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Epitope discovery in arenaviruses

Epitope discovery in arenaviruses. Outline. Introduction to arenaviruses How to find the data? How to predict epitopes What sequences to include? How to estimate conservation? Prediction of epitopes in Junin virus. Why focus on arena virus?. How to get data!.

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Epitope discovery in arenaviruses

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  1. Epitope discovery inarenaviruses

  2. Outline • Introduction to arenaviruses • How to find the data? • How to predict epitopes • What sequences to include? • How to estimate conservation? • Prediction of epitopes in Junin virus

  3. Why focus on arena virus?

  4. How to get data!

  5. NCBI has it all!(http://www.ncbi.nlm.nih.gov/)

  6. NCBI has it all!(http://www.ncbi.nlm.nih.gov/)

  7. NCBI has it all!(http://www.ncbi.nlm.nih.gov/)

  8. How to predict?

  9. Phylogeny Hanta virus Toparafou Hanta Virus Tula Virus Puuma Virus Hanta Virus Lodz-2 Thottapalayam Muleshou Hanta Virus Seoul Virus Laguna Virus AF482715 Dobrava Virus Hantaan Virus

  10. Hanta Segment S conservation • Focus on Segment S protein in Hanta • 7 full length segment S sequences in Swissprot • Pairwise %id > 95% • What is the overlap in 9mers?

  11. Segment D sequences Pergamino Virus Lechiguanas Virus Maciel virus Bermejo Virus Hanta Virus Andes Virus Oran Virus Hanta Virus

  12. Hanta Segment S conservation

  13. Epitope identification • AF482715 contains 420 unique 9mers • AF482712, AF482711, AF291702, AF482717, AF482716, AF482715, AF482714, AF482713, AF324902 contain 734 unique peptides • Only 243 9meric peptides are conserved among all 9 sequences

  14. Viral sequence conservation No two viral strains will “host” the same set of CTL eitopes

  15. HLA supertypes

  16. Epitope predictions • NetCTL • Include all 12 supertypes • Combined score > 1.0 • Identify epitopes that are most conserved in the different proteins in the Junin/Hanta sequences • Verify that the majority of the selected epitopes are present in the Argentina viral strains • Validation will be carried out in Argentina

  17. Promiscuous epitopes

  18. Epitope conservation • 23 of the 23 select L epitopes are present in the 5 L protein sequences • 6 of the 7 selected Z epitopes are present in the 5 Z proteins sequences. 1 epitope is present in 4 Z protein sequence • 26 of the 28 selected GPG epitopes are present in all 9 complete GPC sequences. 1 is present in 4 of the 9. 1 epitope is absent in the complete GPC sequences. • 1 of the selected GPC fragment epitopes is present in only 5 GPC fragment sequences.26 of the selected 27 NP epitopes are present in the 12 complete NP sequences. One is present in only 3. • This latter epitopes is also only present in 7 of the 54 NP fragment sequences.

  19. Overlap with the Argentinean strain • 26 of the 27 epitopes selected from the NP and NP fragment proteins are found in the ABB80080 sequence. (DQ272266 genbank segment S). • 27 of the 28 epitopes selected from the GPC and GPC fragments are found in the NP_899218 sequence. • 7 of the 7 epitopes selected from the Z protein are found in the AAV68494 sequence (AY819707 genbank segment L). • 23 of the 23 epitopes selected form the L protein are found in the AAV68495 sequence (AY819707 genbank segment L).

  20. Whats next • Obtain blood samples from Junin/Hanta infected patients • Elispot immunoassays to validate immunogenecity of predicted epitopes

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