The Department of General Services (DGS) Division of Consolidated Laboratory Services (DCLS) serves as Virginia’s public health (PH) laboratory and has a long-standing partnership with the Virginia Department of Health (VDH) to provide laboratory testing. DGS-DCLS strengthened Virginia academic partnerships during the response to the SARS-CoV-2 (SC2) pandemic to increase public health testing capacity. Collaborating with the University of Virginia (UVA) and Virginia Commonwealth University (VCU) has enhanced and expanded Virginia’s ability to rapidly turn diagnostic testing and sequencing data into PH action. Virginia’s testing network is the “Virginia SARS-CoV-2 Strain Surveillance Network (VAS3)”. Since its inception, UVA and VCU have contributed thousands of sequences to the surveillance system, in addition to the samples sequenced by DCLS. The partnership between DCLS, VDH, UVA, and VCU has allowed Virginia to take academic innovation into the PH sphere. The Pathogen Genomics Centers of Excellence (PGCOE) will further expand the early VAS23 innovation for novel method development and translation for public health adoption beyond pandemic response. Academic partners bring expertise in the areas of clinical application, genomics, metagenomics, and data science.
Department of General Services Division of Consolidated Laboratory Services: The Division of Consolidated Laboratory Services (DCLS) provides around-the-clock, high-quality analytical testing services and support to local, state, and federal agencies that serve to protect the health, safety, and security of the public. The State Laboratory is a national training "Center of Excellence" for the U.S. Centers for Disease Control and Prevention and the U.S. Department of Agriculture and provides certification and accreditation for Virginia environmental laboratories.
DGS-DCLS is the lead agency for the Virginia PGCoE. In this role, DGS-DCLS is expanding internal laboratory capacity for genomic surveillance and public health response, developing and distributing trainings to improve the use of genomic data, guiding research and collaboration with our academic partners, and adapting research for public health use.
DGS-DCLS continues to expand the Advanced Molecular Detection (AMD) NGS program and testing capacity for both surveillance, outbreak response, and enhanced pathogen characterization. Current AMD program initiatives include testing for foodborne, waterborne, respiratory, nosocomial, and antimicrobial-resistant (AMR) pathogens. In addition to the VA PGCoE, DGS-DCLS also serves as the Molecular Subtyping Network for Foodborne Disease Surveillance Regional Laboratory for the Mid-Atlantic Region, Advanced Molecular Detection (AMD) Bioinformatics Regional Resource and Workforce Training Lead for the Mid-Atlantic Region, and the CDC AMD Platform Development Domain Lead for Applied Genomic Epidemiology.
Team members: Alexandra Lorentz, PhD (Genomic Epidemiology Lead Scientist); Lauren Turner, PhD (Advanced Molecular Detection Lead Scientist); Logan Fink, MS (Bioinformatics Lead Scientist); Denise M. Toney, PhD (HCLD) (Laboratory Director); Marilyn Bibbs Freeman, PhD, M(ASCP)(Deputy Director)
Virginia Department of Health: The Virginia Department of Health (VDH) is dedicated to protecting and promoting the health of Virginians. The VDH is made up of a statewide Central Office in Richmond and 35 local health districts. These entities work together to promote healthy lifestyle choices that can combat chronic disease, educate the public about emergency preparedness and threats to their health, and track disease outbreaks in Virginia. The VDH is led by the State Health Commissioner, appointed by the Governor of Virginia. The Commissioner oversees the direction of the agency and provides feedback to the Governor through the Secretary of Health and Human Resources. The Commissioner works alongside numerous Deputy Commissioners and other key figures on the leadership team in heading the VDH in its efforts to navigate the complex health landscape and to promote the well-being of all people in Virginia.
The VDH State Epidemiologist serves on the VA PGCoE Governance Committee along with the DGS DCLS State Public Health Director. VDH provides applied public health relevance and input for the novel research of pathogen genomics proposed and executed by academic partners. VDH supports genomic data integration requirements for PGCoE advancement by implementing public health information exchange and interoperability improvements. VDH contributes to Center of Excellence activities through staff workforce development and training, and by maintaining a joint VDH-DCLS genomics surveillance program.
Team members: Laurie Forlano, DO, MPH (State Epidemiologist, Director Office of Epidemiology (OEPI)); Brandy Darby, DVM, MPH, DACVPM (Director, OEPI Division of Surveillance and Investigation (DSI)); Katherine McCombs, MPH (Deputy Director, DSI Rebecca Early, MPH, CHES Director, Division of Informatics and Information Systems (DIIS)); Jenny Crain, MS, MPH, CPH (Genomic Epidemiologist, DSI); Justin Crowe, MPA (Foresight and Analytics Coordinator, Office of Emergency Preparedness); Merylyn Huitz, DIIS (Messaging Manager); Anup Srikumar (Acting Director, Center for Public Health Informatics (CPHI, within OIM)); Lanora Cooper (Public Health Informatics Data Governance, CPHI); Prabhat Kumar (Office of Information Management (OIM) Technical Project Manager
University of Virginia School of Medicine: The Mathers Lab at the UVA School of Medicine is part of the Division of Infectious Diseases and International Health. The primary emphasis of research centers on the clinical impact, emergence, transmission, and detection of antimicrobial resistance (AMR) in gram-negative pathogens. With experience in infection control and clinical microbiology, they have developed tools for the detection and tracking of antimicrobial-resistant pathogens in hospitalized patients. They have long-standing experience with using whole genome sequencing applications for tracking antimicrobial gene sharing between bacteria. Controlling transmission has prompted specialization in wastewater and plumbing surveillance for these organisms and other pathogens of concern. They have a dedicated sink laboratory in which they can mimic real-world sink conditions in a controlled setting. This experience and background have enabled their hybrid clinical and research lab to quickly pivot and apply genomic surveillance efforts in SARS-CoV-2 sequencing, bacterial strain speciation, and outbreak detection.
As part of the PGCoE effort, they are actively working on the research and development of genomic practices from a clinical setting that can be applied in public health by assessing current practices and developing bioinformatic protocols. In addition to this, they also contribute to research on the development of tools and understanding of the biology of AMR gene movement between bacteria on plasmids. Modeling this transfer will increase the understanding of the spread of these genes, which is a major public health concern. Applying many of the genomic, microbiologic, and molecular tools developed initially for clinical detection of AMR to wastewater, they are also focusing on understanding the use of wastewater monitoring for the detection of AMR as well as other potential pathogens.
Team members: Amy Mathers, MD, D(ABMM) (Associate Professor of Medicine and Pathology, Associate Director of Clinical Microbiology, Medical Director of Antimicrobial Stewardship), Shireen Kotay, PhD (Research Scientist), Emily Snavely, PhD, (ABMM) (Assistant Professor of Pathology), Katie Barry, MS, MB(ASCP) (Senior Laboratory Specialist), Sharvari Narendra (Bioinformatics Analyst), Aubrey Hetzler, MS (Laboratory and Research Specialist)
University of Virginia Biocomplexity Institute: The Biocomplexity Institute (BI) at UVA focuses on interdisciplinary research, bringing together experts from various fields such as biology, computer science, engineering, and other relevant disciplines needed for understanding complex biological systems. BI researchers use computational modeling and simulation techniques to study and analyze biological systems. This involves the use of advanced computing technologies to process and analyze large datasets, simulate complex interactions, and derive meaningful insights. The Institute's research covers a broad range of topics within the realm of biocomplexity, including infectious diseases, environmental science, public health, and social systems.
BI works closely with PGCoE partners to develop cyberinfrastructure to support genomic epidemiological data acquisition, processing, and analysis. BI also develops advanced methods in biosurveillance, forecasting, and epidemiological modeling using synthetic information ("digital twin") to support and advance PGCoE goals. Further, the BI team develops training materials for bioinformatic analysis and coordinates outreach activities to foster collaboration and communication among public health practitioners and researchers.
Team members: Madhav Marathe, PhD (Distinguished Professor in Biocomplexity, Biocomplexity Institute; Professor, Dept. of Computer Science, UVA); Ron Kenyon, MBA (Senior Scientist, UVA-BI); Bryan Lewis, PhD, (Research Associate Professor, UVA-BI); Rebecca Wattam, PhD (Research Associate Professor, UVA-BI); Andrew Warren, PhD (Research Assistant Professor, UVA-BI)
Virginia Commonwealth University Center for Microbiome Engineering and Data Analysis: The Microbiome of the Female Reproductive Tract and Women’s Health. The VCU team in the Center for Microbiome Engineering and Data Analysis has focused its attention on the impact of the microbiome of the female reproductive tract on women’s gynecologic and obstetric well-being. Recipients of two sequential awards from the National Institutes of Health Human (NIH) Microbiome Project and several investigator-initiated research grants from the NIH, NSF, and philanthropic organizations, the team has advanced our understanding of the role of the vaginal and related microbiomes on both day-to-day women’s gynecologic health and the successful progression of pregnancy. Focus has included the prokaryotic, eukaryotic, and viral colonizers of the female reproductive tract. Technology the team has developed in these studies is being applied to the research the team is performing in the Center for Disease Control-funded Virginia Pathogen Genomics Center of Excellence.
SARS-CoV-2 Genome Sequencing. At the initiation of the COVID-19 pandemic, the VCU team focused on the development of strategies for rapid inexpensive sequencing of the virus from nasopharyngeal samples. Supported by funds from the CDC-funded contract awarded to the Virginia Division of Consolidated Laboratory Services, VCU developed and applied the Pathogenic Virus Amplification and Sequencing Protocol (PVASP), which permitted it to rapidly and inexpensively generate genomic sequences of thousands of SARS-CoV-2 sequences from positive samples provided by the VCU Health Center Diagnostic Microbiology Laboratory. This protocol is being adapted for Hepatitis A Virus genome sequencing in the current Virginia Pathogen Genomics Center of Excellence.
Team members: Tom Arodz, PhD (Associate Professor, Computer Science); Alexandra Bryson, PhD (Assistant Professor, Pathology); Gregory Buck, PhD (Professor, Microbiology and Immunology); Christopher Doern, PhD (Associate Professor, Pathology); Jeffrey Donowitz, MD (Associate Professor, Pediatrics (UVA)); Kimberly Jefferson, PhD (Associate Professor, Microbiology and Immunology); Michael McVoy, PhD (Professor, Pediatrics); Myrna Serrano, PhD (Associate Professor, Microbiology and Immunology)
