SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development
Abstract
:1. Introduction
2. Methods
2.1. Consensus Sequence ORF Generation and Entropy Calculation
2.2. Overlapping Peptide Set Design and Variability Plots
2.3. Detection of Conserved Peptides Among Coronavirus
2.4. Identification of Previously Described Epitopes in CoV-2 Conserved Regions
3. Results
3.1. Open Reading Frames and Sequence Isolates for CoV-2-Cons Sequence Creation
3.2. Overlapping Peptides (OLP) Sets Design
3.3. CoV-2-Cons Variability Analysis by Entropy Scores across the Full Genome
3.4. Variant OLP Sequences to Cover CoV-2 Sequence Diversity
3.5. Conserved Protein Sequences Matching Other Coronavirus Family Member and Identification of Pan-Coronavirus Sequences
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene | Start | End | Protein | Protease Products | Frame |
---|---|---|---|---|---|
ORF1a.iORF1.ext | 59 | 136 | upORF1a1 | - | Alternative |
ORF1a.iORF2.ext | 163 | 264 | upORF1a2 | - | Alternative |
ORF1ab | 266 | 13483 | pp1a | leader protein | Canonical |
nsp2 | |||||
nsp3 | |||||
nsp4 | |||||
3C-like proteinase | |||||
nsp6 | |||||
nsp7 | |||||
nsp8 | |||||
nsp9 | |||||
nsp10 | |||||
nsp11 | |||||
ORF1ab | 13468 | 21555 | pp1ab | RNA-dependent RNA polymerase | Canonical |
helicase | |||||
3′-to-5′ exonuclease | |||||
endoRNAse | |||||
2′-O-ribose methyltransferase | |||||
S | 21563 | 25384 | surface glycoprotein | S1 | Canonical |
S2 | |||||
ORFS.iORF1 | 21744 | 21863 | inORFS | - | Alternative |
ORF3a | 25393 | 26220 | ORF3a protein | - | Canonical |
ORF3a.iORF1 | 25457 | 25582 | inORF3a1 | - | Alternative |
ORF3a.iORF2 | 25596 | 25697 | inORF3a2 | - | Alternative |
E | 26245 | 26472 | envelope protein | - | Canonical |
ORFM.ext | 26484 | 27191 | exORFM | - | Alternative |
M | 26523 | 27191 | membrane glycoprotein | - | Canonical |
ORFM.iORF | 27151 | 27195 | inORFM | - | Alternative |
ORF6 | 27202 | 27387 | ORF6 protein | - | Canonical |
ORF7a | 27394 | 27759 | ORF7a protein | - | Canonical |
ORF7b | 27756 | 27887 | ORF7b protein | - | Canonical |
ORF7b.iORF2 | 27862 | 27897 | inORF7b | - | Alternative |
ORF8 | 27894 | 28259 | ORF8 protein | - | Canonical |
ORF8.iORF | 27965 | 27994 | inORF8 | - | Alternative |
N | 28274 | 29533 | nucleocapsid phosphoprotein | - | Canonical |
ORFN.iORF1 | 28284 | 28577 | ORF9b | - | Alternative |
ORF10.upORF | 29538 | 29570 | upORF10 | - | Alternative |
ORF10 | 29558 | 29674 | ORF10 protein | - | Canonical |
Set | Length | Overlapp | Number | Variants |
---|---|---|---|---|
15–11 | 15 | 11 | 2821 | 31 |
15–10 | 15 | 10 | 2262 | 23 |
18–11 | 18 | 11 | 1561 | 22 |
Consensus Sequence | ORF | Consensus Start Position | Alignment Hit | Epitopes | |||||
---|---|---|---|---|---|---|---|---|---|
I | II | III | Unknown | SARS-CoV | Human | Other Coronavirus | |||
VGVLTLDNQDLNG | ORF1b | 193 | 1 | 4 | - | - | |||
TQMNLKYAISAKNRARTVAGVSI | ORF1b | 530 | - | 5 | 2 | - | |||
VIGTSKFYGGW | ORF1b | 580 | - | 3 | - | - | |||
LMGWDYPKCDRAMPN | ORF1b | 605 | 1 | 3 | - | - | |||
LANECAQVL | ORF1b | 646 | - | 1 | - | - | |||
YVKPGGTSSGDATTA | ORF1b | 665 | - | 3 | - | - | |||
KHFSMMILSDDAVVCFN | ORF1b | 743 | - | 2 | 1 | - | |||
LYYQNNVFMS | ORF1b | 778 | - | - | - | - | |||
GPHEFCSQHT | ORF1b | 800 | - | 2 | - | - | |||
LPYPDPSRIL | ORF1b | 820 | - | 2 | 3 | - | |||
ERFVSLAIDAYPL | ORF1b | 849 | - | 5 | - | 1 | |||
SQTSLRCG | ORF1b | 934 | - | 1 | - | - | |||
LYLGGMSYY | ORF1b | 986 | - | 3 | - | - | |||
LKLFAAET | ORF1b | 1054 | - | 4 | - | - | |||
QGPPGTGKSH | ORF1b | 1205 | 1 | 2 | 40 | - | |||
TACSHAAVDALCEKA | ORF1b | 1231 | - | 1 | - | - | |||
GDPAQLPAPR | ORF1b | 1324 | - | 3 | - | - | |||
AVFISPYNSQN | ORF1b | 1432 | - | 4 | 1 | - | |||
NRFNVAITRA | ORF1b | 1483 | - | 2 | - | - | |||
CNLGGAVC | ORF1b | 2002 | - | 1 | - | - | |||
KYTQLCQYLN | ORF1b | 2443 | - | 3 | - | - | |||
RSFIEDLLF | Spike | 815 | - | 2 | - | - | |||
QIDRLITGRL | Spike | 993 | - | 5 | - | 1 | |||
KWPWYIWL | Spike | 1211 | - | - | - | - | |||
WSFNPETN | M | 110 | - | 3 | - | - | |||
PRWYFYYLGTGP | N | 106 | - | 7 | - | - |
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Olvera, A.; Noguera-Julian, M.; Kilpelainen, A.; Romero-Martín, L.; Prado, J.G.; Brander, C. SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development. Vaccines 2020, 8, 444. https://doi.org/10.3390/vaccines8030444
Olvera A, Noguera-Julian M, Kilpelainen A, Romero-Martín L, Prado JG, Brander C. SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development. Vaccines. 2020; 8(3):444. https://doi.org/10.3390/vaccines8030444
Chicago/Turabian StyleOlvera, Alex, Marc Noguera-Julian, Athina Kilpelainen, Luis Romero-Martín, Julia G. Prado, and Christian Brander. 2020. "SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development" Vaccines 8, no. 3: 444. https://doi.org/10.3390/vaccines8030444
APA StyleOlvera, A., Noguera-Julian, M., Kilpelainen, A., Romero-Martín, L., Prado, J. G., & Brander, C. (2020). SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development. Vaccines, 8(3), 444. https://doi.org/10.3390/vaccines8030444