Integrating patient and whole genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses
Integrating patient and whole genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses
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整合患者和全基因组测序数据，深入了解季节性甲型流感 (H3N2) 病毒的流行病学
DOI：
10.1101/121434
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发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Goldstein E
中科院分区：
文献类型：
--
作者：
Goldstein E
季节性流感的基因监测主要集中在血凝素基因的测序上。因此，我们对其余七个基因片段对季节性流感的演变和流行病学动态的贡献的理解相对有限。下一代测序技术的增加使得流感病毒的快速和经济的全基因组测序（WGS）成为可能。在此，使用Illumina MiSeq平台，使用HA 1区域的桑格测序和WGS直接测序了来自苏格兰2014/15季节的150份具有相关流行病学数据的甲型H3 N2流感阳性临床标本。通过两种方法产生的序列高度相关，并且WGS提供平均> 90%的全基因组覆盖率。 如2014/15年其他欧洲国家报告的，所有菌株均属于遗传组3C，其中亚组3C.2a占主导地位。鉴定出多个亚组间重配株，包括3个3C.3病毒，其起源于一个重配事件，在人群中持续存在。严重急性呼吸道疾病病例明显聚集在多个基因片段的遗传上，表明可能的遗传因素，值得进一步研究。严重的病例也更可能与抵抗病毒有关，并在季节晚些时候发生。这些结果表明，WGS提供了一个机会，发展我们的理解之间的关系，流感基因组和疾病的严重程度和流行病学后果的亚型内重配。因此，提高WGS水平，结合临床和流行病学数据，可以改善流感监测。
Genetic surveillance of seasonal influenza is largely focused on sequencing of the haemagglutinin gene. Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited. The increased availability of next-generation sequencing technologies allows rapid and economic whole-genome sequencing (WGS) of influenza virus. Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and WGS using the Illumina MiSeq platform. Sequences generated by the two methods were highly correlated, and WGS provided on average >90 % whole genome coverage. As reported in other European countries during 2014/15, all strains belonged to genetic group 3C, with subgroup 3C.2a predominating. Multiple inter-subgroup reassortants were identified, including three 3C.3 viruses descended from a single reassortment event, which had persisted in the population. Cases of severe acute respiratory illness were significantly clustered on phylogenies of multiple gene segments indicating potential genetic factors warranting further investigation. Severe cases were also more likely to be associated with reassortant viruses and to occur later in the season. These results suggest that WGS provides an opportunity to develop our understanding of the relationship between the influenza genome and disease severity and the epidemiological consequences of within-subtype reassortment. Therefore, increased levels of WGS, linked to clinical and epidemiological data, could improve influenza surveillance.
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影响因子：
4.5
作者：
Neverov AD;Lezhnina KV;Kondrashov AS;Bazykin GA
通讯作者：
Bazykin GA
DOI：
10.1007/978-1-61779-621-0_11
发表时间：
2012-01-01
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Zhou, Bin;Wentworth, David E
通讯作者：
Wentworth, David E
DOI：
10.1136/bmj.f5061
发表时间：
2013-08-23
期刊：
BMJ (Clinical research ed.)
影响因子：
--
作者：
Mertz D;Kim TH;Johnstone J;Lam PP;Science M;Kuster SP;Fadel SA;Tran D;Fernandez E;Bhatnagar N;Loeb M
通讯作者：
Loeb M
影响因子：
10.7
作者：
Simonsen, Lone;Viboud, Cecile;Holmes, Edward C.
通讯作者：
Holmes, Edward C.
影响因子：
4.9
作者：
Tamura, Daisuke;Nguyen, Ha T.;Gubareva, Larisa V.
通讯作者：
Gubareva, Larisa V.