Application of a case–control study design to investigate genotypic signatures of HIV-1 transmission

Subtype B transmission strains had shorter V3 regions than chronic strains (p？=？0.031); subtype C transmission strains had shorter V1 loops than chronic strains (p？=？0.047); subtype B transmission strains had more V3 loop glycosites (p？=？0.024) than chronic strains. Further investigation showed that these statistically significant results were unlikely to be biologically meaningful. Also, there was no difference observed in the prevalence of a histidine at position 12 among transmission strains and controls of either subtype.Although a genetic bottleneck is observed after HIV-1 transmission, our results indicate that summary characteristics of Env hypothesised to be important in transmission are not divergent between transmission and chronic strains of either subtype. The success of a transmission strain to initiate infection may be a random event from the divergent pool of donor viral sequences. The characteristics explored through this study are important, but may not function as genotypic signatures of transmission as previously described.