CAPSID SEQUENCE DIVERSITY IN SMALL ROUND STRUCTURED VIRUSES FROM RECENT UK OUTBREAKS OF GASTROENTERITIS

Genetic typing of small round structured viruses (SRSVs) by reverse tr anscription-polymerase chain reaction (RT-PCR) and sequencing has been confined to analysis of the RNA polymerase because of the considerabl e genome variability outside of this region. To provide capsid sequenc e data for epidemiological studies and outbreak investigations, a broa dly reactive capsid PCR was developed using two sets of degenerate, in osine-containing primers. Primer pairs Capla/Caplb and Caplla/Capllb s pecifically amplify a 223-bp region of the SRSV capsid open reading fr ame from SRSV genetic groups I and II, respectively. The capsid PCR wa s used to investigate SRSVs from nine UK outbreaks of gastroenteritis occurring between 1992 and 1995. Differential amplification by the pri mer 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), whi le those of the group II strains were 75.9% to 98.3% identical with Br i/93/UK (group II). Phylogenetic comparison of the capsid region from the outbreak strains and 13 previously characterised SRSVs revealed cl usters of strains closely related to Bri/93/UK and Tor/77/C within gen etic group II. With the exception of some Bri/93/UK-like strains, ther e was no correlation between capsid sequence and the geographical orig in of SRSVs. UK strains were found with greater than 90% capsid sequen ce identity to SRSVs from various locations worldwide including Austra lia (Cam/94/A), Canada (Tor/77/C), Hawaii (Haw/71/US), and Saudi Arabi a (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 hos pital outbreaks. These Bri/93/UK-like strains appear to be prevalent i n the UK. (C) 1997 Wiley-Liss, Inc.