Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics
Authors: 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 , Hoff Peter De , 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. , 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. , Flores Jocelyn Olivas , Rincon Rodríguez Diana G. , Ibarra Martin Gonzalez , Robles Ibarra Luis C. , Arellano Vera Betsy J. , Garcia Jonathan Gonzalez , 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 
Published: March 2023

SummaryThe 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 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.