Phylogenetic analysis of the caliciviruses

Abstract

A phylogenetic portrait of the genus Calicivirus in the family Caliciviridae was developed based upon published sequences and newly characterized calicivirus (CV) strains, including additional Sapporo-like HuCV strains in pediatric diarrhea stool specimens from South Africa, the United Kingdom, and the United States. Distance and parsimony methods were applied to nucleotide and amino acid sequences of human and animal calicivirus 3D RNA-dependent RNA polymerase (approximately 470nt) and capsid hypervariable regions (approximately 1,200nt) to generate phylogenetic trees. Pairwise amino acid identity in the 3D region among the Sapporo-like strains ranged from 61% to 100%. Human and animal caliciviruses (HuCVs and AnCVs) separated into five genogroups: small round-structured viruses (SRSV), Sapporo-like, and hepatitis E virus (HEV)-like HuCVs and rabbit-, and vesicular exanthema of swine virus (VESV)-like AnCVs, each with a distinct genome organization. Each genogroup, including the Sapporo-like HuCVs, subdivided further into subgenogroups. The capsid region trees had higher levels of confidence than the 3D region trees and limited conclusions about genogroups could be drawn from the 3D region analyses. This analysis suggested that CVs include five potential virus subfamilies.

Characterization of an Enteropathogenic Bovine Calicivirus Representing a Potentially New Calicivirus Genus

“…2. Trees produced for each of the genomic regions evaluated grouped the characterized prototype calicivirus strains similarly to reports of previous phylogenetic analyses (2,4,70). However, phylogenetic classification of the NB virus varied with the genome region evaluated and included placements as a new genus (2C helicase/ATPase), a new SLV genogroup (3C protease), and a new lagovirus genogroup (3D RdRP and VP1 capsid).…”

Genetic classification of "Sapporo-like viruses"

“…Human SLVs have also been reported as genetically diverse and classified into 4 genetic clusters, each of which is represented by Manchester/93 (and/or Sapporo/82), Houston/90 (and/or Parkville/94), Stockholm/97 and London/92, respectively [2,18,27,40]. In addition, a porcine enteric calicivirus (PEC) has recently been shown to be related to the SLV genus and to belong to a fifth genetic cluster [15].…”

Coexistence of Multiple Genotypes, Including Newly Identified Genotypes, in Outbreaks of Gastroenteritis Due to Norovirus in Japan

“…A recently developed reverse transcription-PCR (RT-PCR) assay that targets the RdRp (1,2,10,16,26,27) or capsid gene (4,7,9,11,21,22,28,31,33) and phylogenetic analysis revealed that NV is classified into two genogroups, genogroup I (GI) and genogroup II (GII). In a previous study, we proposed a genotyping scheme for NV based on diversity in the capsid N terminus/shell (N/S) gene and reported nine genotypes in GI and 10 genotypes in GII (19).…”