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RECOVIR: A NOVEL COMPUTATIONAL PLATFORM FOR UNCOVERING RECOMBINATION AND ASSOCIATED AMINO ACID VARIANTS IN ROTAVIRUS

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abstract
Viral replication requires dynamic, multi-faceted interactions among viral genes and their encoded proteins. The prevalence and mutational consequences of recombination within genomic segments and reassortment among segments have remained difficult to detect due to a lack of methods that identify recombination-associated variants. There is currently a need for fast, no-cost computational approaches to identify recombination as well as how viral proteins might participate in functional or physical interactions. We seek to tackle these problems by introducing the RecoVir program (Recombination-associated variants in Viruses), which has identified recombination-associated variants in a dataset of over 2,500 rotavirus A strains. This study demonstrates how reassortment can be detected in viral genomes through incongruencies in phylogenies. It expands upon traditional formats by identifying specific examples of RecAMs (recombination-associated mutations) within previously annotated structural sites responsible for protein function and interaction. Furthermore, this study provides variants for additional analysis to determine if such events and subsequent mutations have a functional impact on viral fitness. The RecoVir program is a novel methodology to expand our understanding of viral evolution. This approach simultaneously identifies unique variants and mutations which are crucial for understanding viral structural biology and guiding future therapies.
subject
computational
evolution
phylogenetic
reassortment
recombination
rotavirus
contributor
Ligon, Roddey Miller (author)
Pease, James B (committee chair)
Lyles, Douglas S (committee member)
date
2021-09-01T08:35:48Z (accessioned)
2021 (issued)
degree
Biology (discipline)
2022-08-31 (liftdate)
embargo
2022-08-31 (terms)
identifier
http://hdl.handle.net/10339/99081 (uri)
language
en (iso)
publisher
Wake Forest University
title
RECOVIR: A NOVEL COMPUTATIONAL PLATFORM FOR UNCOVERING RECOMBINATION AND ASSOCIATED AMINO ACID VARIANTS IN ROTAVIRUS
type
Thesis

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