Huang Weihua, Wang Guiqing, Zhuge Jian, Nolan Sheila M, Dimitrova Nevenka, Fallon John T
Department of Pathology, New York Medical College, Valhalla, New York, United States of America.
Department of Pathology and Clinical Laboratories, Westchester Medical Center, Valhalla, New York, United States of America.
Sci Rep. 2015 Oct 15;5:15223. doi: 10.1038/srep15223.
In the late summer and the fall of 2014, the United States experienced an unprecedented outbreak of enterovirus D68 (EV-D68) infections. During the outbreak, we collected nasopharyngeal swab specimens from patients in the Lower Hudson Valley of New York. Here, we conduct a retrospective study on the genomic diversity of EV-D68 strains. We first employ a metagenomic shotgun sequencing protocol on a total of 93 clinical samples, including 21 negative controls, the results of which allow assembly of 20 EV-D68 genomes, six complete and 14 near-complete. We then investigate their genetic relationships, along with additional 20 EV-D68 strains having whole-genome sequences publicly available. Our comparative genomic analysis uncovers that the majority (26/29) of EV-D68 strains circulating in the 2014 outbreak differ significantly from prior ones, have a main feature of three variables, C1817T, C3277A, and A4020G, and belong to a new clade. C3277A causes amino acid substitution T860N in the protease 2A(pro) cleavage site between VP1 and 2A, whereas A4020G causes S1108G in a 3C(pro) cleavage site between 2B and 2C. The two functional mutations may alter the proteases' cleavage efficiency, leading to increased rate of viral replication and transmission. These provide insights into the evolution of epidemic EV-D68 strains.
2014年夏末秋初，美国经历了肠道病毒D68（EV-D68）感染的前所未有的爆发。在疫情爆发期间，我们从纽约下哈德逊山谷的患者中采集了鼻咽拭子样本。在此，我们对EV-D68毒株的基因组多样性进行了一项回顾性研究。我们首先对总共93份临床样本（包括21份阴性对照）采用宏基因组鸟枪法测序方案，其结果使得能够组装20个EV-D68基因组，其中6个完整，14个接近完整。然后，我们研究它们与另外20个具有公开全基因组序列的EV-D68毒株的遗传关系。我们的比较基因组分析发现，2014年疫情中传播的大多数（26/29）EV-D68毒株与之前的毒株有显著差异，具有C1817T、C3277A和A4020G三个变量的主要特征，并且属于一个新的进化枝。C3277A导致VP1和2A之间蛋白酶2A（pro）切割位点的氨基酸替换T860N，而A4020G导致2B和2C之间3C（pro）切割位点的S1108G。这两个功能性突变可能会改变蛋白酶的切割效率，导致病毒复制和传播速率增加。这些为流行的EV-D68毒株的进化提供了见解。
