Genomic Epidemiology of SARS-CoV-2 in a County Jail

Abstract

Abstract Background In the SARS-CoV-2 pandemic, correctional facilities are potential hotspots for transmission. We examined the genomic epidemiology of SARS-CoV-2 early in the pandemic in one of the country’s largest urban jails. Methods Existing SARS-CoV-2 isolates from 131 detainees at the Cook County Jail in Chicago, IL from March 2020 through May 2020 were analyzed by whole-genome sequencing. Contemporaneous isolates from Rush University Medical Center (Chicago, IL) and Global Initiative on Sharing All Influenza Data (GISAID) were used to identify genetic clusters containing only jail isolates. Transmission windows were identified for each pair of detainees using the date of the COVID-positive test and location data to determine if detainees overlapped in the jail, within a specific building, or within particular living units during transmission windows. Results We identified 29 jail-only clusters that contained 75 of the 132 SARS-CoV-2 isolates from detainees; of these clusters, 17 (58.6%) had individuals who overlapped in the jail during putative transmission windows. Focusing on specific buildings revealed that two buildings, a single and double-cell style type of housing were associated with having detainees infected with similar SARS-CoV-2 genomes during their infectious time period (p < 0.001). Conclusion Our findings suggest that there was transmission of SARS- CoV-2 in the jail, in the setting of extensive importation of COVID from the community. Numerous infection control practices at intake and during incarceration were implemented in the jail to limit viral spread. Our study shows the importance of genomic analysis in this type of settings and how it can be utilized within infection control protocols.