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MBio Mar 2014
Topics: History, 20th Century; History, 21st Century; Host-Pathogen Interactions; Virology; Virus Diseases; Virus Physiological Phenomena; Viruses
PubMed: 24667711
DOI: 10.1128/mBio.01003-14 -
Current Opinion in Microbiology Aug 2013Viral pathogen discovery is of critical importance to clinical microbiology, infectious diseases, and public health. Genomic approaches for pathogen discovery, including... (Review)
Review
Viral pathogen discovery is of critical importance to clinical microbiology, infectious diseases, and public health. Genomic approaches for pathogen discovery, including consensus polymerase chain reaction (PCR), microarrays, and unbiased next-generation sequencing (NGS), have the capacity to comprehensively identify novel microbes present in clinical samples. Although numerous challenges remain to be addressed, including the bioinformatics analysis and interpretation of large datasets, these technologies have been successful in rapidly identifying emerging outbreak threats, screening vaccines and other biological products for microbial contamination, and discovering novel viruses associated with both acute and chronic illnesses. Downstream studies such as genome assembly, epidemiologic screening, and a culture system or animal model of infection are necessary to establish an association of a candidate pathogen with disease.
Topics: Animals; Disease Models, Animal; Drug Contamination; Genomics; Humans; Virology; Virus Diseases; Viruses
PubMed: 23725672
DOI: 10.1016/j.mib.2013.05.001 -
Current Opinion in Virology Dec 2014Recent technological advances have led to an explosion in the system-wide profiling of biological processes in the study of herpesvirus biology, herein referred to as... (Review)
Review
Recent technological advances have led to an explosion in the system-wide profiling of biological processes in the study of herpesvirus biology, herein referred to as '-omics'. In many cases these approaches have revealed novel virus-induced changes to host cell biology that can be targeted with new antiviral therapeutics. Despite these successes, -omics approaches are not widely applied in the study of roseoloviruses. Here we describe examples of how -omics studies have shaped our understanding of herpesvirus biology, and discuss how these approaches might be used to identify host and viral factors that mediate roseolovirus pathogenesis.
Topics: Gene Expression Profiling; Genomics; Host-Pathogen Interactions; Humans; Metabolomics; Proteomics; Roseolovirus; Systems Biology; Virology
PubMed: 25437230
DOI: 10.1016/j.coviro.2014.09.021 -
Upsala Journal of Medical Sciences Apr 2019In this paper I describe aspects of work on the human adenoviruses in which my laboratory has participated. It consists of two sections-one historic dealing with work... (Review)
Review
In this paper I describe aspects of work on the human adenoviruses in which my laboratory has participated. It consists of two sections-one historic dealing with work performed in the previous century, and one dealing with the application of 'omics' technologies to understand how adenovirus-infected cells become reprogrammed to benefit virus multiplication.
Topics: Adenoviridae; Adenoviridae Infections; Apoptosis; Capsid; Gene Expression Profiling; History, 20th Century; History, 21st Century; Humans; Kinetics; Proteome; Proteomics; Signal Transduction; Transcriptome; Viral Proteins; Virology
PubMed: 31142167
DOI: 10.1080/03009734.2019.1613698 -
Cell Host & Microbe Apr 2018The deterministic force of natural selection and stochastic influence of drift shape RNA virus evolution. New deep-sequencing and microfluidics technologies allow us to... (Review)
Review
The deterministic force of natural selection and stochastic influence of drift shape RNA virus evolution. New deep-sequencing and microfluidics technologies allow us to quantify the effect of mutations and trace the evolution of viral populations with single-genome and single-nucleotide resolution. Such experiments can reveal the topography of the genotype-fitness landscapes that shape the path of viral evolution. By combining historical analyses, like phylogenetic approaches, with high-throughput and high-resolution evolutionary experiments, we can observe parallel patterns of evolution that drive important phenotypic transitions. These developments provide a framework for quantifying and anticipating potential evolutionary events. Here, we examine emerging technologies that can map the selective landscapes of viruses, focusing on their application to pathogenic viruses. We identify areas where these technologies can bolster our ability to study the evolution of viruses and to anticipate and possibly intervene in evolutionary events and prevent viral disease.
Topics: Adaptation, Biological; Evolution, Molecular; Genetics, Population; High-Throughput Nucleotide Sequencing; RNA Viruses; Selection, Genetic; Virology
PubMed: 29649440
DOI: 10.1016/j.chom.2018.03.012 -
Proceedings of the National Academy of... Jan 2020Emerging and reemerging viruses are responsible for a number of recent epidemic outbreaks. A crucial step in predicting and controlling outbreaks is the timely and...
Emerging and reemerging viruses are responsible for a number of recent epidemic outbreaks. A crucial step in predicting and controlling outbreaks is the timely and accurate characterization of emerging virus strains. We present a portable microfluidic platform containing carbon nanotube arrays with differential filtration porosity for the rapid enrichment and optical identification of viruses. Different emerging strains (or unknown viruses) can be enriched and identified in real time through a multivirus capture component in conjunction with surface-enhanced Raman spectroscopy. More importantly, after viral capture and detection on a chip, viruses remain viable and get purified in a microdevice that permits subsequent in-depth characterizations by various conventional methods. We validated this platform using different subtypes of avian influenza A viruses and human samples with respiratory infections. This technology successfully enriched rhinovirus, influenza virus, and parainfluenza viruses, and maintained the stoichiometric viral proportions when the samples contained more than one type of virus, thus emulating coinfection. Viral capture and detection took only a few minutes with a 70-fold enrichment enhancement; detection could be achieved with as little as 10 EID/mL (50% egg infective dose per microliter), with a virus specificity of 90%. After enrichment using the device, we demonstrated by sequencing that the abundance of viral-specific reads significantly increased from 4.1 to 31.8% for parainfluenza and from 0.08 to 0.44% for influenza virus. This enrichment method coupled to Raman virus identification constitutes an innovative system that could be used to quickly track and monitor viral outbreaks in real time.
Topics: Humans; Influenza A virus; Microbiological Techniques; Microtechnology; Nanotubes, Carbon; Respiratory Tract Infections; Respirovirus; Rhinovirus; Sensitivity and Specificity; Silicon Dioxide; Spectrum Analysis, Raman; Staining and Labeling; Virion; Virology; Virus Diseases; Viruses
PubMed: 31882450
DOI: 10.1073/pnas.1910113117 -
Journal of Virology Oct 2015Many longstanding questions about dynamics of virus-cell interactions can be answered by combining fluorescence imaging techniques with fluorescent protein (FP) tagging... (Review)
Review
Many longstanding questions about dynamics of virus-cell interactions can be answered by combining fluorescence imaging techniques with fluorescent protein (FP) tagging strategies. Successfully creating a FP fusion with a cellular or viral protein of interest first requires selecting the appropriate FP. However, while viral architecture and cellular localization often dictate the suitability of a FP, a FP's chemical and physical properties must also be considered. Here, we discuss the challenges of and offer suggestions for identifying the optimal FPs for studying the cell biology of viruses.
Topics: Cellular Microenvironment; Luminescent Proteins; Models, Molecular; Optical Imaging; Viral Fusion Proteins; Virology
PubMed: 26202231
DOI: 10.1128/JVI.03489-13 -
Advances in Experimental Medicine and... 2019Virus particles, 'virions', range in size from nano-scale to micro-scale. They have many different shapes and are composed of proteins, sugars, nucleic acids, lipids,...
Virus particles, 'virions', range in size from nano-scale to micro-scale. They have many different shapes and are composed of proteins, sugars, nucleic acids, lipids, water and solutes. Virions are autonomous entities and affect all forms of life in a parasitic relationship. They infect prokaryotic and eukaryotic cells. The physical properties of virions are tuned to the way they interact with cells. When virions interact with cells, they gain huge complexity and give rise to an infected cell, also known as 'virus'. Virion-cell interactions entail the processes of entry, replication and assembly, as well as egress from the infected cell. Collectively, these steps can result in progeny virions, which is a productive infection, or in silencing of the virus, an abortive or latent infection. This book explores facets of the physical nature of virions and viruses and the impact of mechanical properties on infection processes at the cellular and subcellular levels.
Topics: Humans; Virology; Virus Diseases
PubMed: 31317493
DOI: 10.1007/978-3-030-14741-9_1 -
Biochimica Et Biophysica Acta Jul 2016Viruses typically pack their genetic material within a protein capsid. Enveloped viruses also have an outer membrane made up of a lipid bilayer and membrane-spanning... (Review)
Review
Viruses typically pack their genetic material within a protein capsid. Enveloped viruses also have an outer membrane made up of a lipid bilayer and membrane-spanning glycoproteins. X-ray diffraction and cryoelectron microscopy provide high resolution static views of viral structure. Molecular dynamics (MD) simulations may be used to provide dynamic insights into the structures of viruses and their components. There have been a number of simulations of viral capsids and (in some cases) of the inner core of RNA or DNA packaged within them. These simulations have generally focussed on the structural integrity and stability of the capsid and/or on the influence of the nucleic acid core on capsid stability. More recently there have been a number of simulation studies of enveloped viruses, including HIV-1, influenza A, and dengue virus. These have addressed the dynamic behaviour of the capsid, the matrix, and/or of the outer envelope. Analysis of the dynamics of the lipid bilayer components of the envelopes of influenza A and of dengue virus reveals a degree of biophysical robustness, which may contribute to the stability of virus particles in different environments. Significant computational challenges need to be addressed to aid simulation of complex viruses and their membranes, including the need to integrate structural data from a range of sources to enable us to move towards simulations of intact virions. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Topics: Capsid; Computational Biology; Computer Simulation; Lipid Bilayers; Models, Chemical; Models, Molecular; Virology
PubMed: 26874202
DOI: 10.1016/j.bbamem.2016.02.007 -
Current Opinion in Virology Feb 2013Viral entry encompasses the initial steps of infection starting from virion host cell attachment to viral genome release. Given the dynamic interactions between the... (Review)
Review
Viral entry encompasses the initial steps of infection starting from virion host cell attachment to viral genome release. Given the dynamic interactions between the virus and the host, many questions related to viral entry can be directly addressed by live cell imaging. Recent advances in fluorescent labeling of viral and cellular components, fluorescence microscopy with high sensitivity and spatiotemporal resolution, and image analysis enabled studies of a broad spectrum across many viral entry steps, including virus-receptor interactions, internalization, intracellular transport, genomic release, nuclear transport, and cell-to-cell transmission. Collectively, these live cell imaging studies have not only enriched our understandings of the viral entry mechanisms, but also provided novel insights into basic cellular biology processes.
Topics: Cytological Techniques; Image Processing, Computer-Assisted; Microscopy, Fluorescence; Virology; Virus Internalization
PubMed: 23395264
DOI: 10.1016/j.coviro.2013.01.005