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The Journal of General Virology Sep 2012The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance... (Review)
Review
The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture and PCR, next-generation sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination and, to some extent, by their cost, which has restricted their use to relatively small numbers of samples. Challenges remain, including the storage and analysis of the large amounts of data generated. As the chemistries employed mature, costs will decrease. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. An exciting era of viral exploration has begun, and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health.
Topics: Animals; High-Throughput Nucleotide Sequencing; Humans; Sequence Analysis, DNA; Virology; Viruses
PubMed: 22647373
DOI: 10.1099/vir.0.043182-0 -
Viruses Aug 2016The genome of influenza A viruses (IAV) consists of eight single-stranded negative sense viral RNAs (vRNAs) encapsidated into viral ribonucleoproteins (vRNPs). It is now... (Review)
Review
The genome of influenza A viruses (IAV) consists of eight single-stranded negative sense viral RNAs (vRNAs) encapsidated into viral ribonucleoproteins (vRNPs). It is now well established that genome packaging (i.e., the incorporation of a set of eight distinct vRNPs into budding viral particles), follows a specific pathway guided by segment-specific cis-acting packaging signals on each vRNA. However, the precise nature and function of the packaging signals, and the mechanisms underlying the assembly of vRNPs into sub-bundles in the cytoplasm and their selective packaging at the viral budding site, remain largely unknown. Here, we review the diverse and complementary methods currently being used to elucidate these aspects of the viral cycle. They range from conventional and competitive reverse genetics, single molecule imaging of vRNPs by fluorescence in situ hybridization (FISH) and high-resolution electron microscopy and tomography of budding viral particles, to solely in vitro approaches to investigate vRNA-vRNA interactions at the molecular level.
Topics: Electron Microscope Tomography; Humans; In Situ Hybridization, Fluorescence; Influenza A virus; Microscopy, Electron, Transmission; Reverse Genetics; Single Molecule Imaging; Virology; Virus Assembly
PubMed: 27517951
DOI: 10.3390/v8080218 -
Virologica Sinica Feb 2015There are many recent studies regarding the efficacy of bacteriophage-related lytic enzymes: the enzymes of 'bacteria-eaters' or viruses that infect bacteria. By... (Review)
Review
There are many recent studies regarding the efficacy of bacteriophage-related lytic enzymes: the enzymes of 'bacteria-eaters' or viruses that infect bacteria. By degrading the cell wall of the targeted bacteria, these lytic enzymes have been shown to efficiently lyse Gram-positive bacteria without affecting normal flora and non-related bacteria. Recent studies have suggested approaches for lysing Gram-negative bacteria as well (Briersa Y, et al., 2014). These enzymes include: phage-lysozyme, endolysin, lysozyme, lysin, phage lysin, phage lytic enzymes, phageassociated enzymes, enzybiotics, muralysin, muramidase, virolysin and designations such as Ply, PAE and others. Bacteriophages are viruses that kill bacteria, do not contribute to antimicrobial resistance, are easy to develop, inexpensive to manufacture and safe for humans, animals and the environment. The current focus on lytic enzymes has been on their use as anti-infectives in humans and more recently in agricultural research models. The initial translational application of lytic enzymes, however, was not associated with treating or preventing a specific disease but rather as an extraction method to be incorporated in a rapid bacterial detection assay (Bernstein D, 1997).The current review traces the translational history of phage lytic enzymes-from their initial discovery in 1986 for the rapid detection of group A streptococcus in clinical specimens to evolving applications in the detection and prevention of disease in humans and in agriculture.
Topics: Bacteriophages; History, 20th Century; History, 21st Century; Viral Proteins; Virology
PubMed: 25662888
DOI: 10.1007/s12250-014-3549-0 -
Journal of Virology Oct 2018The rise of populist movements worldwide is challenging science and motivating scientists to join the debate and enter politics. Based on my experience, taking a public... (Review)
Review
The rise of populist movements worldwide is challenging science and motivating scientists to join the debate and enter politics. Based on my experience, taking a public stand will not come without slanderous personal and institutional attacks as an attempt to shake scientific credibility. The virology community is at risk of similar misrepresentation; reflection on this topic, particularly on how to address such challenges, should be a priority, given we are in the "post-truth" era.
Topics: Biomedical Research; Politics; Trust; Virology
PubMed: 30089689
DOI: 10.1128/JVI.00757-18 -
Viruses Dec 2012Systems biology approaches in virology aim to integrate viral and host biological networks, and thus model the infection process. The growing availability of... (Review)
Review
Systems biology approaches in virology aim to integrate viral and host biological networks, and thus model the infection process. The growing availability of high-throughput “-omics” techniques and datasets, as well as the ever-increasing sophistication of in silico modeling tools, has resulted in a corresponding rise in the complexity of the analyses that can be performed. The present study seeks to review and organize published evidence regarding virus-host interactions for the arenaviruses, from alterations in the host proteome during infection, to reported protein-protein interactions. In this way, we hope to provide an overview of the interplay between arenaviruses and the host cell, and lay the foundations for complementing current arenavirus research with a systems-level approach.
Topics: Arenavirus; Computational Biology; Host-Pathogen Interactions; Humans; Protein Interaction Maps; Proteomics; Systems Biology; Virology
PubMed: 23342371
DOI: 10.3390/v4123625 -
Journal of Virology Feb 2023Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the...
Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.
Topics: Humans; COVID-19; Information Dissemination; Pandemics; Policy Making; Research; SARS-CoV-2; Virology; Virus Diseases; Viruses
PubMed: 36700640
DOI: 10.1128/jvi.00089-23 -
Proceedings of the National Academy of... Mar 2017
Topics: Germany; History, 20th Century; History, 21st Century; Neoplasms; Slovakia; Virology
PubMed: 28289211
DOI: 10.1073/pnas.1702501114 -
Antiviral Research Mar 2014Reverse genetics allows the generation of recombinant viruses entirely from cDNA. One application of this technology is the creation of reporter-expressing viruses,... (Review)
Review
Reverse genetics allows the generation of recombinant viruses entirely from cDNA. One application of this technology is the creation of reporter-expressing viruses, which greatly increase the detail and ease with which these viruses can be studied. However, there are a number of challenges when working with reporter-expressing viruses. Both the reporter protein itself as well as the genetic manipulations within the viral genome required for expression of this reporter can result in altered biological properties of the recombinant virus, and lead to attenuation in vitro and/or in vivo. Further, instability of reporter expression and purging of the genetic information encoding for the reporter from the viral genome can be an issue. Finally, a practical challenge for in vivo studies lies in the attenuation of light signals when traversing tissues. Novel expression strategies and the continued development of brighter, red and far-red shifted reporters and the increased use of bioluminescent reporters for in vivo applications promise to overcome some of these limitations in future. However, a "one size fits all" approach to the design of reporter-expressing viruses has thus far not been possible. Rather, a reporter suited to the intended application must be selected and an appropriate expression strategy and location for the reporter in the viral genome chosen. Still, attenuating effects of the reporter on viral fitness are difficult to predict and have to be carefully assessed with respect to the intended application. Despite these limitations the generation of suitable reporter-expressing viruses will become more common as technology and our understanding of the intricacies of viral gene expression and regulation improves, allowing deeper insight into virus biology both in living cells and in animals.
Topics: Animals; Gene Expression; Genes, Reporter; Humans; Mononegavirales; Reverse Genetics; Staining and Labeling; Virology
PubMed: 24462694
DOI: 10.1016/j.antiviral.2014.01.003 -
Nature Reviews. Microbiology Jul 2013High-throughput molecular profiling and computational biology are changing the face of virology, providing a new appreciation of the importance of the host in viral... (Review)
Review
High-throughput molecular profiling and computational biology are changing the face of virology, providing a new appreciation of the importance of the host in viral pathogenesis and offering unprecedented opportunities for better diagnostics, therapeutics and vaccines. Here, we provide a snapshot of the evolution of systems virology, from global gene expression profiling and signatures of disease outcome, to geometry-based computational methods that promise to yield novel therapeutic targets, personalized medicine and a deeper understanding of how viruses cause disease. To realize these goals, pipettes and Petri dishes need to join forces with the powers of mathematics and computational biology.
Topics: Animals; Computational Biology; Drug Delivery Systems; High-Throughput Screening Assays; Host-Pathogen Interactions; Humans; Systems Biology; Virology; Virulence; Virus Diseases; Viruses
PubMed: 23728212
DOI: 10.1038/nrmicro3036 -
Journal of Microbiology, Immunology,... Apr 2015Minigenomes (MGs) are complementary DNAs of the synthetic analogs of genomic RNA. MGs are widely used to study the life cycle of the Paramyxoviridae family of viruses.... (Review)
Review
Minigenomes (MGs) are complementary DNAs of the synthetic analogs of genomic RNA. MGs are widely used to study the life cycle of the Paramyxoviridae family of viruses. MG-based studies have provided valuable insights into the mechanisms of viral replication and transcription in this family, including the roles of viral proteins, the location and boundaries of the cis-acting elements, the functional domains of trans-acting proteins, techniques for the measurement of neutralizing antibody, virus-host interactions, and the structure and function of viral RNA. This article provides a brief overview of the principle and application of MG technology in studies involving members of the Paramyxoviridae family. The advantages, potential limitations, and future scope of MG technology are also discussed.
Topics: Genome, Viral; Host-Pathogen Interactions; Molecular Biology; Paramyxoviridae; Virology; Virus Physiological Phenomena
PubMed: 24767419
DOI: 10.1016/j.jmii.2014.02.008