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Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics.
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.
Afiliação
  • Matteson NL; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA. Electronic address: natem@scripps.edu.
  • Hassler GW; Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
  • Kurzban E; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
  • Schwab MA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
  • Perkins SA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
  • Gangavarapu K; Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
  • Levy JI; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
  • Parker E; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
  • Pride D; Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
  • Hakim A; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation
  • De Hoff P; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation
  • Cheung W; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation
  • Castro-Martinez A; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerativ
  • Rivera A; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Veder A; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Rivera A; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Wauer C; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Holmes J; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Wilson J; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Ngo SN; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Plascencia A; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Lawrence ES; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Smoot EW; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Eisner ER; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Tsai R; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Chacón M; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Baer NA; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Seaver P; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Salido RA; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Aigner S; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Ngo TT; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Barber T; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Ostrander T; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Fielding-Miller R; Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA.
  • Simmons EH; Academic Affairs, University of California, San Diego, La Jolla, CA, USA.
  • Zazueta OE; Department of Epidemiology, Secretaria de Salud de Baja California, Tijuana, Baja California, Mexico.
  • Serafin-Higuera I; Centro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico.
  • Sanchez-Alavez M; Centro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico; Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
  • Moreno-Camacho JL; Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico.
  • García-Gil A; Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico.
  • Murphy Schafer AR; County of San Diego Health and Human Services Agency, San Diego, CA, USA.
  • McDonald E; County of San Diego Health and Human Services Agency, San Diego, CA, USA.
  • Corrigan J; County of San Diego Health and Human Services Agency, San Diego, CA, USA.
  • Malone JD; County of San Diego Health and Human Services Agency, San Diego, CA, USA.
  • Stous S; County of San Diego Health and Human Services Agency, San Diego, CA, USA.
  • Shah S; County of San Diego Health and Human Services Agency, San Diego, CA, USA.
  • Moshiri N; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
  • Weiss A; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
  • Anderson C; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
  • Aceves CM; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Cell ; 186(26): 5690-5704.e20, 2023 12 21.
Article em En | MEDLINE | ID: mdl-38101407
ABSTRACT
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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: COVID-19 Limite: Humans Idioma: En Revista: Cell Ano de publicação: 2023 Tipo de documento: Article
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PubMed Links
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: COVID-19 Limite: Humans Idioma: En Revista: Cell Ano de publicação: 2023 Tipo de documento: Article