Abstract：
Diseases caused by Capripoxviruses (CaPVs) are of great economic importance in sheep, goats, and cattle. Since CaPV strains are serologically indistinguishable and genetically highly homologous, typing of closely related strains can only be achieved by whole-genome sequencing. In this chapter, we describe a robust, cost-effective, and widely applicable protocol for reconstructing (nearly) complete CaPV genomes directly from clinical samples or commercial vaccine batches in less than a week. Taking advantage of the genetic similarity of CaPVs, a set of pan-CaPVs long-range PCRs was developed that covers the entire genome with only a limited number of tiled amplicons. The resulting amplicons can be sequenced on all currently available high-throughput sequencing platforms. As an example, we have included a detailed protocol for performing nanopore sequencing and a pipeline for assembling the resulting tiled amplicon data.
摘要：
羊痘病毒（CaPV）引起的疾病在绵羊中具有重要的经济意义，山羊,和牛。由于CaPV菌株在血清学上无法区分，并且在遗传上高度同源，密切相关的菌株的分型只能通过全基因组测序来实现。在这一章中,我们描述了一个健壮的，成本效益高,和广泛适用的方案，用于在不到一周的时间内直接从临床样品或商业疫苗批次中重建（几乎）完整的CaPV基因组。利用CaPVs的遗传相似性，开发了一组泛CaPV远程PCR,其覆盖了仅有有限数量的平铺扩增子的整个基因组.可以在所有当前可用的高通量测序平台上对所得扩增子进行测序。作为一个例子,我们已经包括了用于进行纳米孔测序的详细方案和用于组装所得到的平铺扩增子数据的流水线。
