Biology subjects

Ganga, Y.

Publications and source records attributed to Ganga, Y..

5 recordsLinked to original sources

bioRxiv2022

HIV skews the SARS-CoV-2 B cell response toward an extrafollicular maturation pathway

BackgroundHIV infection dysregulates the B cell compartment, affecting memory B cell formation and the antibody response to infection and vaccination. Understanding the B cell response to SARS-CoV-2 in people living with HIV (PLWH) may explain the increased morbidity, reduced vaccine efficacy, reduced clearance, and intra-host evolution of SARS-CoV-2 observed in some HIV-1 coinfections. MethodsWe compared B cell responses to COVID-19 in PLWH and HIV negative (HIV-ve) patients in a cohort recruited in Durban, South Africa, during the first pandemic wave in July 2020 using detailed flow cytometry phenotyping of longitudinal samples with markers of B cell maturation, homing and regulatory features. ResultsThis revealed a coordinated B cell response to COVID-19 that differed significantly between HIV-ve and PLWH. Memory B cells in PLWH displayed evidence of reduced germinal center (GC) activity, homing capacity and class-switching responses, with increased PD-L1 expression, and decreased Tfh frequency. This was mirrored by increased extrafollicular (EF) activity, with dynamic changes in activated double negative (DN2) and activated naive B cells, which correlated with anti-RBD-titres in these individuals. An elevated SARS-CoV-2 specific EF response in PLWH was confirmed using viral spike and RBD bait proteins. ConclusionsDespite similar disease severity, these trends were highest in participants with uncontrolled HIV, implicating HIV in driving these changes. EF B cell responses are rapid but give rise to lower affinity antibodies, less durable long-term memory, and reduced capacity to adapt to new variants. Further work is needed to determine the long-term effects of HIV on SARS-CoV-2 immunity, particularly as new variants emerge. FundingThis work was supported by a grant from the Wellcome Trust to the Africa Health Research Institute (Wellcome Trust Strategic Core Award [grant number 201433/Z/16/Z]). Additional funding was received from the South African Department of Science and Innovation through the National Research Foundation (South African Research Chairs Initiative, [grant number 64809]), and the Victor Daitz Foundation.

immunology↗

bioRxiv2021

SARS-CoV-2 cell-to-cell spread occurs rapidly and is insensitive to antibody neutralization

Viruses increase the efficiency of close-range transmission between cells by manipulating cellular physiology and behavior, and SARS-CoV-2 uses cell fusion as one mechanism for cell-to-cell spread. Here we visualized infection using time-lapse microscopy of a human lung cell line and used live virus neutralization to determine the sensitivity of SARS-CoV-2 cell-to-cell spread to neutralizing antibodies. SARS-CoV-2 infection rapidly led to cell fusion, forming multinucleated cells with clustered nuclei which started to be detected at 6h post-infection. To compare sensitivity of cell-to-cell spread to neutralization, we infected either with cell-free virus or with single infected cells expressing on their surface the SARS-CoV-2 spike protein. We tested two variants of SARS-CoV-2: B.1.117 containing only the D614G substitution, and the escape variant B.1.351. We used the much smaller area of single infected cells relative to infection foci to exclude any input infected cells which did not lead to transmission. The monoclonal antibody and convalescent plasma we tested neutralized cell-free SARS-CoV-2, with the exception of B.1.351 virus, which was poorly neutralized with plasma from non-B.1.351 infections. In contrast, cell-to-cell spread of SARS-CoV-2 showed no sensitivity to monoclonal antibody or convalescent plasma neutralization. These observations suggest that, once cells are infected, SARS-CoV-2 may be more difficult to neutralize in cell types and anatomical compartments permissive for cell-to-cell spread.

microbiology↗

bioRxiv2021

Aggregated Mycobacterium tuberculosis enhances the inflammatory response

Mycobacterium tuberculosis (Mtb) readily aggregates in culture and Mtb aggregates in the lung were observed in experimental Mtb infection. However, the physiological consequences of Mtb aggregation are incompletely understood. Here we examined the human macrophage transcriptional response to aggregated Mtb relative to infection with non-aggregated single or multiple bacilli per host cell. Infection with aggregated Mtb led to an early upregulation of pro-inflammatory associated genes and enhanced TNF signaling via the NF{kappa}B pathway. Both these pathways were significantly upregulated relative to infection with single bacilli, and TNF signaling was also significantly elevated relative to infection with multiple non-aggregated Mtb. Secretion of TNF and downstream cytokines were also enhanced. On a longer timescale, aggregate infection led to overall increased acidification per macrophage and a high proportion of death in these cells after aggregate phagocytosis. Host cell death did not occur when Mtb aggregates were heat killed despite such clumps being readily picked up. To validate that Mtb aggregates do occur in the human lung, we document Mtb aggregates surrounding a cavity in a human TB lesion. Aggregates may therefore be present in some lesions and elicit a stronger inflammatory response resulting in recruitment of additional phagocytes and their subsequent death, potentially leading to necrosis and transmission.

microbiology↗

bioRxiv2019

The CNS in the face of ART contains T cell origin HIV which can lead to drug resistance

HIV persists despite antiretroviral therapy (ART) in cellular reservoirs thought to occur in distinct anatomical compartments. Therapy failure may occur because of incomplete ART adherence and possibly viral replication at some reservoir sites. The CNS may serve as a reservoir site due to lowered ART penetration and virus production from long-lived tissue resident macrophages. Compelling evidence for the CNS as a reservoir is the existence of individuals where HIV is suppressed below limit of detection in blood but detectable in the cerebrospinal fluid (CSF), termed CSF Escape. Here, we asked whether HIV in CSF Escape individuals is derived from macrophages or persists due to lowered ART. We used cell surface markers on the HIV envelope to determine the cellular source of HIV. We verified detection using in vitro derived virus from infected macrophages and T cells and tested CSF from CSF Escape individuals. We observed host surface markers consistent with T cell origin. We also measured ART concentrations in the CSF and plasma. We found a dramatic decrease in CSF ART concentrations described previously, but no significant difference between CSF Escape versus fully suppressed individuals. To examine the effect of the observed CSF ART concentrations on HIV replication, we used long-term infection with ART in cell culture. CSF Escape ART levels led to either HIV suppression or evolution of drug resistance, but not replication of drug sensitive HIV. These observations argue that persistent CNS viremia despite ART can be T cell generated and may result in drug resistance and therapy failure.

microbiology↗

bioRxiv2017

Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death

HIV has been reported to be cytotoxic in vitro and in lymph node infection models. Using a computational approach, we found that partial inhibition of transmission which involves multiple virions per cell could lead to increased numbers of live infected cells if the number of viral DNA copies remains above one after inhibition, as eliminating the surplus viral copies reduces cell death. Using a cell line, we observed increased numbers of live infected cells when infection was partially inhibited with the antiretroviral efavirenz or neutralizing antibody. We then used efavirenz at concentrations reported in lymph nodes to inhibit lymph node infection by partially resistant HIV mutants. We observed more live infected lymph node cells, but with fewer HIV DNA copies per cell, relative to no drug. Hence, counterintuitively, limited attenuation of HIV transmission per cell may increase live infected cell numbers in environments where the force of infection is high.

bioinformatics↗