Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling
Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling
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DOI：
10.1038/s41591-020-1000-7
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发表时间：
2020-07-09
期刊：
影响因子：
82.9
通讯作者：
Sintchenko, Vitali
中科院分区：
文献类型：
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作者：
Rockett, Rebecca J.;Arnott, Alicia;Sintchenko, Vitali
2020年1月，一种名为严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的新型β冠状病毒（冠状病毒科）被确定为中国湖北省武汉市发生的一组肺炎病例的病原体（1，2）。由SARS-CoV-2感染引起的疾病，即2019冠状病毒病（COVID-19），随后迅速蔓延，导致全球大流行。在这里，我们研究了在澳大利亚COVID-19控制的前10周内，在感染患者亚群中SARS-CoV-2的近实时基因组测序的附加值，并将基因组监测的结果与基于计算代理的模型（ABM）的预测进行了比较。使用澳大利亚人口普查数据，ABM生成了代表澳大利亚人口的2400多万个软件代理，每个代理都具有匿名个人的人口统计属性。然后，它利用不同社会背景下的个人接触率，模拟疾病随时间的传播，从特定的感染源传播。我们报告说，SARS-CoV-2的前瞻性测序澄清了无法确定流行病学联系的病例中可能的感染源，显著降低了有争议联系的COVID-19病例的比例，记录了与几个机构中同时传播相关的基因组相似病例，并确定了以前未怀疑的联系。只有四分之一的测序病例似乎是当地获得的，与ABM的预测一致。这些高分辨率的基因组数据对于追踪当地获得的COVID-19病例以及在边境限制解除、贸易和旅行恢复后及时识别独立输入病例至关重要。在澳大利亚COVID-19遏制的前10周内，对感染患者的SARS-CoV-2进行了近实时的基因组测序，并建立了流行病学模型，这有助于了解COVID-19的动态。19大流行，并可能指导公共卫生决策。
In January 2020, a novel betacoronavirus (familyCoronaviridae), named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of a cluster of pneumonia cases occurring in Wuhan City, Hubei Province, China(1,2). The disease arising from SARS-CoV-2 infection, coronavirus disease 2019 (COVID-19), subsequently spread rapidly causing a worldwide pandemic. Here we examine the added value of near real-time genome sequencing of SARS-CoV-2 in a subpopulation of infected patients during the first 10 weeks of COVID-19 containment in Australia and compare findings from genomic surveillance with predictions of a computational agent-based model (ABM). Using the Australian census data, the ABM generates over 24 million software agents representing the population of Australia, each with demographic attributes of an anonymous individual. It then simulates transmission of the disease over time, spreading from specific infection sources, using contact rates of individuals within different social contexts. We report that the prospective sequencing of SARS-CoV-2 clarified the probable source of infection in cases where epidemiological links could not be determined, significantly decreased the proportion of COVID-19 cases with contentious links, documented genomically similar cases associated with concurrent transmission in several institutions and identified previously unsuspected links. Only a quarter of sequenced cases appeared to be locally acquired and were concordant with predictions from the ABM. These high-resolution genomic data are crucial to track cases with locally acquired COVID-19 and for timely recognition of independent importations once border restrictions are lifted and trade and travel resume.The combination of nearly real-time genome sequencing of SARS-CoV-2 in infected patients during the first 10 weeks of COVID-19 containment in Australia and epidemiological modeling is helping in understanding the dynamics of the COVID-19 pandemic and potentially guiding public health decisions.