Using Barcoded HIV Ensembles (B-HIVE) for Single Provirus Transcriptomics

The latent HIV reservoir is the main barrier to curing AIDS, because infected cells escape the immune system and antiretroviral therapies. Developing new treatment strategies requires technologies to trace latent proviruses. Here, we describe a genome-wide technique called Barcoded HIV Ensembles (B-HIVE) to measure HIV expression at the single provirus level. The principle of B-HIVE is to tag the genome of HIV with DNA barcodes to trace viral transcripts produced by single proviruses in an infected cell population. This in turn reveals which proviruses are active and which are latent or expressed at low level. B-HIVE is a high-throughput method to identify and quantify thousands of individual viral transcripts per round of infection. It can be applied in different conditions, characterizing the response of single proviruses to different treatments. Overall, B-HIVE gives unprecedented insight into the expression of single proviruses in populations of HIV-infected cells. © 2018 by John Wiley & Sons, Inc.