Research Projects

In absence of an effective vaccine, current treatment modality for HIV-1 infection is early initiation of antiretroviral therapy (ART) regardless of CD4 counts or clinical stage. ART reduces viral load in HIV-1 infected children but lifelong adherence is a challenge for children who acquire HIV-1 infection by vertical infection during infancy and are initiated early on ART. In children, apart from viral suppression, recovery of lost B cell functionality and humoral response to other infections are also important. Over recent years, clinical trials have shown efficacy of HIV-1 monoclonal broadly neutralizing antibody (bnAb) cocktail administration as adjuvant to ART. However, it will only be effective as supplementary treatment if patient’s residual viral reservoir is neutralization susceptible to existing HIV-1 bnAbs. Studies have shown natural bnAb production in children against HIV-1, earlier than adults and with less somatic hypermutations in their bnAb BCRs. Children may respond particularly well to current vaccine design strategies which seek to trigger rare B cell precursors and then steer affinity maturation toward the development of bnAbs in a multi-stage approach. The impact of early ART on B cell populations and B Cell Receptor (BCR) repertoire in these children and how it shapes their functionality in eliciting protective broadly neutralizing (bnAb) responses remains to be studied. Chronic high viremia causes persistent polyclonal B cell activation and dilution of bnAb producing clones. On ART, the bnAb producing B cells have more potential to expand and evolve into robust bnAb secreting plasma cells. Early start of ART, by suppressing viremia and limiting diversification of virus in patients, may help restoration and functional activation of bnAb specific B cell clones against founder viruses and their close mutants to persist and mature into HIV-1 bnAb producing B cells. Hence, in this proposed project, we will use high throughput deep sequencing to longitudinally study BCR repertoire lineage and B cell subpopulations in a cohort of 15 HIV-1+ children initiated early on ART, at both pre-ART and post-ART timepoints and also in 15 age-matched healthy controls. In the current set up of Test and Treat policy in India, this will help us define the effects of early ART on restoration of B cell functionality and memory to levels comparable to healthy children, and identify evolving bnAb specific BCR sequences (with details on gene usage, percent SHM, CDR sequences etc) to potentially develop bnAbs. These BCR sequences and the HIV-1 envelop specific epitopes that they are identified to target, and the frequencies of their unmutated common ancestor (UCA) (naïve BCR) in healthy children will be important guides in immunogen design for paediatric vaccines. New BCR lineages identified to appear/expand at post-ART time points will indicate responses generated against epitopes belonging to ART resistant virus and will guide design of epitope-directed therapeutic bnAb regimens in Indian paediatric population, as adjuvant to ART. We will assess B cell phenotypes using flowcytometry and single cell cDNA library based immune discovery panel (CITE-seq) approaches. This will evaluate B cell activation, memory development and exhaustion status using proportions of known B cell subsets and new/rare subsets at pre- and post-ART timepoints in HIV+ children. Combining the sequence and phenotype data we will look at the development/maturation of rare B cell subsets characterized by antigen expression at either time points. All these along with neutralization potency of patient plasma at pre- and post-ART timepoints will wholistically inform the effects of early initiation of the current ART regimen on immune reconstitution in HIV-1 infected children.