Sapporo-like human caliciviruses are genetically and antigenically diverse

Abstract

The Sapporo-like human caliciviruses (HuCVs) comprise one of three genogroups of HuCVs associated with acute gastroenteritis. Phylogenetic analysis has shown that Sapporo-like HuCVs are related more closely to animal caliciviruses than to other known HuCVs. We produced 3.2 kb cDNA fragments from the 3' end to three Sapporo-like HuCVs that were associated with acute gastroenteritis in children (Houston/86, Houston/90, and London/92). Sequence analysis of the 3.2 kb cDNAs showed that two of the three viruses had a genomic organization similar to that of other Sapporo-like strains and the third strain (London/92) lacked an open reading frame overlapping the 5' end of the capsid gene. Alignment of the capsid sequences of these three strains showed 44-78% amino acid identity among the three strains. Phylogenetic analysis of the aligned sequences indicated the three strains are related but each belongs to a distinct genetic cluster. The genetic differences are associated with antigenic differences in that an enzyme immune assay (EIA) specific for the prototype Sapporo/82 strain detected the Houston/86 strain, but not the Houston/90 and London/92 strains. In vitro transcription and translation of viral cDNA containing the predicted capsid gene of Houston/90 resulted in a protein of 63 K, which is immunoprecipitated by sera from children infected with the strain. Genetically and antigenically distinct strains in the Sapporo-like HuCVs have not been described previously and the occurrence of such diverse strains in the same community likely increases the importance of these strains as a cause of illness in children.

Genetic classification of "Sapporo-like viruses"

“…Overall, both the separate and combined alignments of the SLV and NLV sequences showed relatively good concordance with those previously reported [3,13,16,18,27,35,42]. However, the alignment of 10 SLV sequences indicated marked differences in the amino acid and nucleotide sequences of the 3 end of the 3 ORF and the 5 end of the 3 UTR of London/92 strain compared to the remaining 9 SLV strains.…”

“…We therefore replaced the presumably deleted nucleotide with a symbol X, indicating an as yet undetermined nucleotide, and used the revised London/92 sequence (Table 1) to generate new alignments of 3 ORF and 3 UTR sequences. To generate the alignment in the 3 UTR, we also excluded 12 nucleotides located at the 5 end of Houston/86, Houston/90, and Manchester/93 sequences in the alignment reported by Jiang [18], because these nucleotides (including a stop codon) encoded the C-terminal amino acids of the 3 ORF. In the revised alignment of the 3 UTR sequences, Lyon/598/97 and London/92 strains showed, at the 5 end, 45 and 44 additional nucleotides, which were absent in other SLV strains (Fig.…”

“…In SLVs, the polyprotein gene is fused to and in frame with the capsid coding region [24,29]. In addition, in all published SLV strains except a human strain, London/92 and a porcine strain, PEC/Cowden [5,15,18,27,29,40], an additional ORF has been predicted in +1 frame, overlapping the N terminus of the capsid gene (capsid overlap). To date, the sequence of a ∼3-kb region extending from the RNA polymerase gene to the 3 poly(A) tail is available in GenBank for 9 NLV strains, of which 6 have had their entire genome sequenced: Norwalk/68 [17], Southampton/91 [22], Lordsdale/93 [9], Camberwell/94 [3,36], Chiba/87 (GenBank accession number No.…”

“…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].…”

“…To date, human SLVs, within the family Caliciviridae, have often been considered to belong to a single genogroup, GIII, comparable with the two genogroups of NLVs, GI and GII [13,29,40,41]. However, Jiang et al have suggested the possible existence of two genogroups among human SLVs [18]. In addition, the phylogenetic relationship between the genetic cluster represented by the porcine strain PEC/Cowden and the 4 genetic clusters of human SLVs needs clarification.…”