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Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains
Recent increase in the detection of unusual G1P[8], G3P[8], G8P[8], and G9P[4] Rotavirus A (RVA) strains bearing the DS-1-like constellation of the non-G, non-P genes (hereafter referred to as the genotype 2 backbone) requires better understanding of their evolutionary relationship. However, within...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544246/ https://www.ncbi.nlm.nih.gov/pubmed/31150425 http://dx.doi.org/10.1371/journal.pone.0217422 |
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author | Agbemabiese, Chantal Ama Nakagomi, Toyoko Damanka, Susan Afua Dennis, Francis Ekow Lartey, Belinda Larteley Armah, George Enyimah Nakagomi, Osamu |
author_facet | Agbemabiese, Chantal Ama Nakagomi, Toyoko Damanka, Susan Afua Dennis, Francis Ekow Lartey, Belinda Larteley Armah, George Enyimah Nakagomi, Osamu |
author_sort | Agbemabiese, Chantal Ama |
collection | PubMed |
description | Recent increase in the detection of unusual G1P[8], G3P[8], G8P[8], and G9P[4] Rotavirus A (RVA) strains bearing the DS-1-like constellation of the non-G, non-P genes (hereafter referred to as the genotype 2 backbone) requires better understanding of their evolutionary relationship. However, within a genotype, there is lack of a consensus lineage designation framework and a set of common sequences that can serve as references. Phylogenetic analyses were carried out on over 8,500 RVA genotype 2 genes systematically retrieved from the rotavirus database within the NCBI Virus Variation Resource. In line with previous designations, using pairwise comparison of cogent nucleotide sequences and stringent bootstrap support, reference lineages were defined. This study proposes a lineage framework and provides a dataset ranging from 34 to 145 sequences for each genotype 2 gene for orderly lineage designation of global genotype 2 genes of RVAs detected in human and animals. The framework identified five to 31 lineages depending on the gene. The least number of lineages (five to seven) were observed in genotypes A2 (NSP1), T2 (NSP3) and H2 (NSP5) which are limited to human RVA whereas the most number of lineages (31) was observed in genotype E2 (NSP4). Sharing of the same lineage constellations of the genotype 2 backbone genes between recently-emerging, unusual G1P[8], G3P[8], G8P[8] and G9P[4] reassortants and many contemporary G2P[4] strains provided strong support to the hypothesis that unusual genotype 2 strains originated primarily from reassortment events in the recent past involving contemporary G2P[4] strains as one parent and ordinary genotype 1 strains or animal RVA strains as the other. The lineage framework with selected reference sequences will help researchers to identify the lineage to which a given genotype 2 strain belongs, and trace the evolutionary history of common and unusual genotype 2 strains in circulation. |
format | Online Article Text |
id | pubmed-6544246 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-65442462019-06-17 Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains Agbemabiese, Chantal Ama Nakagomi, Toyoko Damanka, Susan Afua Dennis, Francis Ekow Lartey, Belinda Larteley Armah, George Enyimah Nakagomi, Osamu PLoS One Research Article Recent increase in the detection of unusual G1P[8], G3P[8], G8P[8], and G9P[4] Rotavirus A (RVA) strains bearing the DS-1-like constellation of the non-G, non-P genes (hereafter referred to as the genotype 2 backbone) requires better understanding of their evolutionary relationship. However, within a genotype, there is lack of a consensus lineage designation framework and a set of common sequences that can serve as references. Phylogenetic analyses were carried out on over 8,500 RVA genotype 2 genes systematically retrieved from the rotavirus database within the NCBI Virus Variation Resource. In line with previous designations, using pairwise comparison of cogent nucleotide sequences and stringent bootstrap support, reference lineages were defined. This study proposes a lineage framework and provides a dataset ranging from 34 to 145 sequences for each genotype 2 gene for orderly lineage designation of global genotype 2 genes of RVAs detected in human and animals. The framework identified five to 31 lineages depending on the gene. The least number of lineages (five to seven) were observed in genotypes A2 (NSP1), T2 (NSP3) and H2 (NSP5) which are limited to human RVA whereas the most number of lineages (31) was observed in genotype E2 (NSP4). Sharing of the same lineage constellations of the genotype 2 backbone genes between recently-emerging, unusual G1P[8], G3P[8], G8P[8] and G9P[4] reassortants and many contemporary G2P[4] strains provided strong support to the hypothesis that unusual genotype 2 strains originated primarily from reassortment events in the recent past involving contemporary G2P[4] strains as one parent and ordinary genotype 1 strains or animal RVA strains as the other. The lineage framework with selected reference sequences will help researchers to identify the lineage to which a given genotype 2 strain belongs, and trace the evolutionary history of common and unusual genotype 2 strains in circulation. Public Library of Science 2019-05-31 /pmc/articles/PMC6544246/ /pubmed/31150425 http://dx.doi.org/10.1371/journal.pone.0217422 Text en © 2019 Agbemabiese et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Agbemabiese, Chantal Ama Nakagomi, Toyoko Damanka, Susan Afua Dennis, Francis Ekow Lartey, Belinda Larteley Armah, George Enyimah Nakagomi, Osamu Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains |
title | Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains |
title_full | Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains |
title_fullStr | Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains |
title_full_unstemmed | Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains |
title_short | Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains |
title_sort | sub-genotype phylogeny of the non-g, non-p genes of genotype 2 rotavirus a strains |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544246/ https://www.ncbi.nlm.nih.gov/pubmed/31150425 http://dx.doi.org/10.1371/journal.pone.0217422 |
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