{"title":"Experimental Considerations for the Evaluation of Viral Biomolecular Condensates.","authors":"Christine A Roden, Amy S Gladfelter","doi":"10.1146/annurev-virology-093022-010014","DOIUrl":"https://doi.org/10.1146/annurev-virology-093022-010014","url":null,"abstract":"<p><p>Biomolecular condensates are nonmembrane-bound assemblies of biological polymers such as protein and nucleic acids. An increasingly accepted paradigm across the viral tree of life is (<i>a</i>) that viruses form biomolecular condensates and (<i>b</i>) that the formation is required for the virus. Condensates can promote viral replication by promoting packaging, genome compaction, membrane bending, and co-opting of host translation. This review is primarily concerned with exploring methodologies for assessing virally encoded biomolecular condensates. The goal of this review is to provide an experimental framework for virologists to consider when designing experiments to (<i>a</i>) identify viral condensates and their components, (<i>b</i>) reconstitute condensation cell free from minimal components, (<i>c</i>) ask questions about what conditions lead to condensation, (<i>d</i>) map these questions back to the viral life cycle, and (<i>e</i>) design and test inhibitors/modulators of condensation as potential therapeutics. This experimental framework attempts to integrate virology, cell biology, and biochemistry approaches.</p>","PeriodicalId":48761,"journal":{"name":"Annual Review of Virology","volume":"11 1","pages":"105-124"},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142356535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual Review of VirologyPub Date : 2024-09-01Epub Date: 2024-08-30DOI: 10.1146/annurev-virology-100422-012608
Jorge F Guerrero, Sydney L Lesko, Edward L Evans, Nathan M Sherer
{"title":"Studying Retroviral Life Cycles Using Visible Viruses and Live Cell Imaging.","authors":"Jorge F Guerrero, Sydney L Lesko, Edward L Evans, Nathan M Sherer","doi":"10.1146/annurev-virology-100422-012608","DOIUrl":"10.1146/annurev-virology-100422-012608","url":null,"abstract":"<p><p>Viruses exploit key host cell factors to accomplish each individual stage of the viral replication cycle. To understand viral pathogenesis and speed the development of new antiviral strategies, high-resolution visualization of virus-host interactions is needed to define where and when these events occur within cells. Here, we review state-of-the-art live cell imaging techniques for tracking individual stages of viral life cycles, focusing predominantly on retroviruses and especially human immunodeficiency virus type 1, which is most extensively studied. We describe how visible viruses can be engineered for live cell imaging and how nonmodified viruses can, in some instances, be tracked and studied indirectly using cell biosensor systems. We summarize the ways in which live cell imaging has been used to dissect the retroviral life cycle. Finally, we discuss select challenges for the future including the need for better labeling strategies, increased resolution, and multivariate systems that will allow for the study of full viral replication cycles.</p>","PeriodicalId":48761,"journal":{"name":"Annual Review of Virology","volume":" ","pages":"125-146"},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11697243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141321837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual Review of VirologyPub Date : 2024-09-01Epub Date: 2024-08-30DOI: 10.1146/annurev-virology-100422-024648
Benoit de Thoisy, Tiago Gräf, Daniel Santos Mansur, Adriana Delfraro, Claudia Nunes Duarte Dos Santos
{"title":"The Risk of Virus Emergence in South America: A Subtle Balance Between Increasingly Favorable Conditions and a Protective Environment.","authors":"Benoit de Thoisy, Tiago Gräf, Daniel Santos Mansur, Adriana Delfraro, Claudia Nunes Duarte Dos Santos","doi":"10.1146/annurev-virology-100422-024648","DOIUrl":"10.1146/annurev-virology-100422-024648","url":null,"abstract":"<p><p>South American ecosystems host astonishing biodiversity, with potentially great richness in viruses. However, these ecosystems have not yet been the source of any widespread, epidemic viruses. Here we explore a set of putative causes that may explain this apparent paradox. We discuss that human presence in South America is recent, beginning around 14,000 years ago; that few domestications of native species have occurred; and that successive immigration events associated with Old World virus introductions reduced the likelihood of spillovers and adaptation of local viruses into humans. Also, the diversity and ecological characteristics of vertebrate hosts might serve as protective factors. Moreover, although forest areas remained well preserved until recently, current brutal, sudden, and large-scale clear cuts through the forest have resulted in nearly no ecotones, which are essential for creating an adaptive gradient of microbes, hosts, and vectors. This may be temporarily preventing virus emergence. Nevertheless, the mid-term effect of such drastic changes in habitats and landscapes, coupled with explosive urbanization and climate changes, must not be overlooked by health authorities.</p>","PeriodicalId":48761,"journal":{"name":"Annual Review of Virology","volume":" ","pages":"43-65"},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual Review of VirologyPub Date : 2024-09-01Epub Date: 2024-08-30DOI: 10.1146/annurev-virology-111821-101531
Margaret R Dedloff, Helen M Lazear
{"title":"Antiviral and Immunomodulatory Effects of Interferon Lambda at the Maternal-Fetal Interface.","authors":"Margaret R Dedloff, Helen M Lazear","doi":"10.1146/annurev-virology-111821-101531","DOIUrl":"10.1146/annurev-virology-111821-101531","url":null,"abstract":"<p><p>Interferon lambda (IFN-λ, type III IFN, IL-28/29) is a family of antiviral cytokines that are especially important at barrier sites, including the maternal-fetal interface. Recent discoveries have identified important roles for IFN-λ during pregnancy, particularly in the context of congenital infections. Here, we provide a comprehensive review of the activity of IFN-λ at the maternal-fetal interface, highlighting cell types that produce and respond to IFN-λ in the placenta, decidua, and endometrium. Further, we discuss the role of IFN-λ during infections with congenital pathogens including Zika virus, human cytomegalovirus, rubella virus, and <i>Listeria monocytogenes</i>. We discuss advances in experimental models that can be used to fill important knowledge gaps about IFN-λ-mediated immunity.</p>","PeriodicalId":48761,"journal":{"name":"Annual Review of Virology","volume":" ","pages":"363-379"},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual Review of VirologyPub Date : 2024-09-01Epub Date: 2024-08-30DOI: 10.1146/annurev-virology-111821-122718
Anne E Simon, Diego F Quito-Avila, Sayanta Bera
{"title":"Expanding the Plant Virome: Umbra-Like Viruses Use Host Proteins for Movement.","authors":"Anne E Simon, Diego F Quito-Avila, Sayanta Bera","doi":"10.1146/annurev-virology-111821-122718","DOIUrl":"10.1146/annurev-virology-111821-122718","url":null,"abstract":"<p><p>Before the very recent discovery of umbra-like viruses (ULVs), the signature defining feature of all plant RNA viruses was the encoding of specialized RNA-binding movement proteins (MPs) for transiting their RNA genomes through gated plasmodesmata to establish systemic infections. The vast majority of ULVs share umbravirus-like RNA-dependent RNA polymerases and 3'-terminal structures, but they differ by not encoding cell-to-cell and long-distance MPs and by not relying on a helper virus for <i>trans</i>-encapsidation and plant-to-plant transmission. The recent finding that two groups of ULVs do not necessarily encode MPs is expanding our understanding of the minimum requirements for modern plant RNA viruses. ULV CY1 from citrus uses host protein PHLOEM PROTEIN 2 (PP2) for systemic movement, and related ULVs encode a capsid protein, thereby providing an explanation for the lack of helper viruses present in many ULV-infected plants. ULVs thus resemble the first viruses that infected plants, which were likely deposited from feeding organisms and would have similarly required the use of host proteins such as PP2 to exit initially infected cells.</p>","PeriodicalId":48761,"journal":{"name":"Annual Review of Virology","volume":" ","pages":"283-308"},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141321836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual Review of VirologyPub Date : 2024-09-01Epub Date: 2024-08-30DOI: 10.1146/annurev-virology-100422-010336
Alejandro Ortigas-Vasquez, Moriah Szpara
{"title":"Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity.","authors":"Alejandro Ortigas-Vasquez, Moriah Szpara","doi":"10.1146/annurev-virology-100422-010336","DOIUrl":"10.1146/annurev-virology-100422-010336","url":null,"abstract":"<p><p>The arrival of novel sequencing technologies throughout the past two decades has led to a paradigm shift in our understanding of herpesvirus genomic diversity. Previously, herpesviruses were seen as a family of DNA viruses with low genomic diversity. However, a growing body of evidence now suggests that herpesviruses exist as dynamic populations that possess standing variation and evolve at much faster rates than previously assumed. In this review, we explore how strategies such as deep sequencing, long-read sequencing, and haplotype reconstruction are allowing scientists to dissect the genomic composition of herpesvirus populations. We also discuss the challenges that need to be addressed before a detailed picture of herpesvirus diversity can emerge.</p>","PeriodicalId":48761,"journal":{"name":"Annual Review of Virology","volume":" ","pages":"67-87"},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Are There More Human Cancer Viruses Left to Be Found?","authors":"Patrick S Moore, Yuan Chang","doi":"10.1146/annurev-virology-111821-103721","DOIUrl":"https://doi.org/10.1146/annurev-virology-111821-103721","url":null,"abstract":"<p><p>Of the thousands of viruses infecting humans, only seven cause cancer in the general population. Tumor sequencing is now a common cancer medicine procedure, and so it seems likely that more human cancer viruses already would have been found if they exist. Here, we review cancer characteristics that can inform a dedicated search for new cancer viruses, focusing on Kaposi sarcoma herpesvirus and Merkel cell polyomavirus as the most recent examples of successful genomic and transcriptomic searches. We emphasize the importance of epidemiology in determining which cancers to examine and describe approaches to virus discovery. Barriers to virus discovery, such as novel genomes and viral suppression of messenger RNA expression, may exist that prevent virus discovery using existing approaches. Optimally virus hunting should be performed in such a way that if no virus is found, the tumor can be reasonably excluded from having an infectious etiology and new information about the biology of the tumor can be found.</p>","PeriodicalId":48761,"journal":{"name":"Annual Review of Virology","volume":"11 1","pages":"239-259"},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142356534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual Review of VirologyPub Date : 2024-09-01Epub Date: 2024-08-30DOI: 10.1146/annurev-virology-111821-111145
Jingen Zhu, Pan Tao, Ashok K Chopra, Venigalla B Rao
{"title":"Bacteriophage T4 as a Protein-Based, Adjuvant- and Needle-Free, Mucosal Pandemic Vaccine Design Platform.","authors":"Jingen Zhu, Pan Tao, Ashok K Chopra, Venigalla B Rao","doi":"10.1146/annurev-virology-111821-111145","DOIUrl":"10.1146/annurev-virology-111821-111145","url":null,"abstract":"<p><p>The COVID-19 pandemic has transformed vaccinology. Rapid deployment of mRNA vaccines has saved countless lives. However, these platforms have inherent limitations including lack of durability of immune responses and mucosal immunity, high cost, and thermal instability. These and uncertainties about the nature of future pandemics underscore the need for exploring next-generation vaccine platforms. Here, we present a novel protein-based, bacteriophage T4 platform for rapid design of efficacious vaccines against bacterial and viral pathogens. Full-length antigens can be displayed at high density on a 120 × 86 nm phage capsid through nonessential capsid binding proteins Soc and Hoc. Such nanoparticles, without any adjuvant, induce robust humoral, cellular, and mucosal responses when administered intranasally and confer sterilizing immunity. Combined with structural stability and ease of manufacture, T4 phage provides an excellent needle-free, mucosal pandemic vaccine platform and allows equitable vaccine access to low- and middle-income communities across the globe.</p>","PeriodicalId":48761,"journal":{"name":"Annual Review of Virology","volume":" ","pages":"395-420"},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11690488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141072063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual Review of VirologyPub Date : 2024-09-01Epub Date: 2024-08-30DOI: 10.1146/annurev-virology-111821-125122
John M Coffin, Mary F Kearney
{"title":"False Alarm: XMRV, Cancer, and Chronic Fatigue Syndrome.","authors":"John M Coffin, Mary F Kearney","doi":"10.1146/annurev-virology-111821-125122","DOIUrl":"10.1146/annurev-virology-111821-125122","url":null,"abstract":"<p><p>Xenotropic murine leukemia virus (MLV)-related virus (XMRV) was first described in 2006 in some human prostate cancers. But it drew little attention until 2009, when it was also found, as infectious virus and as MLV-related DNA, in samples from people suffering from myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). This discovery was rapidly followed by efforts of the international research community to understand the significance of the association and its potential to spread widely as an important human pathogen. Within a few years, efforts by researchers worldwide failed to repeat these findings, and mounting evidence for laboratory contamination with mouse-derived virus and viral DNA sequences became accepted as the explanation for the initial findings. As researchers engaged in these studies, we present here a historical review of the rise and fall of XMRV as a human pathogen, and we discuss the lessons learned from these events.</p>","PeriodicalId":48761,"journal":{"name":"Annual Review of Virology","volume":" ","pages":"261-281"},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141560121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual Review of VirologyPub Date : 2024-09-01Epub Date: 2024-08-30DOI: 10.1146/annurev-vi-11-060624-100111
Julie K Pfeiffer, Terence S Dermody
{"title":"Artificial Intelligence and Scientific Reviews.","authors":"Julie K Pfeiffer, Terence S Dermody","doi":"10.1146/annurev-vi-11-060624-100111","DOIUrl":"10.1146/annurev-vi-11-060624-100111","url":null,"abstract":"","PeriodicalId":48761,"journal":{"name":"Annual Review of Virology","volume":" ","pages":"iii-iv"},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141321835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}