Identifying the genetic basis of viral spillover using Lassa virus as a test case.
Lassa virus
genome-wide association studies
host shift
single-nucleotide polymorphisms
spillover
zoonosis
Journal
Royal Society open science
ISSN: 2054-5703
Titre abrégé: R Soc Open Sci
Pays: England
ID NLM: 101647528
Informations de publication
Date de publication:
Mar 2023
Mar 2023
Historique:
received:
21
11
2022
accepted:
27
02
2023
entrez:
27
3
2023
pubmed:
28
3
2023
medline:
28
3
2023
Statut:
epublish
Résumé
The rate at which zoonotic viruses spill over into the human population varies significantly over space and time. Remarkably, we do not yet know how much of this variation is attributable to genetic variation within viral populations. This gap in understanding arises because we lack methods of genetic analysis that can be easily applied to zoonotic viruses, where the number of available viral sequences is often limited, and opportunistic sampling introduces significant population stratification. Here, we explore the feasibility of using patterns of shared ancestry to correct for population stratification, enabling genome-wide association methods to identify genetic substitutions associated with spillover into the human population. Using a combination of phylogenetically structured simulations and Lassa virus sequences collected from humans and rodents in Sierra Leone, we demonstrate that existing methods do not fully correct for stratification, leading to elevated error rates. We also demonstrate, however, that the Type I error rate can be substantially reduced by confining the analysis to a less-stratified region of the phylogeny, even in an already-small dataset. Using this method, we detect two candidate single-nucleotide polymorphisms associated with spillover in the Lassa virus polymerase gene and provide generalized recommendations for the collection and analysis of zoonotic viruses.
Identifiants
pubmed: 36968239
doi: 10.1098/rsos.221503
pii: rsos221503
pmc: PMC10031424
doi:
Banques de données
figshare
['10.6084/m9.figshare.c.6461054']
Types de publication
Journal Article
Langues
eng
Pagination
221503Informations de copyright
© 2023 The Authors.
Déclaration de conflit d'intérêts
We declare we have no competing interests.
Références
Emerg Infect Dis. 2015 Apr;21(4):609-18
pubmed: 25811712
Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15376-9
pubmed: 15492220
Infect Genet Evol. 2015 Mar;30:296-307
pubmed: 25541518
Mol Biol Evol. 2016 Jun;33(6):1635-8
pubmed: 26921390
Nat Rev Genet. 2010 Jul;11(7):459-63
pubmed: 20548291
R Soc Open Sci. 2023 Mar 22;10(3):221503
pubmed: 36968239
Genome Biol Evol. 2018 Mar 1;10(3):863-874
pubmed: 29608723
Nat Commun. 2021 Oct 1;12(1):5759
pubmed: 34599162
Lancet. 2012 Dec 1;380(9857):1956-65
pubmed: 23200504
J Virol. 2019 Oct 15;93(21):
pubmed: 31413134
N Engl J Med. 2018 Nov 1;379(18):1745-1753
pubmed: 30332564
Nature. 2020 Mar;579(7800):615-619
pubmed: 32214249
J Immunol. 2021 Jun 1;206(11):2566-2582
pubmed: 33911008
Cell. 2015 Aug 13;162(4):738-50
pubmed: 26276630
Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):955-9
pubmed: 19144928
Nat Commun. 2021 Dec 2;12(1):7018
pubmed: 34857749
Lancet Infect Dis. 2019 Dec;19(12):1371-1378
pubmed: 31588039
Philos Trans R Soc Lond B Biol Sci. 2019 Sep 30;374(1782):20180342
pubmed: 31401951
Nat Rev Microbiol. 2022 May;20(5):299-314
pubmed: 34799704
J Virol. 2013 Jun;87(12):6635-43
pubmed: 23552411
Biology (Basel). 2021 Jan 05;10(1):
pubmed: 33466234
BMC Bioinformatics. 2021 Nov 10;22(1):546
pubmed: 34758743
Sci Rep. 2022 Aug 29;12(1):14683
pubmed: 36038559
Trends Microbiol. 2020 Apr;28(4):293-303
pubmed: 31948728
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
mSphere. 2019 Sep 25;4(5):
pubmed: 31554720
Cell. 2016 Nov 3;167(4):1079-1087.e5
pubmed: 27814505
Bioinformatics. 2014 Aug 1;30(15):2216-8
pubmed: 24728855
Virology. 1989 Feb;168(2):421-5
pubmed: 2916333
PLoS Negl Trop Dis. 2022 Jun 22;16(6):e0010504
pubmed: 35731800
Hum Mol Genet. 2008 Oct 15;17(R2):R143-50
pubmed: 18852203
PLoS Negl Trop Dis. 2019 Jun 27;13(6):e0007393
pubmed: 31246966
Nature. 2014 Dec 18;516(7531):361-6
pubmed: 25409151
Trends Parasitol. 2020 Dec;36(12):970-978
pubmed: 32952060
PLoS Pathog. 2019 May 28;15(5):e1007829
pubmed: 31136637
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12
pubmed: 16845082
Nat Rev Microbiol. 2016 Jul;14(7):448-60
pubmed: 27211789
Viruses. 2020 Apr 13;12(4):
pubmed: 32294960
Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):
pubmed: 33822740
Bioinformatics. 2019 Nov 1;35(21):4453-4455
pubmed: 31070718
J Virol. 2013 Jul;87(13):7200-9
pubmed: 23616660
Nature. 2022 Jul;607(7919):555-562
pubmed: 35483403
BMC Vet Res. 2013 Nov 04;9:223
pubmed: 24188616
One Health Outlook. 2020 Jan 10;2:1
pubmed: 33824944
Nature. 2020 Aug;584(7821):398-402
pubmed: 32759999
J Virol. 1991 Aug;65(8):4242-7
pubmed: 2072451
PLoS Negl Trop Dis. 2014 Mar 20;8(3):e2748
pubmed: 24651047
Nat Rev Genet. 2008 Apr;9(4):267-76
pubmed: 18319742
Proc Natl Acad Sci U S A. 2020 Nov 17;117(46):29190-29201
pubmed: 33139552
PLoS Genet. 2006 Dec;2(12):e190
pubmed: 17194218
Nat Genet. 2006 Aug;38(8):904-9
pubmed: 16862161
Biosaf Health. 2019 Jun;1(1):14-24
pubmed: 32835207
Genet Mol Biol. 2021 Jun 04;44(1 Suppl 1):e20200355
pubmed: 34096963
PLoS Genet. 2009 Oct;5(10):e1000686
pubmed: 19834557
Nat Genet. 2004 May;36(5):512-7
pubmed: 15052271
Nat Rev Microbiol. 2017 Aug;15(8):502-510
pubmed: 28555073
Virology. 2004 Jan 5;318(1):153-68
pubmed: 14972544
Nat Commun. 2017 Oct 24;8(1):1124
pubmed: 29066781