Design of soluble HIV-1 Env trimers from highly neutralisation-resistant HIV-1 strains for the isolation of broadly neutralising antibodies

Abstract

The emergence of circulating HIV-1 strains with decreased sensitivity to clinically relevant broadly neutralising antibodies (bNAbs) poses a significant challenge, suggesting that current bNAbs may lose efficacy against future variants. This highlights the need for new bNAbs capable of neutralising resistant viruses. This study aimed to isolate novel bNAbs using a soluble trimer based on the envelope protein (Env) of a difficult-to-neutralise HIV-1 isolate with intrinsic resistance to several existing bNAbs. A soluble Env trimer derived from the FRESH1388 transmitted founder virus was successfully engineered with multiple stabilising mutations and expressed in mammalian cells. Binding assays revealed the V3 loop – an immunodominant, non-bNAb epitope – was overexposed on this trimer. However further stabilisation within the V3 region reduced this exposure and limited off-target antibody binding. Structural characterisation confirmed that the modified trimer, FRESH1388-2P-316W, adopted a closed, native-like conformation. This trimer was used in cell sorting to isolate 252 memory B cells from a CAPRISA cohort participant living with HIV-1, CAP287 – an individual with previously unmapped responses and 61% neutralisation breadth. Antibodies were expressed from sequenced B cell receptors (BCRs) and screened for neutralisation activity. Multiple clonal lineages were identified from 94 productively rearranged BCRs, with the largest lineage using a rarely used IGHV3-13. Ten antibodies were screened against a diverse subtype six- virus panel and the FRESH1388 virus. Four novel bNAbs were discovered, with breadth up to 67%, and three were able to neutralise FRESH1388. This study demonstrates the potential of resistant Env trimers to isolate novel bNAbs with promising neutralisation profiles.