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Masters Degrees (Virology)

Permanent URI for this collectionhttps://hdl.handle.net/10413/7018

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Browsing Masters Degrees (Virology) by Subject "Antiretroviral therapy."

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    Genetic characterization of viral blips in patients following suppressive HIV ART.
    (2021) Jhamba, Lindiwe Amanda.; Gounder, Kamini.; Ndung'u, Peter Thumbi.
    Antiretroviral therapy (ART) has resulted in the decline of HIV-related mortality worldwide. On initiating treatment, most patients can suppress plasma viral RNA to undetectable levels (<20 copies/mL). Patients on ART frequently experience intermittent viremia (viral blips), however the genetic nature and source of these rebounding viruses while on suppressive ART remains unclear. The study of these genetic characteristics would be essential in the development of targeted vaccines and adjunct treatments. We identified four HIV-1 subtype C infected women from the Females Rising through Education, Support and Health (FRESH) acute infection cohort who experienced viral blips following suppressive ART (median 584 days). Two participants initiated treatment during the chronic infection phase (~625 days post detection) and the other two initiated treatment immediately upon first HIV-1 RNA detection. RNA was extracted from stored plasma samples of participants’ transmitter/founder (T/F) virus (~3 days post detection), pre-treatment initiation and during viral blips (>2,000 copies/mL). Gag and env genes were amplified by single genome amplification followed by sequencing. The protease and reverse transcriptase region of the pol gene were also amplified and bulk sequenced. Phylogenetic relatedness and genetic differences were visualized using Maximum-likelihood trees and Highlighter plots respectively (Los Alamos HIV-1 database). The gag and env blip sequences of the acute-treated participants were similar to those of the T/F, while those of the chronic-treated participants were genetically distinct from the T/F but similar to the pre-treatment initiation virus (PreART). In the acute-treated participants, all transmitted HLA-associated gag cytotoxic CD8+ T lymphocyte (CTL) escape identified was retained in the blip-derived sequences, however the chronic-treated participants experienced an increase of ~0.8% CTL escape at the blip time point. This increase coupled with development of a reduced replication capacity mutation (HLA-B*57:01/58:01 T242N), may be indicative of immune pressure prior to ART initiation. Mutations associated with bnAb escape in the CD4 binding, gp120/gp41 and V1V2 sites were identified only in the PreART and blip sequences of the chronic-treated participants, whereas the acute-treated retained the same amino acid residues at T/F and blip. With the exception of one chronic-treated participant who developed mutations associated with resistance to efavirenz, the viral blips were not associated with mutations linked to drug resistance. This data suggests that those who initiate treatment late are less likely to benefit from an immune response-inducing vaccine or bnAb therapy.
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    Identifying novel transcriptional regulatory elements of HLA-A alleles through the evaluation of the 5’ un-translated region sequences.
    (2020) Singh, Saiyuri.; Ramsuran, Veron.
    Sub-Saharan Africa holds approximately half the population living with human immunodeficiency virus (HIV) in the world (~19.6 million), of which around 7.2 million cases are found in South Africa. Although antiretroviral therapy can suppress viral loads to below detectable levels in most cases, drug resistance is a growing problem. Therefore, identifying novel treatment strategies are warranted against HIV. The strongest human genetic associations with HIV disease have been found within the human leukocyte antigen (HLA) region. The expression levels of various HLA genes have been associated with HIV disease outcomes. Increased HLA-A mRNA expression results in poor HIV outcomes due to the inhibition of natural killer (NK) cells since high mRNA expression of HLA-A results in high protein expression of HLA-E which serves as an inhibitory receptor for NK cells. Identifying factors that regulate the expression of HLA-A has the potential to serve as an avenue for HIV drug target sites. DNA methylation has previously been identified as one of the factors responsible for HLA-A expression regulation. In this study, we aimed to identify additional regulatory mechanisms for the HLA-A gene. The identification of a putative CCCTC-binding factor (CTCF) binding site upstream of HLA-A suggested that CTCF may play a role in regulation of HLA-A. Sequence alignments about 2 kilobases (2KB) upstream of the transcriptional start site (TSS) were analysed for polymorphisms that associate with HLA-A expression. Six HLA-A promoter variants (rs9260084, rs9260086, rs9260092, rs9260101, rs9260116 and rs41560714) were observed to significantly associate with HLA-A mRNA expression. However, only one single nucleotide polymorphism (SNP), rs9260084 (-993G>A), was predicted to disrupt a CTCF binding site. Despite the predicted disrupted binding site, using a chromatin immunoprecipitation (ChIP) assay, we did not detect any difference in CTCF binding across the -993 G>A variants. Additional transcriptional regulators, Nuclear Factor 1 (NF1), Ras related protein (RAP1) and glucocorticoid receptor (GR), were predicted to have differential binding to -993G>A, -226G>A and -885C>G, respectively. The results provided here serve as a basis for further studies exploring the role HLA-A promoter variants have in regulating HLA-A expression. These variants may serve as potential target sites for future therapeutic intervention against HIV.