Phylogenetic analysis of the complete genome of 18 norwalk-like viruses

Kazuhiko Katayama*, Haruko Shirato-Horikoshi, Shigeyuki Kojima, Tsutomu Kageyama, Tomoichiro Oka, Fuminori B. Hoshino, Shuetsu Fukushi, Michiyo Shinohara, Kazue Uchida, Yoshiyuki Suzuki, Takashi Gojobori, Naokazu Takeda

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

260 Scopus citations

Abstract

"Norwalk-like viruses" (NLV), a member of the family Caliciviridae, are the major causative agents of acute gastroenteritis and are genetically divided into two groups, genogroup I (GI) and genogroup II (GII). We have determined the complete nucleotide sequences of 10 new NLV strains. Using this information together with eight known NLV sequences, the criteria to further classify genotypes of NLV were investigated. Validation of the topological error based on the bootstrap value and the branch length (distance) allowed us to identify two potential subgenomic regions suitable for the genotyping. They were the putative 3D-like RNA-dependent RNA polymerase (polymerase) and the capsid N-terminal/Shell domains (capsid N/S domain). When the distance distribution analysis was performed, the polymerase-based classification did not separate the strains into internal clusters within the genogroup. Furthermore, a diversity plot analysis of the complete nucleotide sequences of WUG1, a NLV GI strain, and Saitama U1, a NLV GII strain, indicated that the genotype was different between the polymerase and capsid N/S domain, suggesting that these strains are the genetic recombinants. Therefore, polymerase is not suitable for genotyping. On the other hand, the clustering based on the capsid N/S domain successfully distinguished the NLV as well as the grouping based on the antigenicity, as determined by both antigen and antibody ELISAs with recombinant virus-like particles. As the nucleotide sequences of the primers for the capsid N/S domain are highly conserved among the NLV, the amplification of the unknown genotype can be easily performed. This method will facilitate global surveying as well as epidemiologic study on NLV.

Original languageEnglish (US)
Pages (from-to)225-239
Number of pages15
JournalVirology
Volume299
Issue number2
DOIs
StatePublished - Jan 1 2002

Keywords

  • Complete genome sequence
  • Genotyping
  • Norwalk-like viruses
  • Phylogenetic analysis
  • Recombination

ASJC Scopus subject areas

  • Virology

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