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A critical analysis of the current state of virus taxonomy
Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and a priorism. Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classific...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10435761/ https://www.ncbi.nlm.nih.gov/pubmed/37601376 http://dx.doi.org/10.3389/fmicb.2023.1240993 |
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author | Caetano-Anollés, Gustavo Claverie, Jean-Michel Nasir, Arshan |
author_facet | Caetano-Anollés, Gustavo Claverie, Jean-Michel Nasir, Arshan |
author_sort | Caetano-Anollés, Gustavo |
collection | PubMed |
description | Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and a priorism. Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification. We emphasize that viruses are crucial contributors to the genomic and functional makeup of holobionts, organismal communities that behave as units of biological organization. Consequently, viruses cannot be considered taxonomic units because they challenge crucial concepts of organismality and individuality. Instead, they should be considered processes that integrate virions and their hosts into life cycles. Viruses harbor phylogenetic signatures of genetic transfer that compromise monophyly and the validity of deep taxonomic ranks. A focus on building phylogenetic networks using alignment-free methodologies and molecular structure can help mitigate the impasse, at least in part. Finally, structural phylogenomic analysis challenges the polyphyletic scenario of multiple viral origins adopted by virus taxonomy, defeating a polyphyletic origin and supporting instead an ancient cellular origin of viruses. We therefore, prompt abandoning deep ranks and urgently reevaluating the validity of taxonomic units and principles of virus classification. |
format | Online Article Text |
id | pubmed-10435761 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-104357612023-08-19 A critical analysis of the current state of virus taxonomy Caetano-Anollés, Gustavo Claverie, Jean-Michel Nasir, Arshan Front Microbiol Microbiology Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and a priorism. Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification. We emphasize that viruses are crucial contributors to the genomic and functional makeup of holobionts, organismal communities that behave as units of biological organization. Consequently, viruses cannot be considered taxonomic units because they challenge crucial concepts of organismality and individuality. Instead, they should be considered processes that integrate virions and their hosts into life cycles. Viruses harbor phylogenetic signatures of genetic transfer that compromise monophyly and the validity of deep taxonomic ranks. A focus on building phylogenetic networks using alignment-free methodologies and molecular structure can help mitigate the impasse, at least in part. Finally, structural phylogenomic analysis challenges the polyphyletic scenario of multiple viral origins adopted by virus taxonomy, defeating a polyphyletic origin and supporting instead an ancient cellular origin of viruses. We therefore, prompt abandoning deep ranks and urgently reevaluating the validity of taxonomic units and principles of virus classification. Frontiers Media S.A. 2023-08-03 /pmc/articles/PMC10435761/ /pubmed/37601376 http://dx.doi.org/10.3389/fmicb.2023.1240993 Text en Copyright © 2023 Caetano-Anollés, Claverie and Nasir. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Caetano-Anollés, Gustavo Claverie, Jean-Michel Nasir, Arshan A critical analysis of the current state of virus taxonomy |
title | A critical analysis of the current state of virus taxonomy |
title_full | A critical analysis of the current state of virus taxonomy |
title_fullStr | A critical analysis of the current state of virus taxonomy |
title_full_unstemmed | A critical analysis of the current state of virus taxonomy |
title_short | A critical analysis of the current state of virus taxonomy |
title_sort | critical analysis of the current state of virus taxonomy |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10435761/ https://www.ncbi.nlm.nih.gov/pubmed/37601376 http://dx.doi.org/10.3389/fmicb.2023.1240993 |
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