Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2019
2019
Historique:
received:
25
01
2019
accepted:
08
07
2019
entrez:
19
7
2019
pubmed:
19
7
2019
medline:
4
3
2020
Statut:
epublish
Résumé
Human Parainfluenza viruses (HPIV) type 1 and 3 are important causes of respiratory tract infections in young children globally. HPIV infections do not confer complete protective immunity so reinfections occur throughout life. Since no effective vaccine is available for the two virus subtypes, comprehensive understanding of HPIV-1 and HPIV-3 genetic and epidemic features is important for diagnosis, prevention, and treatment of HPIV-1 and HPIV-3 infections. Relatively few whole genome sequences are available for both HPIV-1 and HPIV-3 viruses, so our study sought to provide whole genome sequences from multiple countries to further the understanding of the global diversity of HPIV at a whole-genome level. We collected HPIV-1 and HPIV-3 samples and isolates from Argentina, Australia, France, Mexico, South Africa, Switzerland, and USA from the years 2003-2011 and sequenced the genomes of 40 HPIV-1 and 75 HPIV-3 viruses with Sanger and next-generation sequencing with the Ion Torrent, Illumina, and 454 platforms. Phylogenetic analysis showed that the HPIV-1 genome is evolving at an estimated rate of 4.97 × 10-4 mutations/site/year (95% highest posterior density 4.55 × 10-4 to 5.38 × 10-4) and the HPIV-3 genome is evolving at a similar rate (3.59 × 10-4 mutations/site/year, 95% highest posterior density 3.26 × 10-4 to 3.94 × 10-4). There were multiple genetically distinct lineages of both HPIV-1 and 3 circulating on a global scale. Further surveillance and whole-genome sequencing are greatly needed to better understand the spatial dynamics of these important respiratory viruses in humans.
Identifiants
pubmed: 31318956
doi: 10.1371/journal.pone.0220057
pii: PONE-D-19-02466
pmc: PMC6638977
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0220057Subventions
Organisme : NIAID NIH HHS
ID : HHSN272200900007C
Pays : United States
Organisme : NIAID NIH HHS
ID : U19 AI110819
Pays : United States
Organisme : NIAID NIH HHS
ID : U01 AI070428
Pays : United States
Organisme : NIAID NIH HHS
ID : U01 AI077988
Pays : United States
Déclaration de conflit d'intérêts
I have read the journal's policy and the authors of this manuscript have the following competing interests: Daniel E. Noyola has participated as a member of the speakers' bureau of AbbVie and speakers' bureau and advisory board for Sanofi Pasteur. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
Références
PLoS One. 2014 Feb 05;9(2):e88342
pubmed: 24505479
J Virol Methods. 1993 May;42(2-3):241-50
pubmed: 8390473
J Med Microbiol. 2014 Apr;63(Pt 4):570-577
pubmed: 24464692
BMC Genomics. 2008 Jan 07;9:5
pubmed: 18179705
PLoS One. 2014 Apr 15;9(4):e94681
pubmed: 24736452
Virology. 1994 Aug 1;202(2):875-84
pubmed: 8030249
Mol Biol Evol. 2005 May;22(5):1208-22
pubmed: 15703242
Virol J. 2012 Nov 06;9:261
pubmed: 23131097
PLoS Genet. 2012;8(7):e1002764
pubmed: 22807683
Pediatr Infect Dis J. 2001 Jul;20(7):646-53
pubmed: 11465835
J Pediatric Infect Dis Soc. 2016 Mar;5(1):7-13
pubmed: 26908486
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Rev Infect Dis. 1990 Nov-Dec;12 Suppl 8:S889-98
pubmed: 2270411
Clin Microbiol Rev. 2003 Apr;16(2):242-64
pubmed: 12692097
Vaccine. 2010 Mar 16;28(13):2550-5
pubmed: 20117263
Sci Rep. 2016 May 23;6:26311
pubmed: 27212633
J Virol Methods. 1999 Aug;81(1-2):77-81
pubmed: 10488764
J Med Microbiol. 2005 Oct;54(Pt 10):969-74
pubmed: 16157552
Bioinformatics. 2010 Oct 1;26(19):2455-7
pubmed: 20671151
J Med Microbiol. 2017 Feb;66(2):160-168
pubmed: 28266286
Pediatr Infect Dis J. 2004 Jan;23(1 Suppl):S11-8
pubmed: 14730265
Virol J. 2011 Feb 09;8:58
pubmed: 21306605
Mol Biol Evol. 2012 Aug;29(8):1969-73
pubmed: 22367748
Bioinformatics. 2010 Oct 1;26(19):2462-3
pubmed: 20798170
Nat Rev Genet. 2008 Apr;9(4):267-76
pubmed: 18319742
J Virol Methods. 2010 May;165(2):254-60
pubmed: 20153377
J Infect Dis. 1997 Dec;176(6):1423-7
pubmed: 9395350
J Virol. 1990 Mar;64(3):1329-34
pubmed: 1689394
Mol Biol Evol. 2013 May;30(5):1196-205
pubmed: 23420840
Wellcome Open Res. 2018 Sep 19;3:118
pubmed: 30569021
Virology. 1986 Jul 15;152(1):241-51
pubmed: 3012869
Sci Rep. 2018 May 1;8(1):6833
pubmed: 29717150
J Virol Methods. 2009 Mar;156(1-2):166-8
pubmed: 19063922
J Mol Evol. 2002 Feb;54(2):156-65
pubmed: 11821909
Infect Control Hosp Epidemiol. 2008 Jun;29(6):556-8
pubmed: 18510465
Pediatr Infect Dis J. 2004 Feb;23(2):118-23
pubmed: 14872176
Intervirology. 2015;58(1):35-40
pubmed: 25592955
mBio. 2018 Jul 3;9(4):
pubmed: 29970463
PLoS One. 2012;7(9):e46048
pubmed: 23029382
J Med Microbiol. 2016 Aug;65(8):793-803
pubmed: 27302417
J Infect Dis. 2012 Dec 15;206 Suppl 1:S159-65
pubmed: 23169964
Virol J. 2011 Dec 13;8:533
pubmed: 22152158
Am J Public Health Nations Health. 1962 Jun;52:907-17
pubmed: 14038204
PLoS One. 2015 Mar 20;10(3):e0120098
pubmed: 25793751
PLoS One. 2012;7(8):e43893
pubmed: 22937119
J Virol Methods. 1994 Dec;50(1-3):87-100
pubmed: 7714062
Infect Genet Evol. 2013 Mar;14:357-60
pubmed: 23305888