An Assessment of Amplicon-Sequencing Based Method for Viral Intrahost Analysis
An Assessment of Amplicon-Sequencing Based Method for Viral Intrahost Analysis
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基于扩增子测序的病毒宿主分析方法的评估。
DOI：
10.1007/s12250-018-0052-z
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发表时间：
2018-11
影响因子：
5.5
通讯作者：
Liu Di
中科院分区：
文献类型：
--
作者：
Ni Ming;Chen Chen;Liu Di
RNA病毒具有每代突变率高的特点，导致高度多样化的种群，这决定了病毒的表型和适应性（Domingo et al. 2012）。深度测序和生物信息学技术的发展为在宿主内水平研究病毒群体遗传学铺平了道路，并为病毒进化提供了新的见解。在Lakdawala et al.（2015），病毒宿主内分析用于监测具有功能突变的流感病毒的快速选择。Debbink及其同事采用类似的方法研究了季节性流感病毒的病毒宿主内异质性，并声称疫苗诱导的免疫对抗原漂移的影响较小（Debbink et al. 2017）。特别是在防治新出现的疫情方面，还进行了宿主内分析，以调查传染病病原体的演变，包括西非的埃博拉病毒（Ni et al. 2016），寨卡病毒（ZIKV）在美洲的传播（Metsky et al. 2017），以及中国的输入性黄热病病毒（YFV）（Chen et al. 2018）。如今，有两种方法可用于从临床样本中有效富集病毒基因组，包括（1）宿主RNA耗尽后的病毒RNA捕获（Matranga et al. 2014; Metsky et al. 2017）和（2）直接病毒特异性基因组扩增（Ni et al. 2016;
RNA virus features the high per-generation mutation rate, resulting in highly diversified population, which determines viral phenotypes and fitness (Domingo et al. 2012). The development of deep sequencing and bioinformatic techniques paves the way to study viral population genetics at an intrahost level, and has provided new insights into viral evolution. In a study conducted by Lakdawala et al.(2015), viral intrahost analysis was applied to monitor rapid selection of influenza virus with functional mutations. With a similar method on seasonal influenza virus, Debbink and colleagues have examined the viral intrahost heterogeneity and claimed that vaccine-induced immunity had minor impact on antigenic drift (Debbink et al. 2017). Particularly, in combating emerging outbreaks, the intrahost analyses have also been conducted to investigate the evolution of infectious disease pathogens, including the Ebola virus (EBOV) in West Africa (Ni et al. 2016), Zika virus (ZIKV) transmission in the Americas (Metsky et al. 2017), and imported yellow fever virus (YFV) in China (Chen et al. 2018).Nowadays, two approaches have been applied to effectively enrich viral genomes from clinical samples, including (1) viral RNA capture following the depletion of host RNA (Matranga et al. 2014; Metsky et al. 2017) and (2) direct viral-specific genomic amplification (Ni et al. 2016;
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DOI：
10.1101/109348
发表时间：
2017-02
期刊：
bioRxiv
影响因子：
--
作者：
Hayden C. Metsky;C. Matranga;S. Wohl;S. Schaffner;C. A. Freije;S. Winnicki;K. West;J. Qu;M. Baniecki;A. Gladden-Young;Aaron E. Lin;C. Tomkins-Tinch;Simon H. Ye;Daniel J. Park;C. Luo;K. Barnes;R. Shah;B. Chak;G. Barbosa-Lima;E. Delatorre;Y. R. Vieira;Lauren M. Paul;A. L. Tan;Carolyn M. Barcellona;M. Porcelli;Chalmers Vasquez;A. Cannons;Marshall R. Cone;K. Hogan;Edgar W. Kopp;J. Anzinger;Kimberly García;L. Parham;Rosa Ramirez;M. Montoya;D. Rojas;Catherine M. Brown;S. Hennigan;B. Sabina;S. Scotland;K. Gangavarapu;N. Grubaugh;G. Oliveira;R. Robles-Sikisaka;A. Rambaut;L. Gehrke;S. Smole;M. Halloran;L. Villar;S. Mattar;I. Lorenzana;J. Cerbino-Neto;C. Valim;W. Degrave;P. Bozza;A. Gnirke;K. Andersen;S. Isern;S. Michael;F. Bozza;T. M. Souza;I. Bosch;N. Yozwiak;B. MacInnis;Pardis C Sabeti
通讯作者：
Hayden C. Metsky;C. Matranga;S. Wohl;S. Schaffner;C. A. Freije;S. Winnicki;K. West;J. Qu;M. Baniecki;A. Gladden-Young;Aaron E. Lin;C. Tomkins-Tinch;Simon H. Ye;Daniel J. Park;C. Luo;K. Barnes;R. Shah;B. Chak;G. Barbosa-Lima;E. Delatorre;Y. R. Vieira;Lauren M. Paul;A. L. Tan;Carolyn M. Barcellona;M. Porcelli;Chalmers Vasquez;A. Cannons;Marshall R. Cone;K. Hogan;Edgar W. Kopp;J. Anzinger;Kimberly García;L. Parham;Rosa Ramirez;M. Montoya;D. Rojas;Catherine M. Brown;S. Hennigan;B. Sabina;S. Scotland;K. Gangavarapu;N. Grubaugh;G. Oliveira;R. Robles-Sikisaka;A. Rambaut;L. Gehrke;S. Smole;M. Halloran;L. Villar;S. Mattar;I. Lorenzana;J. Cerbino-Neto;C. Valim;W. Degrave;P. Bozza;A. Gnirke;K. Andersen;S. Isern;S. Michael;F. Bozza;T. M. Souza;I. Bosch;N. Yozwiak;B. MacInnis;Pardis C Sabeti
DOI：
10.1126/science.1259657
发表时间：
2014-09-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gire SK;Goba A;Andersen KG;Sealfon RS;Park DJ;Kanneh L;Jalloh S;Momoh M;Fullah M;Dudas G;Wohl S;Moses LM;Yozwiak NL;Winnicki S;Matranga CB;Malboeuf CM;Qu J;Gladden AD;Schaffner SF;Yang X;Jiang PP;Nekoui M;Colubri A;Coomber MR;Fonnie M;Moigboi A;Gbakie M;Kamara FK;Tucker V;Konuwa E;Saffa S;Sellu J;Jalloh AA;Kovoma A;Koninga J;Mustapha I;Kargbo K;Foday M;Yillah M;Kanneh F;Robert W;Massally JL;Chapman SB;Bochicchio J;Murphy C;Nusbaum C;Young S;Birren BW;Grant DS;Scheiffelin JS;Lander ES;Happi C;Gevao SM;Gnirke A;Rambaut A;Garry RF;Khan SH;Sabeti PC
通讯作者：
Sabeti PC
影响因子：
12.3
作者：
Matranga, Christian B.;Andersen, Kristian G.;Sabeti, Pardis C.
通讯作者：
Sabeti, Pardis C.
影响因子：
64.5
作者：
Park DJ;Dudas G;Wohl S;Goba A;Whitmer SL;Andersen KG;Sealfon RS;Ladner JT;Kugelman JR;Matranga CB;Winnicki SM;Qu J;Gire SK;Gladden-Young A;Jalloh S;Nosamiefan D;Yozwiak NL;Moses LM;Jiang PP;Lin AE;Schaffner SF;Bird B;Towner J;Mamoh M;Gbakie M;Kanneh L;Kargbo D;Massally JL;Kamara FK;Konuwa E;Sellu J;Jalloh AA;Mustapha I;Foday M;Yillah M;Erickson BR;Sealy T;Blau D;Paddock C;Brault A;Amman B;Basile J;Bearden S;Belser J;Bergeron E;Campbell S;Chakrabarti A;Dodd K;Flint M;Gibbons A;Goodman C;Klena J;McMullan L;Morgan L;Russell B;Salzer J;Sanchez A;Wang D;Jungreis I;Tomkins-Tinch C;Kislyuk A;Lin MF;Chapman S;MacInnis B;Matthews A;Bochicchio J;Hensley LE;Kuhn JH;Nusbaum C;Schieffelin JS;Birren BW;Forget M;Nichol ST;Palacios GF;Ndiaye D;Happi C;Gevao SM;Vandi MA;Kargbo B;Holmes EC;Bedford T;Gnirke A;Ströher U;Rambaut A;Garry RF;Sabeti PC
通讯作者：
Sabeti PC
影响因子：
64.8
作者：
Holmes EC;Dudas G;Rambaut A;Andersen KG
通讯作者：
Andersen KG