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Dec 20, 2024;7 (1): 1687.

Improving the reporting of metagenomic virome-scale data.

Wei-Shan Chang, Erin Harvey, Jackie E Mahar, Cadhla Firth, Mang Shi, Etienne Simon-Loriere, Jemma L Geoghegan, Michelle Wille
Author Information
  1. Wei-Shan Chang: School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia. ORCID
  2. Erin Harvey: School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia. ORCID
  3. Jackie E Mahar: School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia. ORCID
  4. Cadhla Firth: College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Australia. ORCID
  5. Mang Shi: Sun Yat-Sen University, Shenzhen campus of Sun Yat-Sen University, Shenzhen, China. ORCID
  6. Etienne Simon-Loriere: Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France. ORCID
  7. Jemma L Geoghegan: Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand. ORCID
  8. Michelle Wille: School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia. michelle.wille@unimelb.edu.au. ORCID
PMID: 39706917 DOI: 10.1038/s42003-024-07212-3

Abstract

Over the last decade metagenomic sequencing has facilitated an increasing number of virome-scale studies, leading to an exponential expansion in understanding of virus diversity. This is partially driven by the decreasing costs of metagenomic sequencing, improvements in computational tools for revealing novel viruses, and an increased understanding of the key role that viruses play in human and animal health. A central concern associated with this remarkable increase in the number of virome-scale studies is the lack of broadly accepted "gold standards" for reporting the data and results generated. This is of particular importance for animal virome studies as there are a multitude of nuanced approaches for both data presentation and analysis, all of which impact the resulting outcomes. As such, the results of published studies can be difficult to contextualise and may be of reduced utility due to reporting deficiencies. Herein, we aim to address these reporting issues by outlining recommendations for the presentation of virome data, encouraging a transparent communication of findings that can be interpreted in evolutionary and ecological contexts.

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MeSH Term

Animals
Humans
Genome, Viral
Metagenome
Metagenomics
Virome
Viruses
Journal Article
Article has an altmetric score of 7

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