Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient.
Biodata mining
COVID-19
ORF1ab
Protein Modelling
SARS-CoV-2
nsp1
Journal
Biological procedures online
ISSN: 1480-9222
Titre abrégé: Biol Proced Online
Pays: England
ID NLM: 100963717
Informations de publication
Date de publication:
2020
2020
Historique:
received:
16
03
2020
accepted:
08
04
2020
entrez:
28
4
2020
pubmed:
28
4
2020
medline:
28
4
2020
Statut:
epublish
Résumé
Coronavirus disease 2019 (COVID-19) is an emerging zoonotic viral infection, which was started in Wuhan, China, in December 2019 and transmitted to other countries worldwide as a pandemic outbreak. Iran is one of the top ranked countries in the tables of COVID-19-infected and -mortality cases that make the Iranian patients as the potential targets for diversity of studies including epidemiology, biomedical, biodata, and viral proteins computational modelling studies. In this study, we applied bioinformatic biodata mining methods to detect CDS and protein sequences of ORF1ab polyprotein of SARS-CoV-2 isolated from oronasopharynx of an Iranian patient. Then through the computational modelling and antigenicity prediction approaches, the identified polyprotein sequence was analyzed. The results revealed that the identified ORF1ab polyprotein belongs to a part of nonstructural protein 1 (nsp1) with the high antigenicity residues in a glycine-proline or hydrophobic amino acid rich domain. The results revealed that nsp1 as a virulence factor and crucial agent in spreading of the COVID-19 among the society can be a potential target for the future epidemiology, drug, and vaccine studies.
Sections du résumé
BACKGROUND
BACKGROUND
Coronavirus disease 2019 (COVID-19) is an emerging zoonotic viral infection, which was started in Wuhan, China, in December 2019 and transmitted to other countries worldwide as a pandemic outbreak. Iran is one of the top ranked countries in the tables of COVID-19-infected and -mortality cases that make the Iranian patients as the potential targets for diversity of studies including epidemiology, biomedical, biodata, and viral proteins computational modelling studies.
RESULTS
RESULTS
In this study, we applied bioinformatic biodata mining methods to detect CDS and protein sequences of ORF1ab polyprotein of SARS-CoV-2 isolated from oronasopharynx of an Iranian patient. Then through the computational modelling and antigenicity prediction approaches, the identified polyprotein sequence was analyzed. The results revealed that the identified ORF1ab polyprotein belongs to a part of nonstructural protein 1 (nsp1) with the high antigenicity residues in a glycine-proline or hydrophobic amino acid rich domain.
CONCLUSIONS
CONCLUSIONS
The results revealed that nsp1 as a virulence factor and crucial agent in spreading of the COVID-19 among the society can be a potential target for the future epidemiology, drug, and vaccine studies.
Identifiants
pubmed: 32336957
doi: 10.1186/s12575-020-00121-9
pii: 121
pmc: PMC7171442
doi:
Types de publication
Journal Article
Langues
eng
Pagination
8Informations de copyright
© The Author(s) 2020.
Déclaration de conflit d'intérêts
Competing InterestsThe authors declare that they have no conflict of interests.
Références
Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7348-E7357
pubmed: 28807998
mBio. 2013 Sep 10;4(5):e00650-13
pubmed: 24023385
Viruses. 2019 Mar 02;11(3):
pubmed: 30832356
Nature. 2013 Mar 14;495(7440):251-4
pubmed: 23486063
Virol Sin. 2018 Oct;33(5):453-455
pubmed: 30374826
PLoS Pathog. 2014 Aug 21;10(8):e1004250
pubmed: 25144235
Int J Gen Med. 2019 Aug 26;12:305-311
pubmed: 31692574
FEBS Lett. 1990 Dec 10;276(1-2):172-4
pubmed: 1702393
Vaccine. 2014 Oct 14;32(45):5975-82
pubmed: 25192975
Bioinformatics. 2018 Nov 1;34(21):3755-3758
pubmed: 29850778
J Infect Dis. 2019 Oct 8;220(10):1558-1567
pubmed: 30911758
Vaccine. 2014 Apr 11;32(18):2100-8
pubmed: 24560617
Front Biosci. 2008 May 01;13:4873-81
pubmed: 18508552
J Virol. 2017 Jan 3;91(2):
pubmed: 27807241
PLoS One. 2013 Dec 04;8(12):e81587
pubmed: 24324708
J Virol. 2013 Nov;87(21):11950-4
pubmed: 23986586
J Virol. 2015 Apr;89(7):3659-70
pubmed: 25589660
Vaccine. 2018 Mar 27;36(14):1853-1862
pubmed: 29496347
Oncotarget. 2017 Feb 21;8(8):12686-12694
pubmed: 27050368
Virology. 2018 Jan 1;513:65-74
pubmed: 29035787
Vaccine. 2017 Jun 27;35(30):3780-3788
pubmed: 28579232
Allergy. 2020 Feb 19;:
pubmed: 32077115
J Clin Med. 2020 Feb 11;9(2):
pubmed: 32054124
N Engl J Med. 2012 Nov 8;367(19):1814-20
pubmed: 23075143
Vaccine. 2018 Jun 7;36(24):3468-3476
pubmed: 29739720
J Mol Biol. 2017 Jan 20;429(2):261-279
pubmed: 27890783
Viruses. 2012 Jun;4(6):1011-33
pubmed: 22816037
Cell Mol Immunol. 2016 Mar;13(2):180-90
pubmed: 25640653
Immunology. 2015 Aug;145(4):476-84
pubmed: 25762305
Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8738-43
pubmed: 26124093
Vaccine. 2017 Apr 11;35(16):2069-2075
pubmed: 28314561
Hum Vaccin Immunother. 2017 Jul 3;13(7):1615-1624
pubmed: 28277821
Int J Environ Res Public Health. 2020 Mar 03;17(5):
pubmed: 32138266
J Virol. 2015 Aug;89(16):8651-6
pubmed: 26018172
Vaccine. 2017 Jan 3;35(1):10-18
pubmed: 27899228
Parasit Vectors. 2014 Aug 29;7:403
pubmed: 25174433
Nat Microbiol. 2016 Feb 22;1:16004
pubmed: 27572168
Nat Microbiol. 2020 Apr;5(4):562-569
pubmed: 32094589
Front Microbiol. 2019 Aug 02;10:1781
pubmed: 31428074
NPJ Vaccines. 2017 Oct 16;2:28
pubmed: 29263883
Vaccine. 2014 May 30;32(26):3169-3174
pubmed: 24736006
PLoS Biol. 2015 May 05;13(5):e1002140
pubmed: 25942442
Nat Microbiol. 2016 Nov 28;2:16226
pubmed: 27892925
Viruses. 2013 Jan 18;5(1):279-94
pubmed: 23334702
J Virol. 2015 Nov;89(22):11654-67
pubmed: 26355094
Emerg Infect Dis. 2014 Dec;20(12):1999-2005
pubmed: 25418529
Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4970-5
pubmed: 24599590
Protein Sci. 2018 Jan;27(1):135-145
pubmed: 28884485
Emerg Microbes Infect. 2018 Apr 4;7(1):60
pubmed: 29618723
Antiviral Res. 2018 Feb;150:30-38
pubmed: 29246504
Lancet. 2003 Oct 25;362(9393):1353-8
pubmed: 14585636
Nat Rev Microbiol. 2009 Jun;7(6):439-50
pubmed: 19430490
Vaccine. 2014 Oct 21;32(46):6170-6176
pubmed: 25240756
Virology. 2018 Jun 11;521:99-107
pubmed: 29902727
PLoS One. 2014 Nov 18;9(11):e112602
pubmed: 25405618
Virology. 2016 Dec;499:375-382
pubmed: 27750111
EBioMedicine. 2015 Aug 18;2(10):1438-46
pubmed: 26629538
Hum Vaccin Immunother. 2016 Sep;12(9):2351-6
pubmed: 27269431
Viruses. 2018 Aug 23;10(9):
pubmed: 30142928
Emerg Microbes Infect. 2017 Mar 29;6(3):e14
pubmed: 28352124
Trends Microbiol. 2007 Feb;15(2):51-3
pubmed: 17207625
Vaccine. 2017 Mar 14;35(12):1586-1589
pubmed: 28237499
Sci Transl Med. 2015 Aug 19;7(301):301ra132
pubmed: 26290414
mSphere. 2017 Nov 15;2(6):
pubmed: 29152578
Nucleic Acids Res. 2015 Jan;43(Database issue):D571-7
pubmed: 25428358
Front Immunol. 2018 Feb 12;9:205
pubmed: 29483914
Viruses. 2018 Dec 16;10(12):
pubmed: 30558354
Antiviral Res. 2017 Apr;140:55-61
pubmed: 28040513
Parasit Vectors. 2016 Mar 16;9:152
pubmed: 26983858
Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):E3900-9
pubmed: 25197083
PLoS One. 2017 Feb 24;12(2):e0172093
pubmed: 28234937
Cell. 2020 Apr 16;181(2):271-280.e8
pubmed: 32142651
Korean J Parasitol. 2001 Mar;39(1):57-66
pubmed: 11301591
Methods Mol Biol. 2015;1282:1-23
pubmed: 25720466
J Anat. 2010 Mar;216(3):356-67
pubmed: 20070430
Front Immunol. 2018 May 17;9:1093
pubmed: 29868035
Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6335-9
pubmed: 9177218
J Virol. 2008 Dec;82(24):12392-405
pubmed: 18842706
J Virol. 2005 Dec;79(24):15199-208
pubmed: 16306591
Sci Rep. 2017 Mar 23;7:44875
pubmed: 28332568