Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics

Nathaniel L. Matteson, Gabriel W. Hassler, Ezra Kurzban, Madison A. Schwab, Sarah A. Perkins, Karthik Gangavarapu, Joshua I. Levy, Edyth Parker, David Pride, Abbas Hakim, Peter De Hoff, Willi Cheung, Anelizze Castro-Martinez, Andrea Rivera, Anthony Veder, Ariana Rivera, Cassandra Wauer, Jacqueline Holmes, Jedediah Wilson, Shayla N. NgoAshley Plascencia, Elijah S. Lawrence, Elizabeth W. Smoot, Emily R. Eisner, Rebecca Tsai, Marisol Chacón, Nathan A. Baer, Phoebe Seaver, Rodolfo A. Salido, Stefan Aigner, Toan T. Ngo, Tom Barber, Tyler Ostrander, Rebecca Fielding-Miller, Elizabeth H. Simmons, Oscar E. Zazueta, Idanya Serafin-Higuera, Manuel Sanchez-Alavez, Jose L. Moreno-Camacho, Abraham García-Gil, Ashleigh R. Murphy Schafer, Eric McDonald, Jeremy Corrigan, John D. Malone, Sarah Stous, Seema Shah, Niema Moshiri, Alana Weiss, Catelyn Anderson, Christine M. Aceves, Emily G. Spencer, Emory C. Hufbauer, Justin J. Lee, Alison J. King, Karthik S. Ramesh, Kelly N. Nguyen, Kieran Saucedo, Refugio Robles-Sikisaka, Kathleen M. Fisch, Steven L. Gonias, Amanda Birmingham, Daniel McDonald, Smruthi Karthikeyan, Natasha K. Martin, Robert T. Schooley, Agustin J. Negrete, Horacio J. Reyna, Jose R. Chavez, Maria L. Garcia, Jose M. Cornejo-Bravo, David Becker, Magnus Isaksson, Nicole L. Washington, William Lee, Richard S. Garfein, Marco A. Luna-Ruiz Esparza, Jonathan Alcántar-Fernández, Benjamin Henson, Kristen Jepsen, Beatriz Olivares-Flores, Gisela Barrera-Badillo, Irma Lopez-Martínez, José E. Ramírez-González, Rita Flores-León, Stephen F. Kingsmore, Alison Sanders, Allorah Pradenas, Benjamin White, Gary Matthews, Matt Hale, Ronald W. McLawhon, Sharon L. Reed, Terri Winbush, Ian H. McHardy, Russel A. Fielding, Laura Nicholson, Michael M. Quigley, Aaron Harding, Art Mendoza, Omid Bakhtar, Sara H. Browne, Jocelyn Olivas Flores, Diana G. Rincon Rodríguez, Martin Gonzalez Ibarra, Luis C. Robles Ibarra, Betsy J. Arellano Vera, Jonathan Gonzalez Garcia, Alicia Harvey-Vera, Rob Knight, Louise C. Laurent, Gene W. Yeo, Joel O. Wertheim, Xiang Ji, Michael Worobey, Marc A. Suchard, Kristian G. Andersen, Abraham Campos-Romero, Shirlee Wohl, Mark Zeller

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)5690-5704.e20
Issue number26
StatePublished - 21 Dec 2023
Externally publishedYes


  • COVID-19
  • SARS-CoV-2
  • genomic epidemiology
  • mobility
  • phylogenetics
  • travel restrictions
  • viral sequencing


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