HIV-2 amino acid substitutions in Gag and Env proteins occurring simultaneously with viral load upsurge in a drug-naïve patient

It has been reported that the peptides of human immunodeficiency virus type 2 (HIV-2) most frequently recognized by cytotoxic T lymphocytes are firstly in Gag and secondly in Env proteins. In the present case study, we attempted to observe amino acid substitutions in Gag and Env proteins and related parameters possibly associated with an increase in HIV-2 load. A sudden, eightfold, increase in HIV-2 load occurred in a drug-naive patient with human leukocyte antigen-B*5801 during the last phase of a longitudinal observation period from months 29 to 40. The genetic diversity of Gag and Env increased gradually prior to the HIV-2 load increase. The proportions of synonymous substitutions in both Gag and Env were greater than the proportions of nonsynonymous substitutions at every sampling point for 40 months, and the net charge of the V3-loop increased from months 29 to 40. Three amino acid substitutions (V2861 in Gag, K303T and N337 K/R in Env) were observed from months 29 to 40. Only one amino acid substitution (V286I) was observed with an increase in HIV-2 load in the Gag region where the clustering of epitopes was reported. These results suggest that the sites encompassing these three substituted positions are candidates for HIV-2 epitopes, although further careful examinations will be required.