Unusual distribution of mutations associated with serial bottleneck passages of human immunodeficiency virus type 1

Repeated bottleneck passages result in fitness losses of RNA viruses. In th e case of human immunodeficiency virus type 1 (HIV-1), decreases in fitness after a limited number of plaque-to-plaque transfers in MT-4 cells were ve ry drastic. Here we report an analysis of entire genomic nucleotide sequenc es of four HIV-1 clones derived from the same HIV-1 isolate and their low-f itness progeny following 7 to 15 plaque-to-plaque passages. Clones accumula ted 4 to 28 mutations per genome, with dominance of A --> G and G --> A tra nsitions (57% of all mutations) and 49% nonsynonymous replacements. One clo ne-but not three sibling clones-showed an overabundance of G --> A transiti ons, evidencing the highly stochastic nature of some types of mutational bi as. The distribution of mutations along the genome was very unusual in that mutation frequencies in gag were threefold higher than in env. Particularl y striking was the complete absence of replacements in the V3 loop of gp120 , confirmed with partial nucleotide sequences of additional HIV-1 clones su bjected to repeated bottleneck passages. The analyses revealed several amin o acid replacements that have not been previously recorded among natural HI V-1 isolates and illustrate how evolution of an RNA virus genome, with rega rd to constant and variable regions, can be profoundly modified by alterati ons in population dynamics.