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Nature Biotechnology Oct 2018Ambitious efforts to catalog viruses across the globe may facilitate our understanding of viral communities and ecology, boost infectious disease diagnostics and...
Ambitious efforts to catalog viruses across the globe may facilitate our understanding of viral communities and ecology, boost infectious disease diagnostics and surveillance, and spur new therapeutics. Charles Schmidt investigates.
Topics: Animals; Biotechnology; Disease Reservoirs; Disease Vectors; High-Throughput Nucleotide Sequencing; Humans; Microbiota; Virology; Viruses
PubMed: 30307913
DOI: 10.1038/nbt.4268 -
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 -
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 -
International Journal of Biological... 2022The coronavirus disease 2019 (COVID-19) global pandemic evoked by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered a major public health... (Review)
Review
The coronavirus disease 2019 (COVID-19) global pandemic evoked by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered a major public health problem with significant morbidity and mortality. Understanding the pathogenesis and molecular mechanisms underlying this novel virus is crucial for both fundamental research and clinical trials in order to devise effective therapies and vaccination regimens. Basic research on SARS-CoV-2 largely depends on models that allow viral invasion and replication. Organoid models are now emerging as a valuable tool to investigate viral biology and disease progression, serving as an efficient platform to investigate potential therapies for COVID-19. Here, we summarize various human stem cell-derived organoid types employed in SARS-CoV-2 studies. We highlight key findings from these models, including cell tropisms and molecular mechanisms in viral infection. We also describe their use in identifying potential therapeutic agents against SARS-CoV-2. As more and more advanced organoids emerge, they will facilitate the understanding of disease pathogenesis for drug development in this dreaded pandemic.
Topics: COVID-19; Humans; Organoids; SARS-CoV-2; Virology
PubMed: 35173525
DOI: 10.7150/ijbs.64993 -
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 -
The Journal of Pathology Jan 2015Varicelloviruses in primates comprise the prototypic human varicella-zoster virus (VZV) and its non-human primate homologue, simian varicella virus (SVV). Both viruses... (Review)
Review
Varicelloviruses in primates comprise the prototypic human varicella-zoster virus (VZV) and its non-human primate homologue, simian varicella virus (SVV). Both viruses cause varicella as a primary infection, establish latency in ganglionic neurons and reactivate later in life to cause herpes zoster in their respective hosts. VZV is endemic worldwide and, although varicella is usually a benign disease in childhood, VZV reactivation is a significant cause of neurological disease in the elderly and in immunocompromised individuals. The pathogenesis of VZV infection remains ill-defined, mostly due to the species restriction of VZV that impedes studies in experimental animal models. SVV infection of non-human primates parallels virological, clinical, pathological and immunological features of human VZV infection, thereby providing an excellent model to study the pathogenesis of varicella and herpes zoster in its natural host. In this review, we discuss recent studies that provided novel insight in both the virus and host factors involved in the three elementary stages of Varicellovirus infection in primates: primary infection, latency and reactivation.
Topics: Animals; Biopsy; Disease Models, Animal; Genotype; Herpesviridae Infections; Host-Pathogen Interactions; Humans; Pathology, Molecular; Predictive Value of Tests; Primates; Varicellovirus; Virology; Virulence; Virus Activation; Virus Latency
PubMed: 25255989
DOI: 10.1002/path.4451 -
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 -
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 -
Bundesgesundheitsblatt,... Mar 2017
Topics: Communicable Disease Control; Cross Infection; Disinfection; Evidence-Based Medicine; Germany; Humans; Hygiene; Practice Guidelines as Topic; Virology; Virus Diseases
PubMed: 28220216
DOI: 10.1007/s00103-016-2509-2 -
Viruses Dec 2020The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke...
The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.
Topics: COVID-19; Computational Biology; Congresses as Topic; Evolution, Molecular; Genome, Viral; Humans; Metagenomics; RNA Viruses; Virology
PubMed: 33291220
DOI: 10.3390/v12121398