The dissection of HIV-1 reverse transcriptase intracellular error mechanisms is challenging.
A novel system to study mismatch resolution during HIV-1 replication was developed.
Outcomes for wild-type and an AZT-resistant reverse transcriptase were quantified using three approaches.
Most mismatches were extended to similar high extents by both enzymes.
Striking mechanistic differences were revealed during dC–rC mispair resolution.