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Annual Review of Biochemistry 1989
Review
Topics: Amino Acid Sequence; Animals; Antibodies, Viral; Antiviral Agents; Biological Evolution; Capsid; Molecular Sequence Data; Protein Conformation; Protein Processing, Post-Translational; RNA Viruses; RNA, Viral; Receptors, Virus
PubMed: 2673017
DOI: 10.1146/annurev.bi.58.070189.002533 -
The Journal of General Virology Oct 2018Genetic recombination in positive-strand RNA viruses is a significant evolutionary mechanism that drives the creation of viral diversity by the formation of novel... (Review)
Review
Genetic recombination in positive-strand RNA viruses is a significant evolutionary mechanism that drives the creation of viral diversity by the formation of novel chimaeric genomes. The process and its consequences, for example the generation of viruses with novel phenotypes, has historically been studied by analysis of the end products. More recently, with an appreciation that there are both replicative and non-replicative mechanisms at work, and with new approaches and techniques to analyse intermediate products, the viral and cellular factors that influence the process are becoming understood. The major influence on replicative recombination is the fidelity of viral polymerase, although RNA structures and sequences may also have an impact. In replicative recombination the viral polymerase is necessary and sufficient, although roles for other viral or cellular proteins may exist. In contrast, non-replicative recombination appears to be mediated solely by cellular components. Despite these insights, the relative importance of replicative and non-replicative mechanisms is not clear. Using single-stranded positive-sense RNA viruses as exemplars, we review the current state of understanding of the processes and consequences of recombination.
Topics: Evolution, Molecular; Host-Pathogen Interactions; RNA Viruses; RNA, Viral; Recombination, Genetic; Virus Replication
PubMed: 30156526
DOI: 10.1099/jgv.0.001142 -
Methods in Molecular Biology (Clifton,... 2017Self-replicating RNA derived from the genomes of positive strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to... (Review)
Review
Self-replicating RNA derived from the genomes of positive strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to novel safe and effective vaccines. The following chapter summarizes the principles how such RNAs can be established and used for design of vaccines. Due to the large variety of strategies needed to circumvent specific pitfalls in the design of such constructs the technical details of the experiments are not described here but can be found in the cited literature.
Topics: Animals; Humans; RNA Viruses; RNA, Viral; Replicon; Vaccines
PubMed: 27987141
DOI: 10.1007/978-1-4939-6481-9_2 -
Annual Review of Virology Sep 2018RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and frequent recombination. They rapidly adapt to environmental changes, such as... (Review)
Review
RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and frequent recombination. They rapidly adapt to environmental changes, such as shifts in immune pressure or pharmacological challenge. The evolution of RNA viruses has been brought into new focus with the recent developments of genetic and experimental tools to explore and manipulate the evolutionary dynamics of viral populations. These studies have uncovered new mechanisms that enable viruses to overcome evolutionary challenges in the environment and have emphasized the intimate relationship of viral populations with evolution. Here, we review some of the emerging viral and host mechanisms that underlie the evolution of RNA viruses. We also discuss new studies that demonstrate that the relationship between evolutionary dynamics and virus biology spans many spatial and temporal scales, affecting transmission dynamics within and between hosts as well as pathogenesis.
Topics: Adaptation, Biological; Biological Evolution; Host-Pathogen Interactions; Population Dynamics; RNA Viruses
PubMed: 30048219
DOI: 10.1146/annurev-virology-101416-041718 -
PLoS Pathogens Jul 2015
Review
Topics: Animals; Biological Evolution; Host-Parasite Interactions; Humans; Immune Evasion; RNA Virus Infections; RNA Viruses; Reassortant Viruses
PubMed: 26158697
DOI: 10.1371/journal.ppat.1004902 -
Viruses Feb 2021RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the...
RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.
Topics: Models, Molecular; Phylogeny; Protein Conformation, alpha-Helical; Protein Domains; RNA Viruses; RNA-Dependent RNA Polymerase; Viral Proteins
PubMed: 33671332
DOI: 10.3390/v13020313 -
MSphere Apr 2019RNA viruses, particularly genetically diverse members of the , are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal...
RNA viruses, particularly genetically diverse members of the , are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, and RNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans. Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the , and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.
Topics: Evolution, Molecular; Genetic Variation; Genome, Viral; Genotype; Geography; Oceans and Seas; Picornaviridae; Quasispecies; RNA Viruses; Seawater
PubMed: 30944212
DOI: 10.1128/mSphereDirect.00157-19 -
Journal of Natural Products Jan 2021Three families of RNA viruses, the , , and , collectively have great potential to cause epidemic disease in human populations. The current SARS-CoV-2 () responsible for... (Review)
Review
Three families of RNA viruses, the , , and , collectively have great potential to cause epidemic disease in human populations. The current SARS-CoV-2 () responsible for the COVID-19 pandemic underscores the lack of effective medications currently available to treat these classes of viral pathogens. Similarly, the , which includes such viruses as Dengue, West Nile, and Zika, and the , with the Ebola-type viruses, as examples, all lack effective therapeutics. In this review, we present fundamental information concerning the biology of these three virus families, including their genomic makeup, mode of infection of human cells, and key proteins that may offer targeted therapies. Further, we present the natural products and their derivatives that have documented activities to these viral and host proteins, offering hope for future mechanism-based antiviral therapeutics. By arranging these potential protein targets and their natural product inhibitors by target type across these three families of virus, new insights are developed, and crossover treatment strategies are suggested. Hence, natural products, as is the case for other therapeutic areas, continue to be a promising source of structurally diverse new anti-RNA virus therapeutics.
Topics: Animals; Antiviral Agents; Biological Products; Drug Development; Genome, Viral; Humans; RNA Virus Infections; RNA Viruses; Virus Replication; COVID-19 Drug Treatment
PubMed: 33352046
DOI: 10.1021/acs.jnatprod.0c00968 -
Journal of Biological Physics Mar 2013There are two important problems in the assembly of small, icosahedral RNA viruses. First, how does the capsid protein select the viral RNA for packaging, when there are... (Review)
Review
There are two important problems in the assembly of small, icosahedral RNA viruses. First, how does the capsid protein select the viral RNA for packaging, when there are so many other candidate RNA molecules available? Second, what is the mechanism of assembly? With regard to the first question, there are a number of cases where a particular RNA sequence or structure--often one or more stem-loops--either promotes assembly or is required for assembly, but there are others where specific packaging signals are apparently not required. With regard to the assembly pathway, in those cases where stem-loops are involved, the first step is generally believed to be binding of the capsid proteins to these "fingers" of the RNA secondary structure. In the mature virus, the core of the RNA would then occupy the center of the viral particle, and the stem-loops would reach outward, towards the capsid, like stalagmites reaching up from the floor of a grotto towards the ceiling. Those viruses whose assembly does not depend on protein binding to stem-loops could have a different structure, with the core of the RNA lying just under the capsid, and the fingers reaching down into the interior of the virus, like stalactites. We review the literature on these alternative structures, focusing on RNA selectivity and the assembly mechanism, and we propose experiments aimed at determining, in a given virus, which of the two structures actually occurs.
Topics: Genome, Viral; Levivirus; Models, Molecular; RNA Viruses; Tobacco mosaic satellite virus
PubMed: 23860866
DOI: 10.1007/s10867-013-9312-1 -
Annual Review of Microbiology 1972
Review
Topics: Coliphages; DNA-Directed RNA Polymerases; Electrophoresis, Polyacrylamide Gel; Genes; Genetics, Microbial; Orthomyxoviridae; Paramyxoviridae; Peptide Biosynthesis; Picornaviridae; Protein Biosynthesis; RNA Viruses; RNA, Messenger; RNA, Viral; Reoviridae; Templates, Genetic; Transcription, Genetic; Viral Proteins; Virus Replication
PubMed: 4562817
DOI: 10.1146/annurev.mi.26.100172.002343