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Cobbin JC, Charon J, Harvey E, et al. Current challenges to virus discovery by meta-transcriptomics. Curr Opin Virol. 2021;51:48-55doi: 10.1016/j.coviro.2021.09.007.
Cobbin, J. C., Charon, J., Harvey, E., Holmes, E. C., & Mahar, J. E. (2021). Current challenges to virus discovery by meta-transcriptomics. Current opinion in virology, 5148-55. https://doi.org/10.1016/j.coviro.2021.09.007
Cobbin, Joanna Ca, et al. "Current challenges to virus discovery by meta-transcriptomics." Current opinion in virology vol. 51 (2021): 48-55. doi: https://doi.org/10.1016/j.coviro.2021.09.007
Cobbin JC, Charon J, Harvey E, Holmes EC, Mahar JE. Current challenges to virus discovery by meta-transcriptomics. Curr Opin Virol. 2021 Dec;51:48-55. doi: 10.1016/j.coviro.2021.09.007. Epub 2021 Sep 27. PMID: 34592710.
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Curr Opin Virol. 2021 Dec;51:48-55. doi: 10.1016/j.coviro.2021.09.007. Epub 2021 Sep 27.

Current challenges to virus discovery by meta-transcriptomics.

Current opinion in virology

Joanna Ca Cobbin, Justine Charon, Erin Harvey, Edward C Holmes, Jackie E Mahar

Affiliations

  1. Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
  2. Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia. Electronic address: [email protected].

PMID: 34592710 DOI: 10.1016/j.coviro.2021.09.007

Abstract

Meta-transcriptomic next-generation sequencing has transformed virus discovery, dramatically expanding our knowledge of the known virosphere. Nevertheless, the use of meta-transcriptomics for virus discovery faces important challenges. As this technology becomes more widely adopted, the proportion of viral sequences in public databases with incorrect (e.g. mis-assignment of host) or limited information (e.g. lacking taxonomic classification) is likely to grow, limiting their utility in bioinformatic pipelines for virus discovery. In addition, we currently lack the bioinformatic tools that can accurately identify viruses showing little or no sequence similarity to database viruses or those that represent likely reagent contaminants. Herein, we outline some of the challenges to effective meta-transcriptomic virus discovery as well as their potential solutions.

Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.

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