Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
Sci Rep. 2019 Mar 4;9(1):3398. doi: 10.1038/s41598-019-40036-4.
Identification and characterization of novel unknown viruses is of great importance. The introduction of high-throughput sequencing (HTS)-based methods has paved the way for genomics-based detection of pathogens without any prior assumptions about the characteristics of the organisms. However, the use of HTS for the characterization of viral pathogens from clinical samples remains limited. Here, we report the identification of a novel Orthobunyavirus species isolated from horse plasma. The identification was based on a straightforward HTS approach. Following enrichment in cell culture, RNA was extracted from the growth medium and rapid library preparation, HTS and primary bioinformatic analyses were performed in less than 12 hours. Taxonomical profiling of the sequencing reads did not reveal sequence similarities to any known virus. Subsequent application of de novo assembly tools to the sequencing reads produced contigs, of which three showed some similarity to the L, M, and S segments of viruses belonging to the Orthobunyavirus genus. Further refinement of these contigs resulted in high-quality, full-length genomic sequences of the three genomic segments (L, M and S) of a novel Orthobunyavirus. Characterization of the genomic sequence, including the prediction of open reading frames and the inspection of consensus genomic termini and phylogenetic analysis, further confirmed that the novel virus is indeed a new species, which we named Ness Ziona virus.
鉴定和描述新型未知病毒具有重要意义。高通量测序(HTS)方法的引入为基于基因组学的病原体检测铺平了道路,而无需对生物体的特征做出任何预先假设。然而,HTS 用于从临床样本中鉴定病毒病原体的应用仍然有限。在这里,我们报告了从马血浆中分离出的一种新型 Orthobunyavirus 物种的鉴定。鉴定是基于一种直接的 HTS 方法。在细胞培养中富集后,从生长培养基中提取 RNA,并在不到 12 小时内完成快速文库制备、HTS 和初步生物信息学分析。测序reads 的分类分析没有显示与任何已知病毒的序列相似性。随后将从头组装工具应用于测序reads 产生了 contigs,其中三个 contigs 与属于 Orthobunyavirus 属的病毒的 L、M 和 S 片段有一定的相似性。对这些 contigs 的进一步细化产生了三个新型 Orthobunyavirus 的全长基因组序列(L、M 和 S)。对基因组序列的特征描述,包括开放阅读框的预测以及对共识基因组末端和系统发育分析的检查,进一步证实了该新型病毒确实是一个新的物种,我们将其命名为 Ness Ziona 病毒。