Background
Materials and methods
Sample collection source
Sample collection standard
Human papillomavirus DNA extraction
PCR amplification and identification of variants
Sequence and structural analysis
HLA allele retrieval and analysis
Alleles | Average frequency | Alleles | Average frequency | Alleles | Average frequency |
---|---|---|---|---|---|
HLA-A*11:01 | 27.7% | HLA-B*40:01 | 14.9% | HLA-C*01:02 | 16.9% |
HLA-A*24:02 | 17.2% | HLA-B*46:01 | 11.5% | HLA-C*03:04 | 12.8% |
HLA-A*33:03 | 11.5% | HLA-B*58:01 | 8.9% | HLA-C*08:01 | 12.6% |
HLA-A*02:01 | 5.3% | HLA-B*13:01 | 8.2% | HLA-C*03:02 | 8.7% |
HLA-B*15:02 | 7.1% |
Alleles | Average frequency | Alleles | Average frequency | Alleles | Average frequency |
---|---|---|---|---|---|
DRB1*14:01 | 13.4% | DRB1*15:02 | 5.6% | DQB1*02:01 | 9.3% |
DRB1*12:02 | 11.4% | DQB1*05:01 | 10.9% | DPB1*04:01 | 17.1% |
Epitope prediction
T cell antigen epitope
B cell antigen epitope
Data availability
Results
Mutation analysis of E6 and E7
HPV-33 E6 and E7 polymorphism analysis
HPV-33 |
E6
|
E7
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
S. No. | M1 | M2 | M3 | M4 | M5 | M6 | M7 | M8 | M1 | M2 | M3 | M4 |
Position | 213 | 273 | 329 | 364 | 387 | 446 | 542 | 549 | 658 | 706 | 706 | 862 |
Ref | A | A | G | A | A | A | G | T | G | C | C | A |
Normal | – | – | – | – | – | – | – | – | – | – | – | – |
A | – | – | – | – | – | – | – | – | – | – | A | – |
T | – | – | – | – | – | – | T | – | – | T | – | T |
G | – | G | – | – | – | G | – | C | – | – | – | – |
C | C | – | C | C | C | – | – | – | C | – | – | – |
Frequency | 42 | 17 | 7 | 16 | 42 | 16 | 33 | 25 | 16 | 36 | 27 | 19 |
% of Samples | 19.44 | 7.87 | 3.24 | 7.41 | 19.44 | 7.41 | 15.28 | 11.57 | 7.4 | 16.67 | 12.5 | 8.8 |
Amino acid Mutation | K35N | – | S74T | N86H | K93N | Q113R | R145I | – | S29T | A45V | A45E | Q97L |
Secondary structure | C | S | H | C | C | H | C | C | C | C | C | C |
Analysis of HPV-58 E6 and E7 polymorphisms
HPV-58 |
E6
|
E7
| |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
S. No. | M1 | M2 | M3 | M4 | M5 | M6 | M7 | M8 | M1 | M2 | M3 | M4 | M5 | M6 | M7 | M8 | M9 | M10 | M11 | M12 | M13 |
Position | 187 | 203 | 259 | 307 | 367 | 388 | 395 | 543 | 599 | 632 | 694 | 726 | 744 | 755 | 760 | 761 | 763 | 793 | 798 | 801 | 803 |
Ref | C | G | A | C | C | A | T | G | G | C | G | T | T | C | G | G | A | A | C | C | T |
Normal | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
A | – | – | – | – | A | – | – | A | A | – | A | – | – | A | A | A | – | – | – | A | – |
T | T | – | – | T | – | – | – | – | – | T | – | – | – | – | – | – | – | – | T | – | – |
G | – | – | G | – | – | – | – | – | – | – | – | – | G | – | – | – | G | G | – | – | – |
C | – | C | – | – | – | C | C | – | – | – | – | C | – | – | – | – | – | – | – | – | C |
Frequency | 7 | 1 | 2 | 237 | 1 | 111 | 1 | 16 | 13 | 74 | 162 | 7 | 319 | 26 | 74 | 163 | 26 | 1 | 1 | 1 | 82 |
% of Samples | 1.73 | 0.25 | 0.49 | 58.52 | 0.25 | 27.41 | 0.25 | 3.95 | 3.21 | 18.27 | 40.00 | 1.73 | 78.76 | 6.42 | 18.27 | 40.25 | 6.42 | 0.25 | 0.25 | 0.25 | 20.25 |
Amino acid Mutation | – | E32Q | – | – | D86E | K93N | – | R145K | R9K | T20I | G41R | – | – | T61N | G63S | G63D | T64A | T74A | – | D76E | V77A |
Secondary structure | S | C | S | H | C | C | C | C | C | C | C | C | S | C | C | C | C | H | H | H | H |
Structural analysis
HPV-33 E6 and E7 structural analysis
Target protein | Sequence type | No. helix/Helicesa | No. sheet/Sheetsb | No. coil/Coilsc | Accessibility type | |
---|---|---|---|---|---|---|
Burred | Exposed | |||||
HPV-33 E6 | Reference | 41/27.52% | 31/20.80% | 77/51.68% | 50/33.56% | 99/66.44% |
Variant | 42/28.19% | 24/16.11% | 83/55.70% | 49/32.89% | 100/67.11% | |
HPV-58 E6 | Reference | 41/27.52% | 25/16.78% | 83/55.70% | 48/32.22% | 101/67.78% |
Variant | 42/28.19% | 25/16.78% | 82/55.03% | 48/32.22% | 101/67.78% | |
HPV-33 E7 | Reference | 12/12.37% | 16/16.50% | 69/71.13% | 27/27.84% | 70/72.16% |
Variant-1 | 11/11.34% | 16/16.50% | 70/72.16% | 30/30.93% | 67/69.07% | |
Variant-2 | 11/11.34% | 16/16.50% | 70/72.16% | 28/28.87% | 69/71.13% | |
HPV-58 E7 | Reference | 12/12.24% | 17/17.35% | 69/70.41% | 28/28.57% | 70/71.43% |
Variant-1 | 12/12.24% | 17/17.35% | 69/70.41% | 26/26.53% | 72/73.47% | |
Variant-2 | 12/12.24% | 17/17.35% | 69/70.41% | 26/26.53% | 72/73.47% |
HPV-58 E6 and E7 structural analysis
T cell epitope prediction
T cell epitope prediction for HPV-33 E6 and E7
Target protein | Distribution of HLA-I epitopes (epitope’s number) | Distribution of HLA-II epitopes (epitope’s number) |
---|---|---|
HPV-33 E6 | 15~29 (8) | |
36~72 (97) | 38~74 (25) | |
75~85 (2) | ||
96~110 (10) | ||
124~144 (16) | ||
HPV-33 E7 | 52~66 (3) | 3~25 (22) |
77~90 (5) | 46~96 (27) | |
HPV-58 E6 | 5~31 (12) | |
35~84 (96) | 37~85 (53) | |
96~110 (10) | ||
124~144 (17) | ||
HPV-58 E7 | 44~60 (3) | |
78~91 (7) |
Target Protein | Start | Length | Peptide | Percentile Rank | Binding Core in HLA-II predicted epitopes |
---|---|---|---|---|---|
HPV-33 E6 | 41 | 14 | EVYDFAFADLTVVY | 0.1 | YDFAFADLT/DFAFADLTV/FAFADLTVV |
42 | 14 | VYDFAFADLTVVYR | 0.1 | YDFAFADLT/DFAFADLTV/FAFADLTVV | |
43 | 14 | YDFAFADLTVVYRE | 0.1 | YDFAFADLT/DFAFADLTV/FAFADLTVV | |
44 | 14 | DFAFADLTVVYREG | 0.1 | DFAFADLTV/FAFADLTVV | |
45 | 14 | FAFADLTVVYREGN | 0.1 | FAFADLTVV | |
HPV-33 E7 | 52 | 10 | YYIVTCCHTC | 0.6 | YYIVTCCHT |
59 | 8 | HTCNTTVR | 0.6 | ||
77 | 8 | RTIQQLLM | 0.1 | ||
77 | 14 | RTIQQLLMGTVNIV | 0.5 | ||
81 | 10 | QLLMGTVNIV | 0.55 | ||
82 | 9 | LLMGTVNIV | 0.4 |
T cell epitope prediction for HPV-58 E6 and E7
Target protein | Start | Length | Peptide | PercentileRank | Binding Core in HLA-II predicted epitopes |
---|---|---|---|---|---|
HPV-58 E6 | 40 | 11 | SEVYDFVFADL | 0.2 | EVYDFVFAD |
41 | 11 | EVYDFVFADLR | 0.2 | EVYDFVFAD | |
44 | 12 | DFVFADLRIVYR | 0.2 | DFVFADLRI/FVFADLRIV | |
45 | 10 | FVFADLRIVY | 0.1 | FVFADLRIV | |
47 | 14 | FADLRIVYRDGNPF | 0.2 | IVYRDGNPF | |
61 | 12 | AVCKVCLRLLSK | 0.1 | CKVCLRLLS | |
71 | 13 | SKISEYRHYNYSL | 0.1 | ||
HPV-58 E7 | 49 | 12 | ATANYYIVTCCY | 0.5 | |
78 | 8 | RTLQQLLM | 0.2 | ||
78 | 14 | RTLQQLLMGTCTIV | 0.4 | ||
79 | 13 | TLQQLLMGTCTIV | 0.5 | ||
82 | 10 | QLLMGTCTIV | 0.45 | ||
83 | 9 | LLMGTCTIV | 0.4 |