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Sequence variation and consensus sequence of V3 loop on HIV-1 gp120
Haijun Tian1, Canhui Lan, Ying-Hua Chen
1Laboratory of Immunology, Research Centre for Medical Science and Protein Science Laboratory of the Ministry of Education, Tsinghua University, Beijing 100084, People's Republic of China.
Abstract:
Mutation in the V3 loop of HIV-1 gp120 could affect syncytium formation, virus infectivity and neutralization. To acquire more information of the V3 loop mutation, we analyzed amino acid sequences of the V3 loop of 24504 isolates from most HIV-1 clades (including A, B, C, D, E, F, G and H clades). The consensus sequence of the V3 loop of each subtype with the highest frequency emerging on each position is constituted and the conservation of each amino acid in this region is also calculated. Exploring the restricted mutation of the V3 region could help to understand mechanism of HIV entry and to develop new strategy against HIV-1.