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Thesis
Assessment of genes in defective integrated HIV-1 provirus within the PBMC compartment of individuals with neuroHIV
Master of Science (M.S.), Drexel University
Dec 2021
DOI:
https://doi.org/10.17918/00000683
Abstract
The integrated human immunodeficiency virus type 1 (HIV-1) provirus forms a stable but transcriptionally silent viral reservoir in the host. Studies have also shown that this viral reservoir contains both replication-competent and defective-proviral sequences. At least some defective proviruses may still be able to produce viral proteins which may contribute to chronic HIV-1 pathogenesis and disease. We have previously studied genetic variation associated with the expression of the viral accessory protein Tat in an attempt to link this variation to functional outcomes. Sequencing of the HIV-1 genome showed an approximate 40 percent failure rate in amplifying the tat gene region. This could be due to genetic variation at the site of the PCR primer complementarity, low HIV-1 target genome copies in the peripheral blood mononuclear cell (PBMC) population, or a lack of target due to defective provirus. We hypothesized that the reason for such variable results could be due to accumulation of replication incompetent defective proviruses. Given these observations, we used a near-full length (NFL) PCR amplification strategy to examine the full spectrum of integrated proviruses contained within the PBMC compartment of individuals in the absence or presence of neuroHIV. The HIV protein Tat has been linked to cause neuropathogenesis on its own. Tat is the only viral regulatory protein detectable in therapy-controlled individuals. Tat has also been shown to be made in latently infected cells. Given this, we hypothesized that the more the tat gene was present, the more likely it could be for the individual having neurocognitive impairment. Amplicon analyses were conducted utilizing a third-generation sequencing (TGS) platform, Nanopore's MinION. Initial results showed defective virus as the predominant species in most individuals. Further analysis showed a trend toward tat gene presence correlating to neurocognitive impairment.
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Details
- Title
- Assessment of genes in defective integrated HIV-1 provirus within the PBMC compartment of individuals with neuroHIV
- Creators
- Diehl Remedio De Souza
- Contributors
- Srinivas Somarowthu (Advisor)Michael R. Nonnemacher (Advisor)
- Awarding Institution
- Drexel University
- Degree Awarded
- Master of Science (M.S.)
- Publisher
- Drexel University; Philadelphia, Pennsylvania
- Number of pages
- xi, 97 pages
- Resource Type
- Thesis
- Language
- English
- Academic Unit
- Biochemistry and Molecular Biology; College of Medicine; Drexel University
- Other Identifier
- 991016054028404721