Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains

Show simple item record Agbemabiese, C.A. Nakagom, T. Damanka, S.A. Dennis, F.E. Lartey, B.L. Armah, G.E. Nakagomi, O. 2019-09-17T17:00:03Z 2019-09-17T17:00:03Z 2019-05-10
dc.description Research Article en_US
dc.description.abstract 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. en_US
dc.language.iso en en_US
dc.publisher PLoS ONE en_US
dc.relation.ispartofseries 14;5
dc.subject Sub-genotype en_US
dc.subject phylogeny en_US
dc.subject non-G en_US
dc.subject non-P en_US
dc.subject genes of genotype 2 en_US
dc.subject Rotavirus A strains en_US
dc.title Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains en_US
dc.type Article en_US

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  • Electron Microscopy Department [67]
    The main research focus of the Electron Microscopy and Histopathology Department in the past 20 years has been in the areas of enteric diarrhoeas with special emphasis on rotavirus. Through its diarrhoea surveillance studies, the Department has helped to firmly establish rotaviruses as a major cause of diarrhoea in children, and document the circulation of unusual rotavirus genotypes in Ghana. The Department has also recently expanded its diagnostic repertoire to include the identification and characterization of noroviruses, astroviruses, and other enteric viruses.

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