1
|
Barbian HJ, Kittner A, Teran R, Bobrovska S, Qiu X, English K, Green SJ, Ghinai I, Pacilli M, Hayden MK. A response playbook for early detection and population surveillance of new SARS-CoV-2 variants in a regional public health laboratory. BMC Public Health 2024; 24:59. [PMID: 38166805 PMCID: PMC10763119 DOI: 10.1186/s12889-023-17536-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Hannah J Barbian
- Department of Internal Medicine, Regional Innovative Public Health Laboratory, Rush University Medical Center, Jelke 1259, 1750 W Harrison St, Chicago, IL, 60612, USA.
| | - Alyse Kittner
- Department of Internal Medicine, Regional Innovative Public Health Laboratory, Rush University Medical Center, Jelke 1259, 1750 W Harrison St, Chicago, IL, 60612, USA
| | - Richard Teran
- Chicago Department of Public Health, Chicago, IL, USA
| | - Sofiya Bobrovska
- Department of Internal Medicine, Regional Innovative Public Health Laboratory, Rush University Medical Center, Jelke 1259, 1750 W Harrison St, Chicago, IL, 60612, USA
| | - Xueting Qiu
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Kayla English
- Chicago Department of Public Health, Chicago, IL, USA
| | - Stefan J Green
- Department of Internal Medicine, Regional Innovative Public Health Laboratory, Rush University Medical Center, Jelke 1259, 1750 W Harrison St, Chicago, IL, 60612, USA
| | - Isaac Ghinai
- Chicago Department of Public Health, Chicago, IL, USA
| | | | - Mary K Hayden
- Department of Internal Medicine, Regional Innovative Public Health Laboratory, Rush University Medical Center, Jelke 1259, 1750 W Harrison St, Chicago, IL, 60612, USA
| |
Collapse
|