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":"10.1016/j.coviro.2022.101231","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":null,"pages":null},"PeriodicalIF":5.9,"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":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43593351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The enigma of picobirnaviruses: viruses of animals, fungi, or bacteria?","authors":"David Wang","doi":"10.1016/j.coviro.2022.101232","DOIUrl":"10.1016/j.coviro.2022.101232","url":null,"abstract":"<div><p>Picobirnaviruses are small double-stranded RNA viruses first discovered in 1988 in stool samples from patients with diarrhea. It has generally been assumed that picobirnaviruses infect animal hosts and that they are potential agents of diarrhea, but there is still no direct evidence demonstrating that picobirnaviruses infect animals. In the metagenomic era, virome studies have broadened our understanding of picobirnavirus genetic diversity and genome organization, expanded the types of animals in which they have been detected, and identified novel associations with human disease. Most importantly, from the wealth of new sequencing data and comparative genomic analyses, a provocative new hypothesis has emerged that picobirnaviruses may not infect animals, but rather that they may infect evolutionarily simpler denizens of the gastrointestinal tract: bacteria and/or fungi. Depending on whether the true hosts of picobirnaviruses are animals, fungi, or bacteria, the mechanisms by which they impact animal biology will vary dramatically.</p></div>","PeriodicalId":11082,"journal":{"name":"Current opinion in virology","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1879625722000414/pdfft?md5=0345c0a13c88835a50839bb83c1cf145&pid=1-s2.0-S1879625722000414-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42959344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Asymmetry in icosahedral viruses","authors":"Joyce Jose , Susan L. Hafenstein","doi":"10.1016/j.coviro.2022.101230","DOIUrl":"10.1016/j.coviro.2022.101230","url":null,"abstract":"<div><p><span><span>Asymmetric structural elements are typically not readily visualized in icosahedral viruses that have other obvious symmetrical features and most asymmetry has gone unresolved for decades. Asymmetric features may be incorporated during assembly or maturation or develop during key steps in the infectious cycle of the virus. However, resolving asymmetric features requires abandoning capsid-wide symmetry averaging and relying on special applications during single-particle cryogenic </span>electron microscopy (cryo-EM) analysis. Thanks to the advances in the cryo-EM field, we are learning more about asymmetry of viruses. Here we summarize some of what is currently known about asymmetric structural features using as examples members of the </span><span><span><em>Togaviridae</em><em>, </em></span><em>Flaviviridae</em><span><em>, </em><em>Herpesviridae</em><span><em>, </em><em>Parvoviridae</em></span></span></span>, <span><em>and </em><em>Papillomaviridae</em></span>.</p></div>","PeriodicalId":11082,"journal":{"name":"Current opinion in virology","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46270565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Editorial overview: 2022 “Virus–Host Interaction” section of Current Opinion in Virology","authors":"Michaela U Gack , Susan C Baker","doi":"10.1016/j.coviro.2022.101229","DOIUrl":"10.1016/j.coviro.2022.101229","url":null,"abstract":"","PeriodicalId":11082,"journal":{"name":"Current opinion in virology","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1879625722000384/pdfft?md5=3399a765bf2acc865556f6125d2df4bb&pid=1-s2.0-S1879625722000384-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41803183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The road to effective and accessible antibody therapies against Ebola virus","authors":"Hugues Fausther-Bovendo , Gary Kobinger","doi":"10.1016/j.coviro.2022.101210","DOIUrl":"10.1016/j.coviro.2022.101210","url":null,"abstract":"<div><p>Ebola virus (EBOV) outbreaks can claim thousands of lives, cripple healthcare systems and local economies. Effective vaccines and treatments against EBOV are therefore needed to limit the impact of this deadly disease. In 2019, a hallmark clinical trial demonstrated the efficacy of monoclonal antibody (mAb) against EBOV. Despite, this recent success, survival of individuals with high viremia remains low. Effective immunotherapies against other Ebolavirus species are still under pre-clinical development. More importantly, the cost of immunotherapies is prohibitive to most individual and affected countries. Novel manufacturing and administration strategies of mAb protein or genetic information could substantially reduce the cost of immunotherapies; hence making them valuable tools against EBOV and other infectious agents.</p></div>","PeriodicalId":11082,"journal":{"name":"Current opinion in virology","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1879625722000190/pdfft?md5=c0ae1bfacd20a3feddc57027002349ce&pid=1-s2.0-S1879625722000190-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46664778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Said Mougari, Claudia Gonzalez, Olivier Reynard, Branka Horvat
{"title":"Fruit bats as natural reservoir of highly pathogenic henipaviruses: balance between antiviral defense and viral tolerance","authors":"Said Mougari, Claudia Gonzalez, Olivier Reynard, Branka Horvat","doi":"10.1016/j.coviro.2022.101228","DOIUrl":"https://doi.org/10.1016/j.coviro.2022.101228","url":null,"abstract":"<div><p>Bats are the natural reservoir host for a number of zoonotic viruses, including Hendra and Nipah viruses of <em>Henipavirus</em> genus, which are highly pathogenic in humans and numerous other mammalian species. Despite being infected, bats present limited signs of disease but still retain the ability to transmit the infection to other susceptible hosts, presenting thus a permanent source of new viral outbreaks. Different mechanisms have evolved in fruit bats permitting them to efficiently control the <em>Henipavirus</em> infection. These mechanisms likely allow bats to establish an adequate equilibrium between viral tolerance and antiviral defense, enabling them thus to avoid both uncontrollable virus expansion as well as immunopathology linked to excessive antiviral responses.</p></div>","PeriodicalId":11082,"journal":{"name":"Current opinion in virology","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1879625722000372/pdfft?md5=11dd534604a830e51f63c39e0726f6d3&pid=1-s2.0-S1879625722000372-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92016020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Fruit bats as natural reservoir of highly pathogenic henipaviruses: balance between antiviral defense and viral toleranceInteractions between Henipaviruses and their natural host, fruit bats.","authors":"S. Mougari, C. González, O. Reynard, B. Horvat","doi":"10.1016/j.coviro.2022.101228","DOIUrl":"https://doi.org/10.1016/j.coviro.2022.101228","url":null,"abstract":"","PeriodicalId":11082,"journal":{"name":"Current opinion in virology","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2022-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47913470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Clara Torres-Barceló , Paul E Turner , Angus Buckling
{"title":"Mitigation of evolved bacterial resistance to phage therapy","authors":"Clara Torres-Barceló , Paul E Turner , Angus Buckling","doi":"10.1016/j.coviro.2022.101201","DOIUrl":"10.1016/j.coviro.2022.101201","url":null,"abstract":"<div><p><span>The ease with which bacteria can evolve resistance to phages is a key consideration for development of phage therapy<span>. Here, we review recent work on the different evolutionary and ecological approaches to mitigate the problem. The approaches are broadly categorised into two areas: </span></span><em>Minimising</em> evolved phage resistance; and <em>Directing</em> phage-resistance evolution towards therapeutically beneficial outcomes.</p></div>","PeriodicalId":11082,"journal":{"name":"Current opinion in virology","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39935115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Virus genomics: what is being overlooked?","authors":"Kristopher Kieft , Karthik Anantharaman","doi":"10.1016/j.coviro.2022.101200","DOIUrl":"10.1016/j.coviro.2022.101200","url":null,"abstract":"<div><p>Viruses are diverse biological entities that influence all life. Even with limited genome sizes, viruses can manipulate, drive, steal from, and kill their hosts. The field of virus genomics, using sequencing data to understand viral capabilities, has seen significant innovations in recent years. However, with advancements in metagenomic sequencing and related technologies, the bottleneck to discovering and employing the virosphere has become the analysis of genomes rather than generation. With metagenomics rapidly expanding available data, vital components of virus genomes and features are being overlooked, with the issue compounded by lagging databases and bioinformatics methods. Despite the field moving in a positive direction, there are noteworthy points to keep in mind, from how software-based virus genome predictions are interpreted to what information is overlooked by current standards. In this review, we discuss conventions and ideologies that likely need to be revised while continuing forward in the study of virus genomics.</p></div>","PeriodicalId":11082,"journal":{"name":"Current opinion in virology","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10201916/pdf/nihms-1770501.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9498636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Broad neutralizing antibody-based strategies to tackle influenza","authors":"Xiaoyu Sun , Zhiyang Ling , Zhuo Yang, Bing Sun","doi":"10.1016/j.coviro.2022.101207","DOIUrl":"10.1016/j.coviro.2022.101207","url":null,"abstract":"<div><p><span><span>Influenza viruses cause occasional pandemics and annual epidemics, thus persist as a threat to human society. The high variability of viral envelope proteins resulting from </span>antigenic shift and </span>antigenic drift<span><span><span> allows influenza viruses to escape human herd immunity<span><span>. During the past decade, along with the breakthroughs of human monoclonal antibody<span><span> technologies, many broad reactive monoclonal antibodies (mAbs) that neutralize diverse influenza subtypes have been isolated and characterized. The achievements in this field have provided potential candidates of anti-influenza therapeutics and shed light on the design of universal </span>influenza vaccines. Here, we review the broad </span></span>neutralizing antibodies (bnAbs) targeting the </span></span>virus </span>surface proteins, summarize their epitopes, broad spectrum and immunological mechanisms of action and discuss the design of universal influenza vaccines inspired by bnAbs.</span></p></div>","PeriodicalId":11082,"journal":{"name":"Current opinion in virology","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39897908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}