assumed 67% proportional cooling cost with our model-predicted cooling cost for 53 hibernating mammals. Our results indicate that using 67% of warming cost only adequately represents cooling cost in ground squirrel-sized mammals. In smaller species, this value overestimates cooling cost and in larger species, the value underestimates cooling cost. Our model allows for the generalization of energetic costs for multiple species using species-specific physiological and morphometric parameters, and for predictions over variable environmental conditions.

Viruses of the subfamily Orthocoronavirinae can cause mild to severe disease in people, including COVID-19, MERS and SARS. Their most common natural hosts are bat and bird species, which are mostly split across four virus genera. Molecular clock analyses of orthocoronaviruses suggested the most recent common ancestor of these viruses might have emerged either around 10,000 years ago or, using models accounting for selection, many millions of years. Here, we reassess the evolutionary history of these viruses. We present time-aware phylogenetic analyses of a RNA-dependent RNA polymerase locus from 123 orthocoronaviruses isolated from birds and bats, including those in New Zealand, which were geographically isolated from other bats around 35 million years ago. We used this age, as well as the age of the avian-mammals split, to calibrate the molecular clocks, under the assumption that these ages are applicable to the analyzed viruses. We found that the time to the most recent ancestor common for all orthocoronaviruses is likely 150 or more million years, supporting clock analyses that account for selection.

Climate change and disease are threats to biodiversity that may compound and interact with one another in ways that are difficult to predict. White-nose syndrome (WNS), caused by a cold-loving fungus (Pseudogymnoascus destructans), has had devastating impacts on North American hibernating bats, and impact severity has been linked to hibernaculum microclimate conditions. As WNS spreads across the continent and climate conditions change, anticipating these stressors’ combined impacts may improve conservation outcomes for bats. We build on the recent development of winter species distribution models for five North American bat species, which used a hybrid correlative-mechanistic approach to integrate spatially explicit winter survivorship estimates from a bioenergetic model of hibernation physiology. We apply this bioenergetic model given the presence of P. destructans , including parameters capturing its climate-dependent growth as well as its climate-dependent effects on host physiology, under both current climate conditions and scenarios of future climate change. We then update species distribution models with the resulting survivorship estimates to predict changes in winter hibernacula suitability under future conditions. Exposure to P. destructans is generally projected to decrease bats’ winter occurrence probability, but in many areas, changes in climate are projected to lessen the detrimental impacts of WNS. This rescue effect is not predicted for all species or geographies and may arrive too late to benefit many hibernacula. However, our findings offer hope that proactive conservation strategies to minimize other sources of mortality could allow bat populations exposed to P. destructans to persist long enough for conditions to improve.

White‐nose syndrome (WNS) has decimated hibernating bat populations across eastern and central North America for over a decade. Disease severity is driven by the interaction between bat characteristics, the cold‐loving fungal agent, and the hibernation environment. While we further improve hibernation energetics models, we have yet to examine how spatial heterogeneity in host traits is linked to survival in this disease system. Here, we develop predictive spatial models of body mass for the little brown myotis (Myotis lucifugus) and reassess previous definitions of the duration of hibernation of this species. Using data from published literature, public databases, local experts, and our own fieldwork, we fit a series of generalized linear models with hypothesized abiotic drivers to create distribution‐wide predictions of prehibernation body fat and hibernation duration. Our results provide improved estimations of hibernation duration and identify a scaling relationship between body mass and body fat; this relationship allows for the first continuous estimates of prehibernation body mass and fat across the species' distribution. We used these results to inform a hibernation energetic model to create spatially varying fat use estimates for M. lucifugus. These results predict WNS mortality of M. lucifugus populations in western North America may be comparable to the substantial die‐off observed in eastern and central populations., White‐nose syndrome disease severity is driven by the interaction between bat characteristics, the cold‐loving fungal agent, and the hibernation environment. Here, we develop predictive spatial models of body mass for the little brown myotis (Myotis lucifugus) and reassess previous definitions of the duration of hibernation of this species. Our results provide improved estimations of hibernation duration and identify a scaling relationship between body mass and body fat; this relationship allows for the first continuous estimates of prehibernation body mass and fat across the species' distribution.

Giardia is an enteric protozoan parasite that causes gastroenteritis in all classes of vertebrates. It is ranked among the leading causes of death in children under 5 years of age. Giardiasis affects approximately 280 million people worldwide annually, a situation exacerbated by the low availability of effective treatments and the lack of a vaccine. In addition, the parasite is difficult to manipulate in in vitro environments, which hampers the development of effective disease management strategies. This article highlights the development of a method for the purification of viable Giardia cysts from fecal samples, verified by a trypan blue dye exclusion test. This protocol produces a 10-fold increase in yield over current methods. By combining sucrose flotation with gated filtration, the protocol significantly reduces the amount of debris in the purified cysts suspension. Cyst viability is verified by a trypan blue dye exclusion test. The ability to purify large quantities of Giardia from fecal samples could advance the development of effective treatments to target this worldwide prevalent parasite. © 2020 Wiley Periodicals LLC. Basic Protocol: Purification of Giardia cysts from fecal samples Support Protocol: Cyst viability test.

Caves and other subterranean features provide unique environments for many species. The importance of cave microclimate is particularly relevant at temperate latitudes where bats make seasonal use of caves for hibernation. White‐nose syndrome (WNS), a fungal disease that has devastated populations of hibernating bats across eastern and central North America, has brought renewed interest in bat hibernation and hibernaculum conditions. A recent review synthesized current understanding of cave climatology, exploring the qualitative relationship between cave and surface climate with implications for hibernaculum suitability. However, a more quantitative understanding of the conditions in which bats hibernate and how they may promote or mediate WNS impacts is required. We compiled subterranean temperatures from caves and mines across the western United States and Canada to (1) quantify the hypothesized relationship between mean annual surface temperature (MAST) and subterranean temperature and how it is influenced by measurable site attributes, and (2) use readily available gridded data to predict and continuously map the range of temperatures that may be available in caves and mines. Our analysis supports qualitative predictions that subterranean winter temperatures are correlated with MAST, that temperatures are warmer and less variable farther from the surface, and that even deep within‐cave temperatures tend to be lower than MAST. Effects of other site attributes (e.g., topography, vegetation, and precipitation) on subterranean temperatures were not detected. We then assessed the plausibility of model‐predicted temperatures using knowledge of winter bat distributions and preferred hibernaculum temperatures. Our model unavoidably simplifies complex subterranean environments and is not intended to explain all variability in subterranean temperatures. Rather, our results offer researchers and managers improved broad‐scale estimates of the geographic distribution of potential hibernaculum conditions compared to reliance on MAST alone. We expect this information to better support range‐scale estimation of winter bat distributions and projection of likely WNS impacts across the west. We suggest that our model predictions should serve as hypotheses to be further tested and refined as additional data become available.

The recorded number of epidemics from emerging diseases is increasing at alarming rates, posing new threats on human societies. Despite the consensus on the existence of a nexus between emerging diseases and human pressure on the environment, the link to global and regional trends in food demand and agricultural production remains poorly understood. The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) is no difference. SARS-related coronaviruses are mostly discovered in Asian horseshoe bat species. It is unclear to what extent the transmission to humans is facilitated by ongoing land use and animal husbandry trends underlying recent shifts in the food system. Forest fragmentation, human encroachment into wildlife habitats as a result of expanding urbanization, cropland, and concentrated animal farming are hypothesized to favor the emergence of zoonotic diseases. In the regions of the world populated by Asian horseshoe bats (>28.5 million km2), we analyze comprehensive high-resolution (30m-1000m) datasets on forest cover, cropland distribution, livestock density, human population, human settlements, bat species’ distribution, and land-use changes to explain why China was and remains at risk for SARS-coronavirus outbreaks. We show that in China areas populated by horseshoe bats exhibit statistically significant higher forest fragmentation and concentrations of livestock (e.g. poultry and pigs) and humans than other countries. Moreover, regions of China populated by horseshoe bats are hotspots of forest fragmentation, livestock density, and human settlements. These results are consistent with the notion that population growth and increasing meat consumption associated with urbanization and economic growth have expanded the footprint of agriculture, leading to human encroachment in wildlife habitat and increased livestock density in areas adjacent to fragmented forest patches. These results indicate that conditions in China put it at high risk for SARS-related coronavirus transmission to humans because land use patterns reduce the distance between wildlife reservoir species and humans.

The COVID-19 pandemic highlights the substantial public health, economic, and societal consequences of virus spillover from a wildlife reservoir. Widespread human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also presents a new set of challenges when considering viral spillover from people to naïve wildlife and other animal populations. The establishment of new wildlife reservoirs for SARS-CoV-2 would further complicate public health control measures and could lead to wildlife health and conservation impacts. Given the likely bat origin of SARS-CoV-2 and related beta-coronaviruses (β-CoVs), free-ranging bats are a key group of concern for spillover from humans back to wildlife. Here, we review the diversity and natural host range of β-CoVs in bats and examine the risk of humans inadvertently infecting free-ranging bats with SARS-CoV-2. Our review of the global distribution and host range of β-CoV evolutionary lineages suggests that 40+ species of temperate-zone North American bats could be immunologically naïve and susceptible to infection by SARS-CoV-2. We highlight an urgent need to proactively connect the wellbeing of human and wildlife health during the current pandemic and to implement new tools to continue wildlife research while avoiding potentially severe health and conservation impacts of SARS-CoV-2 "spilling back" into free-ranging bat populations.