Genome sequencing reveals Zika virus diversity and spread in the Americas

Genome sequencing reveals Zika virus diversity and spread in the Americas
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DOI：
10.1101/109348
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发表时间：
2017-02
期刊：
bioRxiv
影响因子：
--
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
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
中科院分区：
其他
文献类型：
--
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

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尽管最近在美洲流行的寨卡病毒（ZIKV）引起了极大关注，但其流行病学和进化仍知之甚少，部分原因是缺乏基因组数据。我们应用多种测序方法，从来自 10 个国家和地区的临床和蚊子样本中生成了 100 个 ZIKV 基因组，极大地扩展了此次疫情中观察到的病毒遗传多样性。我们分析了传入不同地理区域的时间和模式，确认了巴西爆发的起源和快速扩张的系统发育证据，以及从巴西多次传入洪都拉斯、哥伦比亚、波多黎各、其他加勒比岛屿和美国大陆的证据。我们发现，在确认第一例本地传播病例之前，ZIKV 在美洲许多地区未经发现地传播了长达一年的时间，这突显了对该病毒进行有效监测的挑战。我们进一步描述了整个疫情期间的遗传变异特征，以确定对 ZIKV 生物学和发病机制可能具有功能影响的突变。
Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas, much remains unknown about its epidemiology and evolution, in part due to a lack of genomic data. We applied multiple sequencing approaches to generate 100 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analyzed the timing and patterns of introductions into distinct geographic regions, confirming phylogenetic evidence for the origin and rapid expansion of the outbreak in Brazil1, and for multiple introductions from Brazil into Honduras, Colombia, Puerto Rico, other Caribbean islands, and the continental US. We find that ZIKV circulated undetected in many regions of the Americas for up to a year before the first locally transmitted cases were confirmed, highlighting the challenge of effective surveillance for this virus. We further characterize genetic variation across the outbreak to identify mutations with possible functional implications for ZIKV biology and pathogenesis.