Characterizing and evaluating the zoonotic potential of novel viruses discovered in vampire bats

Bergner, L. M. , Mollentze, N. , Orton, R. J. , Tello, C., Broos, A. , Biek, R. and Streicker, D. G. (2021) Characterizing and evaluating the zoonotic potential of novel viruses discovered in vampire bats. Viruses, 13(2), 252. (doi: 10.3390/v13020252) (PMID:33562073) (PMCID:PMC7914986)

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Abstract

The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely applied to viruses at the time of their discovery. Here, we characterized viral genomes detected through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) and used these data as a case study in evaluating zoonotic potential using molecular sequencing data. Of 58 detected viral families, including 17 which infect mammals, the only known zoonosis detected was rabies virus; however, additional genomes were detected from the families Hepeviridae, Coronaviridae, Reoviridae, Astroviridae and Picornaviridae, all of which contain human-infecting species. In phylogenetic analyses, novel vampire bat viruses most frequently grouped with other bat viruses that are not currently known to infect humans. In agreement, machine learning models built from only phylogenetic information ranked all novel viruses similarly, yielding little insight into zoonotic potential. In contrast, genome composition-based machine learning models estimated different levels of zoonotic potential, even for closely related viruses, categorizing one out of four detected hepeviruses and two out of three picornaviruses as having high priority for further research. We highlight the value of evaluating zoonotic potential beyond ad hoc consideration of phylogeny and provide surveillance recommendations for novel viruses in a wildlife host which has frequent contact with humans and domestic animals.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Streicker, Dr Daniel and Biek, Professor Roman and Bergner, Dr Laura and Mollentze, Dr Nardus and Broos, Ms Alice and Orton, Dr Richard
Creator Roles:
Bergner, L. M.Conceptualization, Formal analysis, Investigation, Visualization, Writing – original draft, Writing – review and editing
Mollentze, N.Conceptualization, Formal analysis, Methodology, Software, Writing – original draft, Writing – review and editing
Orton, R. J.Conceptualization, Formal analysis, Software, Supervision, Writing – review and editing
Biek, R.Conceptualization, Supervision, Writing – review and editing
Streicker, D. G.Conceptualization, Funding acquisition, Supervision, Writing – original draft, Writing – review and editing
Broos, A.Investigation, Writing – review and editing
Authors: Bergner, L. M., Mollentze, N., Orton, R. J., Tello, C., Broos, A., Biek, R., and Streicker, D. G.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Viruses
Publisher:MDPI
ISSN:1999-4915
ISSN (Online):1999-4915
Published Online:06 February 2021
Copyright Holders:Copyright © 2021 The Authors
First Published:First published in Viruses 13(2): 252
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
169793Managing viral emergence at the interface of bats and livestockDaniel StreickerWellcome Trust (WELLCOTR)102507/Z/13/ZRInstitute of Biodiversity, Animal Health and Comparative Medicine
307106Epidemiology meets biotechnology: preventing viral emergence from batsDaniel StreickerWellcome Trust (WELLCOTR)217221/Z/19/ZInstitute of Biodiversity, Animal Health and Comparative Medicine
Viral Genomics and BioinformaticsAndrew DavisonMedical Research Council (MRC)MC_UU_12014/12III-MRC-GU Centre for Virus Research