# Core 3:  Genomic Sequencing and Population Genetics Core

> **NIH NIH P01** · DUKE UNIVERSITY · 2020 · $33,789

## Abstract

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.

## Key facts

- **NIH application ID:** 9982189
- **Project number:** 5P01AI129859-02
- **Recipient organization:** DUKE UNIVERSITY
- **Principal Investigator:** Sallie R. Permar
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $33,789
- **Award type:** 5
- **Project period:** — → 2020-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9982189

## Citation

> US National Institutes of Health, RePORTER application 9982189, Core 3:  Genomic Sequencing and Population Genetics Core (5P01AI129859-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9982189. Licensed CC0.

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