final program.qxd - Parallels Plesk Panel

PP 5.1
Rational design of HCV antigens to contend with diversity and optimize T cell
reactivity
Yusim K. 1 , Fischer W. 1 , Perkins S. 1 , Frahm N. 2 , Brander C. 2 , Bhattacharya T. 1 , Theiler J. 1 ,
Allen T. 2 , Lauer G. 2 , Kuiken C. 1 , Korber B. 1
1
T-Division, Los Alamos Natl. Laboratory, Los Alamos,
2
AIDS Research Center, Harvard Medical School, Boston, United States
Objectives
Designing an effective vaccine for HIV and HCV is a many-faceted challenge. Potent
vaccines are needed, with optimized vectors, immunization protocols, and adjuvants.
Given enormous sequence diversity of these two viruses, vaccine optimization strategies
will not suffice without the parallel development of strategies that stimulate protection
against the diverse spectrum of circulating viruses. For a CTL based vaccine it means that
cross-recognition between vaccine strains and circulating strains should be maximized.
Prototype natural sequences are being considered for both viruses, but diversity
coverage could be significantly improved using optimized synthetic sequences.
Methods
Since CTL epitopes are usually 9 amino acid long fragments, a computational
optimization method maximizing the population coverage of 9-mers was developed.
Polyvalent vaccine antigens containing sets of "mosaic" proteins assembled from
9-mer fragments of natural sequences are designed in such a way that for each
overlapping 9-mer the frequency of each variant appearing in the input sequence set is
evaluated. Importantly, high-frequency overlapping 9-mers are often not compatible, so
the relative benefit of each amino acid variant is assessed in combination with other
nearby variants. The most beneficial variants are assembled in a mosaic protein in the
order they appear in the natural sequences. Every single 9 amino acid long sequence
fragment in these mosaic proteins exists in a natural sequence, and so mosaic proteins
resemble natural proteins. The method could be used for any pathogen and so far has
been applied to HIV and HCV.
Results
High coverage of circulating proteins is feasible with a small number of mosaic proteins.
For example, in an alignment of 165 sequences representing genotype 1 variation in
NS3-NS5 HCV protein region, 87% of potential epitopes (9-mers) are matched perfectly
within a set of four mosaic proteins, and 98% have at least an 8/9 aa match. In contrast,
with a single genotype 1 natural strain, only up to 65% of potential epitopes could be
matched perfectly and only up to 80% could have 8/9 aa match.
Conclusion
HCV genotype 1 mosaic protein sets provide diversity coverage comparable to hundreds
of separate peptides. By weaving together fragments of proteins derived from natural
sequences, this coverage is achieved with a small number of proteins, tractable the
design of antigens for T cell responses screening and for vaccine design. A vaccine
stimulating polyclonal responses to multiple epitope variants may be beneficial as it could
enable responses to a broader range of circulating variants and it could also prime the
immune system against common escape mutants.
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