Defective HIV-1 envelope gene promotes the evolution of the infectious strain through recombination in vitro

Abstract

Background: HIV-1 produces defective mutants in the process of reproduction. The significance of the mutants has not been well investigated. Methods: The plasmids of wild type (HIV-1 NL4-3) and Env-defective (HIV-1 SG3 ΔEnv) HIV-1 were co-transfected into HEK293T cells. The progeny virus was collected to infect MT4 cells. The env gene and near-full-length genome (NFLG) of HIV-1 were amplified and sequenced. The phylogenetic diversity, recombinant patterns and hotspots, and the functionality of HIV-1 Env were determined. Results: A total of 42 env genes and 8 NFLGs were successfully amplified and sequenced. Five types of recombinant patterns of env were identified and the same recombinant sites were detected in different patterns. The recombination hotspots were found distributing mainly in conservative regions of env. The recombination between genes of HIV-1 NL4-3 and HIV-1 SG3 Δenv increased the variety of viral quasispecies and resulted in progeny viruses with relative lower infectious ability than that of HIV NL4-3. The defective env genes as well as NFLG could be detected after 20 passages. Conclusion: The existence of the defective HIV-1 promotes the phylogenetic evolution of the virus, thus increasing the diversity of virus population. The role of defective genes may be converted from junk genes to useful materials and cannot be neglected in the study of HIV-1 reservoir.

High-throughput single-cell sequencing for retroviral reservoir characterization

“…Phylogenetic reconstruction of the virus evolutionary history within each animal revealed multiple instances of persistence of DRMs among intact viral sequences, but also the emergence of integrase DRM N155K in a defective virus during cART that was shared in related post-cART intact sequences. Though HIV DRMs have been hypothesized to persist through recombination of defective and intact viral genomes during co-infection 16 , the potential for viral RNA transcript production required for this process could not be confirmed for this virus population. Alternatively, the maintenance of "double-deletion" defective genomes with intact RT may be the result of accumulation over time due to limited protein expression, thereby reducing their ability to be cleared.…”

“…Characterization of intact virus may also not be the only solution to the problem of HIV persistence. Whereas integration of viral DNA permits survival of the DNA molecule through long-lived cells or even cellular division, it is not the sole form of survival for individual variants within the DNA - genomic fragments (including drug-resistant mutations sites) can be inherited through the act of recombination, allowing for even defective virus to contribute to successful viral rebound 15,16 .…”

Defective HIV-1 genomes and their potential impact on HIV pathogenesis

“…For example, sequence analysis of HIV proviral sequences obtained from CD4+ T cells from PLWH on ART attributed approximately 40% of the internal deletions detected to negative strand synthesis during reverse transcription [54]. Recombination, a process by which genetic diversity is introduced through template-switching between the two copies of the HIV RNA genome packaged in virions, also contributes to the mutation rate of reverse transcription products [55][56][57][58].…”