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Methods Gag was sequenced from 56 participants with acute HIV infection from the CAPRISA 002 cohort. For the newly identified mutation, replication fitness of viruses in PBMCs was compared in a subtype C infectious molecular clone. Disease progression was compared in participants infected with viruses carrying polymorphisms associated with beneficial HLAB*57/58:01 and B7 supertype (B*39:10/81:01) allelic selective pressure in HLA mismatched participants.

Beneficial HLA-mediated viral polymorphisms on the transmitted virus additively influence disease progression in HIV-1, subtype C infection