Deep sequencing for HIV-1 clinical management

•NGS improves ART outcome predictions in ARV-naïve subjects starting NNRTIs and CCR5 antagonists.•NGS might also be helpful to select salvage ART regimens in ART-experienced subjects.•Transmission of INSTI remains anecdotal; Integrase genotyping is not currently mandatory before initiating INSTIs.•In a scenario where global HIV-1 eradication is now considered possible, making NGS accessible also to LMICs is a priority.•Reductions in NGS costs and increased accessibility to simplified bioinformatic NGS data analysis remain essential to end the HIV-1 pandemic.

The emerging HIV-1 resistance epidemic is threatening the impressive global advances in HIV-1 infection treatment and prevention achieved in the last decade. Next-generation sequencing is improving our ability to understand, diagnose and prevent HIV-1 resistance, being increasingly cost-effective and more accessible. However, NGS still faces a number of limitations that need to be addressed to enable its widespread use. Here, we will review the main NGS platforms available for HIV-1 diagnosis, the factors affecting the clinical utility of NGS testing and the evidence supporting −or not- ultrasensitive genotyping over Sanger sequencing for routine HIV-1 diagnosis. Now that global HIV-1 eradication might be within our reach, making NGS accessible also to LMICs has become a priority. Reductions in sequencing costs, particularly in library preparation, and accessibility to low-cost, robust but simplified automated bioinformatic analyses of NGS data will remain essential to end the HIV-1 pandemic.