EAGER: Temporal Occurrence, Spatial Dynamics, and Host Diversity of Betacoronaviruses, including SARS-CoV-2, with Implications for Mitigating Covid-19 Re-emergence

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Frozen museum collections provide a largely untapped biodiversity infrastructure that would potentially allow for the study of pandemics, like that caused by SARS-CoV-2, in substantially new and different ways. This project will leverage a vast set of frozen samples from wild mammals and engage new expertise to develop powerful interdisciplinary approaches to studying pathogens that emerge from wildlife. This study will examine the frozen tissue collections of the Museum of Southwestern Biology’s Division of Genomic Resources (DGR) with specimens collected from Asian countries near China that are ideal for testing for SARS-CoV-2 virus. Detailed understanding of the distribution of pathogens in the wild and how they cross species boundaries, including switching to infect humans, could provide a critical foundation for prevention and mitigation of future zoonotic infections or reinfections. New workflows that fully leverage this biodiversity and zoonotic pathogen infrastructure will be developed. This project also provides training opportunities for students, including from underrepresented minorities, as well as outreach to the public.During the last few decades, disease ecologists and evolutionary biologists have identified key factors involved in the spillover of pathogens from reservoir host species into human populations. Understanding the distribution of the virus in wild mammals will contribute to a better assessment of the potential for direct contact between human populations and the virus. Pathogen detection will be carried out via molecular methods in tissues from 1,000 target (bar-coded) mammal specimens from eastern Asia with a special focus on SARS-CoV-2 and its coronavirus relatives. For positive tissues, sequencing of whole genomes of viruses will be conducted using established techniques for coronaviruses optimized for downstream comparative analyses. Phylogeographic methods will be used to characterize the geographic variation and historical demography of viruses and associated mammalian hosts. These efforts will leverage already existing natural history collection materials to inform SARS-CoV-2 evolution, Covid-19 emergence, and more generally pathogen emergence and epidemiological models.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.