An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
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DOI：
10.1128/mbio.02107-20
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发表时间：
2020-09-01
期刊：
影响因子：
6.4
通讯作者：
Keim, Paul
中科院分区：
文献类型：
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作者：
Ladner, Jason T.;Larsen, Brendan B.;Keim, Paul
2019 年 12 月，一种新型冠状病毒 SARS-CoV-2 在中国武汉市出现，造成严重的发病和死亡。此后，该病毒席卷全球，造成数百万人确诊感染，数十万人死亡。为了更好地了解大流行的性质以及病毒在亚利桑那州的传入和传播，我们对 TGen North 临床实验室、亚利桑那州卫生服务部测试的临床样本以及作为亚利桑那州立大学和亚利桑那大学社区监测项目一部分收集的样本进行了病毒基因组测序。对亚利桑那州各地 84 个基因组的系统发育分析显示，至少有 11 次不同的引入被推断发生在 2 月和 3 月期间。我们发现，超过 80% 的序列源自最初在欧洲广泛传播但后来在美国疫情中占主导地位的菌株。此外，我们还发现亚利桑那州首例报告的社区传播病例源于二月底发现的华盛顿州疫情。值得注意的是，观察到的传播群在流行病学上均与该州最初的旅行相关病例无关，这表明早期隔离和检疫是成功的。最后，我们使用分子钟分析来证明，2020 年 2 月中旬之前，亚利桑那州缺乏可识别的、广泛的隐秘传播。 重要性 随着 COVID-19 大流行席卷美国，对当地和区域社区产生了巨大的不同影响。纽约是受影响最早和最严重的地区之一，而同时亚利桑那州（例如）的发病率较低。这种情况发生了巨大变化，亚利桑那州现在是全国疾病增长率最高的州。随着疫情持续蔓延并达到新的高度，了解疫情最初几个月的根源至关重要。亚利桑那州 SARS-COV-2 的基因组分析和系统发育模型有助于重建种群组成并预测最早未被发现的引入。随着疫情的持续，这项基础性工作为未来分析和理解奠定了基础。
In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China, causing severe morbidity and mortality. Since then, the virus has swept across the globe, causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, the Arizona Depart-ment of Health Services, and those collected as part of community surveillance projects at Arizona State University and the University of Arizona. Phylogenetic analysis of 84 genomes from across Arizona revealed a minimum of 11 distinct introductions inferred to have occurred during February and March. We show that >80% of our sequences descend from strains that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported case of community transmission in Arizona descended from the Washington state outbreak that was discovered in late February. Notably, none of the observed transmission clusters are epidemiologically linked to the original travel-related case in the state, suggesting successful early isolation and quarantine. Finally, we use molecular clock analyses to demonstrate a lack of identifiable, widespread cryptic transmission in Arizona prior to the middle of February 2020.IMPORTANCE As the COVID-19 pandemic swept across the United States, there was great differential impact on local and regional communities. One of the earliest and hardest hit regions was in New York, while at the same time Arizona (for example) had low incidence. That situation has changed dramatically, with Arizona now having the highest rate of disease increase in the country. Understanding the roots of the pandemic during the initial months is essential as the pandemic continues and reaches new heights. Genomic analysis and phylogenetic modeling of SARS-COV-2 in Arizona can help to reconstruct population composition and predict the earliest un-detected introductions. This foundational work represents the basis for future analysis and understanding as the pandemic continues.