The human immunodeficiency virus (HIV) integrates its genome into that of infected cells and may enter an inactive state of reversible latency that cannot be targeted using antiretroviral therapy. Sequencing such a provirus and the adjacent host junctions in individual cells may elucidate the mechanisms of the persistence of infected cells, but this is difficult owing to the 150-million-fold higher amount of background human DNA. Here we show that full-length proviruses connected to their contiguous HIV–host DNA junctions can be assembled via a high-throughput microfluidic assay where droplet-based whole-genome amplification of HIV DNA in its native context is followed by a polymerase chain reaction (PCR) to tag droplets containing proviruses for sequencing. We assayed infected cells from people with HIV receiving suppressive antiretroviral therapy, resulting in the detection and sequencing of paired proviral genomes and integration sites, 90% of which were not recovered by commonly used nested-PCR methods. The sequencing of individual proviral genomes with their integration sites could improve the genetic analysis of persistent HIV-infected cell reservoirs.

人类免疫缺陷病毒 (HIV) 将其基因组整合到受感染细胞的基因组中，并可能进入一种无法使用抗逆转录病毒疗法靶向的可逆潜伏期的非活动状态。对单个细胞中的这种前病毒和相邻宿主连接进行测序可能会阐明受感染细胞持续存在的机制，但这很困难，因为背景人类 DNA 的量要高出 1.5 亿倍。在这里，我们展示了与其相邻的 HIV-宿主 DNA 接头相连的全长前病毒可以通过高通量微流体分析组装，其中基于液滴的 HIV DNA 在其天然环境中的全基因组扩增，然后是聚合酶链反应。 PCR）标记含有原病毒的液滴进行测序。我们分析了接受抑制性抗逆转录病毒治疗的 HIV 感染者的感染细胞，从而检测和测序了配对的前病毒基因组和整合位点，其中 90% 没有通过常用的巢式 PCR 方法恢复。对单个前病毒基因组及其整合位点进行测序可以改进对持续感染 HIV 的细胞库的遗传分析。