Biology subjects

Abrahams, M.-R.

Publications and source records attributed to Abrahams, M.-R..

4 recordsLinked to original sources

bioRxiv2025

Digital PCR detection of Mycobacterium tuberculosis and HIV-1 co-localization in spinal tuberculosis biopsies

BackgroundMycobacterium tuberculosis (Mtb) and HIV-1 co-infection in tissues is suggested to favour reciprocal replication, infection and reservoir expansion. Yet, confirmation of this detrimental synergism in diseased tissues is limited. MethodsIn this prospective study of 25 adults investigated for spinal tuberculosis (STB) in South Africa (13 (52%) people living with HIV-1 (PLWH), on antiretroviral treatment) 25 open surgery or CT-guided biopsies were collected and portioned into 93 segments. Extracted DNA was analysed by droplet digital PCR (ddPCR) to detect and quantify Mtb complex (MTBC) (rpoB, IS6110), HIV-1 (pol, gag) and Human (RPP30) gene copies. ddPCR sensitivity for Mtb was validated against Xpert-Ultra and culture. Total biopsy and intra-biopsy variation in pathogen DNA abundance, co-detection, and relationships to human cellularity, HIV status, and peripheral viral load (VL) evaluated. ResultsddPCR detected MTBC DNA in biopsies from 10/10 (100%) culture-confirmed STB, 5/6 (83%) Xpert Ultra-confirmed STB and 4/9 (44%) diagnosed Not STB (all 4 with previous pulmonary TB). Detected MTBC ranged from 8-59,144 rpoB copies/biopsy. RpoB copies/million human cells were higher in biopsies from PLWH (p=0.0096) and positively correlated with matched-segment HIV-1 pol copies/million cells (r=0.40; p=0.0003), but not VL. HIV-1 DNA was detected in all PLWH biopsies, four with undetectable VL. HIV-1 pol copies/million cells were higher in segments with MTBC DNA co-detected (p=0.011) and also correlated with VL (r=0.91; p=0.0003). ConclusionsReciprocal relationships exists between Mtb and HIV-1 abundance in spinal tissue. Findings support investigating TB-HIV co-infected tissue segments to characterise how the immune microenvironment impacts HIV-1/Mtb reservoir persistence and/or expansion.

molecular biology↗

bioRxiv2025

HIV-1 Rebound Virus Consists of a Small Number of Lineages That Entered the Reservoir Close to ART Initiation

HIV-1 persists as a latent reservoir during suppressive antiretroviral therapy (ART). Viral rebound occurs upon ART interruption, posing a challenge to cure efforts. Characterizing viral populations fuelling rebound is imperative to curing HIV-1. We used longitudinal samples collected pretherapy from women in the CAPRISA 002 cohort to create an evolutionary time- line to determine the pretherapy timepoint when the rebound virus originally entered the long- lived reservoir. Participants (N=10) were untreated for an average of 5 years then on ART for an average of 2 years before viral rebound (defined as >1000 RNA copies/ml). env sequences were used to characterize the longitudinal pre-ART evolving viral RNA population, the proviral DNA reservoir during ART, and viral RNA in the plasma during rebound. For each participant, between 1 and 3 major viral lineages were identified in the plasma during rebound. A total of 20 rebound virus lineages were examined for the 10 participants, and 19 were found to have entered the reservoir around the time of therapy initiation. The one lineage estimated to enter the reservoir more than a year before therapy was observed in a participant who was untreated for more than 8 years, yet retained moderate CD4 T cell counts. Analysis of the viral DNA reservoir, from which the rebound viruses emanated, revealed that while 95% of rebounding lineages dated to the year before ART initiation, only 61% of unique proviruses dated to that time period. Strikingly, for three participants with DNA reservoirs dominated by viruses from earlier in untreated infection, only 33% of unique proviruses dated to the year before ART initiation, yet 83% of rebounding lineages dated to that time. Our results show that rebound virus almost exclusively comes from the portion of the latent reservoir that formed around the time of therapy initiation, even when the reservoir is composed of diverse sequences from across the pre-ART time period. Author SummaryHIV-1 is maintained in a long-lived reservoir during suppressive therapy. Virus rebounds if therapy is discontinued. We found that in most cases rebound virus comes from a pool of viral sequences that entered the long-lived reservoir around the time of therapy initiation. While the viral DNA reservoir is on average also skewed toward sequences replicating around the time of therapy initiation, the rebound virus almost exclusively comes from this portion of the latent reservoir, even when the reservoir contained proviruses from much earlier in untreated infection. Thus, we hypothesize that there are features of the viruses forming the latent reservoir around the time of therapy initiation, or features of the host at that time, that select these viruses as initiators of rebound during therapy discontinuation.

microbiology↗

bioRxiv2024

The role of Nef in the long-term persistence of the replication-competent HIV reservoir in South African women

HIV-1 Nef mediates immune evasion and viral pathogenesis in part through downregulation of cell surface cluster of differentiation 4 (CD4) and major histocompatibility complex class I (MHC-I) on infected cells. While Nef function of circulating viral populations found early in infection has been associated with reservoir size in early-treated cohorts, there is limited research on how its activity impacts reservoir size in people initiating treatment during chronic infection. In addition, there is little research on its role in persistence of viral variants during long-term antiretroviral therapy (ART). Phylogenetically distinct nef genes (n=82) with varying estimated times of reservoir entry were selected from viral outgrowth variants stimulated from the reservoir of South African women living with HIV who initiated ART during chronic infection (n=16). These nef genes were synthesized and used in a pseudovirus infection assay that measures CD4 and MHC-I downregulation via flow cytometry. Downregulation measures were compared to the size of the replication-competent viral reservoir (RC-VR), estimated by quantitative viral outgrowth assay (QVOA) at 5 years after treatment initiation, as well as proviral survival time. Maximum Nef-mediated MHC-I downregulation was significantly associated with RC-VR size (p=0.034), but this association was not observed for CD4 downregulation. Conversely, we did not find a consistent association between intraparticipant MHC-I or CD4 downregulation and the variant timing of entry into the reservoir. These data support a role for Nef-mediated MHC-I downregulation in determining RC-VR size, but more work is needed to determine Nefs role in the survival of individual viral variants over time. Author summaryUnderstanding the HIV reservoir, including viral determinants of reservoir formation and maintenance, is key for the rational design of cure interventions. In addition, for cure interventions to be equitable, it needs to be broadly applicable. While African women bear the greatest burden of HIV globally, most cure research has been performed in men living in the global North. Our study aims to elucidate attributes of the virus that contribute to reservoir dynamics in South African women on ART. We investigated the ability of the HIV accessory protein Nef to reduce the cell surface levels of two cellular proteins, CD4 and MHC-I, and compared this downregulation capacity with the size of the HIV reservoir and survival of cells infected with a given viral isolate. We found a positive association between an individuals measured reservoir size and MHC-I downregulation, but not CD4 downregulation. There was little evidence for a survival benefit for stronger Nef MHC-I reduction, but more research is needed on this subject. These data support earlier work and suggest that Nefs interaction with MHC-I may be a target to restrict the latent reservoir and inform alternate cure strategies.

pathology↗

bioRxiv2019

The Replication-Competent HIV-1 Latent Reservoir is Primarily Established Near the Time of Therapy Initiation

Although antiretroviral therapy (ART) is highly effective at suppressing HIV-1 replication, the virus persists as a latent reservoir in resting CD4+ T cells during therapy. Little is known about the dynamics of reservoir formation and this reservoir forms even when ART is initiated early after infection. The reservoir of individuals who initiate therapy in chronic infection is generally larger and genetically more diverse than that of individuals who initiate in acute infection, suggesting the reservoir is formed continuously throughout untreated infection. To determine when viruses enter the latent reservoir, we compared sequences of replication-competent viruses from resting CD4+ T cells from nine women on therapy to viral sequences circulating in blood collected longitudinally prior to therapy. We found that 78% of viruses from the latent reservoir were most genetically similar to viruses replicating just prior to therapy initiation. This proportion is far greater than expected if the reservoir forms continuously and is always long-lived. Thus, therapy alters the host environment in a way that allows the formation of a majority of the long-lived latent HIV-1 reservoir.\n\nOne Sentence SummaryMost of the long-lived, replication-competent HIV-1 reservoir is formed at the time of therapy initiation.

microbiology↗