Background:  We analyzed the env and pol genotypic profile in antiretroviral naïve individuals from Santos, Brazil.

Methods:  PBMC were collected and stored from persons testing HIV⁺ at an anonymous HIV testing site from 1999 to 2001. Recently acquired (<170 days) HIV infection was determined using the STARHS. Of 90 HIV⁺ persons, 25 infections had been recently acquired and 65 were of long-standing; all were ART naive. Samples were subjected to DNA sequencing of the V3 region, and the protease/reverse transcriptase (RT) regions.

Results:  In the recently acquired infections and infectins of long-standing, respectively, prevalence of resistance to NRTI was 22.7% and 21.1%, to NNRTI was 0% and 15.7%, and to PI was 13.6% and 8.1%. Cumulatively, 32% of recently acquired HIV infections and 29.2% of long-standing infections presented resistance to at least 1 antiretrovirals class. Frequent observed mutations in the recent and long-standing HIV infections were, respectively, T215Y/F (9.1 and 1.7%), M184V (9.1 and 3.5%), G190A/R (0 and 3.5%), A98G/S (0 and 7%), and M41L (4.5 and 3.5%). Among persons with long-standing HIV infections, 5.3% presented the recently described deletion at codon 67 of RT, that causes multi-drug resistance to NRTI and NNRTI; 47% of the those with recently acquired infections harbored B/B/B viruses (V3/PT/RT), 35.3% had B/F/B, 5.9% F/B/F, and 5.9% F/B/B;  56.2% of those with long-standing infections were infected with B/B/B viruses, 37.5% with B/F/B, and 2.1% with C/C/C viruses.

Conclusions:  Primary resistance was extremely high in this population, including the presence of multi-drug-resistant strains, probably due to the long-term use of antiretrovirals in this area of Brazil.  A high prevalence of HIV-1 B/F recombinant strains was detected.

Keywords: primary infection; genotypic resistance; recombinant subtypes