Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 in a County Jail

Abstract

Background: In the coronavirus disease 2019 (COVID-19) pandemic, correctional facilities are potential hotspots for transmission. We examined the genomic epidemiology of severe acute respiratory syndrome coronavirus 2 (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, Illinois, from March 2020 through May 2020 were analyzed by whole-genome sequencing. Contemporaneous isolates from Rush University Medical Center (Chicago, Illinois) and the 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 SARS-CoV-2-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 2 buildings, a single- and double-cell style of housing. were associated with having detainees infected with similar SARS-CoV-2 genomes during their infectious time period (P < .001).

Conclusions: Our findings suggest that there was transmission of SARS-CoV-2 in the jail, in the setting of extensive importation of COVID-19 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.

Keywords: SARS-CoV-2; genomic epidemiology; jail; pandemic; transmission.

Figure 1.

Time-calibrated whole-genome phylogeny of severe acute respiratory syndrome coronavirus 2 isolates taken from the jail, an urban hospital, and GISAID using TreeTime. Recombination-masked whole-genome alignment was used. The tree is midpoint rooted. The x-axis shows time points in the early phase of the COVID-19 pandemic in date decimal format.

Figure 2.

A whole-genome phylogenetic tree (left) of jail severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolates with tips colored to indicate jail-only clusters. Trace plot (right) aligned with the tree to show whether detainees were within the same building and clusters. Each line represents the location of the detainees during their infectious period, and each dot represents the collection date of the SARS-CoV-2 specimen. The collection dot is colored by which cluster group each isolate was in.