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近期英国肠胃炎暴发中检出的小圆结构病毒的衣壳序列多样性

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

作者信息

Green S M, Lambden P R, Caul E O, Clarke I N

机构信息

Public Health Laboratory, University Medical School, Southampton General Hospital, UK.

出版信息

J Med Virol. 1997 May;52(1):14-9.

PMID:9131452
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.

摘要

由于该区域以外的基因组存在相当大的变异性,通过逆转录聚合酶链反应(RT-PCR)和测序对小圆结构病毒(SRSV)进行基因分型一直局限于对RNA聚合酶的分析。为了提供衣壳序列数据用于流行病学研究和疫情调查,使用两组简并的含次黄苷引物开发了一种广泛反应性的衣壳PCR。引物对Capla/Caplb和Caplla/Capllb分别从SRSV基因I组和II组特异性扩增SRSV衣壳开放阅读框的一个223bp区域。衣壳PCR用于调查1992年至1995年间英国发生的9起肠胃炎疫情中的SRSV。引物对的差异扩增表明,三株菌株属于基因I组,六株属于基因II组。I组菌株的衣壳氨基酸序列与Sot/91/UK(I组)的同一性为75.9%至79.3%,而II组菌株的衣壳氨基酸序列与Bri/93/UK(II组)的同一性为75.9%至98.3%。对疫情菌株和13种先前鉴定的SRSV的衣壳区域进行系统发育比较,发现基因II组内存在与Bri/93/UK和Tor/77/C密切相关的菌株簇。除了一些类似Bri/93/UK的菌株外,衣壳序列与SRSV的地理来源之间没有相关性。发现英国菌株与来自世界各地(包括澳大利亚(Cam/94/A)、加拿大(Tor/77/C)、夏威夷(Haw/71/US)和沙特阿拉伯(DSV395/90/SA))的SRSV的衣壳序列同一性大于90%,以及与已知SRSV衣壳在基因上不同的I组(B447/92/UK)和II组(Yat/94/UK)菌株。三株与Bri/93/UK非常密切相关的SRSV来自英国近期的医院疫情。这些类似Bri/93/UK的菌株似乎在英国很普遍。

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