[Phylogenetic analysis of 14 strains of Norwalk-like viruses: identification of the region in the genome for genotyping]

Abstract

'Norwalk-like viruses(NLV)', a member of the family Caliciviridae, are the major causative agent of acute gastroenteritis and genetically divided into two groups, geno-group I(GI) and genogroup II(GII). We have determined complete nucleotide sequences, of 9 new NLV strains. Using this information together with 5 known NLV sequences, we investigated the criteria to further classify genotypes of NLV. Validation of the topological error based on the bootstrap value and the branch length(distance) identified two potential subgenomic regions suitable for genotyping. They were the RNA dependent RNA polymerase(RdRp) and the capsid N-terminal/Shell domains(capsid N/S). When the distance distribution analysis was performed, the RdRp-based classification did not separate the strains into internal clusters within genogroup. Furthermore, a diversity plot analysis of the complete nucleotide sequences of the GII Saitama U1 strain indicated that the genotype was different between the RdRp and the capsid N/S, suggesting that these strains are the genetic recombinants. Therefore, RdRp is not suitable for genotyping. On the other hand, the clustering based on the capsid N/S successfully distinguished the NLV equally to the cluster according to the antigenicity determined by both antigen and antibody ELISAs with recombinant virus-like particles. We would like to recommend to use the capsid N/S for the genotyping.