Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting

Jocelyn Keehner; Shira R Abeles; Christopher A Longhurst; Lucy E Horton; Frank E Myers; Lindsay Riggs-Rodriguez; Mohammed Ahmad; Sally Baxter; Aaron Boussina; Kalen Cantrell; Priscilla Cardenas; Peter De Hoff; Robert El-Kareh; Jennifer Holland; Daryn Ikeda; Kirk Kurashige; Louise C Laurent; SEARCH Alliance; Andrew Lucas; David Pride; Shashank Sathe; Allen R Tran; Tetyana I Vasylyeva; Gene Yeo; Rob Knight; Joel O Wertheim; Francesca J Torriani

doi:10.1093/cid/ciad738

Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting

Clin Infect Dis. 2024 May 15;78(5):1204-1213. doi: 10.1093/cid/ciad738.

Authors

Jocelyn Keehner^{1

2}, Shira R Abeles^{2

3}, Christopher A Longhurst^{4

5}, Lucy E Horton^{2

3

6}, Frank E Myers³, Lindsay Riggs-Rodriguez⁷, Mohammed Ahmad⁸, Sally Baxter⁹, Aaron Boussina¹⁰, Kalen Cantrell¹¹, Priscilla Cardenas¹², Peter De Hoff^{13

14

15}, Robert El-Kareh^{4

16}, Jennifer Holland¹⁷, Daryn Ikeda¹², Kirk Kurashige¹⁷, Louise C Laurent^{13

14

15}; SEARCH Alliance; Andrew Lucas⁸, David Pride^{2

18}, Shashank Sathe^{13

19

14}, Allen R Tran⁸, Tetyana I Vasylyeva², Gene Yeo^{13

19

14}, Rob Knight^{5

20

21

14

22}, Joel O Wertheim², Francesca J Torriani^{2

3}

Collaborators

SEARCH Alliance:
Stefan Aigner, Kristian G Andersen, Catelyn Anderson, Nathan A Baer, Tom Barber, Marco Bauk, Jennifer N Beck, Pedro Belda-Ferre, Maryann Betty, Amanda Birmingham, Anelizze Castro-Martinez, Willi Cheung, Peter De Hoff, Kathleen M Fisch, Karthik Gangavarapu, Isabella Gargano, Abbas Hakim, Shania Harsono, Benjamin Henson, Charlotte Hobbs, Jacqueline Holmes, Kristen Jepsen, Rob Knight, Ezra Kurzban, Louise C Laurent, Clarisse A Marotz, Nathaniel L Matteson, Niema Moshiri, Toan T Ngo, Tyler R Ostrander, Sarah Perkins, Ashley Plascencia, Andrea Rivera, Ariana Rivera, Rodolfo A Salido, Shashank Sathe, Phoebe Seaver, Madison Schwab, Anthony Veder, Gene W Yeo, Mark Zeller

Affiliations

¹ Division of Infectious Diseases, Department of Medicine, University of California-SanFrancisco, San Francisco, California, USA.
² Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA.
³ Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA.
⁴ Division of Biomedical Informatics, Department of Medicine, UC San Diego Health, La Jolla, California, USA.
⁵ Department of Pediatrics, University of California-San Diego, La Jolla, California, USA.
⁶ Vaccine Research and Development Unit, Pfizer Inc, San Diego, California, USA.
⁷ Population Health Services Organization-Programs and Strategy, UC San Diego Health, San Diego, California, USA.
⁸ Information Services EMR, UC San Diego Health, San Diego, California, USA.
⁹ Division of Biomedical Informatics at the University of California-San Diego, San Diego, California, USA.
¹⁰ Division of Biomedical Informatics, University of California-San Diego, La Jolla, California, USA.
¹¹ Department of Computer Science & Engineering, Jacobs School of Engineering, University of California, San Diego, California, USA.
¹² UC San Diego Health's Contact Tracing Team, Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA.
¹³ Sanford Consortium of Regenerative Medicine, University of California-San Diego, La Jolla, California, USA.
¹⁴ Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California-San Diego, La Jolla, California, USA.
¹⁵ Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, UC San Diego Health, San Diego, California, USA.
¹⁶ Division of Hospital Medicine, Department of Medicine, UC San Diego Health, La Jolla, California, USA.
¹⁷ Analytics and Population Health Department, UC San Diego Health, San Diego, California, USA.
¹⁸ Department of Pathology, UC San Diego Health, La Jolla, California, USA.
¹⁹ Department of Cellular and Molecular Medicine, University of California-San Diego, La Jolla, California, USA.
²⁰ Department of Bioengineering, University of California-San Diego, La Jolla, California, USA.
²¹ Department of Computer Science and Engineering, University of California-San Diego, La Jolla, California, USA.
²² Center for Microbiome Innovation, University of California-San Diego, La Jolla, California, USA.

PMID: 38227643
PMCID: PMC11093679 (available on 2025-01-16)
DOI: 10.1093/cid/ciad738

Abstract

Background: Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2.

Methods: We performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs.

Results: Among 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P < .001).

Conclusions: IP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission.

Keywords: SARS-CoV-2 pandemic; healthcare transmission of SARS-CoV-2; infection prevention precautions; social network analyses and contact tracing; whole-genome sequencing.

MeSH terms

Adolescent
Adult
Aged
Aged, 80 and over
COVID-19* / epidemiology
COVID-19* / transmission
COVID-19* / virology
Child
Child, Preschool
Contact Tracing
Cross Infection / epidemiology
Cross Infection / transmission
Cross Infection / virology
Cross-Sectional Studies
Female
Genome, Viral*
Genomics
Health Personnel*
Humans
Male
Middle Aged
Retrospective Studies
SARS-CoV-2* / genetics
Social Network Analysis
Young Adult

Abstract

MeSH terms

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