title: Whole genome analysis of Vietnamese G2P[4] rotavirus strains possessing the NSP2 gene sharing an ancestral sequence with Chinese sheep and goat rotavirus strains.
abstract: Because imminent introduction into Vietnam of a vaccine against Rotavirus A is anticipated, baseline information on the whole genome of representative strains is needed to understand changes in circulating strains that may occur after vaccine introduction. In this study, the whole genomes of two G2P[4] strains detected in Nha Trang, Vietnam in 2008 were sequenced, this being the last period during which virtually no rotavirus vaccine was used in this country. The two strains were found to be >99.9% identical in sequence and had a typical DS-1 like G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 genotype constellation. Analysis of the Vietnamese strains with >184 G2P[4] strains retrieved from GenBank/EMBL/DDBJ DNA databases placed the Vietnamese strains in one of the lineages commonly found among contemporary strains, with the exception of the NSP2 and NSP4 genes. The NSP2 genes were found to belong to a previously undescribed lineage that diverged from Chinese sheep and goat rotavirus strains, including a Chinese rotavirus vaccine strain LLR with 95% nucleotide identity; the time of their most recent common ancestor was 1975. The NSP4 genes were found to belong, together with Thai and USA strains, to an emergent lineage (VIII), adding further diversity to ever diversifying NSP4 lineages. Thus, there is a need to enhance surveillance of locally-circulating strains from both children and animals at the whole genome level to address the effect of rotavirus vaccines on changing strain distribution.
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.|National Institute of Hygiene and Epidemiology, Hanoi 112-800, Vietnam.
authors.forename: Loan Phuong
authors.initials: LP
authors.lastname: Do
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
authors.forename: Yen Hai
authors.initials: YH
authors.lastname: Doan
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
authors.forename: Toyoko
authors.initials: T
authors.lastname: Nakagomi
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
authors.forename: Punita
authors.initials: P
authors.lastname: Gauchan
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
authors.forename: Miho
authors.initials: M
authors.lastname: Kaneko
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
authors.forename: Chantal
authors.initials: C
authors.lastname: Agbemabiese
authors.affiliation: National Institute of Hygiene and Epidemiology, Hanoi 112-800, Vietnam.
authors.forename: Anh Duc
authors.initials: AD
authors.lastname: Dang
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Nakagomi
mesh_terms: D000818:Animals; D001483:Base Sequence; D002681:China; D016679:Genome, Viral / Q000235:genetics*; D006023:Glycoproteins / Q000235:genetics*; D015511:Goat Diseases / Q000235:genetics / Q000821:virology; D006041:Goats / Q000235:genetics / Q000821:virology; D006801:Humans; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000235:genetics; D016601:RNA-Binding Proteins / Q000235:genetics*; D012401:Rotavirus / Q000145:classification / Q000235:genetics* / Q000276:immunology; D012400:Rotavirus Infections / Q000662:veterinary*; D022243:Rotavirus Vaccines / Q000276:immunology; D017423:Sequence Analysis, RNA; D012756:Sheep / Q000235:genetics / Q000821:virology; D012757:Sheep Diseases; D014118:Toxins, Biological / Q000235:genetics*; D014744:Vietnam; D017361:Viral Nonstructural Proteins / Q000235:genetics*
chemical_list: D006023:Glycoproteins; C081369:NS28 protein, rotavirus; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D022243:Rotavirus Vaccines; D014118:Toxins, Biological; D017361:Viral Nonstructural Proteins; C079234:NS35 protein, rotavirus
keywords: NSP2; NSP4; Vietnam; rotavirus