title: Genomic constellation and evolution of Ghanaian G2P[4] rotavirus strains from a global perspective.
abstract: Understanding of the genetic diversity and evolution of Rotavirus A (RVA) strains, a common cause of severe diarrhoea in children, needs to be based on the analysis at the whole genome level in the vaccine era. This study sequenced the whole genomes of six representative G2P[4] strains detected in Ghana from 2008 to 2013, and analysed them phylogenetically with a global collection of G2P[4] strains and African non-G2P[4] DS-1-like strains. The genotype constellation of the study strains was G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Strains from the same season were highly identical across the whole genome while strains from different seasons were more divergent from each other. The VP7, VP4, VP2, NSP1, and NSP5 genes belonged to lineage IVa; the VP6, VP1, NSP2, and NSP3 genes belonged to lineage V, and all these genes evolved in the same fashion as the global strains. In the NSP4 gene, lineages V (2008) and X (2009) were replaced by VI (2012/2013) whereas in the VP3 gene, lineage V (2008/2009) was replaced by VII (2012/2013) and these replacements coincided with the vaccine introduction period (2012). The evolutionary rate of the NSP4 gene was 1.2×10-3substitutions/site/year and was rather comparable to that of the remaining 10 genes. The multiple NSP4 lineages were explained by intra-genotype reassortment with co-circulating African human DS-1-like strains bearing G2[6], G3P[6], G6[6] and G8. There was no explicit evidence of the contribution of animal RVA strains to the genome of the Ghanaian G2P[4] strains. In summary, this study revealed the dynamic evolution of the G2P[4] strains through intra-genotype reassortment events leading to African specific lineages such IX and X in the NSP4 gene. So far, there was no evidence of a recent direct involvement of animal RVA genes in the genome diversity of African G2P[4] strains.
authors: Leading Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan; Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana.
authors: Chantal Ama
authors: CA
authors: Agbemabiese
authors: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
authors: Toyoko
authors: T
authors: Nakagomi
authors: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
authors: Yen Hai
authors: YH
authors: Doan
authors: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
authors: Loan Phuong
authors: LP
authors: Do
authors: Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana.
authors: Susan
authors: S
authors: Damanka
authors: Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana.
authors: George E
authors: GE
authors: Armah
authors: Leading Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan; Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan. Electronic address: onakagom@nagasaki-u.ac.jp.
authors: Osamu
authors: O
authors: Nakagomi
mesh_terms: D002675:Child, Preschool; D019143:Evolution, Molecular; D016679:Genome, Viral / Q000235:genetics*; D005869:Ghana / Q000453:epidemiology; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D017720:Molecular Epidemiology; D010802:Phylogeny; D016865:Reassortant Viruses / Q000145:classification / Q000235:genetics; D012401:Rotavirus / Q000145:classification / Q000235:genetics*; D012400:Rotavirus Infections / Q000453:epidemiology / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins
keywords: G2P[4]; Ghana; NSP4; Reassortment; Rotavirus; Whole genome evolution