Matteson Nathaniel L, Hassler Gabriel W, Kurzban Ezra, Schwab Madison A, Perkins Sarah A, Gangavarapu Karthik, Levy Joshua I, Parker Edyth, Pride David, Hakim Abbas, De Hoff Peter, Cheung Willi, Castro-Martinez Anelizze, Rivera Andrea, Veder Anthony, Rivera Ariana, Wauer Cassandra, Holmes Jacqueline, Wilson Jedediah, Ngo Shayla N, Plascencia Ashley, Lawrence Elijah S, Smoot Elizabeth W, Eisner Emily R, Tsai Rebecca, Chacón Marisol, Baer Nathan A, Seaver Phoebe, Salido Rodolfo A, Aigner Stefan, Ngo Toan T, Barber Tom, Ostrander Tyler, Fielding-Miller Rebecca, Simmons Elizabeth H, Zazueta Oscar E, Serafin-Higuera Idanya, Sanchez-Alavez Manuel, Moreno-Camacho Jose L, García-Gil Abraham, Murphy Schafer Ashleigh R, McDonald Eric, Corrigan Jeremy, Malone John D, Stous Sarah, Shah Seema, Moshiri Niema, Weiss Alana, Anderson Catelyn, Aceves Christine M, Spencer Emily G, Hufbauer Emory C, Lee Justin J, King Alison J, Ramesh Karthik S, Nguyen Kelly N, Saucedo Kieran, Robles-Sikisaka Refugio, Fisch Kathleen M, Gonias Steven L, Birmingham Amanda, McDonald Daniel, Karthikeyan Smruthi, Martin Natasha K, Schooley Robert T, Negrete Agustin J, Reyna Horacio J, Chavez Jose R, Garcia Maria L, Cornejo-Bravo Jose M, Becker David, Isaksson Magnus, Washington Nicole L, Lee William, Garfein Richard S, Luna-Ruiz Esparza Marco A, Alcántar-Fernández Jonathan, Henson Benjamin, Jepsen Kristen, Olivares-Flores Beatriz, Barrera-Badillo Gisela, Lopez-Martínez Irma, Ramírez-González José E, Flores-León Rita, Kingsmore Stephen F, Sanders Alison, Pradenas Allorah, White Benjamin, Matthews Gary, Hale Matt, McLawhon Ronald W, Reed Sharon L, Winbush Terri, McHardy Ian H, Fielding Russel A, Nicholson Laura, Quigley Michael M, Harding Aaron, Mendoza Art, Bakhtar Omid, Browne Sara H, Olivas Flores Jocelyn, Rincon Rodríguez Diana G, Gonzalez Ibarra Martin, Robles Ibarra Luis C, Arellano Vera Betsy J, Gonzalez Garcia Jonathan, Harvey-Vera Alicia, Knight Rob, Laurent Louise C, Yeo Gene W, Wertheim Joel O, Ji Xiang, Worobey Michael, Suchard Marc A, Andersen Kristian G, Campos-Romero Abraham, Wohl Shirlee, Zeller Mark
Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
Cell. 2023 Dec 21;186(26):5690-5704.e20. doi: 10.1016/j.cell.2023.11.024. Epub 2023 Dec 14.
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.
在过去十年中，基因组监测的成熟使得对疫情的出现和传播进行追踪达到了前所未有的水平。例如，在新冠疫情期间，基因组数据显示，由于新冠疫情防控措施和人员流动变化的综合影响，各地疫情在严重急性呼吸综合征冠状病毒2（SARS-CoV-2）谱系输入频率和持续时间方面存在很大差异。在此，我们表明，本地新冠疫情是由区域传播驱动的，包括跨国传播，但在公共卫生干预措施放松后，可能会与遥远地区的联系日益增加。通过整合基因组、流动性和流行病学数据，我们发现，在动态流动模式的支持下，相邻地区和遥远地区之间都存在大量传播。我们发现，连通性的变化显著影响本地新冠疫情的发病率。我们的研究结果表明，在调查相互关联的疫情时，“本地”具有复杂的含义，并强调了合作干预措施对疫情预防和缓解的重要性。
