Data for: Learning from full characterization of HIV proviruses in people receiving Long-Acting Cabotegravir/Rilpivirine with history of replication on the antiretroviral classes

To better understand factors associated with virological response, we characterized retrospectively HIV proviruses of seven People-With-HIV who received long-acting cabotegravir/rilpivirine (CAB/RPV-LA) selected according the following criteria: virological control achieved despite a history of viral replication on one or both corresponding antiretroviral classes (n=6); virological failure (VF) post CAB/RPV-LA initiation (n=1). The last available blood samples before the initiation of CAB/RPV-LA were analyzed retrospectively. Near full-length HIV-DNA genome haplotypes were inferred from Nanopore sequencing using in-vivo Genome-Diversity-Analyzer (iGDA) to search for archived Drug Resistance Mutations (DRMs) and to evaluate the frequency and the intactness of proviruses harboring DRMs. Archived DRMs including G-to-A mutations were found in samples from three subjects who maintained virological control. Genomes harboring DRMs were majorly in minority variants (<20%) and were defective ..., A near full-length HIV genome nanopore single genome sequencing (NFG) was performed on HIV DNA after limiting dilution to search for archived DRMs, link them with each other, and evaluate the intactness of proviruses harboring these DRMs. A de-hosting step was performed using the VIRiONT pipeline. A custom-designed bioinformatic pipeline adapted from the in-vivo Genome Diversity Analyzer (iGDA) algorithm was developed to recover representative haplotypes using the following initial criteria: Total reads >30, Min length >1,000 bp, Min freq >0.01 (1%), Mean depth >100 reads., , # Data for: Learning from full characterization of HIV proviruses in people receiving Long-Acting Cabotegravir/Rilpivirine with history of replication on the antiretroviral classes

[https://doi.org/10.5061/dryad.9w0vt4bqp](https://doi.org/10.5061/dryad.9w0vt4bqp)

A near full-length HIV genome nanopore single genome sequencing (NFG) was performed on HIV DNA after limiting dilution to search for archived DRMs and to evaluate the intactness of proviruses harboring these DRMs in blood samples taken before the switch to CAB/RPV-LA in 7 People-With-HIV-1 (ID1-7). A de-hosting step was performed using the VIRiONT pipeline (1). A custom-designed bioinformatic pipeline adapted from the in-vivo Genome Diversity Analyzer (iGDA) algorithm was developed to recover representative haplotypes (2) using the following initial criteria: Total reads >30, Min length >1,000 bp, Min freq >0.01 (1%), Mean depth >100 reads.

1.       Charre C, Regue H, Dény P, Josset L, Chemin I, Zoulim F, et al. ...