Core 3: Genomic Sequencing and Population Genetics Core

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ABSTRACT – Genomic Sequencing and Population Genetics Core – Core 3 The Genomic Sequencing and Population Genetics Core (Core 3) supports the Program’s two projects in evaluating and understanding the relationship between cCMV genetic variation, transmission, and immune response. The Core is responsive to the understanding that herpes viruses, and human cytomegalovirus (HCMV) in particular, are large DNA viruses that exhibit surprising levels of sequence diversity: HCMV samples from patients often have 1,000’s polymorphisms at both the consensus and population levels. This level of standing genetic variation is biologically important, as it has been shown to play a significant role in a range of clinical infectious disease challenges. For example, in HCMV, genetic diversity contributes to temporal and compartmental changes in allele frequencies in congenital fetal infections. To support investigations of such dynamics in our RhCMV model, the Genomic Sequencing Core will sequence populations of RhCMV genomes from animals, inoculum, and cultured virus samples provided by Projects 1-2 (Aim 1). Sequence reads will be mapped as RhCMV sequences through an iterative process of reference mediated alignments and de novo contig builds. RhCMV sequence datasets will be used to define an annotated consensus (i.e., the most common) sequence of each sample and provide summary statistics of viral populations. Summary statistics include total number of sequences reads, mapped reads/efficiency, mean coverage, polymorphisms in the consensus relative to the parental virus and population diversity. Results will be made available to the Projects. In addition, the Core will improve workflow by cataloguing an RhCMV saturation dataset, improve processing protocols, and will collaborate with the Viral Pathogen and Analysis Resource (ViPR) to provide RhCMV sequence data and related in vivo data for their simple, searchable format (Aim 2). Bulk sequence data will be submitted to the publicly available NCBI Sequence Read Archive. Finally, the Core will employ population genetics strategies to investigate the patterns of RhCMV evolution in congenital RhCMV models by interrogating viral loads and viral population sequence space to define diversity and mechanisms of divergence amongst maternal and infant viral populations (Aim 3). Other parameters that influence infection, transmission and disease including viral gene deletion strains (Project 2) and altered immunological states (Project 1) will be analyzed for their influence on viral population diversity, founder size and compartmental effects in relation to transmission and disease. Taken together, the Core will provide important understanding of how in vivo evolutionary processes, such as bottlenecks and selective pressure, influence viral transmission and fetal disease.