Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City.
Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City.
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DOI：
10.1371/journal.ppat.1009571
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发表时间：
2021-05
期刊：
影响因子：
6.7
通讯作者：
Heguy A
中科院分区：
文献类型：
--
作者：
Dellicour S;Hong SL;Vrancken B;Chaillon A;Gill MS;Maurano MT;Ramaswami S;Zappile P;Marier C;Harkins GW;Baele G;Duerr R;Heguy A
在COVID-19疫情的第一阶段，纽约市迅速成为美国疫情的中心。虽然分子系统发育分析先前强调了纽约市内的多次引入和一段时间的神秘社区传播，但对SARS-CoV-2在其行政区内和行政区之间的传播知之甚少。我们在这里进行地理调查，以深入了解纽约市疫情爆发的头几个月病毒谱系的传播情况。我们的分析描述了在国家和城市层面的病毒谱系的传播动态，说明周边的样本可能对应于不同的传播事件起源于主要的大都市地区。与该地区记录的高流行率一致，我们的研究结果突出了皇后区作为传播中心的相对重要的作用，该中心与较高的局部循环和病毒谱系向周围行政区的传播相关。在流行病的背景下，对病毒基因组的分析可用于在空间和时间上联系传染病病例。当采样足够密集时，可以进行系统地理调查，以获得病毒谱系的传播历史和动态的估计。在我们的研究中，我们利用从纽约州采样的SARS-CoV-2基因组的综合数据集，分析2020年春季期间病毒的传播情况。我们特别关注当时美国疫情的震中纽约市，以解开病毒谱系在其五个行政区之间的传播，这往往证实了皇后区在整个传播链中的相对重要性。从方法论的角度来看，我们的研究说明了如何利用精细的地理分析来深入了解当地病毒流行病的流行病学动态，这是及时的，但也是标准流行病学方法的补充工具。
During the first phase of the COVID-19 epidemic, New York City rapidly became the epicenter of the pandemic in the United States. While molecular phylogenetic analyses have previously highlighted multiple introductions and a period of cryptic community transmission within New York City, little is known about the circulation of SARS-CoV-2 within and among its boroughs. We here perform phylogeographic investigations to gain insights into the circulation of viral lineages during the first months of the New York City outbreak. Our analyses describe the dispersal dynamics of viral lineages at the state and city levels, illustrating that peripheral samples likely correspond to distinct dispersal events originating from the main metropolitan city areas. In line with the high prevalence recorded in this area, our results highlight the relatively important role of the borough of Queens as a transmission hub associated with higher local circulation and dispersal of viral lineages toward the surrounding boroughs. In the context of epidemics, analyses of viral genomes can be used to link infectious cases in space and time. When the sampling is dense enough, phylogeographic investigations can be performed to obtain estimates of the dispersal history and dynamics of viral lineages. In our study, we take advantage of a comprehensive data set of SARS-CoV-2 genomes sampled from New York State to analyze the circulation of the virus during spring 2020. In particular, we focus on New York City, then the epicenter of the United States epidemic, to unravel the dispersal of viral lineages among its five boroughs, which tends to confirm the relative importance of the Queens area in the overall transmission chain. From a methodological point of view, our study illustrates how fine-scale phylogeographic analyses can be exploited to gain insight into the epidemiological dynamic of local viral epidemics, which constitute timely but also complementary tool to standard epidemiological approaches.
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影响因子：
4.3
作者：
Kalkauskas A;Perron U;Sun Y;Goldman N;Baele G;Guindon S;De Maio N
通讯作者：
De Maio N
SARS-COV-2血统的估计可传播和影响B.1.1.7在英国。
DOI：
10.1126/science.abg3055
发表时间：
2021-04-09
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Davies NG;Abbott S;Barnard RC;Jarvis CI;Kucharski AJ;Munday JD;Pearson CAB;Russell TW;Tully DC;Washburne AD;Wenseleers T;Gimma A;Waites W;Wong KLM;van Zandvoort K;Silverman JD;CMMID COVID-19 Working Group;COVID-19 Genomics UK (COG-UK) Consortium;Diaz-Ordaz K;Keogh R;Eggo RM;Funk S;Jit M;Atkins KE;Edmunds WJ
通讯作者：
Edmunds WJ
影响因子：
10.7
作者：
Dellicour S;Durkin K;Hong SL;Vanmechelen B;Martí-Carreras J;Gill MS;Meex C;Bontems S;André E;Gilbert M;Walker C;Maio N;Faria NR;Hadfield J;Hayette MP;Bours V;Wawina-Bokalanga T;Artesi M;Baele G;Maes P
通讯作者：
Maes P
影响因子：
5.3
作者：
Trovão NS;Baele G;Vrancken B;Bielejec F;Suchard MA;Fargette D;Lemey P
通讯作者：
Lemey P
影响因子：
5.3
作者：
Sagulenko P;Puller V;Neher RA
通讯作者：
Neher RA