Sequencing and Analysis of Globally Obtained Human Respiratory Syncytial Virus A and B Genomes

Background
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.
Methods
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.
Results
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.
Conclusions
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.

背景
人类呼吸道合胞病毒（Human respiratory syncytial virus, RSV）是全球范围内儿童呼吸道感染的首要致病原，几乎所有儿童在两岁前都会感染至少一次该病毒。当前科研工作中常规通过对附着糖蛋白基因进行部分测序以完成基因分型，但可供使用的RSV全基因组序列仍相对匮乏。本研究的目标是对多国采集的RSV毒株进行全基因组测序，以从全基因组层面进一步解析RSV的全球多样性。

方法
我们收集了1998年至2010年间，来自墨西哥、阿根廷、比利时、意大利、德国、澳大利亚、南非以及美国的RSV样本与分离株。分别采用桑格测序（Sanger sequencing）以及基于Illumina、454平台的下一代测序（next-generation sequencing）技术，对RSV A型与B型毒株的全基因组进行测序。系统发育分析采用贝叶斯推断与最大似然推断两种方法开展。

结果
本研究共完成34株RSV A型与23株RSV B型毒株的全基因组测序。系统发育分析显示，RSV A型的进化速率约为6.72×10^-4 替换位点/年（95% HPD：5.61×10^-4 至7.6×10^-4）；RSV B型的进化速率为7.69×10^-4 替换位点/年（95% HPD：6.81×10^-4 至8.62×10^-4）。研究发现，RSV A型与B型均存在多支进化枝在全球范围内共同流行，其中RSV A型的优势进化枝为GA2与GA5，RSV B型的优势进化枝为BA。

结论
本研究分析表明，RSV在全球范围内广泛流行，全球各国检出的优势毒株进化枝类型一致。但随着新毒株的出现，进化枝的分布可快速发生变化。本研究未观察到系统发育树存在显著的空间结构，三类主要的RSV进化枝在全球范围内共同流行，提示RSV的进化并未呈现强烈的区域化特征。