schliessen

Filtern

 

Bibliotheken

Phylogenomic analysis unravels evolution of yellow fever virus within hosts.

The yellow fever virus (YFV) recently reemerged in the large outbreaks in Africa and Brazil, and the first imported patients into Asia have recalled the concerns of YFV evolution. Here we show phylogenomics of YFV with serial clinical samples of the 2016 YFV infections. Phylogenetics exhibited that... Full description

Journal Title: PLoS neglected tropical diseases September 2018, Vol.12(9), p.e0006738
Main Author: Chen, Chen
Other Authors: Jiang, Dong , Ni, Ming , Li, Jing , Chen, Zhihai , Liu, Jingyuan , Ye, Hanhui , Wong, Gary , Li, Wei , Zhang, Yuanyuan , Wang, Beibei , Bi, Yuhai , Chen, Danying , Zhang, Ping , Zhao, Xuesen , Kong, Yaxian , Shi, Weifeng , Du, Pengcheng , Xiao, Gengfu , Ma, Juncai , Gao, George F , Cui, Jie , Zhang, Fujie , Liu, Wenjun , Bo, Xiaochen , Li, Ang , Zeng, Hui , Liu, Di
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1935-2735 ; DOI: 10.1371/journal.pntd.0006738
Link: http://search.proquest.com/docview/2101271004/?pq-origsite=primo
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: proquest2101271004
title: Phylogenomic analysis unravels evolution of yellow fever virus within hosts.
format: Article
creator:
  • Chen, Chen
  • Jiang, Dong
  • Ni, Ming
  • Li, Jing
  • Chen, Zhihai
  • Liu, Jingyuan
  • Ye, Hanhui
  • Wong, Gary
  • Li, Wei
  • Zhang, Yuanyuan
  • Wang, Beibei
  • Bi, Yuhai
  • Chen, Danying
  • Zhang, Ping
  • Zhao, Xuesen
  • Kong, Yaxian
  • Shi, Weifeng
  • Du, Pengcheng
  • Xiao, Gengfu
  • Ma, Juncai
  • Gao, George F
  • Cui, Jie
  • Zhang, Fujie
  • Liu, Wenjun
  • Bo, Xiaochen
  • Li, Ang
  • Zeng, Hui
  • Liu, Di
subjects:
  • Evolution, Molecular–Virology
  • Genome, Viral–Classification
  • High-Throughput Nucleotide Sequencing–Genetics
  • Humans–Isolation & Purification
  • Mutation Rate–Isolation & Purification
  • Phylogeny–Isolation & Purification
  • Polymorphism, Single Nucleotide–Isolation & Purification
  • Yellow Fever–Isolation & Purification
  • Yellow Fever Virus–Isolation & Purification
ispartof: PLoS neglected tropical diseases, September 2018, Vol.12(9), p.e0006738
description: The yellow fever virus (YFV) recently reemerged in the large outbreaks in Africa and Brazil, and the first imported patients into Asia have recalled the concerns of YFV evolution. Here we show phylogenomics of YFV with serial clinical samples of the 2016 YFV infections. Phylogenetics exhibited that the 2016 strains were close to Angola 1971 strains and only three amino acid changes presented new to other lineages. Deep sequencing of viral genomes discovered 101 intrahost single nucleotide variations (iSNVs) and 234 single nucleotide polymorphisms (SNPs). Analysis of iSNV distribution and mutated allele frequency revealed that the coding regions were under purifying selection. Comparison of the evolutionary rates estimated by iSNV and SNP showed that the intrahost rate was ~2.25 times higher than the epidemic rate, and both rates were higher than the long-term YFV substitution rate, as expected. In addition, the result also hinted that short viremia duration of YFV might further hinder the evolution of YFV. Author summary The first importation of infections into China in 2016 and the following outbreaks in Africa and Brazil of yellow fever virus (YFV) have raised again the concerns of the potential viral spread into new territories. In this study, we aimed to know the evolution dynamics of YFV by using intrahost phylogenomics and to assess the risk of virus epidemics. Through deep sequencing of consecutive samples from 12 patients, we identified hundreds of genomic variations (iSNVs and SNPs), and noticed the nearly linear accumulation of variations within individuals. The estimated evolutionary rate within host is much higher than the epidemic evolutionary rate. In comparison with Dengue virus (DENV) and Zika virus (ZIKV), which share similar host vectors (Aedes spp.), life cycles, mutation rates and replication strategies to YFV, the lower epidemic evolutionary rate of YFV might have been hindered by the shorter viremia duration, which decreased the accumulated variations to get into the transmission cycle.
language: eng
source:
identifier: E-ISSN: 1935-2735 ; DOI: 10.1371/journal.pntd.0006738
fulltext: fulltext
issn:
  • 19352735
  • 1935-2735
url: Link


@attributes
ID650479744
RANK0.07
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
LOCALfalse
PrimoNMBib
record
control
sourcerecordid2101271004
sourceidproquest
recordidTN_proquest2101271004
sourcesystemPC
pqid2101271004
galeid557636880
display
typearticle
titlePhylogenomic analysis unravels evolution of yellow fever virus within hosts.
creatorChen, Chen ; Jiang, Dong ; Ni, Ming ; Li, Jing ; Chen, Zhihai ; Liu, Jingyuan ; Ye, Hanhui ; Wong, Gary ; Li, Wei ; Zhang, Yuanyuan ; Wang, Beibei ; Bi, Yuhai ; Chen, Danying ; Zhang, Ping ; Zhao, Xuesen ; Kong, Yaxian ; Shi, Weifeng ; Du, Pengcheng ; Xiao, Gengfu ; Ma, Juncai ; Gao, George F ; Cui, Jie ; Zhang, Fujie ; Liu, Wenjun ; Bo, Xiaochen ; Li, Ang ; Zeng, Hui ; Liu, Di
contributorChen, Chen (correspondence author) ; Chen, Chen (record owner)
ispartofPLoS neglected tropical diseases, September 2018, Vol.12(9), p.e0006738
identifierE-ISSN: 1935-2735 ; DOI: 10.1371/journal.pntd.0006738
subject
languageeng
source
descriptionThe yellow fever virus (YFV) recently reemerged in the large outbreaks in Africa and Brazil, and the first imported patients into Asia have recalled the concerns of YFV evolution. Here we show phylogenomics of YFV with serial clinical samples of the 2016 YFV infections. Phylogenetics exhibited that the 2016 strains were close to Angola 1971 strains and only three amino acid changes presented new to other lineages. Deep sequencing of viral genomes discovered 101 intrahost single nucleotide variations (iSNVs) and 234 single nucleotide polymorphisms (SNPs). Analysis of iSNV distribution and mutated allele frequency revealed that the coding regions were under purifying selection. Comparison of the evolutionary rates estimated by iSNV and SNP showed that the intrahost rate was ~2.25 times higher than the epidemic rate, and both rates were higher than the long-term YFV substitution rate, as expected. In addition, the result also hinted that short viremia duration of YFV might further hinder the evolution of YFV. Author summary The first importation of infections into China in 2016 and the following outbreaks in Africa and Brazil of yellow fever virus (YFV) have raised again the concerns of the potential viral spread into new territories. In this study, we aimed to know the evolution dynamics of YFV by using intrahost phylogenomics and to assess the risk of virus epidemics. Through deep sequencing of consecutive samples from 12 patients, we identified hundreds of genomic variations (iSNVs and SNPs), and noticed the nearly linear accumulation of variations within individuals. The estimated evolutionary rate within host is much higher than the epidemic evolutionary rate. In comparison with Dengue virus (DENV) and Zika virus (ZIKV), which share similar host vectors (Aedes spp.), life cycles, mutation rates and replication strategies to YFV, the lower epidemic evolutionary rate of YFV might have been hindered by the shorter viremia duration, which decreased the accumulated variations to get into the transmission cycle.
version8
lds50peer_reviewed
links
openurl$$Topenurl_article
openurlfulltext$$Topenurlfull_article
backlink$$Uhttp://search.proquest.com/docview/2101271004/?pq-origsite=primo$$EView_record_in_ProQuest_(subscribers_only)
search
creatorcontrib
0Chen, Chen
1Jiang, Dong
2Ni, Ming
3Li, Jing
4Chen, Zhihai
5Liu, Jingyuan
6Ye, Hanhui
7Wong, Gary
8Li, Wei
9Zhang, Yuanyuan
10Wang, Beibei
11Bi, Yuhai
12Chen, Danying
13Zhang, Ping
14Zhao, Xuesen
15Kong, Yaxian
16Shi, Weifeng
17Du, Pengcheng
18Xiao, Gengfu
19Ma, Juncai
20Gao, George F
21Cui, Jie
22Zhang, Fujie
23Liu, Wenjun
24Bo, Xiaochen
25Li, Ang
26Zeng, Hui
27Liu, Di
titlePhylogenomic analysis unravels evolution of yellow fever virus within hosts.
subject
0Evolution, Molecular–Virology
1Genome, Viral–Classification
2High-Throughput Nucleotide Sequencing–Genetics
3Humans–Isolation & Purification
4Mutation Rate–Isolation & Purification
5Phylogeny–Isolation & Purification
6Polymorphism, Single Nucleotide–Isolation & Purification
7Yellow Fever–Isolation...
general
0English
110.1371/journal.pntd.0006738
2MEDLINE (ProQuest)
3ProQuest Biological Science Collection
4ProQuest Natural Science Collection
5ProQuest SciTech Collection
6Biological Science Database
7Natural Science Collection
8SciTech Premium Collection
9Health Research Premium Collection
10Health Research Premium Collection (Alumni edition)
11Biological Science Index (ProQuest)
sourceidproquest
recordidproquest2101271004
issn
019352735
11935-2735
rsrctypearticle
creationdate2018
addtitlePLoS neglected tropical diseases
searchscope
01007527
11007944
21009130
310000004
410000038
510000050
610000120
710000159
810000238
910000253
1010000260
1110000270
1210000271
1310000302
1410000350
15proquest
scope
01007527
11007944
21009130
310000004
410000038
510000050
610000120
710000159
810000238
910000253
1010000260
1110000270
1210000271
1310000302
1410000350
15proquest
lsr43
01007527false
11007944false
21009130false
310000004false
410000038false
510000050false
610000120false
710000159false
810000238false
910000253false
1010000260false
1110000270false
1210000271false
1310000302false
1410000350false
contributorChen, Chen
startdate20180901
enddate20180901
citationpf e0006738 pt e0006738 vol 12 issue 9
lsr30VSR-Enriched:[pqid, issn, description, galeid, orcidid]
sort
titlePhylogenomic analysis unravels evolution of yellow fever virus within hosts.
authorChen, Chen ; Jiang, Dong ; Ni, Ming ; Li, Jing ; Chen, Zhihai ; Liu, Jingyuan ; Ye, Hanhui ; Wong, Gary ; Li, Wei ; Zhang, Yuanyuan ; Wang, Beibei ; Bi, Yuhai ; Chen, Danying ; Zhang, Ping ; Zhao, Xuesen ; Kong, Yaxian ; Shi, Weifeng ; Du, Pengcheng ; Xiao, Gengfu ; Ma, Juncai ; Gao, George F ; Cui,...
creationdate20180901
lso0120180901
facets
frbrgroupid7546565755190089089
frbrtype5
newrecords20181218
languageeng
creationdate2018
topic
0Evolution, Molecular–Virology
1Genome, Viral–Classification
2High-Throughput Nucleotide Sequencing–Genetics
3Humans–Isolation & Purification
4Mutation Rate–Isolation & Purification
5Phylogeny–Isolation & Purification
6Polymorphism, Single Nucleotide–Isolation & Purification
7Yellow Fever–Isolation...
collection
0MEDLINE (ProQuest)
1ProQuest Biological Science Collection
2ProQuest Natural Science Collection
3ProQuest SciTech Collection
4Biological Science Database
5Natural Science Collection
6SciTech Premium Collection
7Health Research Premium Collection
8Health Research Premium Collection (Alumni edition)
9Biological Science Index (ProQuest)
prefilterarticles
rsrctypearticles
creatorcontrib
0Chen, Chen
1Jiang, Dong
2Ni, Ming
3Li, Jing
4Chen, Zhihai
5Liu, Jingyuan
6Ye, Hanhui
7Wong, Gary
8Li, Wei
9Zhang, Yuanyuan
10Wang, Beibei
11Bi, Yuhai
12Chen, Danying
13Zhang, Ping
14Zhao, Xuesen
15Kong, Yaxian
16Shi, Weifeng
17Du, Pengcheng
18Xiao, Gengfu
19Ma, Juncai
20Gao, George F
21Cui, Jie
22Zhang, Fujie
23Liu, Wenjun
24Bo, Xiaochen
25Li, Ang
26Zeng, Hui
27Liu, Di
jtitlePLoS neglected tropical diseases
toplevelpeer_reviewed
delivery
delcategoryRemote Search Resource
fulltextfulltext
addata
aulast
0Chen
1Jiang
2Ni
3Li
4Liu
5Ye
6Wong
7Zhang
8Wang
9Bi
10Zhao
11Kong
12Shi
13Du
14Xiao
15Ma
16Gao
17Cui
18Bo
19Zeng
aufirst
0Chen
1Dong
2Ming
3Jing
4Zhihai
5Jingyuan
6Hanhui
7Gary
8Wei
9Yuanyuan
10Beibei
11Yuhai
12Danying
13Ping
14Xuesen
15Yaxian
16Weifeng
17Pengcheng
18Gengfu
19Juncai
20George F
21Jie
22Fujie
23Wenjun
24Xiaochen
25Ang
26Hui
27Di
au
0Chen, Chen
1Jiang, Dong
2Ni, Ming
3Li, Jing
4Chen, Zhihai
5Liu, Jingyuan
6Ye, Hanhui
7Wong, Gary
8Li, Wei
9Zhang, Yuanyuan
10Wang, Beibei
11Bi, Yuhai
12Chen, Danying
13Zhang, Ping
14Zhao, Xuesen
15Kong, Yaxian
16Shi, Weifeng
17Du, Pengcheng
18Xiao, Gengfu
19Ma, Juncai
20Gao, George F
21Cui, Jie
22Zhang, Fujie
23Liu, Wenjun
24Bo, Xiaochen
25Li, Ang
26Zeng, Hui
27Liu, Di
addauChen, Chen
atitlePhylogenomic analysis unravels evolution of yellow fever virus within hosts.
jtitlePLoS neglected tropical diseases
risdate20180901
volume12
issue9
spagee0006738
epagee0006738
pagese0006738
eissn1935-2735
formatjournal
genrearticle
ristypeJOUR
doi10.1371/journal.pntd.0006738
urlhttp://search.proquest.com/docview/2101271004/
orcidid0000-0003-1765-8899
issn19352727
date2018-09-01