Drug Resistance Mutation Profile and Accumulation Kinetics in Human Immunodeficiency Virus-Positive Individuals Infected with Subtypes B and F Failing Highly Active Antiretroviral Therapy Are Influenced by Different Viral Codon Usage Patterns

The major human immunodeficiency virus type 1 subtype circulating in Brazil is B, followed by F and C. We have genotyped 882 samples from Brazilian patients for whom highly active antiretroviral therapy failed, and we found subtype B and the unique recombinant B/F1 forms circulating. Due to codon usage variation, there is a significantly lower incidence of the substitutions L210W, Q151M, and F116Y in subtype F1 isolates than in the subtype B counterparts.