Background:
The persistence of SIV/HIV reservoirs is the main obstacle to a cure and the cause of viral rebound after ART cessation. However, the source of viral rebound remains elusive. We characterized the proviral landscape in various tissues of virally suppressed SHIV-infected rhesus macaques before ART interruption (ATI) and matched it with the env sequences from plasma viruses during rebound.
Methods:
We used a highly processive and accurate polymerase and PacBio sequencing to obtain near full-length (NFL) genome sequences from blood, lymph node, and gut biopsies in 5 SHIV-infected rhesus macaques who started ART 8 weeks post infection and remained on therapy for 28 weeks. Env sequences (2,554 pb) from plasma rebound viruses 4 weeks after ATI were obtained by single genome sequencing and analyzed using the ElimDupes tool from the HIV Sequences Database to identify matches between intact NFL proviruses and plasma env sequences.
Results:
Using our novel NFL sequencing approach, a total of 144 proviral sequences were obtained (49 from blood, 63 from lymph nodes and 32 from the gut). 35% of all viral sequences were genetically intact, with a lower proportion in the gut (26%) compared to the blood (42%, p=0.04) and the lymph nodes (41%, p=0.04). Overall, only 2.8% of the proviral sequences were 100% identical, indicating that the SHIV reservoir was mainly composed of unique sequences. Overall, we found that rebounding viruses recovered from plasma more frequently matched with pre-ATI intact proviruses derived from lymph nodes (4 pairs of matched sequences) compared to sequences from blood and the gut (1 and 1 pairs of matched sequences, respectively).
Conclusions:
The SHIV reservoir is largely composed of non-clonal proviral sequences, suggesting that clonal expansion of the SHIV reservoir has a minor contribution to viral persistence in this model. Our results further suggest that intact proviruses persisting in the lymph nodes may be a preferential source of viral rebound upon ATI in this model.