Complete genome analysis of a rare G12P[6] rotavirus isolated in Thailand in 2012 reveals a prototype strain of DS-1-like constellation

• Published in: Virus research Vol. 224; pp. 38 - 45
• Main Authors: Saikruang, Wilaiporn, Khamrin, Pattara, Malasao, Rungnapa, Kumthip, Kattareeya, Ushijima, Hiroshi, Maneekarn, Niwat
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.09.2016
• Subjects: Bayes Theorem; Child; Diarrhea - virology; DS-1-like strain; Evolution, Molecular; Feces - virology; G12P; Gastroenteritis - virology; Genome, Viral; Genotype; Human; Humans; Phylogeny; Prevalence; Reoviridae; RNA, Viral - genetics; Rotavirus; Rotavirus - classification; Rotavirus - genetics; Rotavirus - isolation & purification; Rotavirus Infections - virology; Sequence Analysis, DNA; Species A rotaviruses; Thailand; Human; ESS; MCMC; G12P; NSP; Thailand; Species A rotaviruses; tMRCA; DS-1-like strain; RT-PCR; AICc; VP; RVA; BLAST; HPD; ML
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2016.08.002

•Analysis of whole genome sequence of human G12P[6] rotavirus CMHN49-12.•CMHN49-12 exhibits genotype 2 in all non G, non P-genes.•G12 rotaviruses in Thailand have at least three distinct VP7 gene ancestors.•Evolution rate and time of most recent common ancestor were estimated. Species A rotaviruses (RVAs) are a major cause of severe diarrhea in children worldwide. G12 RVA detection is currently increasing and has been reported from many countries around the world. However, few studies have reported whole genome sequences of G12 RVAs. In the present study, the complete genome sequence of a G12P[6] RVA strain (RVA/Human-wt/THA/CMHN49-12/2012/G12P[6]) detected in a stool sample from a child with acute gastroenteritis in 2012 in Thailand was analyzed. In the CMHN49-12 strain, all genome segments had a DS-1-like backbone: G12-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2 indicates that it is most likely the prototype strain of G12P[6] with a DS-1-like genotype constellation. Based on a Bayesian evolutionary analysis of VP7 nucleotide sequence, G12 RVA strains reported previously from Thailand during the period of 2007–2012 could be divided into 3 clusters, indicating that they originated from at least 3 different ancestral G12 strains. The evolutionary rate of G12 calculated by Bayesian Markov Chain Monte Carlo analysis indicated that the nucleotide substitution rate of G12 was 1.11×10−3 mutations/site/year. The finding of a G12P[6] RVA possessing a DS-1-like backbone provides insights into the evolution of global G12 RVAs.