CONICET | Buscador de Institutos y Recursos Humanos

Introduction: In the 75% of HIV transmission events, only one viral variant establishes the infection. To know this specific variant allows performing studies to increase our understanding of transmission. Clinical data analysis can identify patients with evidence of recent infection but are unable to define whether a high degree of viral diversification have already occurred. Here, we propose that direct sequencing of a short hypervariable segment of env allows rapid identification of newly infected patients with very early infection times. Materials and methods: We studied 44 newly diagnosed individuals with clinical evidence of infection time (30-270 days). Blood samples were collected and the viral RNA was extracted from plasma with QIAamp Viral RNA Kit. An hypervariable segment of the env gene (nt. 6858 to 6883 of HXB2) was amplified by nested RT-PCR andsequenced with ?Big Die terminator Kit" and ABI Prism 3100 sequencer. Chromatograms were analyzed with Sequencher 4.10. Results: From the analysis of the sequences of the env segment we found that the number of ambiguities present in the sequences increased with the number of days estimated post-infection. The average number of ambiguities was 0.125 in patients with less than 60 days of infection, 3.71 for 90 days, 13.6 for 120 days, 17.33 for 150 days and largely superior than 17.3 for 270 days post-infection. In addition, in a set of 5 patients we observed that the intra-host diversity of the gag gene (assessed by cloning and sequencing of the quasiespcies) was also correlated with the number of ambiguities in the env segment. Conclusion: We show that it is possible to rapidly identify patients where the founder virus might still be present by sequencing of an hypervariable region of the env gene, which provides an accurate correlate with the infection time estimated from clinical and serological data.