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Capsid sequence diversity in small round structured viruses from recent UK outbreaks of gastroenteritis

Green, Steve M., Lambden, Paul R., Caul, E. Owen and Clarke, Ian N. (1997) Capsid sequence diversity in small round structured viruses from recent UK outbreaks of gastroenteritis Journal of Medical Virology, 52, (1), pp. 14-19. (doi:10.1002/(SICI)1096-9071(199705)52:1<14::AID-JMV3>3.0.CO;2-U). (PMID:9131452).

Record type: Article

Abstract

Genetic typing of small round structured viruses (SRSVs) by reverse transcription-polymerase chain reaction (RT-PCR) and sequencing has been confined to analysis of the RNA polymerase because of the considerable genome variability outside of this region. To provide capsid sequence data for epidemiological studies and outbreak investigations, a broadly reactive capsid PCR was developed using two sets of degenerate, inosine-containing primers. Primer pairs Capla/Caplb and Caplla/Capllb specifically amplify a 223-bp region of the SRSV capsid open reading frame from SRSV genetic groups I and II, respectively. The capsid PCR was used to investigate SRSVs from nine UK outbreaks of gastroenteritis occurring between 1992 and 1995. Differential amplification by the primer pairs suggested that three strains belonged to genetic group I and six to genetic group II. The capsid amino acid sequences of the group I strains were 75.9% to 79.3% identical with Sot/91/UK (group I), while those of the group II strains were 75.9% to 98.3% identical with Bri/93/UK (group II). Phylogenetic comparison of the capsid region from the outbreak strains and 13 previously characterised SRSVs revealed clusters of strains closely related to Bri/93/UK and Tor/77/C within genetic group II. With the exception of some Bri/93/UK-like strains, there was no correlation between capsid sequence and the geographical origin of SRSVs. UK strains were found with greater than 90% capsid sequence identity to SRSVs from various locations worldwide including Australia (Cam/94/A), Canada (Tor/77/C), Hawaii (Haw/71/US), and Saudi Arabia (DSV395/90/SA) together with group I (B447/92/UK) and group II (Yat/94/UK) strains that were genetically distinct from known SRSV capsids. Three SRSVs very closely related to Bri/93/UK were from recent UK hospital outbreaks. These Bri/93/UK-like strains appear to be prevalent in the UK.

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More information

Published date: May 1997
Keywords: calicivirus, capsid sequence, pcr

Identifiers

Local EPrints ID: 194265
URI: http://eprints.soton.ac.uk/id/eprint/194265
ISSN: 0146-6615
PURE UUID: 1e18ad8b-43c2-48e3-b98a-f19364d00fa2
ORCID for Ian N. Clarke: ORCID iD orcid.org/0000-0002-4938-1620

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Date deposited: 26 Jul 2011 12:28
Last modified: 18 Jul 2017 11:27

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Contributors

Author: Steve M. Green
Author: Paul R. Lambden
Author: E. Owen Caul
Author: Ian N. Clarke ORCID iD

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