Superinfection promotes replication and diversification of defective HIV-1 proviruses in people with non-suppressible viraemia

Abstract During replication of some RNA viruses, defective particles can spontaneously arise and interfere with wild-type (WT) virus replication. However, these defective interfering particles (DIPs) have not been reported in people with HIV-1 (PWH). Here we find DIPs in PWH who have a rare, polyclonal form of non-suppressible viraemia (NSV). We characterized the source of NSV in two PWH who never reached undetectable viral load despite adherence to antiretroviral therapy (ART). Remarkably, in each participant, we found a diverse set of defective viral genomes sharing the same fatal deletions. This paradoxical accumulation of mutations by viruses with fatal defects was driven by superinfection with intact viruses, resulting in mobilization of defective genomes and accumulation of additional mutations during untreated infection. These defective proviruses interfere with WT virus replication, conditionally replicate and, in one case, have an R 0 > 1, enabling in vivo spread. Despite this, clinical outcomes showed no beneficial effect of these DIPs. These findings demonstrate that fatally defective proviruses, traditionally considered evolutionary dead ends, can replicate and diversify upon superinfection without preventing disease progression.