Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants

W Fischer, S Perkins, J Theiler, T Bhattacharya… - Nature medicine, 2007 - nature.com
W Fischer, S Perkins, J Theiler, T Bhattacharya, K Yusim, R Funkhouser, C Kuiken…
Nature medicine, 2007nature.com
HIV-1/AIDS vaccines must address the extreme diversity of HIV-1. We have designed new
polyvalent vaccine antigens comprised of sets of'mosaic'proteins, assembled from fragments
of natural sequences via a computational optimization method. Mosaic proteins resemble
natural proteins, and a mosaic set maximizes the coverage of potential T-cell epitopes
(peptides of nine amino acids) for a viral population. We found that coverage of viral diversity
using mosaics was greatly increased compared to coverage by natural-sequence vaccine …
Abstract
HIV-1/AIDS vaccines must address the extreme diversity of HIV-1. We have designed new polyvalent vaccine antigens comprised of sets of 'mosaic' proteins, assembled from fragments of natural sequences via a computational optimization method. Mosaic proteins resemble natural proteins, and a mosaic set maximizes the coverage of potential T-cell epitopes (peptides of nine amino acids) for a viral population. We found that coverage of viral diversity using mosaics was greatly increased compared to coverage by natural-sequence vaccine candidates, for both variable and conserved proteins; for conserved HIV-1 proteins, global coverage may be feasible. For example, four mosaic proteins perfectly matched 74% of 9-amino-acid potential epitopes in global Gag sequences; 87% of potential epitopes matched at least 8 of 9 positions. In contrast, a single natural Gag protein covered only 37% (9 of 9) and 67% (8 of 9). Mosaics provide diversity coverage comparable to that afforded by thousands of separate peptides, but, because the fragments of natural proteins are compressed into a small number of native-like proteins, they are tractable for vaccines.
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