Volume 7, Number 4—August 2001
THEME ISSUE
West Nile Virus
West Nile Virus
Rapid Determination of HLA B*07 Ligands from the West Nile Virus NY99 Genome
Anne S. De Groot*†
, Caitlin Saint-Aubin*, Andrew Bosma*, Hakima Sbai*, James Rayner†, and William Martin†
, Caitlin Saint-Aubin*, Andrew Bosma*, Hakima Sbai*, James Rayner†, and William Martin†
Table 3
West Nile virus T2B7 binding assay results
| Fluorescence ratio (peptide/negative control) |
Fluorescence ratio comparisons (p value) |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Peptide no. | AA sequence | EBPa | Avg. fold inc. @200b | Avg. MFI | 10 | 20 | 200 | control -10 | control -20 | control -200 | Summary |
| WNB7 0004 | AVKDELNTLL | 47.77 | 1.0 | 842.5 | 0.91 | 0.89 | 0.90 | 0.021 | 0.007 | 0.009 | None |
| WNB7 0005 | APAYSFNCLG | 47.03 | 1.2 | 743.5 | 0.96 | 1.09 | 1.14 | 0.511 | 0.127 | 0.020 | Weak |
| WNB7 0006 | AAKKKGASLL | 45.3 | 1.2 | 708.1 | 1.01 | 1.04 | 1.19 | 0.717 | 0.100 | 0.000 | Weak |
| WNB7 0007 | NPMILAAGLI | 36.60 | 1.1 | 944.6 | 0.89 | 0.92 | 1.00 | 0.008 | 0.051 | 0.949 | None |
| WNB7 0008 | IPAGFEPEML | 36.02 | 1.9 | 1,207.4 | 1.03 | 1.18 | 1.89 | 0.468 | 0.000 | 0.000 | Moderate |
| WNB7 0009 | TPAAPSYTLK | 35.68 | 1.5 | 954.5 | 1.03 | 1.13 | 1.55 | 0.372 | 0.001 | 0.000 | Moderate |
| WNB7 0010 | VPCRGQDELV | 32.57 | 1.0 | 658.6 | 1.05 | 1.06 | 1.04 | 0.053 | 0.015 | 0.118 | None |
| WNB7 0011 | GPGHEEPQLV | 32.35 | 1.0 | 848.9 | 1.01 | 1.03 | 0.98 | 0.759 | 0.521 | 0.689 | None |
| WNB7 0012 | AGMLLLSLLL | 31.17 | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| WNB7 0013 | EPPEGVKYVL | 31.07 | 1.1 | 681.7 | 1.08 | 1.10 | 1.06 | 0.004 | 0.000 | 0.023 | Weak |
| WNB7 0014 | MPAILIALLV | 30.23 | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| WNB7 0015 | KPTGSASSLV | 28.79 | 1.7 | 1,070.2 | 1.04 | 1.08 | 1.68 | 0.243 | 0.012 | 0.000 | Weak |
| WNB7 0017 | RPRWIDARVY | 23.99 | 1.9 | 1,714.0 | 1.18 | 1.43 | 1.97 | 0.003 | 0.000 | 0.000 | Strong |
| WNB7 0018 | VPGTKIAGML | 23.10 | 1.7 | 1,088.4 | 0.98 | 1.06 | 1.54 | 0.533 | 0.058 | 0.000 | Weak |
| WNB7 0019 | RPQRHDEKTL | 22.49 | 2.8 | 1,644.6 | 1.32 | 1.57 | 2.77 | 0.000 | 0.000 | 0.000 | Strong |
| WNB7 0020 | SPHRVPNYNL | 22.40 | 2.5 | 1,607.9 | 1.37 | 1.59 | 2.44 | 0.000 | 0.000 | 0.000 | Strong |
| WNB7 0021 | IPMTIAGLMF | 22.32 | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| WNB7 0023 | RPAADGRTVM | 20.89 | 1.5 | 979.1 | 1.68 | 2.01 | 2.90 | 0.000 | 0.000 | 0.000 | Strong |
| WNB7 0024 | TPGLRCLNLD | 20.73 | 1.0 | 849.6 | 1.09 | 1.11 | 1.01 | 0.037 | 0.015 | 0.821 | Weak |
| WNB7 0025 | SVNMTSQVLL | 20.09 | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| WNB7 3399 | PEDIDCWCTK | 0.00 | 1.1 | 990.3 | 0.97 | 0.96 | 0.94 | 0.448 | 0.396 | 0.145 | None |
| WNB7 3403 | PETPQGLAKI | 0.00 | 1.0 | 588.9 | 1.02 | 1.02 | 0.99 | 0.484 | 0.395 | 0.716 | None |
| WNB7 3411 | PFPESNSPIS | 0.00 | 1.0 | 626.7 | 0.90 | 0.86 | 0.90 | 0.020 | 0.001 | 0.019 | None |
| WNB7 3415 | PRTNTILEDN | 0.00 | 0.9 | 778.6 | 0.92 | 0.91 | 0.90 | 0.041 | 0.020 | 0.008 | None |
| HIV-1 B7 1291 | GPGHKARVLA | 28.0 | 2.2 | 1,423.8 | 1.16 | 1.20 | 1.72 | 0.002 | 0.000 | 0.000 | Strong |
| 1.5 | 1,370.9 | 1.12 | 1.14 | 1.78 | 0.000 | 0.000 | 0.000 | Strong | |||
| 1.6 | 1,003.9 | 0.98 | 1.06 | 1.66 | 0.720 | 0.195 | 0.000 | Weak | |||
aEBP = estimated binding potential; MFI = mean fluorescence index and T2B7 binding assay results for each of the peptides.
bAverage fold increase in fluorescence of cells incubated with peptide at 200 µg/mL.
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