Biosecurity Research Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney NSW 2052, Australia.
School of Public Health and Community Medicine, Faculty of Medicine, University of New South Wales, Sydney NSW 2052, Australia.
Viruses. 2020 May 14;12(5):540. doi: 10.3390/v12050540.
This study compared the phylogeography of MERS-CoV between hospital outbreak-associated cases and sporadic cases in Saudi Arabia. We collected complete genome sequences from human samples in Saudi Arabia and data on the multiple risk factors of human MERS-CoV in Saudi Arabia reported from 2012 to 2018. By matching each sequence to human cases, we identified isolates as hospital outbreak-associated cases or sporadic cases. We used Bayesian phylogenetic methods including temporal, discrete trait analysis and phylogeography to uncover transmission routes of MERS-CoV isolates between hospital outbreaks and sporadic cases. Of the 120 sequences collected between 19 June 2012 and 23 January 2017, there were 64 isolates from hospital outbreak-associated cases and 56 from sporadic cases. Overall, MERS-CoV is fast evolving at 7.43 × 10 substitutions per site per year. Isolates from hospital outbreaks showed unusually fast evolutionary speed in a shorter time-frame than sporadic cases. Multiple introductions of different MERS-CoV strains occurred in three separate hospital outbreaks. MERS-CoV appears to be mutating in humans. The impact of mutations on viruses transmissibility in humans is unknown.
本研究比较了沙特阿拉伯医院暴发相关病例和散发病例中东呼吸综合征冠状病毒（MERS-CoV）的系统地理学特征。我们收集了 2012 年至 2018 年期间沙特阿拉伯人类样本的完整基因组序列和沙特阿拉伯报告的人类 MERS-CoV 多种危险因素的数据。通过将每个序列与人类病例相匹配，我们将分离株鉴定为医院暴发相关病例或散发病例。我们使用贝叶斯系统地理学方法，包括时间、离散性状分析和系统地理学，揭示了 MERS-CoV 分离株在医院暴发和散发病例之间的传播途径。在 2012 年 6 月 19 日至 2017 年 1 月 23 日期间收集的 120 个序列中，有 64 个分离株来自医院暴发相关病例，56 个来自散发病例。总体而言，MERS-CoV 的进化速度很快，每年每个位点有 7.43×10 个取代。与散发病例相比，医院暴发相关的分离株在较短的时间内表现出异常快的进化速度。在三次不同的医院暴发中，都有不同的 MERS-CoV 株的多次传入。MERS-CoV 似乎在人类中发生突变。突变对病毒在人类中的传染性的影响尚不清楚。
