Current challenges to virus discovery by metatranscriptomics
Current challenges to virus discovery by metatranscriptomics
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DOI：
10.1016/j.coviro.2021.09.007
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发表时间：
2021-09-27
影响因子：
5.9
通讯作者：
Mahar, Jackie E.
中科院分区：
文献类型：
--
作者：
Cobbin, Joanna C. A.;Charon, Justine;Mahar, Jackie E.
下一代元转录组测序已经改变了病毒的发现，极大地扩展了我们对已知病毒圈的了解。然而，使用元转录组学发现病毒面临着重要的挑战。随着这项技术被越来越广泛地采用，公共数据库中具有不正确（例如宿主的错误分配）或有限信息（例如缺乏分类学分类）的病毒序列的比例可能会增加，从而限制了它们在病毒发现的生物信息学管道中的效用。此外，我们目前缺乏生物信息学工具，可以准确地识别与数据库病毒或代表可能的试剂污染物的病毒显示很少或没有序列相似性的病毒。在此，我们概述了有效的元转录组病毒发现的一些挑战以及它们的潜在解决方案。
Meta-transcriptomic next-generation sequencing has transformed virus discovery, dramatically expanding our knowledge of the known virosphere. Nevertheless, the use of meta-transcriptomics for virus discovery faces important challenges. As this technology becomes more widely adopted, the proportion of viral sequences in public databases with incorrect (e.g. mis-assignment of host) or limited information (e.g. lacking taxonomic classification) is likely to grow, limiting their utility in bioinformatic pipelines for virus discovery. In addition, we currently lack the bioinformatic tools that can accurately identify viruses showing little or no sequence similarity to database viruses or those that represent likely reagent contaminants. Herein, we outline some of the challenges to effective meta-transcriptomic virus discovery as well as their potential solutions.