Emerging technologies in the study of the virome

IF 5.7 2区 医学 Q1 VIROLOGY
Sophie E Smith , Wanqi Huang , Kawtar Tiamani , Magdalena Unterer , Mohammadali Khan Mirzaei , Li Deng
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引用次数: 13

Abstract

Despite the growing interest in the microbiome in recent years, the study of the virome, the major part of which is made up of bacteriophages, is relatively underdeveloped compared with their bacterial counterparts. This is due in part to the lack of a universally conserved marker such as the 16S rRNA gene. For this reason, the development of metagenomic approaches was a major milestone in the study of the viruses in the microbiome or virome. However, it has become increasingly clear that these wet-lab methods have not yet been able to detect the full range of viruses present, and our understanding of the composition of the virome remains incomplete. In recent years, a range of new technologies has been developed to further our understanding. Direct RNA-Seq technologies bypass the need for cDNA synthesis, thus avoiding biases subjected to this step, which further expands our understanding of RNA viruses. The new generation of amplification methods could solve the low biomass issue relevant to most virome samples while reducing the error rate and biases caused by whole genome amplification. The application of long-read sequencing to virome samples can resolve the shortcomings of short-read sequencing in generating complete viral genomes and avoid the biases introduced by the assembly. Novel experimental methods developed to measure viruses' host range can help overcome the challenges of assigning hosts to many phages, specifically unculturable ones.

病毒研究中的新兴技术。
尽管近年来人们对微生物组的兴趣日益浓厚,但与细菌相比,以噬菌体为主要组成部分的病毒组的研究相对不发达。这部分是由于缺乏一种普遍保守的标记,如16S rRNA基因。因此,宏基因组方法的发展是微生物组或病毒组中病毒研究的一个重要里程碑。然而,越来越清楚的是,这些湿实验室方法还不能检测到存在的所有病毒,我们对病毒组组成的理解仍然不完整。近年来,一系列新技术的发展进一步加深了我们的认识。直接RNA- seq技术绕过了cDNA合成的需要,从而避免了这一步骤所带来的偏见,这进一步扩展了我们对RNA病毒的理解。新一代的扩增方法可以解决与大多数病毒样本相关的低生物量问题,同时降低全基因组扩增引起的错误率和偏差。将长读段测序应用于病毒体样本,可以解决短读段测序在生成完整病毒基因组方面的不足,避免组装带来的偏差。测量病毒宿主范围的新实验方法可以帮助克服将宿主分配给许多噬菌体的挑战,特别是不可培养的噬菌体。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
11.80
自引率
5.10%
发文量
76
审稿时长
83 days
期刊介绍: Current Opinion in Virology (COVIRO) is a systematic review journal that aims to provide specialists with a unique and educational platform to keep up to date with the expanding volume of information published in the field of virology. It publishes 6 issues per year covering the following 11 sections, each of which is reviewed once a year: Emerging viruses: interspecies transmission; Viral immunology; Viral pathogenesis; Preventive and therapeutic vaccines; Antiviral strategies; Virus structure and expression; Animal models for viral diseases; Engineering for viral resistance; Viruses and cancer; Virus vector interactions. There is also a section that changes every year to reflect hot topics in the field.
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