Search

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. [ABSTRACT FROM AUTHOR]

Background: Timely genomic surveillance is required to inform public health responses to new SARS-CoV-2 variants. However, the processes involved in local genomic surveillance introduce inherent time constraints. The Regional Innovative Public Health Laboratory in Chicago developed and employed a genomic surveillance response playbook for the early detection and surveillance of emerging SARS-CoV-2 variants. Methods: The playbook outlines modifications to sampling strategies, laboratory workflows, and communication processes based on the emerging variant's predicted viral characteristics, observed public health impact in other jurisdictions and local community risk level. The playbook outlines procedures for implementing and reporting enhanced and accelerated genomic surveillance, including supplementing whole genome sequencing (WGS) with variant screening by quantitative PCR (qPCR). Results: The ability of the playbook to improve the response to an emerging variant was tested for SARS-CoV-2 Omicron BA.1. Increased submission of clinical remnant samples from local hospital laboratories enabled detection of a new variant at an average of 1.4% prevalence with 95% confidence rather than 3.5% at baseline. Genotyping qPCR concurred with WGS lineage assignments in 99.9% of 1541 samples with results by both methods, and was more sensitive, providing lineage results in 90.4% of 1833 samples rather than 85.1% for WGS, while significantly reducing the time to lineage result. Conclusions: The genomic surveillance response playbook provides a structured, stepwise, and data-driven approach to responding to emerging SARS-CoV-2 variants. These pre-defined processes can serve as a template for other genomic surveillance programs to streamline workflows and expedite the detection and public health response to emerging variants. Based on the processes piloted during the Omicron BA.1 response, this method has been applied to subsequent Omicron subvariants and can be readily applied to future SARS-CoV-2 emerging variants and other public health surveillance activities. [ABSTRACT FROM AUTHOR]