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

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

作者单位：Rady Children?ˉs Institute for Genomic MedicineExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoUniHealthMx||Instituto de Seguridad y Servicios Sociales de los Trabajadores del EstadoHerbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego||Division of Infectious Disease and Global Public Health, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoReturn to Learn, University of California San DiegoInstituto de Diagn¨?stico y Referencia Epidemiol¨?gicos (InDRE)Instituto de Diagn¨?stico y Referencia Epidemiol¨?gicos (InDRE)Instituto de Diagn¨?stico y Referencia Epidemiol¨?gicos (InDRE)UniHealthMx||SIMNSADepartment of Pediatrics, University of California San Diego||Department of Computer Science and Engineering, University of California San Diego||Department of Bioengineering, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoCounty of San Diego Health and Human Services AgencyDepartment of Immunology and Microbiology, Scripps ResearchDepartment of Immunology and Microbiology, Scripps ResearchDepartment of Immunology and Microbiology, Scripps ResearchDepartment of Pathology, University of California San DiegoDepartment of Pediatrics, University of California San DiegoDivision of Infectious Disease and Global Public Health, University of California San DiegoDivision of Infectious Disease and Global Public Health, University of California San DiegoFacultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las PalmasFacultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja CaliforniaHelix, San MateoHelix, San MateoHelix, San MateoInnovation and Research DepartmentInnovation and Research DepartmentInstitute for Genomic Medicine, University of California San DiegoAcademic Affairs, University of California San DiegoCentro de Diagnostico COVID-19 UABC TijuanaCounty of San Diego Health and Human Services AgencyCounty of San Diego Health and Human Services AgencyDepartment of Computer Science and Engineering, University of California San DiegoDepartment of Immunology and Microbiology, Scripps ResearchUniHealthMx||Facultad de Medicina, Universidad XochicalcoDepartment of Mathematics, School of Science and Engineering, Tulane UniversityDepartment of Human Genetics, University of CaliforniaInnovation and Research DepartmentReturn to Learn, University of California San DiegoReturn to Learn, University of California San DiegoScripps HealthSharp HealthcareSharp HealthcareUniHealthMx||Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja CaliforniaUniHealthMx||Facultad de Medicina, Universidad XochicalcoDepartment of Immunology and Microbiology, Scripps ResearchDepartment of Immunology and Microbiology, Scripps ResearchDepartment of Immunology and Microbiology, Scripps ResearchExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego||Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego||Sanford Consortium of Regenerative Medicine, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoInstituto de Diagn¨?stico y Referencia Epidemiol¨?gicos (InDRE)Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoDepartment of Computational Medicine, University of CaliforniaDepartment of Pediatrics, University of California San DiegoCounty of San Diego Health and Human Services AgencyExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoDepartment of Immunology and Microbiology, Scripps ResearchDepartment of Biomathematics, David Geffen School of Medicine at UCLA, University of California||Department of Immunology and Microbiology, Scripps ResearchDepartment of Immunology and Microbiology, Scripps ResearchExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoDepartment of Immunology and Microbiology, Scripps ResearchHelix, San MateoDepartment of Ecology and Evolutionary Biology, University of ArizonaExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoUniversity of California San DiegoReturn to Learn, University of California San DiegoScripps HealthFacultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las PalmasExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego||Sanford Consortium of Regenerative Medicine, University of California San Diego||Department of Cellular and Molecular Medicine, University of California San DiegoDepartment of Epidemiology. Secretaria de Salud de Baja CaliforniaHerbert Wertheim School of Public Health and Human Longevity Science, University of California San DiegoSharp HealthcareReturn to Learn, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoSpecialist in Global Health||Division of Infectious Disease and Global Public Health, University of California San DiegoDepartment of Immunology and Microbiology, Scripps ResearchExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego||Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego||COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public HealthDepartment of Immunology and Microbiology, Scripps ResearchDepartment of Pediatrics, University of California San DiegoDepartment of Immunology and Microbiology, Scripps ResearchScripps HealthDepartment of Immunology and Microbiology, Scripps ResearchDepartment of Immunology and Microbiology, Scripps ResearchCentro de Diagnostico COVID-19 UABC Tijuana||Department of Molecular Medicine, Scripps ResearchExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoUniHealthMx||Instituto Mexicano del Seguro SocialCounty of San Diego Health and Human Services AgencyClinical Laboratory DepartmentScripps HealthDepartment of Immunology and Microbiology, Scripps ResearchDepartment of Immunology and Microbiology, Scripps ResearchInstitute for Genomic Medicine, University of California San DiegoInstituto de Diagn¨?stico y Referencia Epidemiol¨?gicos (InDRE)Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego||Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego||COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public HealthDepartment of Pathology, University of California San Diego||Department of Medicine, University of California San DiegoDepartment of Medicine, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego||Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego||COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public HealthReturn to Learn, University of California San DiegoReturn to Learn, University of California San DiegoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San DiegoClinical Laboratory DepartmentReturn to Learn, University of California San DiegoCounty of San Diego Health and Human Services AgencyFacultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las PalmasDepartment of Immunology and Microbiology, Scripps ResearchFacultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las PalmasDepartment of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego||Center for Computational Biology and Bioinformatics, University of California San DiegoDepartment of Immunology and Microbiology, Scripps ResearchExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego||Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego||Sanford Consortium of Regenerative Medicine, University of California San Diego

DOI：10.1101/2023.03.14.23287217

学科分类：医学研究方法预防医学生物科学研究方法、生物科学研究技术

英文关键词：SARS-CoV-2genomic epidemiologyphylogeneticsmobilitytravel restrictionsviral sequencing

推荐引用：Kingsmore Stephen F.,Ngo Toan T.,Ostrander Tyler,Wauer Cassandra,Robles Ibarra Luis C.,Fielding-Miller Rebecca,Rivera Ariana,Pradenas Allorah,Barrera-Badillo Gisela,Lopez-Mart¨anez Irma,Flores-Le¨?n Rita,Garcia Jonathan Gonzalez,Knight Rob,Lawrence Elijah S.,Smoot Elizabeth W.,Eisner Emily R.,Tsai Rebecca,Chac¨?n Marisol,Baer Nathan A.,Barber Tom,Shah Seema,Lee Justin J.,Ramesh Karthik S.,Saucedo Kieran,Gonias Steven L.,McDonald Daniel,Martin Natasha K.,Schooley Robert T.,Chavez Jose R.,Cornejo-Bravo Jose M.,Becker David,Isaksson Magnus,Washington Nicole L.,Luna-Ruiz Esparza Marco A.,Alc¨￠ntar-Fern¨￠ndez Jonathan,Jepsen Kristen,Simmons Elizabeth H.,Serafin-Higuera Idanya,Corrigan Jeremy,Malone John D.,Moshiri Niema,Anderson Catelyn,Rincon Rodr¨aguez Diana G.,Ji Xiang,Suchard Marc A.,Campos-Romero Abraham,McLawhon Ronald W.,Winbush Terri,Quigley Michael M.,Harding Aaron,Bakhtar Omid,Flores Jocelyn Olivas,Ibarra Martin Gonzalez,Kurzban Ezra,Schwab Madison A.,Levy Joshua I.,Castro-Martinez Anelizze,Holmes Jacqueline,Ram¨arez-Gonz¨￠lez Jos¨| E.,Seaver Phoebe,Hassler Gabriel W.,Karthikeyan Smruthi,Stous Sarah,Rivera Andrea,Zeller Mark,Gangavarapu Karthik,Robles-Sikisaka Refugio,Veder Anthony,Wohl Shirlee,Lee William,Worobey Michael,Aigner Stefan,Harvey-Vera Alicia,Matthews Gary,Fielding Russel A.,Garcia Maria L.,Yeo Gene W.,Zazueta Oscar E.,Garfein Richard S.,Mendoza Art,Hale Matt,Plascencia Ashley,Wilson Jedediah,Browne Sara H.,Aceves Christine M.,Hoff Peter De,Spencer Emily G.,Birmingham Amanda,Parker Edyth,Nicholson Laura,Perkins Sarah A.,Matteson Nathaniel L.,Sanchez-Alavez Manuel,Salido Rodolfo A.,Arellano Vera Betsy J.,Murphy Schafer Ashleigh R.,Garc¨aa-Gil Abraham,McHardy Ian H.,Weiss Alana,Nguyen Kelly N.,Henson Benjamin,Olivares-Flores Beatriz,Hakim Abbas,Pride David,Wertheim Joel O.,Cheung Willi,White Benjamin,Sanders Alison,Ngo Shayla N.,Moreno-Camacho Jose L.,Reed Sharon L.,McDonald Eric,Reyna Horacio J.,Andersen Kristian G.,Negrete Agustin J.,Fisch Kathleen M.,Hufbauer Emory C.,Laurent Louise C..Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics[EB/OL].(2025-03-28)[2025-06-15].https://www.medrxiv.org/content/10.1101/2023.03.14.23287217.点此复制