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Journal of Virological Methods Jun 2014Comparing sequences of archived viruses collected over many years to the present allows the study of viral evolution and contributes to the design of new vaccines....
Comparing sequences of archived viruses collected over many years to the present allows the study of viral evolution and contributes to the design of new vaccines. However, the difficulty, time and expense of generating full-length sequences individually from each archived sample have hampered these studies. Next generation sequencing technologies have been utilized for analysis of clinical and environmental samples to identify viral pathogens that may be present. This has led to the discovery of many new, uncharacterized viruses from a number of viral families. Use of these sequencing technologies would be advantageous in examining viral evolution. In this study, a sequencing procedure was used to sequence simultaneously and rapidly multiple archived samples using a single standard protocol. This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3'-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. This conferred sequence independence by random priming both first and second strand cDNA synthesis. Viral stocks were treated with a nuclease cocktail to reduce the presence of host nucleic acids. Viral RNA was extracted, followed by single tube random-primed double-stranded cDNA synthesis. The resultant cDNAs were amplified by primer-specific PCR, pooled, size fractionated and sequenced on the Ion Torrent PGM platform. The individual virus genomes were readily assembled by both de novo and template-assisted assembly methods. This procedure consistently resulted in near full length, if not full-length, genomic sequences and was used to sequence multiple bovine pestivirus and coronavirus isolates simultaneously.
Topics: Genome, Viral; High-Throughput Nucleotide Sequencing; RNA Viruses; RNA, Viral; Virology
PubMed: 24589514
DOI: 10.1016/j.jviromet.2014.02.016 -
Journal of Virology Oct 2014A faculty position at a primarily undergraduate institution requires working with undergraduates in both the classroom and the research lab. Graduate students and... (Review)
Review
A faculty position at a primarily undergraduate institution requires working with undergraduates in both the classroom and the research lab. Graduate students and postdoctoral fellows who are interested in such a career should understand that faculty at these institutions need to teach broadly and devise research questions that can be addressed safely and with limited resources compared to a research I university. Aspects of, and ways to prepare for, this career will be reviewed herein.
Topics: Education, Medical, Undergraduate; Faculty; Humans; Students; Universities; Virology; Workforce
PubMed: 25056885
DOI: 10.1128/JVI.01880-14 -
Applied and Environmental Microbiology Mar 2012Hypersaline close-to-saturation environments harbor an extremely high concentration of virus-like particles, but the number of haloviruses isolated so far is still very... (Review)
Review
Hypersaline close-to-saturation environments harbor an extremely high concentration of virus-like particles, but the number of haloviruses isolated so far is still very low. Haloviruses can be directly studied from natural samples by using different culture-independent techniques that include transmission electron microscopy, pulsed-field gel electrophoresis, and different metagenomic approaches. Here, we review the findings of these studies, with a main focus on the metagenomic approaches. The analysis of bulk viral nucleic acids directly retrieved from the environment allows estimations of viral diversity, activity, and dynamics and tentative host assignment. Results point to a diverse and active viral community in constant interplay with its hosts and to a "hypersalineness" quality common to viral assemblages present in hypersaline environments that are thousands of kilometers away from each other.
Topics: Biodiversity; Electrophoresis, Gel, Pulsed-Field; Environmental Microbiology; Metagenomics; Microscopy, Electron, Transmission; Virology; Viruses
PubMed: 22247131
DOI: 10.1128/AEM.07175-11 -
Virus Research Sep 2018Click chemistry involves reactions that were originally introduced and used in organic chemistry to generate substances by joining small units together with heteroatom... (Review)
Review
Click chemistry involves reactions that were originally introduced and used in organic chemistry to generate substances by joining small units together with heteroatom linkages (C-X-C). Over the last few decades, click chemistry has been widely used in virus-related research. Using click chemistry, the virus particle as well as viral protein and nucleic acids can be labeled. Subsequently, the labeled virions or molecules can be tracked in real time. Here, we reviewed the recent applications of click reactions in virus-related research, including viral tracking, the design of antiviral agents, the diagnosis of viral infection, and virus-based delivery systems. This review provides an overview of the general principles and applications of click chemistry in virus-related research.
Topics: Antiviral Agents; Click Chemistry; Drug Discovery; Staining and Labeling; Virology; Viruses
PubMed: 30081058
DOI: 10.1016/j.virusres.2018.08.003 -
Journal of Virology Sep 2022Curriculum guidelines for virology are needed to best guide student learning due to the continuous and ever-increasing volume of virology information, the need to ensure...
Curriculum guidelines for virology are needed to best guide student learning due to the continuous and ever-increasing volume of virology information, the need to ensure that undergraduate and graduate students have a foundational understanding of key virology concepts, and the importance in being able to communicate that understanding to both other virologists and nonvirologists. Such guidelines, developed by virology educators and the American Society for Virology Education and Career Development Committee, are described herein.
Topics: Curriculum; Education, Graduate; United States; Universities; Virology
PubMed: 36094313
DOI: 10.1128/jvi.01305-22 -
Antiviral Research Aug 2012The European Virus Archive (EVA) was conceived as a direct response to the need for a coordinated and readily accessible collection of viruses that could be made... (Review)
Review
The European Virus Archive (EVA) was conceived as a direct response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry, initially within Europe, but ultimately throughout the world. Although scientists worldwide have accumulated virus collections since the early twentieth century, the quality of the collections and the viruses collected may vary according to the personal interests and agenda of the scientists. Moreover, when laboratories are re-organised or closed, collections are no longer maintained and gradually cease to exist. The tragedy of 9/11 and other disruptive activities have also meant that some previously available biological reagents are no longer openly exchanged between countries. In 2008, funding under the FP7-EU infrastructure programme enabled the initiation of the EVA. Within three years, it has developed from a consortium of nine European laboratories to encompass associated partners in Africa, Russia, China, Turkey, Germany and Italy. There is every reason to believe that EVA will continue to expand and ultimately exist as a globally networked, quality-controlled non-profit archive for the benefit of science. Organizations or individuals who would like to be considered as contributors are invited to contact the EVA coordinator, Jean-Louis Romette, at [email protected].
Topics: Biological Specimen Banks; Biomedical Research; Europe; Humans; Virology
PubMed: 22626637
DOI: 10.1016/j.antiviral.2012.05.005 -
Journal of Virology Dec 2015Gain-of-function (GoF) studies to understand factors affecting transmissibility of potentially pandemic pathogens are controversial. The European Academies Science... (Review)
Review
Gain-of-function (GoF) studies to understand factors affecting transmissibility of potentially pandemic pathogens are controversial. The European Academies Science Advisory Council (EASAC) recently published consensus recommendations relating to GoF research review and management on self-regulation and harmonization; bioethical considerations; benefit-risk assessment; biosafety, and biosecurity advisory options; and publication of sensitive information. A layered approach to integration of responsibilities must include conforming to the stringent rules and guidance already existing. Further commitment is essential to extend the debate on issues worldwide.
Topics: Academies and Institutes; Biomedical Research; Disease Transmission, Infectious; Europe; Humans; Influenza, Human; Orthomyxoviridae; Orthomyxoviridae Infections; Pandemics; Virology; Virulence
PubMed: 26699646
DOI: 10.1128/JVI.03045-15 -
Journal of Clinical Virology : the... Jan 2004Microarrays of DNA probes have at least three roles in clinical virology. These are: firstly, in diagnosis, to recognise the causative agent of an illness; secondly, for... (Review)
Review
Microarrays of DNA probes have at least three roles in clinical virology. These are: firstly, in diagnosis, to recognise the causative agent of an illness; secondly, for molecular typing for (i) patient management, (ii) epidemiological reasons (e.g. investigating routes of transmission), (iii) purposes related to vaccine use; and thirdly, in research, to investigate the interactions between the virus and the host cell. Microarrays intended for syndromic diagnostic purposes require genome specific probes to capture the unknown target viral sequences and thereby reveal the presence of that virus in a test sample. Microarrays intended for typing and patient management, e.g. monitoring antiviral drug resistant mutations require a set of probes representing the important sequence variants of one or more viral genes. Microarrays intended for research into virus-host interactions require probes representative of each individual gene or mRNA of either the virus or the host genome. Diagnostic microarrays are dependent for their utility and versatility on generic, multiplex or random polymerase chain reactions that will amplify any of several (unknown) viral target sequences from a patient sample. In this review, the existing and potential applications of microarrays in virology, and the problems that need to be overcome for future success, are discussed.
Topics: DNA, Viral; Humans; Oligonucleotide Array Sequence Analysis; Research; Virology; Virus Diseases; Viruses
PubMed: 14675863
DOI: 10.1016/j.jcv.2003.08.002 -
Journal of Virological Methods Mar 2015Unbiased metagenomic sequencing holds significant potential as a diagnostic tool for the simultaneous detection of any previously genetically described viral nucleic...
Unbiased metagenomic sequencing holds significant potential as a diagnostic tool for the simultaneous detection of any previously genetically described viral nucleic acids in clinical samples. Viral genome sequences can also inform on likely phenotypes including drug susceptibility or neutralization serotypes. In this study, different variables of the laboratory methods often used to generate viral metagenomics libraries were compared for their abilities to detect multiple viruses and generate full genome coverage. A biological reagent consisting of 25 different human RNA and DNA viral pathogens was used to estimate the effect of filtration and nuclease digestion, DNA/RNA extraction methods, pre-amplification and the use of different library preparation kits on the detection of viral nucleic acids. Filtration and nuclease treatment led to slight decreases in the percentage of viral sequence reads and number of viruses detected. For nucleic acid extractions silica spin columns improved viral sequence recovery relative to magnetic beads and Trizol extraction. Pre-amplification using random RT-PCR while generating more viral sequence reads resulted in detection of fewer viruses, more overlapping sequences, and lower genome coverage. The ScriptSeq library preparation method retrieved more viruses and a greater fraction of their genomes than the TruSeq and Nextera methods. Viral metagenomics sequencing was able to simultaneously detect up to 22 different viruses in the biological reagent analyzed including all those detected by qPCR. Further optimization will be required for the detection of viruses in biologically more complex samples such as tissues, blood, or feces.
Topics: Humans; Indicators and Reagents; Metagenomics; Specimen Handling; Virology; Virus Diseases; Viruses
PubMed: 25497414
DOI: 10.1016/j.jviromet.2014.12.002 -
Viruses Mar 2021The year 2020 was profoundly marked by the emergence and spread of SARS-CoV-2, causing COVID-19, which represents the greatest pandemic of the 21st century until now,...
The year 2020 was profoundly marked by the emergence and spread of SARS-CoV-2, causing COVID-19, which represents the greatest pandemic of the 21st century until now, and a major challenge for virologists in the scientific and medical communities. Increased numbers of SARS-CoV-2 infection all over the world imposed social and travel restrictions, including avoidance of face-to-face scientific meetings. Therefore, for the first time in history, the 2020 edition of the Brazilian Society of Virology (SBV) congress was totally online. Despite the challenge of the new format, the Brazilian society board and collaborators were successful in virtually congregating more than 921 attendees, which was the greatest SBV participant number ever reached. Seminal talks from prominent national and international researchers were presented every night, during a week, and included discussions about environmental, basic, animal, human, plant and invertebrate virology. A special roundtable debated exclusively new data and perspectives regarding COVID-19 by some of the greatest Brazilian virologists. Women scientists were very well represented in another special roundtable called "Young Women Inspiring Research", which was one of the most viewed and commented section during the meeting, given the extraordinary quality of the presented work. Finally, SBV offered the Helio Gelli Pereira award for one graduate and one undergraduate student, which has also been a fruitful collaboration between the society and journal. The annual SBV meeting has, therefore, reached its goals to inspire young scientists, stimulate high-quality scientific discussion and to encourage global collaboration between virologists.
Topics: Brazil; Group Processes; Humans; Societies, Scientific; User-Computer Interface; Virology
PubMed: 33807596
DOI: 10.3390/v13030414