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

SUBMITTER: Whittaker GR

PROVIDER: S-EPMC5750389 | biostudies-literature | 2018 Jan-Feb

REPOSITORIES: biostudies-literature

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Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <i>Alphacoronavirus 1</i> Species.

Whittaker Gary R GR André Nicole M NM Millet Jean Kaoru JK

mSphere 20180103 1

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 <i>Alpha ...[more]

PMID: 29299531

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Project description:The cosmopolitan subfamily Acidocerinae (Coleoptera: Hydrophilidae) is one of the largest and most taxonomically challenging lineages of water scavenger beetles. Recent phylogenetic studies have substantially advanced our understanding of acidocerine relationships but also illuminated the twin challenges of poorly delineated generic concepts and a classification broadly incompatible with the phylogeny. Here, these two challenges are addressed by providing a comprehensive synthesis and taxonomic tools for the Acidocerinae, including (1) a brief history and the current state of acidocerine classification, (2) a review of acidocerine ecology and collection methods, (3) the current knowledge of larval and fossil acidocerines, (4) a morphological primer on characters of taxonomic and systematic importance within the lineage, (5) a key to the world genera of Acidocerinae, (6) diagnoses, habitus, and aedeagal images, distribution maps, and summary of knowledge for each of the 23 extant genera in the subfamily, and (7) a complete annotated taxonomic catalog including the published distributions, synonyms, and references for all described 541 acidocerine species recognized as of 1 April 2021. The following nomenclatural acts are proposed to bring the phylogeny and classification into alignment: Colossochares gen. nov. is established to accommodate two African species previously described as Helochares (s. str.); Novochares gen. nov. is newly established to accommodate 15 Neotropical species previously included in Helochares (s. str.); the remaining Helochares subgenera Helocharimorphus Kuwert syn. nov. and Hydrobaticus MacLeay syn. nov. are synonymized with Helochares Mulsant. Peltochares Régimbart sensu nov. is redefined to include eight Old World species previously included in Helochares (s. str.). A lectotype is designated for Peltochares conspicuus Régimbart, the type species of the genus. The taxonomic and morphological circumscription of Helochares sensu nov. is narrowed and redefined.

Dataset Information

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

Publications

Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the <i>Alphacoronavirus 1</i> Species.

Similar Datasets

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