Tracking echovirus eleven outbreaks in Guangdong, China: a metatranscriptomic, phylogenetic, and epidemiological study
Tracking echovirus eleven outbreaks in Guangdong, China: a metatranscriptomic, phylogenetic, and epidemiological study
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追踪中国广东省埃可病毒十一次爆发：一项宏转录组学、系统发育和流行病学研究
DOI：
10.1093/ve/veaa029
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发表时间：
2020-01-01
期刊：
影响因子：
5.3
通讯作者：
Zheng, Huanying
中科院分区：
文献类型：
--
作者：
Lu, Jing;Kang, Min;Zheng, Huanying
摘要 2019年4月，中国广东省新生儿科报告疑似聚集性肠道病毒病例，造成5人死亡。我们的目的是通过结合宏转录组学、系统发育和流行病学分析来研究致命病例的病原体概况、病毒的传播和传播模式。使用宏转录组测序来表征肠道病毒。对当地人群进行临床和环境监测，以了解当地人群中病毒的流行情况和遗传多样性。通过整合当前疫情、当地回顾性监测和公共数据库的基因组，研究了病毒的可能来源、进化、传播和重组。宏转录组分析在三例死亡病例中发现了埃可病毒 11 (E11)。在3-15岁普通人群中，E11中和抗体的血清阳性率为35%至44%，并且该病毒与各种临床症状相关。从病毒系统发育来看，确定了医院传播，2019 年所有 E11 暴发毒株均与 2017-19 年当地人群中传播的 E11 毒株密切相关。 2019年广东E11暴发毒株与肠道病毒B种各基因型之间发生频繁重组。本研究提供了在传染病暴发期间将先进基因技术与流行病学监测相结合进行病原体诊断、来源和传播追踪的示例。该结果凸显了中国年轻人群中隐藏的E11循环以及病毒传播和感染的风险。广东样毒株与其他肠道病毒基因型之间的频繁重组也意味着这些新出现的 E11 毒株的流行。
Abstract In April 2019, a suspect cluster of enterovirus cases was reported in a neonatology department in Guangdong, China, resulting in five deaths. We aimed to investigate the pathogen profiles in fatal cases, the circulation and transmission pattern of the viruses by combining metatranscriptomic, phylogenetic, and epidemiological analyses. Metatranscriptomic sequencing was used to characterize the enteroviruses. Clinical and environmental surveillance in the local population was performed to understand the prevalence and genetic diversity of the viruses in the local population. The possible source(s), evolution, transmission, and recombination of the viruses were investigated by incorporating genomes from the current outbreak, from local retrospective surveillance, and from public databases. Metatranscriptomic analysis identified Echovirus 11 (E11) in three fatal cases. Seroprevalence of neutralization antibody to E11 was 35 to 44 per cent in 3–15 age groups of general population, and the viruses were associated with various clinical symptoms. From the viral phylogeny, nosocomial transmissions were identified and all E11 2019 outbreak strains were closely related with E11 strains circulating in local population 2017–19. Frequent recombination occurred among the 2019 Guangdong E11 outbreak strains and various genotypes in enterovirus B species. This study provides an example of combining advanced genetic technology and epidemiological surveillance in pathogen diagnosis, source(s), and transmission tracing during an infectious disease outbreak. The result highlights the hidden E11 circulation and the risk of viral transmission and infection in the young age population in China. Frequent recombination between Guangdong-like strains and other enterovirus genotypes also implies the prevalence of these emerging E11 strains.