Virus Influenza Porcin (VIP), initiatives du Québec

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===== Épitopes =====

Un épitope, aussi appelé déterminant antigénique, est une molécule qui peut être reconnue par un paratope (partie variable d'un anticorps ou d'un récepteur membranaire des lymphocytes B : BCR), pour déterminer si elle appartient au domaine du soi ou au domaine du non-soi. Un antigène est caractérisé par ses épitopes, si ses épitopes sont reconnus comme appartenant au non-soi alors il est lui-même immédiatement reconnu comme appartenant au non-soi. Cette reconnaissance épitope/paratope est donc à la base de la réponse immunitaire spécifique : elle permet la sélection clonale, c’est-à-dire la sélection des acteurs capables de s'attaquer spécifiquement à l'antigène correspondant à un épitope particulier [[https://fr.wikipedia.org/wiki/%C3%89pitope|Wikipédia]].

Plusieurs auteurs ont publié de l'information sur la localisation des acides aminés de certains épitopes qui pourraient être impliqués dans le développement de la réponse immunitaire de l'hôte envers les virus influenza.     

===== Épitopes influenza H1 =====
Pour chaque épitope, chaque numéro de la série de nombre représente la position d'un acide aminé sur la séquence du gène HA. Les  

**#Caton & Brownlee 1982, Cell 31:417-427**
  * Caton_epitope_Sa_H1 = [128, 129, 158,160,162,163, 165, 166, 167]
  * Caton_epitope_Sb_H1 = [156,159,192, 193, 196, 198]
  * Caton_epitope_Ca1_H1 = [169, 173, 207, 240]
  * Caton_epitope_Ca2_H1 = [140, 143, 145, 224, 225]
  * Caton_epitope_Cb_H1 = [78, 79, 81, 82, 83, 122]

**# Browlee & Fodor 2001, Phil. Trans. R. Soc. Lond. B  356, 1871-1876, doi 10.1098/rstb.2001.1001**
  * Browlee_epitope_Sa_H1 = [128, 129, 156, 158, 159,160,162,163, 165, 166, 167]
  * Browlee_epitope_Sb_H1 = [187,188,189,192, 193, 196, 198]
  * Browlee_epitope_Ca1_H1 = [169, 170,171, 172,173,178, 206,207, 239,240]
  * Browlee_epitope_Ca2_H1 = [140, 141,142,143,144, 145, 224, 225]
  * Browlee_epitope_Cb_H1 = [78, 79, 80, 81, 82, 83, 122]


**#Qi & Lu 2006.Genetic characterization of novel reassortant H1N2 influenza A viruses isolated from pigs in southeastern China. Arch Virol (2006) 151: 2289–2299, DOI 10.1007/s00705-006-0796-x**
  * Qi_epitope_Sa_H1 = [121,124.125,154,155,157,158,159,160,161,162,163,164]
  * Qi_epitope_Sb_H1 = [153,156,186,189,190,191,193,194,195]
  * Qi_epitope_Ca_H1 = [137,138,1329,140,142,166,168,169,170,204,205,221,222,237]
  * Qi_epitope_Cb_H1 = [69,70,71,72,73,74,75,115]

**#Deem & Pan 2009. Protein Engineering, Design & Selection vol. 22 no. 9 pp. 543–546**
  * A (Sa) = [118, 120, 121, 122, 126, 127, 128, 129, 132, 133, 134, 135, 137, 139, 140, 141, 142, 143, 146, 147, 149, 165, 252, 253]
  * B (Sb) =[124, 125, 15,2 153, 154, 155, 156, 157, 160, 162, 183, 184, 185, 186, 187, 189, 190, 191, 193, 194, 195, 196]
  * C = [34, 35, 3,6 37, 38, 40, 41, 43, 44, 45, 269, 270, 271, 272, 273, 274, 276, 277, 278, 283, 288, 292, 295, 297, 298, 302, 303, 305, 306, 307, 308, 309, 310]
  * D (Ca) = [89, 94, 95, 96, 113, 117, 163, 164, 166, 167, 168, 169, 170, 171, 172, 173, 174, 176, 179, 198, 200, 202, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 222, 223, 224, 225, 226, 227, 235, 237, 241, 24,3 244, 245]
  * E (Cb) = [47, 4,8 5, 51, 53, 54, 56, 57, 58, 66, 68, 69, 70, 71, 72, 73, 74, 75, 78, 79, 80, 82, 83, 84, 85, 86, 102, 257, 258, 259, 260, 261, 263, 267]


**#Stray and Pittman Virology Journal 2012, 9:91 complete list**

  * Stray_epitope_Sa_H1 = [ 128, 129, 163, 165, 166, 167, 247, 248]
  * Stray_epitope_Sb_H1 = [156, 159, 189, 190, 192, 193, 196, 197, 198]
  * Stray_epitope_Ca1_H1 = [169, 173, 207, 212, 240, 241, 242, 243, 244, 245]
  * Stray_epitope_Ca2b_H1 = [132, 133, 140, 143,144, 145, 149, 224, 225]
  * Stray_epitope_Cb_H1 = [51, 74, 75, 77, 78, 79, 117, 149, 255, 256, 259, 260, 261, 262, 263, 264, 265, 266]
  * Stray_epitope_H1C_H1 = [86, 272, 273,274,275,276,277, 279,280, 281,282, 286]



**# Skowronski et al. 2014.   Journal of Infectious Diseases 210:126–37**

  * Skowronski_epitope_Sa_H1 = [124,125,128,153,154,155,156,157,159,160,161,162,163,164]
  * Skowronski_epitope_Sb_H1 = [184,185,186,187,188,189,190,191,192, 193,194,195]
  * Skowronski_epitope_Ca1_H1 = [166,167,168,169,170,235,236,237]
  * Skowronski_epitope_Ca2_H1 = [137,138,139,140, 141,142,221,222]
  * Skowronski_epitope_Cb_H1 = [70,71,72,73,74,75]

----

===== Épitopes influenza H3 =====
Pour chaque épitope, chaque numéro de la série de nombre représente la position d'un acide aminé sur la séquence du gène HA.

**# Lee M, Chen JS. Predicting Antigenic Variants of Influenza A/H3N2 Viruses. Emerg Infect Dis. 2004;10(8):1385-1390. https://dx.doi.org/10.3201/eid1008.040107**
 
  * epitope_A_H3 = [122,124,126,130,131,132,133,135,137,138,140,142,143,144,145,146,150,152,168]
  * epitope_B_H3 = [128,129,155,156,157,158,159,160,163,165,186,187,188,189,190,192,193,194,196,197,198]
  * epitope_C_H3 = [44,45,46,47,48,50,51,53,54,273,275,276,278,279,280,294,297,299,300,304,305,307,308,309,310,311,312]
  * epitope_D_H3 = [96,102,103,117,121,167,170,171,172,173,174,175,176,177,179,182,201,203,207,208,209,212,213,214,215,216,217,218,219,226,227,228,229,230,238,240,242,244,246,247,248]
  * epitope_E_H3 = [57,59,62,63,67,75,78,80,81,82,83,86,87,88,91,92,94,109,260,261,262,265]

**# Lee et al. 2010 BIOINFORMATICS 26:1403–1408 doi:10.1093/bioinformatics/btq160 241 residues**

  * Lee_epitopeA = [71, 72, 98, 122, 124, 126,127, 130,131,132,133, 135,137, 138, 140, 141,142,143,144,145,146,148,149, 150,151,152, 168, 255]
  * Lee_epitopeB = [128, 129, 155–160,161,162, 163,164,165,186,187,188,189,190, 192–194, 196,197,198,199]
  * Lee_epitopeC = [41,42,43,44,45,46,47,48,49, 50, 51,52, 53, 54, 55,271,272,273,274, 275, 276, 278,280,282, 284,285, 287,288,289,290,291,292,293, 294,295,296, 297, 298,299, 300,301,303, 304, 305, 307,308,309,310,311,312, 313, 314]
  * Lee_epitopeD = [95,96, 97,99,100,101, 102, 103, 104, 105, 107,117,118, 120, 121, 167, 166, 169,
  * 170,171,172,173,174,175,176,177,178, 179, 180, 182,183,184, 200,201, 203,204,205,206,
  * 207,208,209,210,211, 212,213, 214,215,216,217,218,219, 220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,
  * 238, 239,240, 242, 243,244,245, 246,247,248,248, 257,258]
  * Lee_epitopeE = [56,57,58, 59, 60,62, 63,64, 65,67, 68,69,70,73,74,75, 76,77, 78,79,80,81,82,83,84,85, 86,87,88,89,90, 91, 92,  93,94,109, 110,11,112,113,114,115,119,259,260,261,262,263,264,  265, 267,268,269,270]



**# Stray and Pittman 2012 Virology Journal 9:91**

  * epitope_A_H3 = [121,122,123,124,125,126,127,129,131,132,133,134,135,136,137,138,140,142,143,144,145,146]
  * epitope_B_H3 = [155,156,157,158,159,160,186,188,189,190,192,193,194,196,197,198,199,246,247]
  * epitope_C_H3 = [49,50,53,54,271,273,275,276,278]
  * epitope_D_H3 = [167,201,202,203,204,205,206,207,214,216,217,218,219,220,222,223,225,226,227,242]
  * epitope_E_H3 = [62,63,75,78,79,80,81,82,83,91,92,94]



**# Skowronski et al. 2014.   Journal of Infectious Diseases 210:126–37**

  * epitope_A_H3 = [122,124,126,130,131,132,133,135,137,138,140,142,143,144,145,146,150,152,168]
  * epitope_B_H3 = [128,129,155,156,157,158,159,160,163,164,165,186,187,188,189,190,192,193,194,196,197,198]
  * epitope_C_H3 = [44,45,46,47,48,50,51,53,54,273,275,276,278,279,280,294,297,299,300,304,305,307,308,309,310,311,312]
  * epitope_D_H3 = [96,102,103,117,121,167,170,171,172,173,174,175,176,177,179,182,201,203,207,208,209,212,213,214,215,216,217,218,219,226,227,228,229,230,238,240,242,244,246,247,248]
  * epitope_E_H3 = [57,59,62,63,67,75,78,80,81,82,83,86,87,88,91,92,94,109,260,261,262,265]


**#Pepitope calculator  http://www.mwdeem.rice.edu/pepitope/**
  * epitopeA = [122, 124, 126, 130, 131, 132, 133, 135, 137, 138, 140, 142, 143, 144, 145, 146, 150, 152, 168]
  * epitopeB = [128,129,155,156,157,158,159,160,163,165,186,187,188,189,190,192,193,194,196,197,198]
  * epitopeC = [44,45,46,47,48,50,51,53,54,273,275,276,278,279,280,294,297,299,300,304,305,307,308,309,310,311,312]
  * epitopeD = [96,	102,103,117,121,167,170,171,172,173,174,175,176,177,179,182,201,203,207,208,209,212,213,214,215,216,217,218,219,226,227,228,229,230,238,240,242,244,246,247,248]
  * epitopeE = [57,59,62,63,67,75,78,80,81,82,83,86,87,88,91,92,94,109,260,261,262,265]