Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models.
Adaptive mutation
COVID-19
Coronavirus
Local adaptation
Molecular evolution
SARS-CoV-2
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
23 12 2020
23 12 2020
Historique:
received:
05
08
2020
accepted:
29
10
2020
entrez:
28
12
2020
pubmed:
29
12
2020
medline:
9
1
2021
Statut:
epublish
Résumé
A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic. Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.
Sections du résumé
BACKGROUND
A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic.
RESULTS
Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp
CONCLUSIONS
These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.
Identifiants
pubmed: 33357233
doi: 10.1186/s13059-020-02191-0
pii: 10.1186/s13059-020-02191-0
pmc: PMC7756312
doi:
Substances chimiques
Viral Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
304Subventions
Organisme : U.S. Department of Energy
ID : LOIS:10074
Pays : International
Organisme : U.S. Department of Energy
ID : Office of Science through the National Virtual Biotechnology Laboratory
Pays : International
Références
Exp Mol Pathol. 2012 Aug;93(1):74-81
pubmed: 22537547
Protein Sci. 2020 Jul;29(7):1596-1605
pubmed: 32304108
Science. 2020 Mar 13;367(6483):1260-1263
pubmed: 32075877
Can J Microbiol. 2009 Mar;55(3):254-60
pubmed: 19370068
J Virol. 2004 Oct;78(19):10628-35
pubmed: 15367630
Sci Rep. 2018 Oct 11;8(1):15177
pubmed: 30310104
Virus Res. 2007 Jul;127(1):71-80
pubmed: 17499376
J Virol. 2015 Dec;89(23):11820-33
pubmed: 26378163
Mol Biol Evol. 1999 Jan;16(1):37-48
pubmed: 10331250
J Biol Chem. 2014 May 2;289(18):12535-49
pubmed: 24668816
J Gen Virol. 2008 Aug;89(Pt 8):1960-1969
pubmed: 18632968
PLoS Pathog. 2013;9(12):e1003760
pubmed: 24348241
J Exp Biol. 2012 Jun 1;215(Pt 11):1837-46
pubmed: 22573762
J Virol. 2010 Nov;84(21):11575-9
pubmed: 20739524
J Biol Chem. 2009 Jun 12;284(24):16202-9
pubmed: 19380580
Emerg Microbes Infect. 2020 Dec;9(1):221-236
pubmed: 31987001
Am J Respir Cell Mol Biol. 2007 Jul;37(1):9-19
pubmed: 17413032
J Hum Genet. 2014 Feb;59(2):66-77
pubmed: 24304692
J Virol. 2009 Mar;83(5):2368-73
pubmed: 19091867
Cell. 2020 May 14;181(4):914-921.e10
pubmed: 32330414
J Virol. 2007 Jan;81(2):718-31
pubmed: 17079322
Gene Rep. 2020 Jun;19:100682
pubmed: 32300673
Curr Pharm Des. 2013;19(23):4191-213
pubmed: 23170892
PLoS One. 2012;7(2):e31231
pubmed: 22363587
J Virol. 2004 Jul;78(14):7833-8
pubmed: 15220459
Biochem Biophys Res Commun. 2004 Apr 2;316(2):476-83
pubmed: 15020242
Cell. 2020 Apr 16;181(2):281-292.e6
pubmed: 32155444
Nature. 2020 Aug;584(7819):154-156
pubmed: 32438371
Genes (Basel). 2020 Jul 07;11(7):
pubmed: 32646049
Cell. 2020 Aug 20;182(4):812-827.e19
pubmed: 32697968
J Immunol. 2014 Sep 15;193(6):3080-9
pubmed: 25135833
J Virol. 2009 Mar;83(5):2255-64
pubmed: 19052082
J Virol. 2009 Dec;83(24):12998-3008
pubmed: 19828617
Cell. 1999 Apr 2;97(1):75-84
pubmed: 10199404
Nat Struct Mol Biol. 2005 Nov;12(11):980-6
pubmed: 16228002
J Virol. 2006 Aug;80(16):7902-8
pubmed: 16873247
Mol Biol Evol. 2020 Sep 17;:
pubmed: 32941612
Cell Mol Life Sci. 2017 Sep;74(17):3175-3183
pubmed: 28597296
J Virol. 2007 May;81(10):5423-6
pubmed: 17344286
Nat Struct Mol Biol. 2009 Nov;16(11):1134-40
pubmed: 19838190
J Gen Virol. 2000 Apr;81(Pt 4):853-79
pubmed: 10725411
J Med Virol. 2020 Jun;92(6):667-674
pubmed: 32167180
Proc Natl Acad Sci U S A. 2020 Jan 21;117(3):1496-1503
pubmed: 31896580
Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12540-5
pubmed: 16894145
J Virol. 2015 Aug;89(16):8416-27
pubmed: 26041293
FEBS Lett. 1987 Dec 10;225(1-2):163-7
pubmed: 3121390
Nat Commun. 2019 May 28;10(1):2342
pubmed: 31138817
mBio. 2013 Aug 13;4(4):
pubmed: 23943763
Structure. 2004 Feb;12(2):341-53
pubmed: 14962394
J Virol. 2004 Sep;78(18):9977-86
pubmed: 15331731
Antiviral Res. 2014 Mar;103:39-50
pubmed: 24418573
Euro Surveill. 2017 Mar 30;22(13):
pubmed: 28382917
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
J Virol. 2005 Sep;79(17):11476-86
pubmed: 16103198
J Biol Chem. 2015 Jan 30;290(5):3172-82
pubmed: 25505178
Nucleic Acids Res. 2019 Jul 9;47(12):6538-6550
pubmed: 31131400
Science. 2020 Sep 25;369(6511):1586-1592
pubmed: 32694201
Science. 2003 Jun 13;300(5626):1763-7
pubmed: 12746549
Structure. 2005 Nov;13(11):1665-75
pubmed: 16271890
J Struct Biol. 2011 Apr;174(1):11-22
pubmed: 21130884
J Virol. 2008 Jun;82(11):5279-94
pubmed: 18367524
Chem Sci. 2018 Mar 20;9(15):3710-3715
pubmed: 29780502
Science. 2020 May 15;368(6492):779-782
pubmed: 32277040
PLoS Genet. 2006 Sep 22;2(9):e148
pubmed: 17044736
R Soc Open Sci. 2014 Oct 01;1(2):140172
pubmed: 26064538
PLoS One. 2011;6(8):e24109
pubmed: 21909381
Nat Rev Microbiol. 2009 Jun;7(6):439-50
pubmed: 19430490
Cells. 2018 Nov 29;7(12):
pubmed: 30501123
Adv Exp Med Biol. 2006;581:115-20
pubmed: 17037516
PLoS Pathog. 2011 May;7(5):e1002059
pubmed: 21637813
PLoS Pathog. 2010 Apr 22;6(4):e1000863
pubmed: 20421945
Science. 2020 Mar 27;367(6485):1444-1448
pubmed: 32132184
Cell Host Microbe. 2020 Mar 11;27(3):325-328
pubmed: 32035028
PLoS Biol. 2018 Aug 13;16(8):e3000003
pubmed: 30102691
PLoS One. 2014 Jun 25;9(6):e100940
pubmed: 24963780
Genes (Basel). 2019 Dec 02;10(12):
pubmed: 31810264
Front Genet. 2019 May 31;10:487
pubmed: 31214244
FEBS J. 2008 Aug;275(16):4152-63
pubmed: 18631359
Virology. 2014 Jun;458-459:125-35
pubmed: 24928045
PLoS Genet. 2008 Dec;4(12):e1000304
pubmed: 19081788
Cell. 2020 Oct 29;183(3):739-751.e8
pubmed: 32991842
J Med Virol. 2007 Oct;79(10):1431-9
pubmed: 17705188
RNA. 2000 May;6(5):755-67
pubmed: 10836796
PLoS One. 2012;7(5):e36521
pubmed: 22615777
Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17668-73
pubmed: 17971437
Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):E3900-9
pubmed: 25197083
Cell. 2020 Apr 16;181(2):271-280.e8
pubmed: 32142651
J Virol. 2013 Aug;87(16):9159-72
pubmed: 23760243
Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10383-8
pubmed: 10984534
J Chem Phys. 2007 Jan 7;126(1):014101
pubmed: 17212484
FEBS Lett. 2006 Dec 22;580(30):6807-12
pubmed: 17141229
Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):9436-41
pubmed: 26159422
J Comput Chem. 2013 Sep 30;34(25):2135-45
pubmed: 23832629
Science. 2020 Oct 30;370(6516):571-575
pubmed: 32913002
PLoS One. 2007 May 23;2(5):e459
pubmed: 17520018
Mol Biol Evol. 2020 Jul 20;:
pubmed: 32687176
Nature. 2020 Jul;583(7816):459-468
pubmed: 32353859
Antiviral Res. 2018 Jan;149:58-74
pubmed: 29128390
J Biochem Mol Biol. 2007 Sep 30;40(5):649-55
pubmed: 17927896
Biochem Biophys Res Commun. 2004 Sep 3;321(4):994-1000
pubmed: 15358126
J Transl Med. 2020 Apr 22;18(1):179
pubmed: 32321524
PLoS One. 2009 Dec 17;4(12):e8342
pubmed: 20020050
J Mol Biol. 2008 Nov 28;383(5):1081-96
pubmed: 18694760