P-A11 An End-To-End Solution in Deep Sequencing of HIV

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HIV drug resistance testing has become an integral part of the management of patients infected with HIV. A new pipeline combining Miseq instrument with DeepChek-HIV (RUO) via BaseSpace as an alternative to Sanger sequencing, opens a new domain of analysing minor HIV variant detection to <1% of the viruses' population. HIV-1 samples were sequenced via a MiSeq instrument (allowing a sensitive and reliable identification of HIV nucleotide variants even below 1%). In this study, nucleotides sequences were automatically uploaded onto BaseSpace via MiSeq Reporter and analysed by the DeepChek-HIV (RUO) software application. Compatible with all the key genomic regions for drug resistance testing of HIV (Reverse transcriptase, Protease, Integrase, GP41 and GP120/V3) in either BAM of FASTQ formats, several types of analyses were performed like a high resolution subtyping of each individual read, a population variants calling and a fully automated reporting. The outcomes of those data processing steps were then interpreted for drug resistance determination using a panel of guidelines part of the system. Results were produced and formatted in a simplified manner, directly compatible with an optimal, reliable, accurate, cost effective interpretation of minor variants even below 1% though efficient workflow, for research applications. This study illustrates the benefits of combining sensitive sequencing methods with software applications tailored for NGS data genotyping and interpretation. In addition to the reliability of the results, we showed that the performances of such a pipeline are compatible with the constraints related to HIV care in research uses.