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

Autor: 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, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA., 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, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA., 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, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA., 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 Regenerative Medicine, 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., 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., Spencer EG; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA., Hufbauer EC; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA., Lee JJ; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA., King AJ; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA., Ramesh KS; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA., Nguyen KN; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA., Saucedo K; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA., Robles-Sikisaka R; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA., Fisch KM; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA., Gonias SL; Department of Pathology, University of California, San Diego, La Jolla, CA, USA., Birmingham A; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA., McDonald D; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA., Karthikeyan S; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA., Martin NK; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA., Schooley RT; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA., Negrete AJ; Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico., Reyna HJ; Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico., Chavez JR; Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico., Garcia ML; Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico., Cornejo-Bravo JM; Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico., Becker D; Helix, San Mateo, CA, USA., Isaksson M; Helix, San Mateo, CA, USA., Washington NL; Helix, San Mateo, CA, USA., Lee W; Helix, San Mateo, CA, USA., Garfein RS; Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA., Luna-Ruiz Esparza MA; Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico., Alcántar-Fernández J; Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico., Henson B; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA., Jepsen K; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA., Olivares-Flores B; Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico., Barrera-Badillo G; Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico., Lopez-Martínez I; Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico., Ramírez-González JE; Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico., Flores-León R; Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico., Kingsmore SF; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA., Sanders A; Return to Learn, University of California, San Diego, La Jolla, CA, USA., Pradenas A; Return to Learn, University of California, San Diego, La Jolla, CA, USA., White B; Return to Learn, University of California, San Diego, La Jolla, CA, USA., Matthews G; Return to Learn, University of California, San Diego, La Jolla, CA, USA., Hale M; Return to Learn, University of California, San Diego, La Jolla, CA, USA., McLawhon RW; Return to Learn, University of California, San Diego, La Jolla, CA, USA., Reed SL; Return to Learn, University of California, San Diego, La Jolla, CA, USA., Winbush T; Return to Learn, University of California, San Diego, La Jolla, CA, USA., McHardy IH; Scripps Health, La Jolla, San Diego, CA, USA., Fielding RA; Scripps Health, La Jolla, San Diego, CA, USA., Nicholson L; Scripps Health, La Jolla, San Diego, CA, USA., Quigley MM; Scripps Health, La Jolla, San Diego, CA, USA., Harding A; Sharp Healthcare, San Diego, CA, USA., Mendoza A; Sharp Healthcare, San Diego, CA, USA., Bakhtar O; Sharp Healthcare, San Diego, CA, USA., Browne SH; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA; Specialist in Global Health, Encinitas, CA, USA., Olivas Flores J; Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico; University of HealthMx, Tijuana, Baja California, Mexico., Rincon Rodríguez DG; University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico., Gonzalez Ibarra M; University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico., Robles Ibarra LC; University of HealthMx, Tijuana, Baja California, Mexico; Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tijuana, Baja California, Mexico., Arellano Vera BJ; University of HealthMx, Tijuana, Baja California, Mexico; Instituto Mexicano del Seguro Social, Tijuana, Baja California, Mexico., Gonzalez Garcia J; University of HealthMx, Tijuana, Baja California, Mexico; SIMNSA, Tijuana, Baja California, Mexico., Harvey-Vera A; University of California, San Diego, La Jolla, CA, USA., Knight R; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Laurent LC; 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 Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA., Yeo GW; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA., Wertheim JO; Department of Medicine, University of California, San Diego, La Jolla, CA, USA., Ji X; Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA., Worobey M; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA., Suchard MA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA., Andersen KG; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA. Electronic address: andersen@scripps.edu., Campos-Romero A; Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico., Wohl S; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA., Zeller M; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA. Electronic address: zellerm@scripps.edu.

Publikováno v: Cell [Cell] 2023 Dec 21; Vol. 186 (26), pp. 5690-5704.e20. Date of Electronic Publication: 2023 Dec 14.