Molecular epidemiology of norovirus GII.15 in Qingdao City

中华传染病杂志 Pub Date : 2019-12-15 DOI:10.3760/CMA.J.ISSN.1000-6680.2019.12.007

Dan Zhao, Weisen Yu, Xiaoyue Zhang, Z. Su, Ruiqin Sun, Zhaoguo Wang

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Abstract

Objective To analyze the molecular epidemiology of norovirus (NoV) genotype GⅡ.15 in Qingdao City. Methods One thousand four hundred and twelve stool samples were collected from suspected NoV infected patients and detected by real-time polymerase chain reaction (PCR). Open reading frame (ORF)1-ORF2 and VP1 gene were amplified by reverse transcription (RT)-PCR and sequenced for genotyping, evolutionary analysis and homology modeling. Results Seven cases of GⅡ.15 type were detected including four sporadic cases and one outbreak.The VP1 gene was highly homologous and had little variation compared with early strain J23/US/1999. The differences of amino acids between strains in Qingdao City were mainly asparagine/asparticacid(N/D)300 and proline/serine(P/S)302.Homology modeling suggested that VP1 of GⅡ.15 strain was composed of S domain and P domain (P1 subdomain included 224-276 and 431-555, P2 subdomain included 277-430). S domain contained eight anti-parallel β-sandwiches and two α-helixes, and P1 subdomain contained one α-helix and seven β-strands, and the P2 subdomain folded into a compact barrel-like structure consisting of six β-strands.Argnine (R)-glycine (G)-valine (V)-motif (289-291) and three specific loci including glutarnine (Q)313, asparagine (N)349 and Q389 were located in the P2 subdomain, with NGR-motif (265-267) located at 22nd upstream of RGV-motif.Site I (SNR-alanine(A)- histidine(H)357-361), Site Ⅱ (D388) and Site Ⅲ (G454, G455) were the main characteristic sites of histo-blood group antigens (HBGA) binding interface, which may be similar to the binding pattern of GⅡ.4 type VA387 and HBGA. Conclusion Although GⅡ.15 type NoV evolves very slowly, it may still have the risk to become an epidemic strain, which needs to be monitored and further studied. Key words: Norovirus GⅡ.15; Epidemiology, molecular

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青岛市诺如病毒GII.15的分子流行病学研究

目的分析诺如病毒(NoV) G基因型Ⅱ的分子流行病学。在青岛市有15个。方法收集疑似新型冠状病毒感染患者粪便1412份，采用实时聚合酶链反应(PCR)检测。采用逆转录-PCR扩增开放阅读框(ORF)1-ORF2和VP1基因，并测序进行基因分型、进化分析和同源性建模。结果7例GⅡ。发现15种类型，包括4例散发病例和1例暴发。VP1基因同源性高，与早期菌株J23/US/1999相比差异不大。青岛市菌株间氨基酸差异主要为天冬氨酸/天冬氨酸(N/D)300和脯氨酸/丝氨酸(P/S)302。同源性建模表明GⅡ的VP1。15株菌株由S域和P域组成(P1子域包括224-276和431-555,P2子域包括277-430)。S结构域包含8个反平行的β-三明治和2个α-螺旋，P1子结构域包含1个α-螺旋和7条β-链，P2子结构域折叠成由6条β-链组成的致密桶状结构。Argnine (R)-glycine (G)-valine (V)-motif(289-291)和glutarnine (Q)313、asparagine (N)349和Q389三个特异位点位于P2亚结构域，NGR-motif(265-267)位于RGV-motif上游的第22位。Site I (snr -丙氨酸(A)-组氨酸(H)357-361)、SiteⅡ(D388)和SiteⅢ(G454、G455)是组织血型抗原(HBGA)结合界面的主要特征位点，可能与GⅡ的结合模式相似。4型VA387和HBGA。结论虽然GⅡ。15型新型冠状病毒演变非常缓慢，可能仍有成为流行毒株的风险，需要进一步监测和研究。关键词:诺如病毒GⅡ.15;流行病学、分子

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来源期刊

中华传染病杂志

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5280

期刊介绍： The Chinese Journal of Infectious Diseases was founded in February 1983. It is an academic journal on infectious diseases supervised by the China Association for Science and Technology, sponsored by the Chinese Medical Association, and hosted by the Shanghai Medical Association. The journal targets infectious disease physicians as its main readers, taking into account physicians of other interdisciplinary disciplines, and timely reports on leading scientific research results and clinical diagnosis and treatment experience in the field of infectious diseases, as well as basic theoretical research that has a guiding role in the clinical practice of infectious diseases and is closely integrated with the actual clinical practice of infectious diseases. Columns include reviews (including editor-in-chief reviews), expert lectures, consensus and guidelines (including interpretations), monographs, short monographs, academic debates, epidemic news, international dynamics, case reports, reviews, lectures, meeting minutes, etc.