Wastewater-based genomic surveillance uncovers broader SARS-CoV-2 diversity and spatial transmission dynamics in Georgia, January 2023–July 2024
Year: 2026
Type: article
Abstract: Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using next-generation sequencing (NGS) enables real-time monitoring of circulating and emerging variants, often providing earlier detection than clinical reporting while capturing presymptomatic, asymptomatic, and symptomatic infections. However, the correlation between lineage abundance in wastewater and clinical specimens from corresponding sewersheds in Georgia remains understudied. From January 2023 through July 2024, the Georgia Public Health Laboratory (GPHL) sequenced SARS-CoV-2 from 669 wastewater samples collected across 17 treatment facilities in 15 counties. These data were compared with 325 clinical specimens from corresponding sewersheds to assess early detection potential. Nucleic acids were extracted using the KingFisher Apex platform, followed by genomic library preparation and paired-end whole-genome sequencing on the Illumina NextSeq 2000. Variant calling and lineage abundance estimation using Freyja identified 2,218 SARS-CoV-2 lineages and sub-lineages, 1,769 in 2023, and 1,255 in 2024, with 806 co-circulating across both years. Clinical sequences spanned 135 lineages/sub-lineages across 15 clades, with >70% in clades 24A (27.4%), 23A (19.4%), 23F (13.5%), and 22E (10.2%). Predominant lineages included XBB.1.5 (11.4%), JN.1 (6.8%), and JN.1.4 (6.2%), reflecting broader clinical trends in Georgia. Clinical data also reflected distinct transmission patterns, including viral introduction and spread within and between counties. Overall, this study provides important insights into the introduction and dissemination of SARS-CoV-2 lineages in Georgia. Expanding wastewater surveillance to include other emerging and reemerging pathogens of public health importance will be particularly valuable during periods of low disease incidence, serving as an early warning system when clinical testing is limited and enabling timely public health responses.IMPORTANCEWastewater-based surveillance of SARS-CoV-2 provides a noninvasive, cost-effective, population-level method for detecting viral genetic material independent of clinical testing. Next-generation sequencing enables timely monitoring of circulating lineages by public health laboratories. The Georgia National Wastewater Surveillance System (GA-NWSS) established in 2021 through collaboration between the Georgia Department of Public Health (DPH) Epidemiology and the Georgia Public Health Laboratory (GPHL) collects weekly samples from 17 wastewater treatment facilities across 15 counties. From January 2023 through July 2024, GPHL sequenced 669 wastewater samples, identifying 2,218 SARS-CoV-2 lineages and sub-lineages, compared with 135 lineages detected in 325 clinical specimens from corresponding sewersheds. Spatial analysis highlights viral spread across state boundaries and within Georgia catchment areas, illustrating evolving transmission patterns. These results demonstrate that wastewater sequencing captures broader genomic diversity than clinical sampling alone, emphasizing its critical role in pathogen genomic surveillance and supporting data-driven public health response to SARS-CoV-2.
Source: Microbiology Spectrum
Institution: Georgia Department of Public Health
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $2,500
Awards: CK19-1904 EPIDEMIOLOGY AND LABORATORY CAPACITY FOR PREVENTION AND CONTROL OF EMERGING INFECTIOUS DISEASES (ELC), G9000474977, GENOMIC CENTER OF EXCELLENCE-PUBLIC HEALTH PATHOGENS: TRANSLATION, EDUCATION, RESPONSE BASE, RESPONSE IMPLEMENTATION, LEAD PGCOE EDUCATION - GEORGIA DEPARTMENT OF PUBLIC HEALTH US PUBLIC HEALTH PATHOGENS GENOMICS CENTERS OF EXCELLENCE PURPOSE: THIS PROPOSAL SUPPORTS IMPLEMENTATION OF THE CENTER FOR APPLIED PATHOGEN EPIDEMIOLOGY AND OUTBREAK CONTROL (CAPE) A CENTER OF EXCELLENCE THAT HAS THREE MAIN COMPONENTS, TRANSLATION OF INNOVATIVE RESEARCH TO PUBLIC HEALTH; EDUCATION OF THE PUBLIC HEALTH WORKFORCE; AND PREPARATION AND RESPONSE TO INFECTIOUS DISEASE THREATS. AS A CENTER OF EXCELLENCE, CAPE WILL ADDRESS BOTH NEAR AND LONG-TERM GENOMIC CHALLENGES THROUGH BROADLY APPLICABLE, INNOVATIVE SOLUTIONS FOR THE PUBLIC HEALTH COMMUNITY. OUR INNOVATIVE TEAMING STRATEGY ALLOWS FOR A RESPONSIVE NETWORK THAT CAN DEVELOP CUTTING EDGE SOLUTIONS AND BEST PRACTICES FOR USING PATHOGEN SEQUENCE DATA TO INFORM PUBLIC HEALTH RESPONSE AND POLICY. THIS APPLICATION IS FOR THE MANDATORY COMPONENTS (CORE, RESPONSE IMPLEMENTATION) AND INCLUDES THE OPTIONAL COMPONENT (LEAD PGCOE FOR EDUCATION). STRATEGY: THE GEORGIA DEPARTMENT OF PUBLIC HEALTH (GDPH) IN COLLABORATION WITH SIX MAJOR ACADEMIC INSTITUTIONS (AUGUSTA UNIVERSITY, EMORY UNIVERSITY, GEORGIA INSTITUTE OF TECHNOLOGY, UNIVERSITY OF GEORGIA, GEORGIA STATE UNIVERSITY, AND THE UNIVERSITY OF TEXAS, WILL JOINTLY SUPPORT CAPE. COORDINATING WITH THE CENTERS FOR DISEASE CONTROL AND PREVENTION AND THE OTHER CENTERS OF EXCELLENCE PARTNERS, THE CAPE PUBLIC HEALTH TEAM WILL CONDUCT A PUBLIC HEALTH NEEDS ASSESSMENT TO GUIDE CENTER INITIATIVES. THE ASSESSMENT WILL PROVIDE THE FOUNDATION FOR SUBSEQUENT PLANNING AND PRIORITIZATION FOR THE NETWORK. THIS APPROACH REPRESENTS THE WAY WE WILL ADDRESS SOLUTION DEVELOPMENT, OPERATIONS, AND IMPLEMENTATION. THE CAPE PRINCIPAL AND CO-PRINCIPAL INVESTIGATORS WILL LEVERAGE THE STRENGTH AND EXPERTISE OF THE OTHER CAPE NETWORK MEMBERS TO ADDRESS THE CORE ACTIVITIES. CORE 1.1 FOCUSES ON DEVELOPING NEW SEQUENCING APPROACHES WITH STREAMLINED METHODOLOGIES THAT ARE PATHOGEN AGNOSTIC. CORE 1.2 FOCUSES ON BIOINFORMATIC SOLUTIONS THAT CAN IMMEDIATELY SUPPORT PUBLIC HEALTH DEPARTMENT REPORTING NEEDS. CORE 1.3 FOCUSES ON DEVELOPMENT OF AN INFORMATIC INFRASTRUCTURE THAT CAN LINK MULTIPLE DATA STREAMS, INTEGRATE BIOINFORMATIC SOLUTIONS WHILE PRIORITIZING DATA SECURITY AND INTEGRITY. PRIOR TO DEVELOPING THIS PROPOSAL, AS A SOLUTIONING TEAM, WE SURVEYED EXISTING WORK TO PROPOSE ACTIVITIES IN CORE 1.4 THAT COULD ADDRESS PRIORITY RESEARCH AREAS AND CHALLENGES ENCOUNTERED IN THE SARS-COV-2 RESPONSE. CORE 1.5 EXPANDS ON CURRENT SURVEILLANCE ACTIVITIES BY EXPLOITING WASTEWATER / ENVIRONMENTAL SAMPLING AND DEVELOPING PROTOCOLS FOR DATA AND SAMPLE SHARING TO INTEGRATE HOSPITAL-BASED SURVEILLANCE AND THE CLINICAL PATHOLOGY NETWORK INTO THE OVERALL PUBLIC HEALTH SURVEILLANCE NETWORK. CORE 1.6 DEVELOPS TRAINING MATERIALS, INCLUDING ONLINE ON-DEMAND MATERIALS FOR WORKFORCE DEVELOPMENT, INTERNSHIPS FOR APPLIED PUBLIC HEALTH PRACTICE EXPERIENCE AND TRANSLATION FROM CAPE TO OUR PUBLIC HEALTH PARTNERS AND WORKSHOPS ON MOLECULAR EPIDEMIOLOGY. CORE 1.7 PROPOSES SPECIFIC ACTIVITIES FOR RESPONSE IMPLEMENTATION. ACTIVITIES WILL INCLUDE ENSURING ALL ADMINISTRATIVE AGREEMENTS ARE IN PLACE TO ENSURE SEAMLESS TRANSFER OF DATA, REAGENTS OR SAMPLE MATERIALS IS POSSIBLE BETWEEN PARTICIPATING LABS. IN CORE 2, CAPE WILL LEVERAGE OUR EXPERTISE TO COORDINATE RESPONSE ACTIVITIES, INCLUDING ANALYTICAL AND MODELING CAPABILITIES. OUTCOME: CAPE WILL WORK WITH CDC AND OTHER CENTERS OF EXCELLENCE, ACADEMIC CENTERS, CLINICAL SITES, AND PUBLIC HEALTH LABORATORIES TO SUPPORT INNOVATIONS IN SEQUENCING, BIOINFORMATICS, GENOMIC SURVEILLANCE, DATA INTEGRATION AND VISUALIZATION, AND WORKFORCE DEVELOPMENT, WITH THE OBJECTIVE OF STRENGTHENING THE CAPACITY TO RESPOND TO PUBLIC HEALTH THREATS AND ADVANCE DAY TO DAY OPERATIONS.
OpenAlex ID: W7214781908