The VA PGCoE publishes manuscripts and makes presentations relevant to the use of genomics in public health. The following have been developed as part of the work done in the Center. Other relevant publications and presentations from team members are also provided.
Publications
Chen J, Espinoza B, Chou J, Gumel AB, Levin SA, Marathe MV. A simple model of coupled individual behavior and its impact on epidemic dynamics. Mathematical Biosciences. V. 380, Feb 2025, 109345.
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Espinoza B, Chen J, Orr M, Saad-Roy CM, Levin SA, Marathe MV. The impact of risk compensation adaptive behavior on the final epidemic size. Mathematical Biosciences. V. 380, Feb 2025, 109370.
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Espinoza B, Adiga A, Venkatramanan S, Warren AS, Chen J, Lewis BL, Vullikanti A, Swarup S, Moon S, Barrett CL, Athreya S, Sundaresan R, Chandru V, Laxminarayan R, Schaffer B, Poor HV, Levin SA, Marathe MV. Coupled models of genomic surveillance and evolving pandemics with applications for timely public health interventions. PNAS. 2023.
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Espinoza B, Saad-Roy CM, Grenfell BT, Levin, SA, Marathe M. (2024). Adaptive human behaviour modulates the impact of immune life history and vaccination on long-term epidemic dynamics. Proceedings B, 291(2033), 20241772.
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Mathers AJ, Li TJ, He Q, Narendra S, Stoesser N, Eyre DW, Walker AS, Barry KE, Castañeda-Barba S, Huang FW, Parikh H. Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir. npj Antimicrobials and Resistance. 2024 Dec 30;2(1):50.
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Saad-Roy CM, Morris SE, Boots M, Baker RE, Lewis BL, Farrar J, Marathe MV, Graham AL, Levin SA, Wagner CE, Metcalf CJ. Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy. PLoS computational biology. 2024 Aug 5;20(8):e1012211.
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Presentations and Webinars
Applying Concepts of Genomic Epidemiology in Public Health - Michigan Perspective. Presentation by Arianna Miles-Jay (standing in for Heather Blankenship), Michigan Department of Health and Human Services, on May 2, 2025, as part of the VDH Genomic Epi Webinar Series.
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Study design considerations for genomic epidemiology. Presentation by Shirlee Wohl, PhD (Brigham and Women's Hospital, Massachusetts Department of Public Health) on April 4, 2025, as part of the VDH Genomic Epidemiology Training Series.
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Genomic epidemiology in practice: tracing a multi-state Pseudomonas aeruginosa outbreak. Presentation by Krisandra Allen, MB (Digital Epidemiology Services, Inc.) on December 6, 2024, as part of the VDH Genomic Epidemiology Training Series.
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Understanding the process of generating and viewing a phylogenetic tree, and other implications. Rebecca Wattam, PhD (University of Virginia Biocomplexity Institute) presentation as part of the 2024 Regional Advanced Genomic Epidemiology Training Series on October 11, 2024.
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Comparison as a Means to Optimization: A Ring Trial of Whole Genome Sequencing for Outbreak Detection in U.S. Public Health Laboratories. Shavari Narendra, MS (University of Virginia School of Medicine) poster at the ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines in Washington, DC, on October 15, 2024.
Abstract
Efficacy of Hybrid Capture Based Metagenomic Sequencing for Monitoring Antimicrobial Resistance in Wastewater. Shireen Kotay, PhD (University of Virginia School of Medicine) poster at the ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines in Washington, DC, on October 15, 2024.
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Composite-Sample Complex: Building a genomics model to understand the evolutionary history of antimicrobial resistance gene movement. Amy Mathers, MD (University of Virginia School of Medicine) presentation for the International Society for Plasmid Biology in Hamamatsu, Japan, on September 4, 2024.
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MicrobeTrace: An Essential Tool for Outbreak Response. Anupama Shankar (CDC, NCHHSTP/DHP/Lab Branch) presentation at the Virginia Department of Health (VDH) Genomic Epi Seminar Series on July 12, 2024.
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The Interplay Between Genomic Surveillance and Public Health Interventions. Baltazar Espinoza, PhD and Madhav Marathe, PhD (Biocomplexity Institute of University of Virginia) presentation for the National Biosurveillance Integration Center (NBIC) on June 20, 2024.
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Investigating the link between Sneathia, Human Papillomavirus, and preterm birth. Kim Jefferson, PhD (Associate Professor, Microbiology and Immunology, VCU) presentation at the VDH Genomic Epi Seminar Series, June 14, 2024.
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Designing Genomic Epidemiologic Studies for Public Health Application. Alli Black, MS, PhD (Molecular Epidemiology Program, WA Department of Health; Project Director, Northwest PGCoE) presentation at the Virginia Department of Health (VDH) Genomic Epi Seminar Series, on March 22, 2024.
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Transmission of antimicrobial resistance and the importance of horizontal gene transfer. Dr. Amy Mathers of the University of Virginia School of Medicine (UVA SOM) presents results from her group's research into antimicrobial resistance transmission via mobile genetic elements. This presentation was made as part of the Virginia Department of Health (VDH) Genomic Epi Seminar Series on December 15, 2023.
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Phylogeny for Pathogen Identification. What is a phylogenetic tree? What is it based on? How can you generate it? And what do those odd-looking things mean? These, and many more questions, are addressed in this webinar. This presentation was made by Dr. Rebecca Wattam of the University of Virginia Biocomplexity Institute (UVA BI) as part of the Virginia Department of Health (VDH) Genomic Epi Seminar Series on September 22, 2023.
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