Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <italic toggle="yes">Alphacoronavirus 1</italic> Species

ABSTRACT The difficulties related to virus taxonomy have been amplified by recent advances in next-generation sequencing and metagenomics, prompting the field to revisit the question of what constitutes a useful viral classification. Here, taking a challenging classification found in coronaviruses,...

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Autores principales:	Gary R. Whittaker, Nicole M. André, Jean Kaoru Millet
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	alphacoronavirus Alphacoronavirus 1 biotype canine coronavirus clade classification Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/73d3eafeb8604e5e8349dbe9f9a1702e
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spelling	oai:doaj.org-article:73d3eafeb8604e5e8349dbe9f9a1702e2021-11-15T15:22:01ZImproving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <italic toggle="yes">Alphacoronavirus 1</italic> Species10.1128/mSphereDirect.00463-172379-5042https://doaj.org/article/73d3eafeb8604e5e8349dbe9f9a1702e2018-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphereDirect.00463-17https://doaj.org/toc/2379-5042ABSTRACT The difficulties related to virus taxonomy have been amplified by recent advances in next-generation sequencing and metagenomics, prompting the field to revisit the question of what constitutes a useful viral classification. Here, taking a challenging classification found in coronaviruses, we argue that consideration of biological properties in addition to sequence-based demarcations is critical for generating useful taxonomy that recapitulates complex evolutionary histories. Within the Alphacoronavirus genus, the Alphacoronavirus 1 species encompasses several biologically distinct viruses. We carried out functionally based phylogenetic analysis, centered on the spike gene, which encodes the main surface antigen and primary driver of tropism and pathogenesis. Within the Alphacoronavirus 1 species, we identify clade A (encompassing serotype I feline coronavirus [FCoV] and canine coronavirus [CCoV]) and clade B (grouping serotype II FCoV and CCoV and transmissible gastroenteritis virus [TGEV]-like viruses). We propose this clade designation, along with the newly proposed Alphacoronavirus 2 species, as an improved way to classify the Alphacoronavirus genus. IMPORTANCE Our work focuses on improving the classification of the Alphacoronavirus genus. The Alphacoronavirus 1 species groups viruses of veterinary importance that infect distinct mammalian hosts and includes canine and feline coronaviruses and transmissible gastroenteritis virus. It is the prototype species of the Alphacoronavirus genus; however, it encompasses biologically distinct viruses. To better characterize this prototypical species, we performed phylogenetic analyses based on the sequences of the spike protein, one of the main determinants of tropism and pathogenesis, and reveal the existence of two subgroups or clades that fit with previously established serotype demarcations. We propose a new clade designation to better classify Alphacoronavirus 1 members.Gary R. WhittakerNicole M. AndréJean Kaoru MilletAmerican Society for MicrobiologyarticlealphacoronavirusAlphacoronavirus 1biotypecanine coronaviruscladeclassificationMicrobiologyQR1-502ENmSphere, Vol 3, Iss 1 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	alphacoronavirus Alphacoronavirus 1 biotype canine coronavirus clade classification Microbiology QR1-502
spellingShingle	alphacoronavirus Alphacoronavirus 1 biotype canine coronavirus clade classification Microbiology QR1-502 Gary R. Whittaker Nicole M. André Jean Kaoru Millet Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <italic toggle="yes">Alphacoronavirus 1</italic> Species
description	ABSTRACT The difficulties related to virus taxonomy have been amplified by recent advances in next-generation sequencing and metagenomics, prompting the field to revisit the question of what constitutes a useful viral classification. Here, taking a challenging classification found in coronaviruses, we argue that consideration of biological properties in addition to sequence-based demarcations is critical for generating useful taxonomy that recapitulates complex evolutionary histories. Within the Alphacoronavirus genus, the Alphacoronavirus 1 species encompasses several biologically distinct viruses. We carried out functionally based phylogenetic analysis, centered on the spike gene, which encodes the main surface antigen and primary driver of tropism and pathogenesis. Within the Alphacoronavirus 1 species, we identify clade A (encompassing serotype I feline coronavirus [FCoV] and canine coronavirus [CCoV]) and clade B (grouping serotype II FCoV and CCoV and transmissible gastroenteritis virus [TGEV]-like viruses). We propose this clade designation, along with the newly proposed Alphacoronavirus 2 species, as an improved way to classify the Alphacoronavirus genus. IMPORTANCE Our work focuses on improving the classification of the Alphacoronavirus genus. The Alphacoronavirus 1 species groups viruses of veterinary importance that infect distinct mammalian hosts and includes canine and feline coronaviruses and transmissible gastroenteritis virus. It is the prototype species of the Alphacoronavirus genus; however, it encompasses biologically distinct viruses. To better characterize this prototypical species, we performed phylogenetic analyses based on the sequences of the spike protein, one of the main determinants of tropism and pathogenesis, and reveal the existence of two subgroups or clades that fit with previously established serotype demarcations. We propose a new clade designation to better classify Alphacoronavirus 1 members.
format	article
author	Gary R. Whittaker Nicole M. André Jean Kaoru Millet
author_facet	Gary R. Whittaker Nicole M. André Jean Kaoru Millet
author_sort	Gary R. Whittaker
title	Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <italic toggle="yes">Alphacoronavirus 1</italic> Species
title_short	Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <italic toggle="yes">Alphacoronavirus 1</italic> Species
title_full	Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <italic toggle="yes">Alphacoronavirus 1</italic> Species
title_fullStr	Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <italic toggle="yes">Alphacoronavirus 1</italic> Species
title_full_unstemmed	Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <italic toggle="yes">Alphacoronavirus 1</italic> Species
title_sort	improving virus taxonomy by recontextualizing sequence-based classification with biologically relevant data: the case of the <italic toggle="yes">alphacoronavirus 1</italic> species
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/73d3eafeb8604e5e8349dbe9f9a1702e
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Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <italic toggle="yes">Alphacoronavirus 1</italic> Species

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