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Rapid taxonomic categorization of short, abundant virus sequences for ecological analyses
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  • Anna Sjodin,
  • Michael Willig,
  • Armando Rodríguez-Durán ,
  • Simon Anthony
Anna Sjodin
University of Connecticut

Corresponding Author:sjodin.anna@epa.gov

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Michael Willig
University of Connecticut
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Armando Rodríguez-Durán
Inter American University of Puerto Rico
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Simon Anthony
Columbia University
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Abstract

Public health concerns about recent viral epidemics have motivated researchers to seek novel ways to understand pathogen infection in native, wildlife hosts. With its deep history of tools and perspectives for understanding the abundance and distribution of organisms, ecology can shed new light on viral infection dynamics. However, datasets allowing deep explorations of viral communities from an ecological perspective are lacking. We sampled 1,086 bats from two, adjacent Puerto Rican caves and tested them for infection by herpesviruses, resulting in 3,131 short, viral sequences. Using percent identity of nucleotides and a machine learning algorithm (affinity propagation), we categorized herpesviruses into 43 operational taxonomic units (OTUs), to be used in place of species in subsequent ecological analyses. Herpesvirus metacommunities demonstrated long-tailed rank frequency distributions at all analyzed levels of host organization (i.e., individual, population, and community). Although 13 herpesvirus OTUs were detected in more than one host species, OTUs generally exhibited host specificity by infecting a single core host species at a significantly higher prevalence than in all satellite species combined. We describes the natural history of herpesvirus metacommunities in Puerto Rican bats and suggest that viruses follow the general law that communities comprise few common and many rare species. To guide future efforts in the field of viral ecology, hypotheses are presented regarding mechanisms that contribute to these patterns.
27 Sep 2023Submitted to Ecology and Evolution
04 Oct 2023Submission Checks Completed
04 Oct 2023Assigned to Editor
04 Oct 2023Review(s) Completed, Editorial Evaluation Pending
09 Oct 2023Reviewer(s) Assigned
08 May 20241st Revision Received
16 May 2024Editorial Decision: Accept