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Volume 7, Number 4—August 2001
West Nile Virus
West Nile Virus

Rapid Determination of HLA B*07 Ligands from the West Nile Virus NY99 Genome

Anne S. De Groot*†Comments to Author , Caitlin Saint-Aubin*, Andrew Bosma*, Hakima Sbai*, James Rayner†, and William Martin†
Author affiliations: *Brown University, Providence, Rhode Island, USA; †EpiVax, Inc., Providence, Rhode Island, USA

Main Article

Table 1

Scoring overlapping peptides by the EpiMatrix motif HLA B*07 EpiMatrix analysis of West Nile virus protein NS-1

AA start Peptide no. (B*07 rank) Sequence EBPa
1123 WNB7 3119 GMEIRPQRHD 0.04
1124 WNB7 2818 MEIRPQRHDE 0.08
1125 WNB7 0591 EIRPQRHDEK 1.12
1126 WNB7 2660 IRPQRHDEKT 0.10
1127 WNB7 0019 RPQRHDEKTL 22.49
1128 WNB7 2661 PQRHDEKTLV 0.10

aEBP = estimated binding potential, which is the value that EpiMatrix uses to describe the probability that the peptide will bind to B*07 in vitro and in vivo. In this example, six overlapping peptides in the region of the WNV sequence coding for the NS-1 protein (WNV genome AA 1123 to 1128) are shown. WNVB7 0019 received the best EpiMatrix score (22.49) and was therefore selected for in vitro studies.

Main Article

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