Real-time Analysis for the Phylogenetic Investigation of Drug-resistant HIV clusters (RAPID-HIV)

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Project Abstract The overall aim of this project is to enable real-time surveillance of HIV-1 drug resistance and transmission clusters using an integrated computational pipeline and novel amplicon approach that we have developed for nanopore sequencing. This project is important because globally the rise of resistance to ART is threating the significant progress made in suppressing the virus. In Africa, this threat is particularly acute where several countries have reported levels of pre-treatment HIV resistance exceeding 10% to the standard first-line therapy. The advent of portable sequencing technology means viral genomic sequencing is now positioned to exert a greater impact on the public health response to the upsurge in resistance. In this proposal we will use the MinION sequencing device and assess the performance characteristics (accuracy, specificity, sensitivity) of a novel amplicon-based approach in order to accurately characterize HIV-1 diversity using full-length pol amplicons. Owing to the biased nucleotide composition of the HIV-1 genome and the complexity of the raw nanopore data we will identify how we can improve raw read accuracy and simplify the analysis of nanopore sequencing data by non-bioinformatics experts. Based on the elevated HIV-1 risks within Ugandan fishing communities we hypothesize that viral clusters from fisherfolk frequently harbor drug-resistance mutations and act as reservoirs of resistance. Thus, we need to understand the transmission dynamics and evolution of transmitted drug resistance within HIV-1 infected fishing communities around Lake Victoria. This proposal will integrate sequencing, basecalling, and analysis in near real-time using an integrated workflow to enable HIV-1 drug resistance surveillance and the detection of transmission clusters. To achieve these objectives, we will use a panel of HIV-1 samples comprising locally circulating strains in order to evaluate the performance characteristics of our amplicon sequencing approach to accurately characterize HIV-1 diversity using full-length pol amplicons. We will develop custom trained basecalling models specific to HIV-1 to accurately quantify drug resistance and implement an integrated analysis pipeline for real-time genotyping and drug resistance reporting to simplify the analysis of nanopore sequencing data by non-bioinformatics experts. Lastly, we will use our recently developed amplicon sequencing approach coupled with our real-time analysis pipeline to understand the transmission dynamics and evolution of transmitted drug resistance within HIV-1 infected individuals from fishing communities around Lake Victoria. Together, these results will advance our understanding of the transmission dynamics of HIV-1 among fishing communities and evaluate the burden of resistance among this high-risk sub-population.