Sequencing and analysis of globally obtained human respiratory syncytial virus A and B genomes.
Sequencing and analysis of globally obtained human respiratory syncytial virus A and B genomes.
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DOI：
10.1371/journal.pone.0120098
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Henrickson KJ
中科院分区：
文献类型：
--
作者：
Bose ME;He J;Shrivastava S;Nelson MI;Bera J;Halpin RA;Town CD;Lorenzi HA;Noyola DE;Falcone V;Gerna G;De Beenhouwer H;Videla C;Kok T;Venter M;Williams JV;Henrickson KJ
人类呼吸道合胞病毒(RSV)是全球儿童呼吸道感染的主要原因，几乎所有儿童在两岁之前都经历了至少一次感染。对附着糖蛋白基因的部分测序是常规的基因分型方法，但相对较少的全基因组序列可用于RSV。本研究的目的是对来自多个国家的RSV毒株的基因组进行测序，以便在全基因组水平上进一步了解RSV的全球多样性。我们收集了1998-2010年间来自墨西哥、阿根廷、比利时、意大利、德国、澳大利亚、南非和美国的RSV样本和分离株。用Illumina和454平台对RSV A和B的全基因组进行了测序，并用贝叶斯和最大似然法进行了系统发育分析。我们测定了34株RSVA病毒和23株RSVB病毒的基因组序列。系统发育分析表明，RSVA基因组的进化速率为6.72×10-4个置换/位点/年(95%HPD为5.61×10-4~7.6×10-4)，RSVB基因组的进化速率为7.69×10-4个置换/位点/年(95%HPD为6.81×10-4~8.62×10-4)。我们发现RSV A和B的多个分支在全球范围内共同循环，RSVA的优势分支是GA2和GA5，RSVB的优势分支是BA。我们的分析表明，RSV在全球范围内传播，在世界各国也发现了同样的主要病毒分支。然而，随着新菌株的出现，分支的分布可能会迅速变化。我们没有在我们的树木中观察到强烈的空间结构，相同的三个主要RSV分支在全球范围内共同循环，这表明RSV的进化不是强烈的区域化。
Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in children globally, with nearly all children experiencing at least one infection by the age of two. Partial sequencing of the attachment glycoprotein gene is conducted routinely for genotyping, but relatively few whole genome sequences are available for RSV. The goal of our study was to sequence the genomes of RSV strains collected from multiple countries to further understand the global diversity of RSV at a whole-genome level. We collected RSV samples and isolates from Mexico, Argentina, Belgium, Italy, Germany, Australia, South Africa, and the USA from the years 1998-2010. Both Sanger and next-generation sequencing with the Illumina and 454 platforms were used to sequence the whole genomes of RSV A and B. Phylogenetic analyses were performed using the Bayesian and maximum likelihood methods of phylogenetic inference. We sequenced the genomes of 34 RSVA and 23 RSVB viruses. Phylogenetic analysis showed that the RSVA genome evolves at an estimated rate of 6.72 × 10-4 substitutions/site/year (95% HPD 5.61 × 10-4 to 7.6 × 10-4) and for RSVB the evolutionary rate was 7.69 × 10-4 substitutions/site/year (95% HPD 6.81 × 10-4 to 8.62 × 10-4). We found multiple clades co-circulating globally for both RSV A and B. The predominant clades were GA2 and GA5 for RSVA and BA for RSVB. Our analyses showed that RSV circulates on a global scale with the same predominant clades of viruses being found in countries around the world. However, the distribution of clades can change rapidly as new strains emerge. We did not observe a strong spatial structure in our trees, with the same three main clades of RSV co-circulating globally, suggesting that the evolution of RSV is not strongly regionalized.
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影响因子：
3.7
作者：
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通讯作者：
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