title: Genetic characterization of group A rotavirus strains circulating among children with acute gastroenteritis in Japan in 2004-2005.
abstract: A total of 752 fecal specimens collected from July 2004 to June 2005 from children with acute gastroenteritis in four localities in Japan (Maizuru, Tokyo, Sapporo, and Osaka) were screened for group A rotavirus by RT-PCR. It was found that 82 (10.9%) specimens were positive for group A rotavirus. The G-(VP7 genotypes) and P-(VP4 genotypes) types were further investigated. The P-types of 18 rotavirus strains, which could not be typed by RT-PCR, were determined by sequencing analysis. Of these, 94% (17/18) were P[8] with multiple point mutations at the VP4 primer-binding site. Another sample turned out to be a rare genotype P[9], which was closely related to feline rotavirus. The predominant genotype was G1P[8] (46.4%), followed by G3P[8] (32.9%) and G2P[4] (12.2%). A number of unusual combinations including, G1P[4] (1.2%), G2P[8] (1.2%), G3P[9] (1.2%), G1G3P[8] (1.2%), and G2G3P[8] (3.7%), were also detected. A new nomenclature of P[8] was proposed, in which worldwide rotavirus P[8] strains were classified into four sub-lineages, namely IA, IB, IIA, and IIB. A wide range of amino acid substitutions (up to 22) specific for P[8] lineages and sub-lineages were also identified. Interestingly, only short amino acid motifs located at positions 32-35, 121-135, and 195-236 of VP4 correctly defined the phylogenetic P[8] lineages and sub-lineages. Of note, at least two distinct clusters of rotavirus P[8] were co-circulating in the Japanese pediatric population studied.
authors.affiliation: Department of Developmental Medical Sciences, Institute of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
authors.forename: Tung Gia
authors.initials: TG
authors.lastname: Phan
authors.forename: Pattara
authors.initials: P
authors.lastname: Khamrin
authors.forename: Duy Quang
authors.initials: DQ
authors.lastname: Trinh
authors.forename: Shuvra Kanti
authors.initials: SK
authors.lastname: Dey
authors.forename: Fumihiro
authors.initials: F
authors.lastname: Yagyu
authors.forename: Shoko
authors.initials: S
authors.lastname: Okitsu
authors.forename: Osamu
authors.initials: O
authors.lastname: Nishio
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ushijima
mesh_terms: D000208:Acute Disease; D000595:Amino Acid Sequence; D002648:Child; D003967:Diarrhea / Q000821:virology; D005243:Feces / Q000821:virology; D005759:Gastroenteritis / Q000453:epidemiology / Q000821:virology*; D006801:Humans; D007564:Japan; D008969:Molecular Sequence Data; D010802:Phylogeny; D015995:Prevalence; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012401:Rotavirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012400:Rotavirus Infections / Q000453:epidemiology / Q000821:virology*; D017423:Sequence Analysis, RNA