Novel methods in HIV-1 strain detection and clonal population identification using next-generation sequencing data

HIV-1is a highly recombinant retrovirus that constantly mutates and diverges, thus giving rise to new clonal populations, as well as recombinant subtypes. There has not been one consistent pipeline established, that can not only identify what strains or populations are in a sample, but also the recombination rate and type, in addition to the occurrence of quasi speciation. The pipeline discussed in this paper does both these tasks using the High Performance Virtual Environment (HIVE).The result of the recombination analysis is that recombination events are clearly identified and represented in the mutual reading frame of all possible genomes. The clonal discovery utility presents all bifurcations among different populations within the sample; producing multiple quasi specie trajectories along the length of the mutual reading frame. The implications of this work are very significant with regards to HIV treatment and vaccine discovery. The hope is that by producing an HIV-1 detection pipeline that specifically identifies HIV strains, recombination and quasi speciation therapies can be more optimally planned and carried out, and vaccine research can advance at a faster pace.

Author

• Voskanian, Alin

Language

• en

Keyword

• Clonal
• Recombination
• HIVE
• HIV-1

Date created

• 2015

Type of Work

• Master's Thesis

License

• All rights reserved

Rights statement

• In Copyright

GW Unit

• Biochemistry and Molecular Biology

Degree

• M.S.

Advisor

• Mazumder, Raja

Committee Member(s)

• Simonyan, Vahan

Persistent URL

•  https://scholarspace.library.gwu.edu/etd/8p58pd11q