Measuring the HIV-1 Reservoir in the Context of Eradication and Pathogen Co-Infection

Infection with human immunodeficiency virus type-1 (HIV-1) causes progressive destruction of the host immune system due to increased loss of the virus’s target cells, CD4 T lymphocytes. Natural HIV-1 infection progresses to a disease known as acquired immunodeficiency syndrome (AIDS), characterised by increased susceptibility to opportunistic infections and cancers. Whilst HIV-1/AIDS was previously a terminal diagnosis, the development of antiretroviral therapy (ART) has drastically reduced HIV-1 associated mortality by providing sustained suppression of virus replication. Nevertheless, ART is unable to eradicate HIV-1 infection due to long-lived cells that harbour transcriptionally silent but inducible provirus, known as the latent reservoir (LR). HIV-1 eradication strategies therefore target latently infected cells for clearance and such studies require robust and sensitive assays to detect small changes in the viral reservoir. Therefore, two prominent HIV-1 quantification assays and widely used calibration standards were compared for their ability to quantify intracellular HIV-1 DNA in patient samples. Based on this analysis, an assay was selected for improvement by redesigning primers to improve the specificity of the method. Further, this work demonstrated the potential for HIV-1 transcript quantification using nanopore based next generation sequencing. Due to overlapping transmission routes and shared regions of high prevalence, HIV-1 infection is frequently associated with co-infections of pathogens such as Mycobacterium tuberculosis (Mtb) and hepatitis C virus (HCV). In both cases, co-infection with HIV-1 leads to more severe prognosis and increased rate of disease progression through disruption of the immune response, however, the effect of these pathogens on HIV-1 disease outcome is not well characterised. To quantify the impact of Mtb on HIV-1 replication, virus production was measured in cells that were infected in the presence of liposomes that mimic the cell wall glycolipid of variant Mycobacteria strains. This analysis demonstrates heterogenous effects of Mycobacteria derived liposomes on HIV-1 infection that is dependent on the tropism of the virus, the strain of Mycobacteria and the method of infection. Based on previous research, which showed that HCV envelope (Env) glycoprotein expression causes downmodulation of HIV-1 LTR driven transcription through disruption of NF-κB, the aim was to measure the effect of exogenous HCV glycoprotein production on HIV-1 activation and replication. Additionally, the effect of HCV glycoprotein expression on the transcriptome of the host cell was investigated using nanopore based RNAseq. Through this analysis, clear upregulation of endoplasmic reticulum stress response pathways in the presence of the HCV Env was observed. These pathways, or individual genes in these pathways, such as the stress response gene, activating transcription factor 3 (ATF3), are potential mediators of HCV induced downmodulation of NF-κB signalling and suggest that through these pathways, HCV may inhibit host immune signalling