Genomic signatures of recent selection at HIV host susceptibility genes in a Central African human population

Multiple independent transfers of simian immunodeficiency virus (SIV) strains from chimpanzees to human populations produced the current HIV-1 pandemic. We hypothesized that Central African human populations may have been exposed to SIV prior to the current pandemic, and that previous local outbreaks may have selected for genetic resistance to immunodeficiency viruses. To test this hypothesis, I examined the genomes of Biaka Western pygmies, who historically have resided in forests within the range of the only chimpanzee subspecies (Pan troglodytes troglodytes) that carries strains of SIV ancestral to HIV-1. SNP genotypes of the Biaka were compared to those of an Eastern pygmy population and to other African groups residing outside the range of P. t. troglodytes. Genomic regions showing signatures of selection were compared to the genomic locations of AIDS restriction genes (ARGs), genes with known variants that affect HIV-1 infection or AIDS progression. In the Biaka, a strong signal of selection was detected at the ARG CUL5, with a modest signal of selection at the ARG TRIM5. Using a different test of selection, Biaka genomes showed a strong signal of selection at the ARG TSG101. Pygmies have also been found to carry genotypes protective against HIV-1 for the ARGs CCR2, CCL3L1 and CCR5.

Name thesis:degree_name

M.S.

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Bioinformatics

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2012

Author dc:creator

• Zhao, Kai

Contributors dc:contributor

• Roca, Alfred L.

• Bioinformatics
• Acquired immune deficiency syndrome (AIDS)
• Human immunodeficiency virus (HIV)
• AIDS Restriction Genes
• Biaka
• Selection
• Cullin-5 (CUL5)
• Tripartite motif-containing protein 5 (TRIM5)
• HIV dependency factor (HDF)

Statement dc:rights

• Copyright 2011 Kai Zhao

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/29582

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/29582