Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residencesResearch in context
Summary: Background: Congregate living provides an ideal setting for SARS-CoV-2 transmission in which many outbreaks and superspreading events occurred. To avoid large outbreaks, universities turned to remote operations during the initial COVID-19 pandemic waves in 2020 and 2021. In late-2021, the...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-06-01
|
| Series: | EBioMedicine |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352396425001732 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849728177313677312 |
|---|---|
| author | Joel O. Wertheim Tetyana I. Vasylyeva Robert J. Wood Kalen Cantrell Soraya Piña Contreras Aryeh Feldheim Ravi Goyal Jennifer L. Havens Rob Knight Louise C. Laurent Niema Moshiri Robert Neuhard Shashank Sathe Alysson Satterlund Angela Scioscia Angela Y. Song Robert T. Schooley Cheryl M. Anderson Natasha K. Martin Stefan Aigner Kristian G. Andersen Nathan A. Baer Maryann Betty Amanda Birmingham Anelizze Castro-Martinez Willi Cheung Peter De Hoff Kathleen M. Fisch Alison J. King Karthik Gangavarapu Abbas Hakim Benjamin Henson Kristen Jepsen Christina H. Mac Toan T. Ngo Kelly N. Nguyen Tyler R. Ostrander Sarah Perkins Ashley Plascencia Andrea Rivera Ariana Rivera Rodolfo A. Salido Kieran C. Saucedo Madison Schwab Allison L. Steedman Anthony Veder Alana Weiss Gene W. Yeo Mark Zeller |
| author_facet | Joel O. Wertheim Tetyana I. Vasylyeva Robert J. Wood Kalen Cantrell Soraya Piña Contreras Aryeh Feldheim Ravi Goyal Jennifer L. Havens Rob Knight Louise C. Laurent Niema Moshiri Robert Neuhard Shashank Sathe Alysson Satterlund Angela Scioscia Angela Y. Song Robert T. Schooley Cheryl M. Anderson Natasha K. Martin Stefan Aigner Kristian G. Andersen Nathan A. Baer Maryann Betty Amanda Birmingham Anelizze Castro-Martinez Willi Cheung Peter De Hoff Kathleen M. Fisch Alison J. King Karthik Gangavarapu Abbas Hakim Benjamin Henson Kristen Jepsen Christina H. Mac Toan T. Ngo Kelly N. Nguyen Tyler R. Ostrander Sarah Perkins Ashley Plascencia Andrea Rivera Ariana Rivera Rodolfo A. Salido Kieran C. Saucedo Madison Schwab Allison L. Steedman Anthony Veder Alana Weiss Gene W. Yeo Mark Zeller |
| author_sort | Joel O. Wertheim |
| collection | DOAJ |
| description | Summary: Background: Congregate living provides an ideal setting for SARS-CoV-2 transmission in which many outbreaks and superspreading events occurred. To avoid large outbreaks, universities turned to remote operations during the initial COVID-19 pandemic waves in 2020 and 2021. In late-2021, the University of California San Diego (UC San Diego) facilitated the return of students to campus with comprehensive testing, vaccination, masking, wastewater surveillance, and isolation policies. Methods: We performed molecular epidemiological and phylogeographic analysis of 4418 SARS-CoV-2 genomes sampled from UC San Diego students during the Omicron waves between December 2021 and September 2022, representing 58% of students with confirmed SARS-CoV-2 infection. We overlaid these analyses across on-campus residential information to assess the spread and persistence of SARS-CoV-2 within university residences. Findings: Within campus residences, SARS-CoV-2 transmission was frequent among students residing in the same room or suite. However, a quarter of pairs of suitemates with concurrent infections had distantly related viruses, suggesting separate sources of infection during periods of high incidence in the surrounding community. Students with concurrent infections residing in the same building were not at substantial increased probability of being members of the same transmission cluster. Genetic network and phylogeographic inference indicated that only between 3.1 and 12.4% of infections among students could be associated with transmission within buildings outside of individual suites. The only super-spreading event we detected was related to a large event outside campus residences. Interpretation: We found little evidence for sustained SARS-CoV-2 transmission within individual buildings, aside from students who resided in the same suite. Even in the face of heightened community transmission during the 2021–2022 Omicron waves, congregate living did not result in a heightened risk for SARS-CoV-2 transmission in the context of the multi-pronged mitigation strategy. Funding: SEARCH Alliance: Centers for Disease Control and Prevention (CDC) BAA (75D301-22-R-72097) and the Google Cloud Platform Research Credits Program. J.O.W.: NIH–NIAID (R01 AI135992). T.I.V.: Branco Weiss Fellowship and Newkirk Fellowship. L.L.: University of California San Diego. |
| format | Article |
| id | doaj-art-644046116f234a73a63a1d2b2fc3bc36 |
| institution | DOAJ |
| issn | 2352-3964 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | EBioMedicine |
| spelling | doaj-art-644046116f234a73a63a1d2b2fc3bc362025-08-20T03:09:37ZengElsevierEBioMedicine2352-39642025-06-0111610572910.1016/j.ebiom.2025.105729Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residencesResearch in contextJoel O. Wertheim0Tetyana I. Vasylyeva1Robert J. Wood2Kalen Cantrell3Soraya Piña Contreras4Aryeh Feldheim5Ravi Goyal6Jennifer L. Havens7Rob Knight8Louise C. Laurent9Niema Moshiri10Robert Neuhard11Shashank Sathe12Alysson Satterlund13Angela Scioscia14Angela Y. Song15Robert T. Schooley16Cheryl M. Anderson17Natasha K. Martin18Stefan AignerKristian G. AndersenNathan A. BaerMaryann BettyAmanda BirminghamAnelizze Castro-MartinezWilli CheungPeter De HoffKathleen M. FischAlison J. KingKarthik GangavarapuAbbas HakimBenjamin HensonKristen JepsenChristina H. MacToan T. NgoKelly N. NguyenTyler R. OstranderSarah PerkinsAshley PlascenciaAndrea RiveraAriana RiveraRodolfo A. SalidoKieran C. SaucedoMadison SchwabAllison L. SteedmanAnthony VederAlana WeissGene W. YeoMark ZellerDepartment of Medicine, University of California San Diego, La Jolla, CA, USA; Corresponding author.Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Population Health and Disease Prevention, University of California Irvine, Irvine, CA, USAHerbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USADepartment of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USAHerbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USAHerbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USADepartment of Medicine, University of California San Diego, La Jolla, CA, USABioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USADepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USASanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA; University of California San Diego, La Jolla, CA, USADepartment of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USAUniversity of California San Diego, La Jolla, CA, USASanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA; University of California San Diego, La Jolla, CA, USAUniversity of California San Diego, La Jolla, CA, USADepartment of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USAUniversity of California San Diego, La Jolla, CA, USADepartment of Medicine, University of California San Diego, La Jolla, CA, USAHerbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USADepartment of Medicine, University of California San Diego, La Jolla, CA, USASummary: Background: Congregate living provides an ideal setting for SARS-CoV-2 transmission in which many outbreaks and superspreading events occurred. To avoid large outbreaks, universities turned to remote operations during the initial COVID-19 pandemic waves in 2020 and 2021. In late-2021, the University of California San Diego (UC San Diego) facilitated the return of students to campus with comprehensive testing, vaccination, masking, wastewater surveillance, and isolation policies. Methods: We performed molecular epidemiological and phylogeographic analysis of 4418 SARS-CoV-2 genomes sampled from UC San Diego students during the Omicron waves between December 2021 and September 2022, representing 58% of students with confirmed SARS-CoV-2 infection. We overlaid these analyses across on-campus residential information to assess the spread and persistence of SARS-CoV-2 within university residences. Findings: Within campus residences, SARS-CoV-2 transmission was frequent among students residing in the same room or suite. However, a quarter of pairs of suitemates with concurrent infections had distantly related viruses, suggesting separate sources of infection during periods of high incidence in the surrounding community. Students with concurrent infections residing in the same building were not at substantial increased probability of being members of the same transmission cluster. Genetic network and phylogeographic inference indicated that only between 3.1 and 12.4% of infections among students could be associated with transmission within buildings outside of individual suites. The only super-spreading event we detected was related to a large event outside campus residences. Interpretation: We found little evidence for sustained SARS-CoV-2 transmission within individual buildings, aside from students who resided in the same suite. Even in the face of heightened community transmission during the 2021–2022 Omicron waves, congregate living did not result in a heightened risk for SARS-CoV-2 transmission in the context of the multi-pronged mitigation strategy. Funding: SEARCH Alliance: Centers for Disease Control and Prevention (CDC) BAA (75D301-22-R-72097) and the Google Cloud Platform Research Credits Program. J.O.W.: NIH–NIAID (R01 AI135992). T.I.V.: Branco Weiss Fellowship and Newkirk Fellowship. L.L.: University of California San Diego.http://www.sciencedirect.com/science/article/pii/S2352396425001732SARS-CoV-2UniversityPhylogeographyTransmission clusterMitigation |
| spellingShingle | Joel O. Wertheim Tetyana I. Vasylyeva Robert J. Wood Kalen Cantrell Soraya Piña Contreras Aryeh Feldheim Ravi Goyal Jennifer L. Havens Rob Knight Louise C. Laurent Niema Moshiri Robert Neuhard Shashank Sathe Alysson Satterlund Angela Scioscia Angela Y. Song Robert T. Schooley Cheryl M. Anderson Natasha K. Martin Stefan Aigner Kristian G. Andersen Nathan A. Baer Maryann Betty Amanda Birmingham Anelizze Castro-Martinez Willi Cheung Peter De Hoff Kathleen M. Fisch Alison J. King Karthik Gangavarapu Abbas Hakim Benjamin Henson Kristen Jepsen Christina H. Mac Toan T. Ngo Kelly N. Nguyen Tyler R. Ostrander Sarah Perkins Ashley Plascencia Andrea Rivera Ariana Rivera Rodolfo A. Salido Kieran C. Saucedo Madison Schwab Allison L. Steedman Anthony Veder Alana Weiss Gene W. Yeo Mark Zeller Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residencesResearch in context EBioMedicine SARS-CoV-2 University Phylogeography Transmission cluster Mitigation |
| title | Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residencesResearch in context |
| title_full | Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residencesResearch in context |
| title_fullStr | Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residencesResearch in context |
| title_full_unstemmed | Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residencesResearch in context |
| title_short | Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residencesResearch in context |
| title_sort | phylogeographic and genetic network assessment of covid 19 mitigation protocols on sars cov 2 transmission in university campus residencesresearch in context |
| topic | SARS-CoV-2 University Phylogeography Transmission cluster Mitigation |
| url | http://www.sciencedirect.com/science/article/pii/S2352396425001732 |
| work_keys_str_mv | AT joelowertheim phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT tetyanaivasylyeva phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT robertjwood phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT kalencantrell phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT sorayapinacontreras phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT aryehfeldheim phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT ravigoyal phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT jenniferlhavens phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT robknight phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT louiseclaurent phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT niemamoshiri phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT robertneuhard phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT shashanksathe phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT alyssonsatterlund phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT angelascioscia phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT angelaysong phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT roberttschooley phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT cherylmanderson phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT natashakmartin phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT stefanaigner phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT kristiangandersen phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT nathanabaer phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT maryannbetty phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT amandabirmingham phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT anelizzecastromartinez phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT willicheung phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT peterdehoff phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT kathleenmfisch phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT alisonjking phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT karthikgangavarapu phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT abbashakim phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT benjaminhenson phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT kristenjepsen phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT christinahmac phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT toantngo phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT kellynnguyen phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT tylerrostrander phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT sarahperkins phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT ashleyplascencia phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT andrearivera phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT arianarivera phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT rodolfoasalido phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT kierancsaucedo phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT madisonschwab phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT allisonlsteedman phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT anthonyveder phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT alanaweiss phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT genewyeo phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext AT markzeller phylogeographicandgeneticnetworkassessmentofcovid19mitigationprotocolsonsarscov2transmissioninuniversitycampusresidencesresearchincontext |