Phylogenomic analysis unravels evolution of yellow fever virus within hosts.
Phylogenomic analysis unravels evolution of yellow fever virus within hosts.
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系统基因组分析揭示了黄热病病毒在宿主内的进化。
DOI：
10.1371/journal.pntd.0006738
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发表时间：
2018-09
影响因子：
3.8
通讯作者：
Liu D
中科院分区：
文献类型：
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作者：
Chen C;Jiang D;Ni M;Li J;Chen Z;Liu J;Ye H;Wong G;Li W;Zhang Y;Wang B;Bi Y;Chen D;Zhang P;Zhao X;Kong Y;Shi W;Du P;Xiao G;Ma J;Gao GF;Cui J;Zhang F;Liu W;Bo X;Li A;Zeng H;Liu D
黄热病病毒(YFV)最近在非洲和巴西的大规模暴发中重新出现，第一批输入亚洲的患者回忆起对YFV进化的担忧。在这里，我们用2016年YFV感染的一系列临床样本展示了YFV的系统基因组学。系统发育分析表明，2016年的毒株与安哥拉1971年的毒株接近，只有3个氨基酸变化是其他谱系的新发现。对病毒基因组的深度测序发现了101个宿主内单核苷酸变异(ISNV)和234个单核苷酸多态(SNPs)。ISNV分布和突变等位基因频率分析表明，编码区处于纯化选择状态。ISNV和SNP估计的进化速率的比较表明，寄主内的进化速率是流行率的2.25倍，两者都高于YFV的长期替代率，正如预期的那样。此外，该结果还提示YFV病毒血症持续时间短可能进一步阻碍YFV的进化。2016年中国首次输入感染病例，以及随后在非洲和巴西爆发的黄热病病毒再次引发了人们对这种病毒可能传播到新地区的担忧。在这项研究中，我们旨在通过宿主内系统基因组学来了解YFV的进化动态，并评估病毒流行的风险。通过对12名患者的连续样本进行深度测序，我们识别了数百种基因组变异(iSNV和SNPs)，并注意到个体内变异的近似线性积累。估计的宿主内进化速率远高于流行进化速率。与登革病毒(DENV)和寨卡病毒(ZIKV)具有相似的宿主媒介(伊蚊)、生活史、突变率和复制策略相比，YFV较低的流行进化率可能是因为病毒血症持续时间较短，从而减少了进入传播周期的累积变异。
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. 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.
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DOI：
10.1126/science.aaf5036
发表时间：
2016-04-15
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Faria NR;Azevedo RDSDS;Kraemer MUG;Souza R;Cunha MS;Hill SC;Thézé J;Bonsall MB;Bowden TA;Rissanen I;Rocco IM;Nogueira JS;Maeda AY;Vasami FGDS;Macedo FLL;Suzuki A;Rodrigues SG;Cruz ACR;Nunes BT;Medeiros DBA;Rodrigues DSG;Queiroz ALN;da Silva EVP;Henriques DF;da Rosa EST;de Oliveira CS;Martins LC;Vasconcelos HB;Casseb LMN;Simith DB;Messina JP;Abade L;Lourenço J;Alcantara LCJ;de Lima MM;Giovanetti M;Hay SI;de Oliveira RS;Lemos PDS;de Oliveira LF;de Lima CPS;da Silva SP;de Vasconcelos JM;Franco L;Cardoso JF;Vianez-Júnior JLDSG;Mir D;Bello G;Delatorre E;Khan K;Creatore M;Coelho GE;de Oliveira WK;Tesh R;Pybus OG;Nunes MRT;Vasconcelos PFC
通讯作者：
Vasconcelos PFC
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
13.2
作者：
Chen, Zhihai;Liu, Lin;Lv, Yanning;Zhang, Wei;Li, Jiandong;Zhang, Yi;Di, Tian;Zhang, Shuo;Liu, Jingyuan;Li, Jie;Qu, Jing;Hua, Wenhao;Li, Chuan;Wang, Peng;Zhang, Quanfu;Xu, Yanli;Jiang, Rongmeng;Wang, Qin;Chen, Lijuan;Wang, Shiwen;Pang, Xinghuo;Liang, Mifang;Ma, Xuejun;Li, Xingwang;Wang, Quanyi;Zhang, Fujie;Li, Dexin
通讯作者：
Li, Dexin
影响因子：
5.4
作者：
Mutebi, JP;Wang, HM;Barrett, ADT
通讯作者：
Barrett, ADT
影响因子：
5.4
作者：
Stock, Nina K.;Laraway, Hewad;Sall, Amadou A.
通讯作者：
Sall, Amadou A.