Evidence map›Paper›PMID 38101407›Full record

ArticleCell2023

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 and 109 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

9 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

119 authors.

Nathaniel L MattesonDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA. Electronic address: natem@scripps.edu.
Gabriel W HasslerDepartment of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
Ezra KurzbanDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Madison A SchwabDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Sarah A PerkinsDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Karthik GangavarapuDepartment 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.
Joshua I LevyDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Edyth ParkerDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
David PrideDepartment of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
Abbas HakimExpedited 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.
Peter De HoffExpedited 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.
Willi CheungExpedited 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.
Anelizze Castro-MartinezExpedited 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.
Andrea RiveraExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Anthony VederExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Ariana RiveraExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Cassandra WauerExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Jacqueline HolmesExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Jedediah WilsonExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Shayla N NgoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Ashley PlascenciaExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Elijah S LawrenceExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Elizabeth W SmootExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Emily R EisnerExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Rebecca TsaiExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Marisol ChacónExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Nathan A BaerExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Phoebe SeaverExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Rodolfo A SalidoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Stefan AignerExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Toan T NgoExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Tom BarberExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Tyler OstranderExpedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Rebecca Fielding-MillerHerbert 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.
Elizabeth H SimmonsAcademic Affairs, University of California, San Diego, La Jolla, CA, USA.
Oscar E ZazuetaDepartment of Epidemiology, Secretaria de Salud de Baja California, Tijuana, Baja California, Mexico.
Idanya Serafin-HigueraCentro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico.
Manuel Sanchez-AlavezCentro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico; Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
Jose L Moreno-CamachoClinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico.
Abraham García-GilClinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico.
Ashleigh R Murphy SchaferCounty of San Diego Health and Human Services Agency, San Diego, CA, USA.
Eric McDonaldCounty of San Diego Health and Human Services Agency, San Diego, CA, USA.
Jeremy CorriganCounty of San Diego Health and Human Services Agency, San Diego, CA, USA.
John D MaloneCounty of San Diego Health and Human Services Agency, San Diego, CA, USA.
Sarah StousCounty of San Diego Health and Human Services Agency, San Diego, CA, USA.
Seema ShahCounty of San Diego Health and Human Services Agency, San Diego, CA, USA.
Niema MoshiriDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Alana WeissDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Catelyn AndersonDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Christine M AcevesDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Emily G SpencerDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Emory C HufbauerDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Justin J LeeDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Alison J KingDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Karthik S RameshDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Kelly N NguyenDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Kieran SaucedoDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Refugio Robles-SikisakaDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Kathleen M FischDepartment 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.
Steven L GoniasDepartment of Pathology, University of California, San Diego, La Jolla, CA, USA.
Amanda BirminghamDepartment of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Daniel McDonaldDepartment of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Smruthi KarthikeyanDepartment of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Natasha K MartinDivision of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA.
Robert T SchooleyDivision of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA.
Agustin J NegreteFacultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico.
Horacio J ReynaFacultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico.
Jose R ChavezFacultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico.
Maria L GarciaFacultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico.
Jose M Cornejo-BravoFacultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico.
David BeckerHelix, San Mateo, CA, USA.
Magnus IsakssonHelix, San Mateo, CA, USA.
Nicole L WashingtonHelix, San Mateo, CA, USA.
William LeeHelix, San Mateo, CA, USA.
Richard S GarfeinHerbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA.
Marco A Luna-Ruiz EsparzaInnovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico.
Jonathan Alcántar-FernándezInnovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico.
Benjamin HensonInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
Kristen JepsenInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
Beatriz Olivares-FloresInstituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico.
Gisela Barrera-BadilloInstituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico.
Irma Lopez-MartínezInstituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico.
José E Ramírez-GonzálezInstituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico.
Rita Flores-LeónInstituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico.
Stephen F KingsmoreRady Children's Institute for Genomic Medicine, San Diego, CA, USA.
Alison SandersReturn to Learn, University of California, San Diego, La Jolla, CA, USA.
Allorah PradenasReturn to Learn, University of California, San Diego, La Jolla, CA, USA.
Benjamin WhiteReturn to Learn, University of California, San Diego, La Jolla, CA, USA.
Gary MatthewsReturn to Learn, University of California, San Diego, La Jolla, CA, USA.
Matt HaleReturn to Learn, University of California, San Diego, La Jolla, CA, USA.
Ronald W McLawhonReturn to Learn, University of California, San Diego, La Jolla, CA, USA.
Sharon L ReedReturn to Learn, University of California, San Diego, La Jolla, CA, USA.
Terri WinbushReturn to Learn, University of California, San Diego, La Jolla, CA, USA.
Ian H McHardyScripps Health, La Jolla, San Diego, CA, USA.
Russel A FieldingScripps Health, La Jolla, San Diego, CA, USA.
Laura NicholsonScripps Health, La Jolla, San Diego, CA, USA.
Michael M QuigleyScripps Health, La Jolla, San Diego, CA, USA.
Aaron HardingSharp Healthcare, San Diego, CA, USA.
Art MendozaSharp Healthcare, San Diego, CA, USA.
Omid BakhtarSharp Healthcare, San Diego, CA, USA.
Sara H BrowneDivision of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA; Specialist in Global Health, Encinitas, CA, USA.
Jocelyn Olivas FloresFacultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico; University of HealthMx, Tijuana, Baja California, Mexico.
Diana G Rincon RodríguezUniversity of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico.
Martin Gonzalez IbarraUniversity of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico.
Luis C Robles IbarraUniversity of HealthMx, Tijuana, Baja California, Mexico; Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tijuana, Baja California, Mexico.
Betsy J Arellano VeraUniversity of HealthMx, Tijuana, Baja California, Mexico; Instituto Mexicano del Seguro Social, Tijuana, Baja California, Mexico.
Jonathan Gonzalez GarciaUniversity of HealthMx, Tijuana, Baja California, Mexico; SIMNSA, Tijuana, Baja California, Mexico.
Alicia Harvey-VeraUniversity of California, San Diego, La Jolla, CA, USA.
Rob KnightDepartment 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.
Louise C LaurentExpedited 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.
Gene W YeoExpedited 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.
Joel O WertheimDepartment of Medicine, University of California, San Diego, La Jolla, CA, USA.
Xiang JiDepartment of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA.
Michael WorobeyDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
Marc A SuchardDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
Kristian G AndersenDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA. Electronic address: andersen@scripps.edu.
Abraham Campos-RomeroInnovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico.
Shirlee WohlDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
Mark ZellerDepartment of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA. Electronic address: zellerm@scripps.edu.

Funding

Technology CoreU19AI135995 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Kristian Graugaard Andersen · 2018 to 2026
$32.0M
Scripps Translational Science InstituteUL1TR002550 · NCATS · SCRIPPS RESEARCH INSTITUTE, THE · PI TOPOL, ERIC JEFFREY · 2018 to 2022
$28.9M
Scripps Clinical and Translational Science HubUM1TR004407 · NCATS · SCRIPPS RESEARCH INSTITUTE, THE · PI Eric Jeffrey Topol · 2023 to 2026
$24.2M
West African Emerging Infectious Disease Research Center (WA-EIDRC)U01AI151812 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI ANDERSEN, KRISTIAN GRAUGAARD, GARRY, ROBERT F · 2020 to 2024
$13.2M
Statistical Innovation to Integrate Sequences and Phenotypes for Scalable Phylodynamic InferenceR01AI153044 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Marc A. Suchard · 2021 to 2026
$2.4M
SASEAU01HD108787 · NICHD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FIELDING-MILLER, REBECCA KATHLEEN · 2022 to 2023
$2.4M
Scalable Inference in Statistical Models of Viral Evolution and Human HealthF31AI154824 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI HASSLER, GABRIEL WILLIAM · 2021 to 2022
$64k
NCATS NIH HHS UL1 TR002550NCATS NIH HHS UM1 TR004407NIAID NIH HHS F31 AI154824NIAID NIH HHS R01 AI153044NIAID NIH HHS U01 AI151812NIAID NIH HHS U19 AI135995NICHD NIH HHS U01 HD108787
6 · The paper itself

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.

Indexed as

COVID-19GenomicsGeographyHumansInfection ControlPandemicsPublic HealthSARS-CoV-2COVID-19genomic epidemiologymobilityphylogeneticsSARS-CoV-2travel restrictionsviral sequencing

Identifiers

PMID38101407
PMCPMC10795731

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.