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In this study the predicted epitopes of C2-V3-C3 domains of gp120 of HIV-1, present in Iran, were compared to the epitopes of the homologous domains in subtypes A, B, C, D, E, F, G, H and I of this virus. Since epitopes are regions between the sequences with secondary structure which are hydrophilic and accessible, these parameters were used to predict the epitopes. The number of predicted helix (one) and sheet (five) regions in the Iranian isolate was equal to these numbers in subtypes A and F. Hubbard method recognized seven potential glycosylation sites on the Iranian isolate. In all other HIV-1 viruses, the number of putative glycosylation sites was less. In all subtypes, including the Iranian one, an epitope in the same region was predicted. In all analyzed sequences (excluding the Iranian one and subtypes D and H) a single long epitope was predicted in another region. In subtype H no epitope was predicted in that region. Similar to subtype D in the Iranian subtype B, two short epitopes were predicted in the same part. The computational analysis predicted similarities and dissimilarities between the locations of epitopes of the Iranian and other HIV-1 viruses. Although the primary structure of gp120 of the Iranian HIV-1 is highly related to subtype B, some differences were even predicted between the secondary and tertiary structure of the Iranian and consensus subtype B.

Keywords: HIV-1, Secondary structure, Computational prediction, gp120, Genomic diversity

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