Comparative analysis of pre-existing HIV drug resistance mutations in proviral DNA via Next-Generation Sequencing and routine HIV RNA genotyping

by Selleckchem | May 08 2023

Background: We investigated whether deep sequencing of archived HIV DNA of antiretroviral-naïve persons with acute/early HIV infection could identify transmitted drug resistance mutations (DRM), per the IAS drug resistance algorithm, that are not detected by routine bulk (consensus) sequencing.

Methods: Deep sequencing of HIV DNA from peripheral blood mononuclear cells and consensus sequencing from concurrent blood plasma (BP) was performed from antiretroviral (ART)-naïve adults with recent infection. We compared the prevalence of low-frequency (2-20%) and high-frequency (>20%) non-nucleoside reverse transcriptase inhibitor (NNRTI), nucleoside reverse transcriptase inhibitor (NRTI), and protease inhibitor (PI) DRM.

Results: Overall, 190 individuals were included, 72 (37.9%) with acute, 20 (10.5%) very early, and 98 (51.6%) with recent HIV infection. While all DRM detected in plasma appeared in archived proviral DNA, 9 high-frequency mutations were only detected in HIV DNA. These included 3 NRTI mutations, 4 NNRTI mutations, 1 PI mutation, and 1 H221Y (associated rilpivirine resistance) mutation. When considering DRM <20%, 11 NNRTI and 7 NRTI, 6 PI, and 3 F227L (associated doravirine resistance) mutations were found exclusively in HIV DNA. Interestingly, while 2 high-frequency M184V appeared in both DNA and RNA, low-frequency M184I were exclusive to HIV DNA (n=6). No participants experienced virologic failure after initiating ART during the median 25.39 ± 3.13 months of follow-up on treatment.

Conclusion: Although most high-frequency DRMs were consistently detected in HIV RNA and HIV DNA, the presence of low-frequency DRM in proviral DNA may be relevant for clinicians as these mutations could become dominant under drug selection pressure.

Comments：

The study investigated the ability of deep sequencing of archived HIV DNA to identify transmitted drug resistance mutations (DRM) that are not detected by routine bulk sequencing in antiretroviral-naïve individuals with acute/early HIV infection. The prevalence of low-frequency (2-20%) and high-frequency (>20%) non-nucleoside reverse transcriptase inhibitor (NNRTI), nucleoside reverse transcriptase inhibitor (NRTI), and protease inhibitor (PI) DRM was compared between deep sequencing of HIV DNA from peripheral blood mononuclear cells and consensus sequencing from concurrent blood plasma (BP).

The study included 190 individuals, and while all DRM detected in plasma appeared in archived proviral DNA, 9 high-frequency mutations were only detected in HIV DNA, including 3 NRTI mutations, 4 NNRTI mutations, 1 PI mutation, and 1 H221Y mutation associated with rilpivirine resistance. When considering DRM <20%, 11 NNRTI and 7 NRTI, 6 PI, and 3 F227L mutations associated with doravirine resistance were found exclusively in HIV DNA. Additionally, low-frequency M184I mutations were exclusive to HIV DNA.

The presence of low-frequency DRM in proviral DNA may be relevant for clinicians, as these mutations could become dominant under drug selection pressure. No participants experienced virologic failure after initiating ART during the median 25.39 ± 3.13 months of follow-up on treatment.