ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
Veterinary Pathology Centre, University of Utrecht, the Netherlands.
Infect Genet Evol. 2019 Sep;73:49-54. doi: 10.1016/j.meegid.2019.04.015. Epub 2019 Apr 20.
Recently, protocols for amplicon based whole genome sequencing using Nanopore technology have been described for Ebola virus, Zika virus, yellow fever virus and West Nile virus. However, there is some debate regarding reliability of sequencing using this technology, which is important for applications beyond diagnosis such as linking lineages to outbreaks, tracking transmission pathways and pockets of circulation, or mapping specific markers. To our knowledge, no in depth analyses of the required read coverage to compensate for the error profile in Nanopore sequencing have been described. Here, we describe the validation of a protocol for whole genome sequencing of USUV using Nanopore sequencing by direct comparison to Illumina sequencing. To that point we selected brain tissue samples with high viral loads, typical for birds which died from USUV infection. We conclude that the low-cost MinION Nanopore sequencing platform can be used for characterization and tracking of Usutu virus outbreaks.
最近，已经有使用纳米孔技术进行基于扩增子的全基因组测序的方案被描述用于埃博拉病毒、寨卡病毒、黄热病病毒和西尼罗河病毒。然而，对于这种技术的测序可靠性存在一些争议，这对于诊断以外的应用非常重要，例如将谱系与疫情爆发、传播途径和循环点联系起来，或者绘制特定的标记物。据我们所知，还没有对使用纳米孔测序来补偿误差的所需读长覆盖范围进行深入分析的描述。在这里，我们通过与 Illumina 测序的直接比较，描述了使用纳米孔测序对 USUV 进行全基因组测序的方案的验证。为此，我们选择了病毒载量高的脑组织样本，这是死于 USUV 感染的鸟类的典型特征。我们的结论是，低成本的 MinION 纳米孔测序平台可用于对乌苏图病毒疫情的特征描述和追踪。
