PHYLOGENETIC ANALYSIS OF THE CALICIVIRUSES

A phylogenetic portrait of the genus Calicivirus in the family Caliciv iridae was developed based upon published sequences and newly characte rized 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 anima l calicivirus 3D RNA-dependent RNA polymerase (similar to 470nt) and c apsid hypervariable regions (similar to 7,200nt) to generate phylogene tic trees. Pair-wise amino acid identity in the 3D region among the Sa pporo-like strains ranged from 61% to 100%. Human and animal calicivir uses (HuCVs and AnCVs) separated into five genogroups: small round-str uctured 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, incl uding the Sapporo-like HuCVs, subdivided further into subgenogroups. T he capsid region trees had higher levels of confidence than the 3D reg ion trees and limited conclusions about genogroups could be drawn from the 3D region analyses. This analysis suggested that CVs include five potential virus subfamilies. (C) 1997 Wiley-Liss, Inc.