Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck’s Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family
Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular g...
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ftdoajarticles:oai:doaj.org/article:96e9e9e34a9f46d7a05a81102fe4599d 2024-01-07T09:46:17+01:00 Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck’s Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family Alina Matsvay Marina Dyachkova Anna Sai Valentina Burskaia Ilya Artyushin German Shipulin 2022-07-01T00:00:00Z https://doi.org/10.3390/microorganisms10081540 https://doaj.org/article/96e9e9e34a9f46d7a05a81102fe4599d EN eng MDPI AG https://www.mdpi.com/2076-2607/10/8/1540 https://doaj.org/toc/2076-2607 doi:10.3390/microorganisms10081540 2076-2607 https://doaj.org/article/96e9e9e34a9f46d7a05a81102fe4599d Microorganisms, Vol 10, Iss 8, p 1540 (2022) Caliciviridae Sanovirus Temminck’s stint calicivirus genome annotation phylogenetics Biology (General) QH301-705.5 article 2022 ftdoajarticles https://doi.org/10.3390/microorganisms10081540 2023-12-10T01:44:07Z Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular genetics and bioinformatics methods can shed light on their genetic architecture and evolutionary relationships. Here, we present and characterize the complete genome sequence of calicivirus isolated from a sandpiper—Temminck’s stint ( Calidris temminckii ), preliminarily named Temminck’s stint calicivirus (TsCV). Its genome is a linear, non-segmented, single-stranded (+sense) RNA with genome organization typical of avian caliciviruses. Comparative studies have shown significant divergence of the nucleotide sequence of the TsCV genome, as well as the amino acid sequence of the major capsid protein from all publicly available genomic and protein sequences, with the highest genome sequence similarity to unclassified Ruddy turnstone calicivirus A (43.68%) and the lowest pairwise divergence of the major capsid protein with unclassified goose calicivirus (57.44%). Phylogenetic analysis, as well as a comparative analysis of the homologous proteins, showed evidence of another separate genus within the Caliciviridae family—previously proposed, but not yet accepted by International Committee on Taxonomy of Viruses (ICTV)—the Sanovirus genus, which combines seven previously unclassified genomic sequences of avian caliciviruses, including the newly discovered TsCV, which we propose to consider as a separate species. Article in Journal/Newspaper Ruddy Turnstone Directory of Open Access Journals: DOAJ Articles Microorganisms 10 8 1540 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Caliciviridae Sanovirus Temminck’s stint calicivirus genome annotation phylogenetics Biology (General) QH301-705.5 |
spellingShingle |
Caliciviridae Sanovirus Temminck’s stint calicivirus genome annotation phylogenetics Biology (General) QH301-705.5 Alina Matsvay Marina Dyachkova Anna Sai Valentina Burskaia Ilya Artyushin German Shipulin Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck’s Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family |
topic_facet |
Caliciviridae Sanovirus Temminck’s stint calicivirus genome annotation phylogenetics Biology (General) QH301-705.5 |
description |
Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular genetics and bioinformatics methods can shed light on their genetic architecture and evolutionary relationships. Here, we present and characterize the complete genome sequence of calicivirus isolated from a sandpiper—Temminck’s stint ( Calidris temminckii ), preliminarily named Temminck’s stint calicivirus (TsCV). Its genome is a linear, non-segmented, single-stranded (+sense) RNA with genome organization typical of avian caliciviruses. Comparative studies have shown significant divergence of the nucleotide sequence of the TsCV genome, as well as the amino acid sequence of the major capsid protein from all publicly available genomic and protein sequences, with the highest genome sequence similarity to unclassified Ruddy turnstone calicivirus A (43.68%) and the lowest pairwise divergence of the major capsid protein with unclassified goose calicivirus (57.44%). Phylogenetic analysis, as well as a comparative analysis of the homologous proteins, showed evidence of another separate genus within the Caliciviridae family—previously proposed, but not yet accepted by International Committee on Taxonomy of Viruses (ICTV)—the Sanovirus genus, which combines seven previously unclassified genomic sequences of avian caliciviruses, including the newly discovered TsCV, which we propose to consider as a separate species. |
format |
Article in Journal/Newspaper |
author |
Alina Matsvay Marina Dyachkova Anna Sai Valentina Burskaia Ilya Artyushin German Shipulin |
author_facet |
Alina Matsvay Marina Dyachkova Anna Sai Valentina Burskaia Ilya Artyushin German Shipulin |
author_sort |
Alina Matsvay |
title |
Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck’s Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family |
title_short |
Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck’s Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family |
title_full |
Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck’s Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family |
title_fullStr |
Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck’s Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family |
title_full_unstemmed |
Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck’s Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family |
title_sort |
complete genome sequence, molecular characterization and phylogenetic relationships of a temminck’s stint calicivirus: evidence for a new genus within caliciviridae family |
publisher |
MDPI AG |
publishDate |
2022 |
url |
https://doi.org/10.3390/microorganisms10081540 https://doaj.org/article/96e9e9e34a9f46d7a05a81102fe4599d |
genre |
Ruddy Turnstone |
genre_facet |
Ruddy Turnstone |
op_source |
Microorganisms, Vol 10, Iss 8, p 1540 (2022) |
op_relation |
https://www.mdpi.com/2076-2607/10/8/1540 https://doaj.org/toc/2076-2607 doi:10.3390/microorganisms10081540 2076-2607 https://doaj.org/article/96e9e9e34a9f46d7a05a81102fe4599d |
op_doi |
https://doi.org/10.3390/microorganisms10081540 |
container_title |
Microorganisms |
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10 |
container_issue |
8 |
container_start_page |
1540 |
_version_ |
1787428038696239104 |