CID：全基因组深度测序或可鉴定诺如病毒传播方向

诺如病毒具高度传染性，是院内肠胃炎的主要病原之一，甚至可能导致患者住院或医院病房暂时关闭。当怀疑爆发医院感染时，及时判断病毒传播途径是非常重要的，这有助于医院迅速采取适当措施以控制感染。为研究发生于骨髓移植儿童中的一组诺如病毒病例，来自英国伦敦大学学院感染与免疫科的Samit Kundu博士等人采用新一代测序技术对诺如病毒基因组进行测序。研究结果在线发表于2013年5月3日的《临床感染性疾病》（Clinical Infectious Diseases）杂志上。对深度测序数据的分析使得研究人员能够确认诺如病毒传播的可能方向。
研究人员从5例rtPCR结果阳性的患者收集到13份粪便样品，采用重叠PCR法扩增诺如病毒cDNA。使用Roche 454系统测定扩增子的序列，从头组装病毒基因组并根据系统进化分析数据。
详细比较2例关联病例的序列数据使研究人员得以鉴别诺如病毒的可能传播方向。系统进化分析表明，感染这些患者的病毒与4种不同的GII.4亚型诺如病毒相似，有2例患者因感染相同病毒而相关联。在2株关联病毒基因组的共有序列中，有14个位点存在差异，其中9个在患者A或患者B中存在少量突变。进一步分析确证，患者B所有9个位点的突变体在患者A中均以共有序列的形式存在。
系统进化分析排除这一诺如病毒暴发是由常见感染源引起。住在同一病房的3名患者中，有2例感染了紧密相关的病毒，尽管采取了保护性隔离措施，但仍存在交叉感染的可能。对深度测序数据的分析使得研究人员能够确认诺如病毒传播的可能方向。

Next generation whole genome sequencing identifies the direction of norovirus transmission in linked patients.
Background
Noroviruses are a highly transmissible and a major cause of nosocomial gastroenteritis resulting in bed and hospital-ward closures. Where hospital outbreaks are suspected, it is important to determine the routes of spread so that appropriate infection control procedures can be implemented. To investigate a cluster of norovirus cases occurring in bone marrow transplant children, we undertook norovirus genome sequencing by next generation methods. Detailed comparison of sequence data from two linked cases enabled us to identify the likely direction of spread.
Methods
Norovirus cDNA was amplified by overlapping PCR from 13 stool samples from five diagnostic rtPCR positive patients. The amplicons were sequenced by Roche 454, the genomes assembled by de novo assembly and the data analysed phylogenetically.
Results
Phylogenetic analysis indicated that patients were infected by viruses similar to four distinct GII.4 subtypes and two patients were linked by the same virus. Of the 14 sites at which there were differences between the consensus sequences of the two linked viral genomes, nine had minor variants present within one or other patient. Further analysis confirmed that minor variants at all nine sites in patient B were present as the consensus sequence in patient A.
Conclusions
Phylogenetic analysis excluded a common source of infection in this apparent outbreak. Two of three patients on the same ward had closely related viruses, raising the possibility of cross infection despite protective isolation. Analysis of deep sequence data enabled us to establish the likely direction of nosocomial transmission.