Characterization of a novel human calicivirus that may be a naturally occurring recombinant

Abstract

We identified a Norwalk-like calicivirus (CV) whose genome likely was derived from naturally occurring recombination. This strain (Arg320) was detected by the EIA developed against recombinant Mexico virus (rMxV) capsids, but the viral RNA polymerase sequence was closer to Lordsdale virus, in a separate genetic cluster of Norwalk-like viruses. A 3.3 kb cDNA from the RNA polymerase region to the 3' end of the genome of Arg320 was cloned and sequenced. The sequence demonstrated that the capsid region of Arg320 shared 95% amino acid identity with MxV, but 68% identity with Lordsdale virus, while the RNA polymerase region shared 95% identity with Lordsdale virus, but 87% identity with MxV. Pair-wise sequence comparisons identified a potential recombination site at the polymerase/capsid junction. This is the first example of a naturally occurring recombinant in the CV family. Further studies to search for and characterize other strains may be necessary for understanding the genetic diversity of the family.

Feline calicivirus

“…In addition, the high prevalence of FCV in such colonies provides an ideal environment for mixed infections. As a result recombination events between strains, similar to those reported for other caliciviruses [7,46,50,73], have been identified in such colonies, and provide a further mechanism for the diversification of viruses [16]. Whether these evolutionary events are associated with the selection of more virulent, faster replicating viral variants remains to be determined.…”

Genetic classification of "Sapporo-like viruses"

“…Previously, the genetic classification of NLVs based on the RNA polymerase sequences had been reported as being essentially identical to that based on the capsid protein sequences [41], and the strains which did not agree with this rule were considered as possible recombinants [16,19]. Our results may provide an alternative explanation to discrepant genetic grouping patterns, i.e grouping of RNA polymerase sequence of individual strains may not be necessarily concordant with that of the capsid sequence because of a difference in genetic characteristics between NLVs and SLVs.…”

Detection of caliciviruses associated with acute infantile gastroenteritis in Salvador, an urban center in Northeast Brazil

“…The 139 fecal samples were tested by PCR using two different sets of primers: i) 289/290, which detects both NoVs (319-bp amplicons) and SaVs (331-bp amplicons) (17) and ii) a generic NoV PCR system based on the degenerate primers Mon 431/Mon 433 and Mon 432/Mon 434 of region B within 3'-end of ORF1 (RNA polymerase) (18). To avoid false-positive and -negative results, previously typed NoV GI/2a and NoV GII/4 strains and Milli-Q water were used as positive and negative controls, respectively.…”