![]() Unlike single sampling studies, spatiotemporal designs can identify seasonal and environmental drivers of viral prevalence and shedding intensity, but they are logistically challenging and often have either spatial or temporal replication but not both 6. Single sampling events can bias prevalence estimates in biologically meaningful ways, for example if sampling is more convenient in one season over another, and may lead to non-randomly missing data. For example, comparative analyses of bat filovirus and henipavirus positivity have shown that only a small fraction of studies report longitudinal data, limiting inference into temporal dynamics of infection in bats 6. However, field sampling is often carried out opportunistically in response to concerns about spillover, and capacity for systematic sampling is financially or logistically constrained 7. Research into the natural origins of SARS-CoV-2 and continuing interest in coronavirus ecology and evolution have highlighted the value of wild bat surveillance. Owing to this, coronaviruses, along with other clades of zoonotic viruses including filoviruses, lyssaviruses and henipaviruses, continue to be extensively monitored in wild bats 6. ![]() While alpha- and betacoronaviruses can infect many different hosts, substantial diversity of coronaviruses occurs in bats, which are probably the ancestral hosts of these coronavirus genera 4, 5. Betacoronaviruses include SARS-CoV, Middle East respiratory syndrome-related coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), all of which have caused morbidity and mortality in humans 3. The alpha- and betacoronaviruses contain all other known human-infective coronaviruses. ![]() The delta- and gammacoronaviruses are primarily bird pathogens, although they also infect some mammals notably, porcine deltacoronavirus was reported to infect humans in 2021 (ref. The group comprises four genera containing an estimated hundreds, or thousands, of viruses 1. Since the emergence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) in 2002, coronaviruses (Coronaviridae: Orthocoronavirinae) have been recognized as potential pandemic threats. We propose that surveillance strategies should address these gaps to improve global health security and enable the origins of zoonotic coronaviruses to be identified. ![]() We show that bat sampling before the SARS-CoV-2 pandemic was concentrated in China, with research gaps in South Asia, the Americas and sub-Saharan Africa, and in subfamilies of phyllostomid bats. Fewer than one in five studies collected and reported longitudinal data, and euthanasia did not improve virus detection. Meta-analysis identified sample type and sampling design as the best predictors of prevalence, with virus detection maximized in rectal and faecal samples and by repeat sampling of the same site. We found substantial heterogeneity in viral prevalence across studies, reflecting spatiotemporal variation in viral dynamics and methodological differences. We compiled 2,274 records of infection prevalence at the finest methodological, spatiotemporal and phylogenetic level of detail possible from public records into an open, static database named datacov, together with metadata on sampling and diagnostic methods. We identified 110 studies published between 20 that collectively reported positivity from 89,752 bat samples. We performed a systematic review of coronavirus sampling (testing for RNA positivity) in bats globally. The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses.
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