• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Journal of Veterinary Research >Evaluation of direct metagenomics and target enriched approaches for high-throughput sequencing of field rabies viruses
【24h】

Evaluation of direct metagenomics and target enriched approaches for high-throughput sequencing of field rabies viruses

机译：野生狂犬病病毒高通量测序的直接偏见和靶向富集谱的评价

获取原文
获取原文并翻译 | 示例
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Introduction: High-throughput sequencing (HTS) identifies random viral fragments in environmental samples metagenomically. High reliability gains it broad application in virus evolution, host-virus interaction, and pathogenicity studies. Deep sequencing of field samples with content of host genetic material and bacteria often produces insufficient data for metagenomics and must be preceded by target enrichment. The main goal of the study was the evaluation of HTS for complete genome sequencing of field-case rabies viruses (RABVs). Material and Methods: The material was 23 RABVs isolated mainly from red foxes and one European bat lyssavirus-1 isolate propagated in neuroblastoma cells. Three methods of RNA isolation were tested for the direct metagenomics and RABV-enriched approaches. Deep sequencing was performed with a MiSeq sequencer (Illumina) and reagent v3 kit. Bioinformatics data were evaluated by Kraken and Centrifuge software and de novo assembly was done with metaSPAdes. Results: Testing RNA extraction procedures revealed the deep sequencing scope superiority of the combined TRIzol/column method. This HTS methodology made it possible to obtain complete genomes of all the RABV isolates collected in the field. Significantly greater rates of RABV genome coverages (over 5,900) were obtained with RABV enrichment. Direct metagenomic studies sequenced the full length of 6 out of 16 RABV isolates with a medium coverage between 1 and 71. Conclusion: Direct metagenomics gives the most realistic illustration of the field sample microbiome, but with low coverage. For deep characterisation of viruses, e.g. for spatial and temporal phylogeography during outbreaks, target enrichment is recommended as it covers sequences much more completely.
机译：介绍：高通量测序（HTS）识别在肉桂度上的环境样本中的随机病毒片段。高可靠性在病毒演化，宿主病毒相互作用和致病性研究中获得广泛应用。具有宿主遗传物质和细菌的含量的田间样品的深度测序通常产生偏心组学的不足，并且必须先通过靶向富集。该研究的主要目的是评估HTS，用于完全基因组序列的田间情况狂犬病病毒（RABV）。材料和方法：该材料主要来自红狐狸和一个欧洲蝙蝠Lysaavirus-1分离物，在神经母细胞瘤细胞中繁殖。测试了三种RNA分离的方法，用于直接偏见和富含饲料的方法。用MiSeq测序仪（Illumina）和试剂V3试剂盒进行深度测序。 Bioinformatics数据通过克拉肯和离心机软件评估，De Novo装配是用离婚者完成的。结果：检测RNA提取程序揭示了三种三唑/柱法的深度测序范围优越性。该HTS方法使得可以获得在该领域收集的所有RABV分离物的完整基因组。用Rabv富集获得RABV基因组覆盖率的显着更大的rABV基因组覆盖率。直接偏见的研究用16个兔子分离物中的全长6分，介质覆盖率在1和71之间。结论：直接偏心组学提供了田间样本微生物组的最逼真的例证，但覆盖率低。例如，用于病毒的深度表征，例如，对于在爆发期间的空间和时间播种地理，建议使用鉴定序列更完全。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号