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

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. Graphical Abstract Graphical Abstract This graphical abstract is also available at Tidbit: https://tidbitapp.io/tidbits/integrated-genomic-and-social-network-analyses-of-sars-cov-2-transmission-in-the-healthcare-setting-1d3824e5-4e59-4391-a778-4f9205ecca0a Genomic/social network analyses and contact tracing data were used to identify healthcare transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rare transmissions were associated with lapses in infection prevention (IP) protocols. Transmission was mitigated when IP protocols were followed.