Methods to determine HIV-1 ex vivo fitness

The fitness of human immunodeficiency virus type-1 (HIV-1) appears to be an important piece of the puzzle in understanding the global HIV-1 epidemic and disease progression in infected individuals. We have developed a dual infection/competition assay followed by a sensitive heteroduplex tracking assay (HTA) to measure the relative fitness of any HIV-1 isolate. Differences in fitness between wild-type and drug-resistant HIV-1 isolates can also be used as indicators of the emergence of drug-resistant isolates. This chapter describes the methods utilized to measure viral fitness (relative replicative capacity) during growth competition experiments. HTA is used to evaluate the production of HIV-1 variants in a competition, which can then be used to estimate ex vivo viral fitness.