HIV Reverse-Transcriptase Drug Resistance Mutations During Early Infection Reveal Greater Transmission Diversity Than in Envelope Sequences

Background. Drug resistance mutations (DRMs) can serve as distinct, nonpolymorphic markers for evaluating diversity of expressed HIV-1. We screened for DRMs during early-acute viremia and examined the diversity in reverse transcriptase (RT) relative to envelope (env) in cases of transmitted drug resistance. Methods. We evaluated 111 longitudinal plasma samples collected every 2–7 days from 15 individuals who seroconverted for HIV-1 infection in 1994–2000. The samples were screened with sensitive polymerase chain reaction assays for the commonly transmitted M41L and K70R mutations and for K65R, which was undetected by bulk sequencing. Mutation-positive samples were further characterized by clonal sequencing of RT and env V1–V3. Results. Drug resistance mutations were detected in 4 of 15 seroconverters at 5–50 days of viral nucleic acid expression; most mutations disappeared about the time of seroconversion. Clonal sequencing verified low-level K65R at frequencies of 0.4%–4.9%. In each case, K65R coexisted unlinked with variants carrying 2–5 thymidine analog mutations at frequencies of 1.6%–23.0%. In one seroconverter, variants with M184V and nonnucleoside RT inhibitor mutations were also identified at first RNA expression. Each seroconverter displayed a homogeneous V1–V3 env population. Conclusions. Reverse-transcriptase DRMs demonstrate that the breadth of variants in transmission may be greater than what is reflected in envelope sequences.