The novel coronavirus SARS-CoV-2 has now infected more than 6,000,000 people worldwide, 370,000 of whom have died. Coronaviruses are notorious for jumping into new host species; indeed SARS-CoV-2 originated via spillover from a wildlife reservoir species, most likely a species of Old World bat, into humans. Arrival of SARS-CoV-2 in the Americas has created an opportunity for the virus to jump into New World bats, which could severely complicate the current public health emergency and threaten bat conservation. A major barrier to identifying which North American bat species are at greatest risk of SARS-CoV-2 ?spillback? is the current lack of knowledge about the distribution of coronaviruses in North American bats. To close this knowledge gap 17 target bat species in the Southwest U.S.A. will be characterized for their ?viromes? with an emphasis on coronaviruses, and also their the sequence of their cellular receptor, ACE-2, to which SARS-CoV-2 binds. Within species, bats of different sexes, ages and breeding status will be sampled. Molecular data will be combined with information on bat behaviors, migration, group size, and tendency to live near humans, to predict risk of spillback of SARS-CoV-2. Per the NSF-DCL, the results of the project will be used to model and understand the spread of COVID-19. As an additional broader impact, training of a graduate student will be supported by these funds.

This project focuses on characterizing the susceptibility of North American bats to SARS-CoV-2 infections. Specifically, two hypotheses will be tested: (i) that susceptibility of New World bat species may be based on genetics, behavior and life stage of each bat species, and (ii) that bat species with a high prevalence and diversity of native coronaviruses may be intrinsically resistant to SARS-CoV-2 infection due to competitive exclusion. Serum, rectal and oral swab samples, wing punches and peripheral blood mononuclear cells (PBMCs), will be collected from 17 bat species across a spectrum of behaviors (sociality, migration, peridomesticity). Within each species, fifty individuals, including, when possible, both sexes and all age and breeding stages, will be sampled in sites of human-bat overlap in New Mexico, Arizona, and Colorado. Samples will be processed for virome characterization using metagenomics based on next-generation DNA sequencing, incorporating recently developed methods that enrich clinical samples for coronaviruses and enable rapid whole-genome sequencing of known and unknown coronaviruses. Additionally, ACE-2 will be sequenced from a subset of individuals in each species. Associations between virus occurrence, prevalence and mean load and behavioral traits and life stage will be analyzed using phylogenetic generalized mixed models and information theory. This study will shed light on how bat behavior, ecology, infection, and ACE-2 sequence may enable or prevent spillback of introduced viruses, with SARS-CoV-2 serving as a critically important study system. This RAPID award is made by the Physiological and Structural Systems Cluster in the BIO Division of Integrative Organismal Systems, using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

National Science Foundation (NSF)
Division of Integrative Organismal Systems (IOS)
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Joanna Shisler
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New Mexico State University
Las Cruces
United States
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