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Epidemiology of human sapporo-like caliciviruses in the South West of England: molecular characterisation of a genetically distinct isolate

Epidemiology of human sapporo-like caliciviruses in the South West of England: molecular characterisation of a genetically distinct isolate
Epidemiology of human sapporo-like caliciviruses in the South West of England: molecular characterisation of a genetically distinct isolate
Human enteric caliciviruses have been assigned to two distinct genera: the Norwalk-like viruses (NLVs) and the Sapporo-like viruses (SLVs). During a 3-year surveillance of gastroenteritis in the South West of England during November 1997-2000, a total of 27 clinical samples containing SLVs were collected. PCR amplicons covering a region of the RNA polymerase gene were obtained from 18 of the SLV samples. Sequence analysis of the PCR products indicated that the SLV isolates could be assigned to one of the two major genetic groups represented by Sapporo and London/92 caliciviruses. One of these isolates belonging to the London/92 group (Bristol/98) was subjected to a complete genome sequence analysis. The full genomic sequence of the Bristol/98 isolate was determined from RNA extracted from a single stool sample and consists of 7490 nucleotides, excluding the poly(A) tail. The genome is organised into two open reading frames (ORFs), similar to that of Manchester SLV although the small ORF overlapping the region encoding the capsid protein observed in Manchester SLV is absent in Bristol/98 SLV. The polyprotein (ORF1) of Bristol/98 SLV consists of 2,280 amino acids and, as observed in all SLVs, the structural protein is encoded in frame and contiguous with the 3' terminus of the ORF1. Phylogenetic studies based on complete capsid sequences and genome arrangements within the SLVs indicate that the human enteric viruses within the "Sapporo-like" virus clade should be divided into two distinct genetic groups analogous to the assignment of the Norwalk-like viruses.
gastroenteritis, calicivirus, sequence, phylogeny, epidemiology
0146-6615
282-288
Robinson, Samantha
4ef22161-0375-4d64-a699-6c9e33cd174a
Clarke, Ian N.
ff6c9324-3547-4039-bb2c-10c0b3327a8b
Vipond, I. Barry
ff5d900a-c164-4c67-b770-53f3d6ec2b42
Caul, E. Owen
177391c9-26e2-4c94-a459-d9353c2daa61
Lambden, Paul R.
4fcd536e-2d9a-4366-97c6-386e6b005698
Robinson, Samantha
4ef22161-0375-4d64-a699-6c9e33cd174a
Clarke, Ian N.
ff6c9324-3547-4039-bb2c-10c0b3327a8b
Vipond, I. Barry
ff5d900a-c164-4c67-b770-53f3d6ec2b42
Caul, E. Owen
177391c9-26e2-4c94-a459-d9353c2daa61
Lambden, Paul R.
4fcd536e-2d9a-4366-97c6-386e6b005698

Robinson, Samantha, Clarke, Ian N., Vipond, I. Barry, Caul, E. Owen and Lambden, Paul R. (2002) Epidemiology of human sapporo-like caliciviruses in the South West of England: molecular characterisation of a genetically distinct isolate. Journal of Medical Virology, 67 (2), 282-288. (doi:10.1002/jmv.2219).

Record type: Article

Abstract

Human enteric caliciviruses have been assigned to two distinct genera: the Norwalk-like viruses (NLVs) and the Sapporo-like viruses (SLVs). During a 3-year surveillance of gastroenteritis in the South West of England during November 1997-2000, a total of 27 clinical samples containing SLVs were collected. PCR amplicons covering a region of the RNA polymerase gene were obtained from 18 of the SLV samples. Sequence analysis of the PCR products indicated that the SLV isolates could be assigned to one of the two major genetic groups represented by Sapporo and London/92 caliciviruses. One of these isolates belonging to the London/92 group (Bristol/98) was subjected to a complete genome sequence analysis. The full genomic sequence of the Bristol/98 isolate was determined from RNA extracted from a single stool sample and consists of 7490 nucleotides, excluding the poly(A) tail. The genome is organised into two open reading frames (ORFs), similar to that of Manchester SLV although the small ORF overlapping the region encoding the capsid protein observed in Manchester SLV is absent in Bristol/98 SLV. The polyprotein (ORF1) of Bristol/98 SLV consists of 2,280 amino acids and, as observed in all SLVs, the structural protein is encoded in frame and contiguous with the 3' terminus of the ORF1. Phylogenetic studies based on complete capsid sequences and genome arrangements within the SLVs indicate that the human enteric viruses within the "Sapporo-like" virus clade should be divided into two distinct genetic groups analogous to the assignment of the Norwalk-like viruses.

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More information

Published date: 2002
Keywords: gastroenteritis, calicivirus, sequence, phylogeny, epidemiology

Identifiers

Local EPrints ID: 27382
URI: http://eprints.soton.ac.uk/id/eprint/27382
ISSN: 0146-6615
PURE UUID: fc09d63c-6525-494d-963a-a9ea70d76a08
ORCID for Ian N. Clarke: ORCID iD orcid.org/0000-0002-4938-1620

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Date deposited: 27 Apr 2006
Last modified: 16 Mar 2024 02:33

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Contributors

Author: Samantha Robinson
Author: Ian N. Clarke ORCID iD
Author: I. Barry Vipond
Author: E. Owen Caul
Author: Paul R. Lambden

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