Real-world prevalence of non-integrase INSTI resistance-associated mutations and virological outcomes in people who have recently acquired HIV-1 in the UK

Introduction: Integrase strand transfer inhibitors(INSTIs) are the mainstay of antiretroviral therapy(ART) globally. Virological breakthrough is uncommon but often manifests as low level viraemia and only 50% of cases have identified drug resistance mutations in the integrase gene. Non-integrase mutations in the Gag-nucleocapsid protein (NC), envelope glycoprotein (Env) and 3'polypurine tract (3'PPT) have been identified in vitro. Methods: Between 2015 and 2021, HIV-1 whole genome sequencing was performed on samples from people with recently acquired HIV-1 in the UK. Sequences were linked to demographic and clinical data within the UK Health Security Agency's HIV and AIDS Reporting System. The relationship between non-integrase enzyme mutations and virological outcomes was assessed.375 (34%) of 1106 participants started an INSTI-based regimen. Of these, 337 (90%) were men and 196 (52%) were living with subtype B. The median age was 33 years and number of viral loads within 24 months of starting ART was 4. Results: Overall, Env Y61H (33, 10%) and A539V (16, 5.0%), 3'PPT c9053t (17, 5.0%), and NC N8S (16, 4.8%) were the most prevalent non-integrase enzyme mutations. Univariable and multivariable Cox regression did not identify significant associations between the presence of these mutations individually and time to viral suppression, or to viral blip. Interestingly, accessory INSTI mutations were found significantly more frequently in people whose virus also harboured the Env mutation A539V (p=0.002). Conclusion: Several non-integrase mutations were prevalent, but we found no evidence of an impact upon virological outcomes within treatment-naïve individuals on INSTI-based regimens who had recently acquired HIV.