About: Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the Alphacoronavirus 1 Species

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About: Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the Alphacoronavirus 1 Species Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the Alphacoronavirus 1 Species
Creator	Millet, Jean André, Nicole Whittaker, Gary
Source	Medline; PMC
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.
has issue date	2018-01-03(xsd:dateTime)
bibo:doi	10.1128/mspheredirect.00463-17
bibo:pmid	29299531
has license	cc-by
sha1sum (hex)	1340cfab5e9d9c4e29144766f379fe8f10e4cc29
schema:url	https://doi.org/10.1128/mspheredirect.00463-17
resource representing a document's title	Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the Alphacoronavirus 1 Species
has PubMed Central identifier	PMC5750389
has PubMed identifier	29299531
schema:publication	mSphere
resource representing a document's body	covid:1340cfab5e9d9c4e29144766f379fe8f10e4cc29#body_text
is schema:about of	named entity 'species' named entity 'pathogenesis' named entity 'species' named entity 'fit' named entity 'transmissible' named entity 'advances' named entity 'clade' named entity 'members' named entity 'Alphacoronavirus' named entity 'Taxonomy' named entity 'Case' named entity 'ALPHACORONAVIRUS 1' named entity 'BASED' named entity 'TAXONOMY' named entity 'IDENTIFY' named entity 'WORK' named entity 'CARRIED' named entity 'INCLUDES' named entity 'WAY' named entity 'TRANSMISSIBLE GASTROENTERITIS VIRUS' named entity 'HAVE' named entity 'RECENT' named entity 'FIT' named entity 'ADDITION' named entity 'CANINE' named entity 'CLASSIFY' named entity 'REVEAL' named entity 'GENE' named entity 'TAXONOMY' named entity 'NEW' named entity 'PRIMARY' named entity 'MEMBERS' named entity 'GENERATING' named entity 'ALPHACORONAVIRUS' named entity 'GROUPS' named entity 'ESTABLISHED' named entity 'DESIGNATION' named entity 'AMPLIFIED' named entity 'NEWLY' named entity 'PHYLOGENETIC ANALYSIS' named entity 'PATHOGENESIS' named entity 'PREVIOUSLY' named entity 'QUESTION' named entity 'SEROTYPE' named entity 'VETERINARY' named entity 'GENUS' named entity 'BIOLOGICALLY' named entity 'WHAT' named entity 'PROTOTYPE' named entity 'COMPLEX' named entity 'DIFFICULTIES' named entity 'VIRUSES' named entity 'ALPHACORONAVIRUS 1' named entity 'RELATED' named entity 'SPIKE PROTEIN' named entity 'CLASSIFICATION' named entity 'LIKE' named entity 'SEQUENCES' named entity 'RELEVANT' named entity 'OUR' named entity 'FIELD' named entity 'DRIVER' named entity 'TROPISM' named entity 'CONSIDERATION' named entity 'CANINE CORONAVIRUS' named entity 'MAMMALIAN' named entity 'USEFUL' named entity 'BETTER' named entity 'CRITICAL' named entity 'NEXT-GENERATION SEQUENCING' named entity 'DISTINCT' named entity 'SPIKE' named entity 'SURFACE ANTIGEN' named entity 'DETERMINANTS' named entity 'HOSTS' named entity 'BIOLOGICALLY' named entity 'VIRUS' named entity 'CORONAVIRUSES' named entity 'CLASSIFICATION'

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