No part gets left behind: Tiled nanopore sequencing of whole ASFV genomes stitched together using Lilo
No part gets left behind: Tiled nanopore sequencing of whole ASFV genomes stitched together using Lilo
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不遗余力：使用 Lilo 将整个 ASFV 基因组拼接在一起进行平铺纳米孔测序
DOI：
10.1101/2021.12.01.470769
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Warr A
中科院分区：
文献类型：
--
作者：
Warr A
非洲猪瘟病毒（ASFV）是一种致命的泛动物源性疾病的病原体，感染野生和驯养的猪群。2007年在格鲁吉亚爆发了一种传染性特别强的变异病毒，这种病毒在非洲大陆被控制了很长一段时间，引发了该病毒在地球仪的传播，严重影响了猪肉生产和当地经济。该病毒具有高度传染性，家猪的死亡率高达100%。至关重要的是要跟踪病毒的传播，检测与病理学相关的变异，并以最有效的方式实施生物安全措施以限制其传播。由于它的大小和其他限制，170- 190 kbp的大DNA病毒还没有很好地测序，公共知识库中的基因组序列不到200个。在这里，我们提出了一种高效，低成本的测序ASFV的方法。该方法使用平铺PCR扩增病毒，以实现更大的覆盖范围，多重性和准确性的便携式测序仪比使用鸟枪测序。我们还介绍了Lilo，这是一种用于从病毒或微生物基因组中组装平铺扩增子数据的管道，而无需依赖于参考抛光，允许结构变异和高变区
African Swine Fever virus (ASFV) is the causative agent of a deadly, panzootic disease, infecting wild and domesticated suid populations. Contained for a long time to the African continent, an outbreak of a particularly infectious variant in Georgia in 2007 initiated the spread of the virus around the globe, severely impacting pork production and local economies. The virus is highly contagious and has a mortality of up to 100% in domestic pigs. It is critical to track the spread of the virus, detect variants associated with pathology, and implement biosecurity measures in the most effective way to limit its spread. Due to its size and other limitations, the 170-190kbp large DNA virus has not been well sequencedwith fewer than 200 genome sequences available in public repositories. Here we present an efficient, low-cost method of sequencing ASFV at scale. The method uses tiled PCR amplification of the virus to achieve greater coverage, multiplexability and accuracy on a portable sequencer than achievable using shotgun sequencing. We also present Lilo, a pipeline for assembling tiled amplicon data from viral or microbial genomes without relying on polishing against a reference, allowing for structural variation and hypervariable region
影响因子：
23.2
作者：
Xu Tian;Stephan von Cramon
通讯作者：
Stephan von Cramon