Biotechnology Bulletin ›› 2024, Vol. 40 ›› Issue (5): 300-309.doi: 10.13560/j.cnki.biotech.bull.1985.2023-1006
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XIE Shuang1(), CHEN Yao2, HUANG Jun-qiong1()
Received:
2023-10-30
Online:
2024-05-26
Published:
2024-04-25
Contact:
HUANG Jun-qiong
E-mail:1172143123@qq.com;junqiongh@aliyun.com
XIE Shuang, CHEN Yao, HUANG Jun-qiong. Prediction of H5Nx Avian Influenza Virus Cross-reactivity CD4+ T-cell Epitopes[J]. Biotechnology Bulletin, 2024, 40(5): 300-309.
蛋白片段Protein segment | 蛋白序列数 Protein sequence number | |||||||
---|---|---|---|---|---|---|---|---|
sH1N1 | pH1N1 | H3N2 | H5N1 | H5N6 | H5N8 | Total | ||
HA | 1994 | 43360 | 62270 | 517 | 37 | 1 | 108179 | |
NA | 2803 | 39867 | 56908 | 477 | 37 | 1 | 100093 | |
M1 | 1645 | 28497 | 44559 | 394 | 37 | 1 | 75133 | |
M2 | 1645 | 28496 | 44569 | 404 | 37 | 1 | 75152 | |
NS1 | 872 | 22279 | 33622 | 391 | 37 | 1 | 57202 | |
NEP | 872 | 22279 | 33624 | 389 | 37 | 1 | 57202 | |
NP | 881 | 22047 | 35759 | 384 | 37 | 1 | 59109 | |
PA | 877 | 22522 | 35229 | 386 | 37 | 1 | 59052 | |
PB1 | 871 | 20601 | 34524 | 371 | 37 | 1 | 56405 | |
PB2 | 900 | 21837 | 34855 | 371 | 37 | 1 | 58001 |
Table 1 Protein sequence analysis datasets of sH1N1, pH-1N1, H3N2, H5N1, H5N6 and H5N8 virus subtypes
蛋白片段Protein segment | 蛋白序列数 Protein sequence number | |||||||
---|---|---|---|---|---|---|---|---|
sH1N1 | pH1N1 | H3N2 | H5N1 | H5N6 | H5N8 | Total | ||
HA | 1994 | 43360 | 62270 | 517 | 37 | 1 | 108179 | |
NA | 2803 | 39867 | 56908 | 477 | 37 | 1 | 100093 | |
M1 | 1645 | 28497 | 44559 | 394 | 37 | 1 | 75133 | |
M2 | 1645 | 28496 | 44569 | 404 | 37 | 1 | 75152 | |
NS1 | 872 | 22279 | 33622 | 391 | 37 | 1 | 57202 | |
NEP | 872 | 22279 | 33624 | 389 | 37 | 1 | 57202 | |
NP | 881 | 22047 | 35759 | 384 | 37 | 1 | 59109 | |
PA | 877 | 22522 | 35229 | 386 | 37 | 1 | 59052 | |
PB1 | 871 | 20601 | 34524 | 371 | 37 | 1 | 56405 | |
PB2 | 900 | 21837 | 34855 | 371 | 37 | 1 | 58001 |
蛋白片段 Protein segment | 氨基酸序列同源性 Amino acid sequence identity/% | |||||
---|---|---|---|---|---|---|
sH1N1 | pH1N1 | H3N2 | H5N1 | H5N6 | ||
HA | 50.5-56.2 | 47.1-55.4 | 32.8-55.6 | 88.4-94.2 | 92.5-99.3 | |
NA | 16.7-39.4 | 32.6-39.7 | 19.1-37.0 | 38.2-43.1 | 18.7-22.6 | |
M1 | 92.2-96.8 | 91.3-95.5 | 90.0-96.8 | 92.5-97.1 | 93.4-100.0 | |
M2 | 73.7-91.4 | 80.7-91.4 | 72.4-93.6 | 79.1-92.2 | 80.7-100.0 | |
NS1 | 76.2-86.2 | 72.3-80.7 | 72.6-86.7 | 80.6-89.8 | 58.5-93.2 | |
NEP | 85.8-93.2 | 79.9-89.6 | 82.9-91.4 | 82.5-92.3 | 76.9-96.6 | |
NP | 90.5-96.3 | 90.3-94.5 | 88.5-95.7 | 96.4-98.4 | 93.4-97.6 | |
PA | 91.6-96.7 | 93.5-97.0 | 92.2-97.0 | 94.5-98.3 | 95.1-98.0 | |
PB1 | 93.9-97.3 | 93.9-96.4 | 93.7-98.0 | 96.0-98.3 | 96.0-98.5 | |
PB2 | 93.5-96.1 | 92.9-96.9 | 87.7-97.2 | 95.0-97.9 | 95.7-98.4 |
Table 2 Amino acid sequence identity of A/Astrakhan/3212/2020(H5N8)with sH1N1, pH1N1 and H3N2 virus subtypes
蛋白片段 Protein segment | 氨基酸序列同源性 Amino acid sequence identity/% | |||||
---|---|---|---|---|---|---|
sH1N1 | pH1N1 | H3N2 | H5N1 | H5N6 | ||
HA | 50.5-56.2 | 47.1-55.4 | 32.8-55.6 | 88.4-94.2 | 92.5-99.3 | |
NA | 16.7-39.4 | 32.6-39.7 | 19.1-37.0 | 38.2-43.1 | 18.7-22.6 | |
M1 | 92.2-96.8 | 91.3-95.5 | 90.0-96.8 | 92.5-97.1 | 93.4-100.0 | |
M2 | 73.7-91.4 | 80.7-91.4 | 72.4-93.6 | 79.1-92.2 | 80.7-100.0 | |
NS1 | 76.2-86.2 | 72.3-80.7 | 72.6-86.7 | 80.6-89.8 | 58.5-93.2 | |
NEP | 85.8-93.2 | 79.9-89.6 | 82.9-91.4 | 82.5-92.3 | 76.9-96.6 | |
NP | 90.5-96.3 | 90.3-94.5 | 88.5-95.7 | 96.4-98.4 | 93.4-97.6 | |
PA | 91.6-96.7 | 93.5-97.0 | 92.2-97.0 | 94.5-98.3 | 95.1-98.0 | |
PB1 | 93.9-97.3 | 93.9-96.4 | 93.7-98.0 | 96.0-98.3 | 96.0-98.5 | |
PB2 | 93.5-96.1 | 92.9-96.9 | 87.7-97.2 | 95.0-97.9 | 95.7-98.4 |
蛋白片段 Protein segment | (A)预测的CD4+ T细胞表位 (A)Predicted CD4+ T-cell epitopes | (B)保守表位(%=B/A*100) (B)Conserved predicted epitopes(% = B/A*100) | (C)交叉反应性表位(%=C/B*100) (C)Cross-reactivity epitopes(%= C/B*100) | 已验证的表位(来源:IEDB,免疫表位数据库) Experimentally defined epitopes/% (Source: IEDB, immune epitope database) | ||
---|---|---|---|---|---|---|
(D)CD4+ T细胞表位(%=D/C*100) (D)CD4+ T-cell epitopes(%=D/C*100) | (E)CD8+ T细胞表位(%=E/D*100) (E)CD8+ T-cell epitopes(%=E/D*100) | (F)B细胞表位(%=F/E*100) (F)B-cell epitopes(%=F/E*100) | ||||
HA | 102 | 24 | 7 | 7 | 7 | 2 |
NA | 56 | 0 | 0 | 0 | 0 | 0 |
M1 | 77 | 47 | 47 | 40 | 29 | 3 |
M2 | 8 | 0 | 0 | 0 | 0 | 0 |
NS1 | 46 | 4 | 4 | 4 | 0 | 0 |
NEP | 29 | 8 | 6 | 4 | 4 | 0 |
NP | 118 | 98 | 75 | 57 | 49 | 0 |
PA | 122 | 104 | 104 | 32 | 21 | 0 |
PB1 | 158 | 138 | 138 | 63 | 42 | 0 |
PB2 | 179 | 132 | 132 | 27 | 20 | 0 |
Total | 895 | 555(62.0) | 513(92.4) | 234(45.6) | 172(73.5) | 5(2.9) |
Table 3 Predicted CD4+ T-cell epitopes of A/Astrakhan/3212/2020(H5N8)
蛋白片段 Protein segment | (A)预测的CD4+ T细胞表位 (A)Predicted CD4+ T-cell epitopes | (B)保守表位(%=B/A*100) (B)Conserved predicted epitopes(% = B/A*100) | (C)交叉反应性表位(%=C/B*100) (C)Cross-reactivity epitopes(%= C/B*100) | 已验证的表位(来源:IEDB,免疫表位数据库) Experimentally defined epitopes/% (Source: IEDB, immune epitope database) | ||
---|---|---|---|---|---|---|
(D)CD4+ T细胞表位(%=D/C*100) (D)CD4+ T-cell epitopes(%=D/C*100) | (E)CD8+ T细胞表位(%=E/D*100) (E)CD8+ T-cell epitopes(%=E/D*100) | (F)B细胞表位(%=F/E*100) (F)B-cell epitopes(%=F/E*100) | ||||
HA | 102 | 24 | 7 | 7 | 7 | 2 |
NA | 56 | 0 | 0 | 0 | 0 | 0 |
M1 | 77 | 47 | 47 | 40 | 29 | 3 |
M2 | 8 | 0 | 0 | 0 | 0 | 0 |
NS1 | 46 | 4 | 4 | 4 | 0 | 0 |
NEP | 29 | 8 | 6 | 4 | 4 | 0 |
NP | 118 | 98 | 75 | 57 | 49 | 0 |
PA | 122 | 104 | 104 | 32 | 21 | 0 |
PB1 | 158 | 138 | 138 | 63 | 42 | 0 |
PB2 | 179 | 132 | 132 | 27 | 20 | 0 |
Total | 895 | 555(62.0) | 513(92.4) | 234(45.6) | 172(73.5) | 5(2.9) |
蛋白片段 Protein segment | H5Nx预测表位 H5Nx predicted epitopes | 与H5Nx的交叉表位 Cross-epitopes with H5Nx | |||
---|---|---|---|---|---|
sH1N1 | pH1N1 | H3N2 | |||
HA head | 8 | 0 | 0 | 0 | |
HA stem | 16 | 7 | 4 | 0 | |
NA | 0 | 0 | 0 | 0 | |
M1 | 47 | 41 | 45 | 40 | |
M2 | 0 | 0 | 0 | 0 | |
NS1 | 4 | 4 | 4 | 4 | |
NEP | 8 | 6 | 6 | 6 | |
NP | 98 | 61 | 66 | 52 | |
PA | 104 | 95 | 96 | 93 | |
PB1 | 138 | 129 | 122 | 138 | |
PB2 | 132 | 120 | 128 | 121 | |
Total | 555 | 463 | 471 | 454 |
Table 4 Cross-reactivity between CD4+ T-cell epitopes of H5Nx and seasonal IAV
蛋白片段 Protein segment | H5Nx预测表位 H5Nx predicted epitopes | 与H5Nx的交叉表位 Cross-epitopes with H5Nx | |||
---|---|---|---|---|---|
sH1N1 | pH1N1 | H3N2 | |||
HA head | 8 | 0 | 0 | 0 | |
HA stem | 16 | 7 | 4 | 0 | |
NA | 0 | 0 | 0 | 0 | |
M1 | 47 | 41 | 45 | 40 | |
M2 | 0 | 0 | 0 | 0 | |
NS1 | 4 | 4 | 4 | 4 | |
NEP | 8 | 6 | 6 | 6 | |
NP | 98 | 61 | 66 | 52 | |
PA | 104 | 95 | 96 | 93 | |
PB1 | 138 | 129 | 122 | 138 | |
PB2 | 132 | 120 | 128 | 121 | |
Total | 555 | 463 | 471 | 454 |
Fig. 2 Locating nested epitopes in 3D model of A/Astrakhan/3212/2020(H5N8)HA-A and M1-D A marks the HA head and stem domains in light gray and dark gray respectively; green marks CD4+ T-cell epitopes, light blue marks nested CD8+ T-cell epitopes, and purple marks nested B-cell epitopes; D marks other amino acid residues of M1 in brown; B, C and E, F are respectively cartoon and sticks representation of CD4+ T-cell epitopes nested with both CD8+ T-cell and B-cell epitopes. The dashed lines represent hydrogen bonds
Fig. 4 Population coverage of identified cross-reactivity CD4+ T-cell epitopes A: All ethnicities groups. B: Eight proteins in H5N8. The identified cross-reactivity CD4+ T-cell epitopes provide broad population coverage. Based on the binding data for each HLA class II-restricted DRB1 alleles, theoretical population coverage was calculated. The number of possible epitope-HLA allele combinations as a function of the fraction of each ethnic population(%)and each protein(%)is shown
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