Dissertation/Thesis Abstract

Quantifying Nucleotide Variation in RNA Virus Populations by Next-generation Sequencing
by Fedewa, Gregory, Ph.D., University of California, San Francisco, 2018, 69; 10936274
Abstract (Summary)

RNA viruses include several notable human pathogens including HIV, hepatitis C virus, West Nile virus, influenza, and Ebola virus. This group of viruses includes viruses with incredibly diverse genome structures, such as single-stranded genomes, double-stranded genomes, multipart genomes, negative-stranded genomes, and positive-stranded genomes. They also exist as heterogeneous populations that can mutate and rapidly evolve due to their error-prone polymerases. These errors then accumulate as they are passed down through generation. They can, therefore, be used as a historical marker for genetic relationships. If these errors result in a change of fitness for the virus they can then be used to locate areas in the genome that are undergoing selection pressures.

In this work, I use these principles to examine what changes are necessary for Ebola virus to infect boa constrictor cells and how high priority RNA viruses mutate as a function of routine viral passaging and propagation. In Chapter 2, I show that Ebola virus requires no additional mutations in order to replicate efficiently in boa constrictor cells. In Chapter 3, I show that SNV analysis can be used to track the identity and passage history of different RNA viruses.

Indexing (document details)
Advisor: DeRisi, Joseph L.
Commitee: Ahituv, Nadav, Cox, Jeffery S., Frankel, Alan
School: University of California, San Francisco
Department: Biological and Medical Informatics
School Location: United States -- California
Source: DAI-B 80/02(E), Dissertation Abstracts International
Subjects: Genetics, Bioinformatics, Virology
Keywords: Boa constrictor, Ebola virus, Filovirus, Malaria, RNA, SNV
Publication Number: 10936274
ISBN: 9780438474772
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