Sophie E Smith , Wanqi Huang , Kawtar Tiamani , Magdalena Unterer , Mohammadali Khan Mirzaei , Li Deng
{"title":"Emerging technologies in the study of the virome","authors":"Sophie E Smith , Wanqi Huang , Kawtar Tiamani , Magdalena Unterer , Mohammadali Khan Mirzaei , Li Deng","doi":"10.1016/j.coviro.2022.101231","DOIUrl":null,"url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":11082,"journal":{"name":"Current opinion in virology","volume":"54 ","pages":"Article 101231"},"PeriodicalIF":5.7000,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1879625722000402/pdfft?md5=942c14c91b8ff050f65841d391a117ad&pid=1-s2.0-S1879625722000402-main.pdf","citationCount":"13","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current opinion in virology","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1879625722000402","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"VIROLOGY","Score":null,"Total":0}
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.
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.