Background
HIV-2 infection is considered as an attenuated viral infection. PBMC HIV-2 reservoir has been shown to be smaller than that of HIV-1 with a higher proportion of APOBEC3-induced defective proviruses. The aim of this study was to characterise the composition of the HIV-2 cellular reservoir by identifying the different forms of defective proviruses.
Methods
ARV-naive participants were recruited from the ANRS national HIV-2 cohort during 2020. Sequencing of protease, RT and integrase was performed using GridION (Oxford Nanopore Technologies, detection threshold: 5%). We considered all hypermutated pol sequences and those containing a stop codon as defective. We set up a specific HIV-2 Intact Proviral DNA Assay (IPDA), for both HIV-2 A and B groups, targeting the Psi and env to quantify 5’- and 3’-defective (due to large internal deletions), env APOBEC3-hypermutated and intact proviral DNA.
Results
Fifty-seven participants were recruited (median age: 56 years, 61% female), all with spontaneously undetectable viral load (<40 c/mL) except two (<200 c/mL). Among the 32 participants with successful prot-RT amplification, the median ratio of APOBEC3-induced mutations to the number of potential APOBEC3 mutation sites was significantly higher in RT than in protease (18% [IQR=17%-21%] vs. 11% [IQR=6%-16%], respectively; p=0.0001). Overall, five (16%) participants had APOBEC3-induced defective proviruses due to the presence of either hypermutations or stop codons in prot-RT. Of the 20 integrase sequences generated, only one participant was found to have APOBEC3-induced defective sequences. Of the 30 participants with IPDA results, 19 (63%) harboured env-hypermutated proviruses, 15 (50%) harboured proviruses defective at either the 5′ or 3′ end. Intact proviruses were detected in only one participant. Median HIV-2 total DNA level was 303 c/106 PBMC (IQR=189-764) consisting on average of 12% 3’-defective proviruses, 19% 5’-defective proviruses and 67% env-hypermutated proviruses.
Conclusions
In this cross-sectional analysis, we were able to describe the composition of part of the HIV-2 viral reservoir. This study describes for the first time the proportion of defective and intact HIV-2 proviruses within the viral reservoir and shows that a very small proportion of ARV-naïve individuals harbours intact proviruses and that most of the proviruses constituting the reservoir are hypermutated or carry large internal deletions. These findings are consistent with the attenuated profile of HIV-2 infection.