Inference of Nipah virus evolution, 1999-2015.
Nipah virus
phylogeography
selective pressure
virus evolution
Journal
Virus evolution
ISSN: 2057-1577
Titre abrégé: Virus Evol
Pays: England
ID NLM: 101664675
Informations de publication
Date de publication:
Jan 2021
Jan 2021
Historique:
entrez:
23
8
2021
pubmed:
24
8
2021
medline:
24
8
2021
Statut:
epublish
Résumé
Despite near-annual human outbreaks of Nipah virus (NiV) disease in Bangladesh, typically due to individual spillover events from the local bat population, only twenty whole-genome NiV sequences exist from humans and ten from bats. NiV whole-genome sequences from annual outbreaks have been challenging to generate, primarily due to the low viral load in human throat swab and serum specimens. Here, we used targeted enrichment with custom NiV-specific probes and generated thirty-five additional unique full-length genomic sequences directly from human specimens and viral isolates. We inferred the temporal and geographic evolutionary history of NiV in Bangladesh and expanded a tool to visualize NiV spatio-temporal spread from a Bayesian continuous diffusion analysis. We observed that strains from Bangladesh segregated into two distinct clades that have intermingled geographically in Bangladesh over time and space. As these clades expanded geographically and temporally, we did not observe evidence for significant branch and site-specific selection, except for a single site in the
Identifiants
pubmed: 34422315
doi: 10.1093/ve/veaa062
pii: veaa062
pmc: PMC7947586
doi:
Types de publication
Journal Article
Langues
eng
Pagination
veaa062Informations de copyright
Published by Oxford University Press 2020. This work is written by a US Government employee and is in the public domain in the US.
Références
Transbound Emerg Dis. 2020 Jan;67(1):121-132
pubmed: 31408582
Virus Evol. 2018 Jun 08;4(1):vey016
pubmed: 29942656
Emerg Infect Dis. 2011 May;17(5):907-9
pubmed: 21529409
Emerg Infect Dis. 2005 Oct;11(10):1594-7
pubmed: 16318702
Science. 2000 May 26;288(5470):1432-5
pubmed: 10827955
Bioinformatics. 2012 Dec 15;28(24):3248-56
pubmed: 23064000
J Virol. 2010 Jan;84(2):765-72
pubmed: 19889759
J Virol. 1998 Feb;72(2):1482-90
pubmed: 9445051
Vector Borne Zoonotic Dis. 2010 Mar;10(2):183-90
pubmed: 19402762
Vector Borne Zoonotic Dis. 2012 Jan;12(1):65-72
pubmed: 21923274
Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):15066-71
pubmed: 22927414
Epidemiol Infect. 2016 Jan;144(2):371-80
pubmed: 26122675
Emerg Infect Dis. 2004 Dec;10(12):2082-7
pubmed: 15663842
Syst Biol. 2018 Sep 1;67(5):901-904
pubmed: 29718447
PLoS Pathog. 2010 Oct 28;6(10):e1001166
pubmed: 21060816
J Infect Dis. 2019 May 24;219(12):1867-1878
pubmed: 30364984
Emerg Infect Dis. 2013 Feb;19(2):210-7
pubmed: 23347678
Virol J. 2016 Mar 25;13:53
pubmed: 27016237
Emerg Infect Dis. 2006 Feb;12(2):235-40
pubmed: 16494748
Virology. 2001 Aug 15;287(1):192-201
pubmed: 11504554
Cell. 2015 Jun 18;161(7):1516-26
pubmed: 26091036
Int J Infect Dis. 2021 Jan;102:144-151
pubmed: 33129964
Microbes Infect. 2002 Feb;4(2):145-51
pubmed: 11880045
Science. 2018 Aug 31;361(6405):894-899
pubmed: 30139911
Virology. 2000 Jun 5;271(2):334-49
pubmed: 10860887
PLoS One. 2011;6(9):e25275
pubmed: 21980413
Mol Ecol. 2018 Feb;27(3):773-788
pubmed: 29274171
Cell Host Microbe. 2015 Dec 9;18(6):659-69
pubmed: 26651942
Emerg Infect Dis. 2012 Feb;18(2):248-55
pubmed: 22304936
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Curr Protoc Bioinformatics. 2020 Mar;69(1):e96
pubmed: 32162851
Emerg Infect Dis. 2005 Jul;11(7):1042-7
pubmed: 16022778
Virus Evol. 2015 May 26;1(1):vev003
pubmed: 27774277
Emerg Infect Dis. 2019 Jan;25(1):166-170
pubmed: 30561301
J Gen Virol. 2009 Feb;90(Pt 2):398-404
pubmed: 19141449
Nature. 2017 Apr 20;544(7650):309-315
pubmed: 28405027
Emerg Infect Dis. 2017 Sep;23(9):1446-1453
pubmed: 28820130
PLoS Pathog. 2019 Dec 6;15(12):e1007976
pubmed: 31809523
Emerg Infect Dis. 2016 Apr;22(4):664-70
pubmed: 26981928
Mol Ecol. 2004 Apr;13(4):745-56
pubmed: 15012753
Emerg Infect Dis. 2005 Dec;11(12):1949-51
pubmed: 16485487
MMWR Morb Mortal Wkly Rep. 1999 Apr 9;48(13):265-9
pubmed: 10227800
PLoS One. 2012;7(8):e42532
pubmed: 22880021
J Virol. 2010 Oct;84(19):9967-77
pubmed: 20631128
Emerg Infect Dis. 2014 Jun;20(6):1064-6
pubmed: 24865545
Emerg Infect Dis. 2019 May;25(5):1003-1006
pubmed: 31002049
Genome Res. 2018 Jun;28(6):869-877
pubmed: 29703817
Mol Biol Evol. 2020 Feb 1;37(2):599-603
pubmed: 31633786
Nat Commun. 2012 Apr 24;3:796
pubmed: 22531181
Virus Evol. 2016 Apr 09;2(1):vew007
pubmed: 27774300
Lancet. 1999 Oct 9;354(9186):1257-9
pubmed: 10520635
Methods Mol Biol. 2017;1525:433-460
pubmed: 27896731
Mol Biol Evol. 2017 Oct 1;34(10):2563-2571
pubmed: 28651357
Emerg Infect Dis. 2015 Feb;21(2):349-51
pubmed: 25625615
Bioinformatics. 2016 Oct 15;32(20):3204-3206
pubmed: 27334476
Mol Ecol. 2020 Mar;29(5):970-985
pubmed: 31652377
PLoS One. 2013 Jul 22;8(7):e69544
pubmed: 23894501
Emerg Infect Dis. 2009 Aug;15(8):1229-35
pubmed: 19751584
J Med Virol. 2016 Mar;88(3):380-8
pubmed: 26252523
PLoS Pathog. 2012;8(8):e1002836
pubmed: 22879820
Int J Epidemiol. 2019 Aug 1;48(4):1219-1227
pubmed: 30977803
Epidemiol Infect. 2010 Nov;138(11):1630-6
pubmed: 20380769
MMWR Morb Mortal Wkly Rep. 1999 Apr 30;48(16):335-7
pubmed: 10366143
J Gen Virol. 2001 Sep;82(Pt 9):2151-2155
pubmed: 11514724