The main obstacle to curing HIV is the presence of latent proviruses in the bodies of infected patients. The partial success of reactivation therapies suggests that the genomic context of integrated proviruses can interfere with treatment. Here we developed a method called Barcoded HIV ensembles (B-HIVE) to map the chromosomal locations of thousands of individual proviruses while tracking their transcriptional activities in an infected cell population. B-HIVE revealed that, in Jurkat cells, the expression of HIV is strongest close to endogenous enhancers. The insertion site also affects the response to latency-reversing agents, because we found that phytohemagglutinin and vorinostat reactivated proviruses inserted at distinct genomic locations. From these results, we propose that combinations of drugs targeting all areas of the genome will be most effective. Overall, our data suggest that the insertion context of HIV is a critical determinant of the viral response to reactivation therapies.

This research was supported by the Government of Catalonia and the Spanish Ministry of Economy and Competitiveness (Plan Nacional BFU2012-37168, Centro de Excelencia Severo Ochoa 2013-2017 SEV-2012-0208). J.P.M. and A.M. were supported by a grant from the Spanish Ministry of Economy and Competitiveness and FEDER (SAF2013-46077-R). E.Z. and G.J.F. are supported by the European Research Council (Synergy Grant 609989).