Introduction: A cross sectional study was conducted from 2002-2004 to record the evolution of HIV-1 infection in Puerto Rico by monitoring the expression of antiretroviral resistance-associated mutations.

Methods: Samples were analyzed by using the TRUGENE HIV-1 Genotyping Kit and the OpenGene DNA Sequencing System.

Results: Mutations in the HIV-1 virus were detected in 92.7% of men and 94.8% of women. Of these, 75.1% of men and 72.4% of women had HIV-1 with resistance to at least one medication. The average number of HIV mutations was 6.1 in men and 5.3 in women. In 2002 and 2003, strains were most frequently resistant to the antiretroviral drugs zalcitabine, lamivudine and didanosine, while in 2004, strains were most frequently resistant to zalcitabine, lamivudine, and efavirenz. The most prevalent mutations in the reverse transcriptase gene were M184V, K103N, T215Y, and M41L. The most prevalent mutations in the protease gene were L63P, M361, L90M, A71V, and L101.

Conclusions: Significant differences between men and women were recorded in the levels of HIV-1 expressed mutations and resistance. When comparing these results with data from 2000 and 2001, results indicate that expression of resistant mutations has remained constant.

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