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Genetics Dec 2018RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their... (Review)
Review
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using and laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
Topics: Evolution, Molecular; Genetic Variation; Genome, Viral; High-Throughput Nucleotide Sequencing; History, 20th Century; History, 21st Century; Metagenomics; Phylogeny; RNA Viruses; Virology
PubMed: 30523166
DOI: 10.1534/genetics.118.301556 -
Mass Spectrometry Reviews Sep 2020Virology, as a branch of the life sciences, discovered mass spectrometry (MS) to be the pivotal tool around two decades ago. The technique unveiled the complex network... (Review)
Review
Virology, as a branch of the life sciences, discovered mass spectrometry (MS) to be the pivotal tool around two decades ago. The technique unveiled the complex network of interactions between the living world of pro- and eukaryotes and viruses, which delivered "a piece of bad news wrapped in protein" as defined by Peter Medawar, Nobel Prize Laureate, in 1960. However, MS is constantly evolving, and novel approaches allow for a better understanding of interactions in this micro- and nanoworld. Currently, we can investigate the interplay between the virus and the cell by analyzing proteomes, interactomes, virus-cell interactions, and search for the compounds that build viral structures. In addition, by using MS, it is possible to look at the cell from the broader perspective and determine the role of viral infection on the scale of the organism, for example, monitoring the crosstalk between infected tissues and the immune system. In such a way, MS became one of the major tools for the modern virology, allowing us to see the infection in the context of the whole cell or the organism. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
Topics: Capsid; Host-Pathogen Interactions; Humans; Mass Spectrometry; Polymerase Chain Reaction; Protein Processing, Post-Translational; Viral Proteins; Viral Vaccines; Virology; Virus Diseases; Viruses
PubMed: 31876329
DOI: 10.1002/mas.21617 -
Viruses Jun 2016The highly pathogenic Marburg virus (MARV) is a member of the Filoviridae family and belongs to the group of nonsegmented negative-strand RNA viruses. Reverse genetics... (Review)
Review
The highly pathogenic Marburg virus (MARV) is a member of the Filoviridae family and belongs to the group of nonsegmented negative-strand RNA viruses. Reverse genetics systems established for MARV have been used to study various aspects of the viral replication cycle, analyze host responses, image viral infection, and screen for antivirals. This article provides an overview of the currently established MARV reverse genetic systems based on minigenomes, infectious virus-like particles and full-length clones, and the research that has been conducted using these systems.
Topics: Marburgvirus; Reverse Genetics; Virology
PubMed: 27338448
DOI: 10.3390/v8060178 -
Viruses May 2016Single-cell sequencing technologies, i.e., single cell analysis followed by deep sequencing investigate cellular heterogeneity in many biological settings. It was only... (Review)
Review
Single-cell sequencing technologies, i.e., single cell analysis followed by deep sequencing investigate cellular heterogeneity in many biological settings. It was only in the past year that single-cell sequencing analyses has been applied in the field of virology, providing new ways to explore viral diversity and cell response to viral infection, which are summarized in the present review.
Topics: Genomics; Host-Pathogen Interactions; Humans; Single-Cell Analysis; Virology; Viruses
PubMed: 27153082
DOI: 10.3390/v8050123 -
Viruses Oct 2015Pollination of flowering plants is an important ecosystem service provided by wild insect pollinators and managed honey bees. Hence, losses and declines of pollinating...
Pollination of flowering plants is an important ecosystem service provided by wild insect pollinators and managed honey bees. Hence, losses and declines of pollinating insect species threaten human food security and are of major concern not only for apiculture or agriculture but for human society in general. Honey bee colony losses and bumblebee declines have attracted intensive research interest over the last decade and although the problem is far from being solved we now know that viruses are among the key players of many of these bee losses and bumblebee declines. With this special issue on bee viruses we, therefore, aimed to collect high quality original papers reflecting the current state of bee virus research. To this end, we focused on newly discovered viruses (Lake Sinai viruses, bee macula-like virus), or a so far neglected virus species (Apis mellifera filamentous virus), and cutting edge technologies (mass spectrometry, RNAi approach) applied in the field.
Topics: Animals; Bees; Biomedical Research; Virology; Viruses
PubMed: 26702462
DOI: 10.3390/v7102885 -
The Journal of Nutrition, Health & Aging 2020A new coronavirus, called SARS-CoV-2, was identified in Wuhan, China, in December 2019. The SARS-CoV-2 spread very rapidly, causing a global pandemic, Coronavirus... (Review)
Review
A new coronavirus, called SARS-CoV-2, was identified in Wuhan, China, in December 2019. The SARS-CoV-2 spread very rapidly, causing a global pandemic, Coronavirus Disease 2019 (COVID-19). Older adults have higher peak of viral load and, especially those with comorbidities, had higher COVID-19-related fatality rates than younger adults. In this Perspective paper, we summarize current knowledge about SARS-CoV-2 and aging, in order to understand why older people are more affected by COVID-19. We discuss about the possibility that the so-called "immunosenescence" and "inflammaging" processes, already present in a fraction of frail older adults, could allow the immune escape of SARS-CoV-2 leading to COVID-19 serious complications. Finally, we propose to use geroscience approaches to the field of COVID-19.
Topics: Aged; Aging; Betacoronavirus; COVID-19; Coronavirus Infections; Geriatrics; Humans; Inflammation; Pandemics; Pneumonia, Viral; SARS-CoV-2; Virology
PubMed: 32744561
DOI: 10.1007/s12603-020-1416-2 -
Transfusion Clinique Et Biologique :... Feb 2016The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new... (Review)
Review
The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new potential threats for blood transfusion safety. Currently, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) can be considered as under control in high-resource countries. However, other viruses unknown or unsuspected may be transmitted to recipients by blood-derived products. This is particularly relevant considering that a significant proportion of transfused patients are immunocompromised and more frequently subjected to fatal outcomes. Several measures to prevent transfusion transmission of unknown viruses have been implemented including the exclusion of at-risk donors, leukocyte reduction of donor blood, and physicochemical treatment of the different blood components. However, up to now there is no universal method for pathogen inactivation, which would be applicable for all types of blood components and, equally effective for all viral families. In addition, among available inactivation procedures of viral genomes, some of them are recognized to be less effective on non-enveloped viruses, and inadequate to inactivate higher viral titers in plasma pools or derivatives. Given this, there is the need to implement new methodologies for the discovery of unknown viruses that may affect blood transfusion. Viral metagenomics combined with High Throughput Sequencing appears as a promising approach for the identification and global surveillance of new and/or unexpected viruses that could impair blood transfusion safety.
Topics: Blood Safety; Communicable Diseases, Emerging; Computational Biology; DNA, Viral; Gene Library; Genes, Viral; High-Throughput Nucleotide Sequencing; Humans; Immunocompromised Host; Metagenome; Metagenomics; Population Surveillance; RNA, Viral; Specimen Handling; Transfusion Reaction; Viremia; Virology; Virus Inactivation
PubMed: 26778104
DOI: 10.1016/j.tracli.2015.12.002 -
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 -
Journal of Clinical Virology : the... Jun 2019Molecular diagnostic methods have evolved and matured considerably over the last several decades and are constantly being evaluated and adopted by clinical laboratories... (Review)
Review
Molecular diagnostic methods have evolved and matured considerably over the last several decades and are constantly being evaluated and adopted by clinical laboratories for the identification of infectious pathogens. Advancement in other technologies such as fluorescence, electronics, instrumentation, automation, and sensors have made the overall diagnostic process more accurate, sensitive, and rapid. Nucleic acid based detection procedures, which rely on the fundamental principles of DNA replication have emerged as a popular and standard diagnostic method, and several commercial assays are currently available based on different nucleic acid amplification techniques. This review focuses on the major amplification chemistries that are used for developing commercial assays and discusses their application in the clinical virology laboratory.
Topics: Clinical Laboratory Techniques; Humans; Molecular Diagnostic Techniques; Nucleic Acid Amplification Techniques; Sensitivity and Specificity; Virology; Virus Diseases; Viruses
PubMed: 30953805
DOI: 10.1016/j.jcv.2019.03.015 -
Viruses Jul 2016Several arenaviruses cause hemorrhagic fever (HF) disease in humans and pose an important public health problem in their endemic regions. To date, no Food and Drug... (Review)
Review
Several arenaviruses cause hemorrhagic fever (HF) disease in humans and pose an important public health problem in their endemic regions. To date, no Food and Drug Administration (FDA)-licensed vaccines are available to combat human arenavirus infections, and current anti-arenaviral drug therapy is limited to an off-label use of ribavirin that is only partially effective. The development of arenavirus reverse genetic approaches has provided investigators with a novel and powerful approach for the study of arenavirus biology including virus-host interactions underlying arenavirus induced disease. The use of cell-based minigenome systems has allowed examining the cis- and trans-acting factors involved in arenavirus replication and transcription, as well as particle assembly and budding. Likewise, it is now feasible to rescue infectious arenaviruses containing predetermined mutations in their genomes to investigate virus-host interactions and mechanisms of pathogenesis. The use of reverse genetics approaches has also allowed the generation of recombinant arenaviruses expressing additional genes of interest. These advances in arenavirus molecular genetics have also facilitated the implementation of novel screens to identify anti-arenaviral drugs, and the development of novel strategies for the generation of arenavirus live-attenuated vaccines. In this review, we will summarize the current knowledge on reporter-expressing, replicating-competent arenaviruses harboring reporter genes in different locations of the viral genome and their use for studying and understanding arenavirus biology and the identification of anti-arenaviral drugs to combat these important human pathogens.
Topics: Animals; Arenavirus; Genes, Reporter; Humans; Reverse Genetics; Staining and Labeling; Virology; Virus Replication
PubMed: 27447662
DOI: 10.3390/v8070197