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Quantifying nucleotide variation in RNA virus populations by next-generation sequencing

  • Author(s): Fedewa, Gregory Robert
  • Advisor(s): DeRisi, Joseph L
  • et al.

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 Chapter2, I show that Ebola virus requires no additional mutations in order to replicate efficiently in boa constrictor cells. In Chapter3, I show that SNV analysis can be used to track the identity and passage history of different RNA viruses.

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