The Experts below are selected from a list of 93264 Experts worldwide ranked by ideXlab platform
Edward C Holmes - One of the best experts on this subject based on the ideXlab platform.
-
the diversity evolution and origins of vertebrate RNA Viruses
Current Opinion in Virology, 2018Co-Authors: Yongzhen Zhang, Weichen Wu, Edward C HolmesAbstract:Despite a substantial increase in our knowledge of the biodiversity and evolution of vertebrate RNA Viruses, far less is known about the diversity, evolution and origin of RNA Viruses across the diverse phylogenetic range of Viruses, and particularly in healthy animals that are often only rarely utilized for virological sampling. Fortunately, recent advances in virus discovery using metagenomic approaches are beginning to reveal a multitude of RNA Viruses in vertebrates other than birds and mammals. In particular, fish harbor a remarkable array of RNA Viruses, including the relatives of important pathogens. In addition, despite frequent cross-species transmission, the RNA Viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years.
-
the evolutionary history of vertebrate RNA Viruses
Nature, 2018Co-Authors: Xiao Chen, Edward C Holmes, John-sebastian Eden, Junhua Tian, Liangjun Chen, Kun Li, Wen Wang, Jinjin ShenAbstract:Our understanding of the diversity and evolution of vertebrate RNA Viruses is largely limited to those found in mammalian and avian hosts and associated with overt disease. Here, using a large-scale meta-transcriptomic approach, we discover 214 vertebrate-associated Viruses in reptiles, amphibians, lungfish, ray-finned fish, cartilaginous fish and jawless fish. The newly discovered Viruses appear in every family or genus of RNA virus associated with vertebrate infection, including those containing human pathogens such as influenza virus, the Arenaviridae and Filoviridae families, and have branching orders that broadly reflected the phylogenetic history of their hosts. We establish a long evolutionary history for most groups of vertebrate RNA virus, and support this by evaluating evolutionary timescales using dated orthologous endogenous virus elements. We also identify new vertebrate-specific RNA Viruses and genome architectures, and re-evaluate the evolution of vector-borne RNA Viruses. In summary, this study reveals diverse virus–host associations across the entire evolutionary history of the vertebrates.
-
A rticle Fast T rack Gene Duplication Is Infrequent in the Recent Evolutionary History of RNA Viruses
2016Co-Authors: Etienne Simon-loriere, Edward C HolmesAbstract:Gene duplication generates genetic novelty and redundancy and is a major mechanism of evolutionary change in bacteria and eukaryotes. To date, however, gene duplication has been reported only rarely in RNA Viruses. Using a conservative BLAST approach we systematically screened for the presence of duplicated (i.e., paralogous) proteins in all RNA Viruses for which full genome sequences are publicly available. Strikingly, we found only nine significantly supported cases of gene duplication, two of which are newly described here—in the 25 and 26kDa proteins of Beet necrotic yellow vein virus (genus Benyvirus) and in the U1 and U2 proteins of Wongabel virus (family Rhabdoviridae). Hence, gene duplication has occurred at a far lower frequency in the recent evolutionary history of RNA Viruses than in other organisms. Although the rapidity of RNA virus evolution means that older gene duplication events will be difficult to detect through sequence-based analyses alone, it is likely that specific features of RNA virus biology, and particularly intrinsic constraints on genome size, reduce the likelihood of the fixation and maintenance of duplicated genes. Key words: RNA virus, gene duplication, genome size, genetic redundancy
-
genomic analysis of the emergence evolution and spread of human respiratory RNA Viruses
Annual Review of Genomics and Human Genetics, 2016Co-Authors: Tommy Tsanyuk Lam, H Zhu, Yi Guan, Edward C HolmesAbstract:The emergence and reemergence of rapidly evolving RNA Viruses-particularly those responsible for respiratory diseases, such as influenza Viruses and coronaViruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as sampling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA Viruses, as well as the major challenges in such genomic analyses.
-
endogenous RNA Viruses of plants in insect genomes
Virology, 2012Co-Authors: Jie Cui, Edward C HolmesAbstract:Endogenous viral elements (EVEs) derived from RNA Viruses with no DNA stage are rare, especially those where the parental Viruses possess single-strand positive-sense (ssRNA+) genomes. Here we provide evidence that EVEs that share a sequence similarity to ssRNA+Viruses of plants are integrated into the genomes of a number of insects, including mosquito, fruit flies, bees, ant, silkworm, pea aphid, Monarch butterfly, and wasps. A preliminary phylogenetic analysis places these EVEs as divergent relatives of the Virgaviridae and three currently unclassified plant viral species.
Yongzhen Zhang - One of the best experts on this subject based on the ideXlab platform.
-
the diversity evolution and origins of vertebrate RNA Viruses
Current Opinion in Virology, 2018Co-Authors: Yongzhen Zhang, Weichen Wu, Edward C HolmesAbstract:Despite a substantial increase in our knowledge of the biodiversity and evolution of vertebrate RNA Viruses, far less is known about the diversity, evolution and origin of RNA Viruses across the diverse phylogenetic range of Viruses, and particularly in healthy animals that are often only rarely utilized for virological sampling. Fortunately, recent advances in virus discovery using metagenomic approaches are beginning to reveal a multitude of RNA Viruses in vertebrates other than birds and mammals. In particular, fish harbor a remarkable array of RNA Viruses, including the relatives of important pathogens. In addition, despite frequent cross-species transmission, the RNA Viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years.
-
unprecedented genomic diversity of RNA Viruses in arthropods reveals the ancestry of negative sense RNA Viruses
eLife, 2015Co-Authors: Mang Shi, Junhua Tian, Xiandan Lin, Yanjun Kang, Liangjun Chen, Xincheng Qin, Yongzhen ZhangAbstract:Many illnesses, including influenza, hemorrhagic fever, and rabies, are caused by a group of Viruses called negative-sense RNA Viruses. The genetic information—or genome—of these Viruses is encoded in strands of RNA that must be copied before they can be translated into the proteins needed to build new Viruses. It is currently known that there are at least eight different families of these Viruses, which have a wide range of shapes and sizes and arrange their RNA in different ways. Insects, spiders, and other arthropods carry many different RNA Viruses. Many of these Viruses have not previously been studied, and those that have been studied so far are mainly those that cause diseases in humans and other vertebrates. Researchers therefore only know a limited amount about the diversity of the negative-sense RNA Viruses that arthropods harbor and how these Viruses evolved. Studying how Viruses evolve helps scientists to understand what makes some Viruses deadly and others harmless and can also help develop treatments or vaccines for the diseases caused by the Viruses. Li, Shi, Tian, Lin, Kang et al. collected 70 species of insects, spiders, centipedes, and other arthropods in China and sequenced all the negative-sense RNA Viruses in the creatures. This revealed an enormous number of negative-sense RNA Viruses, including 112 new Viruses. Many of the newly discovered arthropod Viruses appear to be the ancestors of disease-causing Viruses, including influenza Viruses and the filoViruses—the group that includes the Ebola virus. Indeed, it appears that arthropods host many—if not all—of the negative-sense RNA Viruses that cause disease in vertebrates and plants. While documenting the new RNA Viruses and how they are related to each other, Li et al. found many different genome structures. Some genomes were segmented, which may play an important role in evolution as segments can be easily swapped to create new genetic combinations. Non-segmented and circular genomes were also found. This genetic diversity suggests that arthropods are likely to have played a key role in the evolution of new Viruses by acting as a site where many different Viruses can interact and exchange genetic information.
Gareth M Jenkins - One of the best experts on this subject based on the ideXlab platform.
-
the extent of codon usage bias in human RNA Viruses and its evolutionary origin
Virus Research, 2003Co-Authors: Gareth M Jenkins, Edward C HolmesAbstract:Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution. Herein, we report the results of a survey of codon usage bias in a wide range of genetically and ecologically diverse human RNA Viruses. This analysis showed that the overall extent of codon usage bias in RNA Viruses is low and that there is little variation in bias between genes. Furthermore, the strong correlation between base and dinucleotide composition and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed. However, we also detected correlations between codon usage bias and some characteristics of viral genome structure and ecology, with increased bias in segmented and aerosol-transmitted Viruses and decreased bias in vector-borne Viruses. This suggests that translational selection may also have some influence in shaping codon usage bias.
-
rates of molecular evolution in RNA Viruses a quantitative phylogenetic analysis
Journal of Molecular Evolution, 2002Co-Authors: Gareth M Jenkins, Andrew Rambaut, Oliver G Pybus, Edward C HolmesAbstract:The study of rates of nucleotide substitution in RNA Viruses is central to our understanding of their evolution. Herein we report a comprehensive analysis of substitution rates in 50 RNA Viruses using a recently developed maximum likelihood phylogenetic method. This analysis revealed a significant relationship between genetic divergence and isolation time for an extensive array of RNA Viruses, although more rate variation was usually present among lineages than would be expected under the constraints of a molecular clock. Despite the lack of a molecular clock, the range of statistically significant variation in overall substitution rates was surprisingly narrow for those Viruses where a significant relationship between genetic divergence and time was found, as was the case when synonymous sites were considered alone, where the molecular clock was rejected less frequently. An analysis of the ecological and genetic factors that might explain this rate variation revealed some evidence of significantly lower substitution rates in vector-borne Viruses, as well as a weak correlation between rate and genome length. Finally, a simulation study revealed that our maximum likelihood estimates of substitution rates are valid, even if the molecular clock is rejected, provided that sufficiently large data sets are analyzed.
Mehul S Suthar - One of the best experts on this subject based on the ideXlab platform.
-
mechanisms of innate immune evasion in re emerging RNA Viruses
Current Opinion in Virology, 2015Co-Authors: Daphne Y, Mehul S SutharAbstract:Recent outbreaks of Ebola, West Nile, Chikungunya, Middle Eastern Respiratory and other emerging/re-emerging RNA Viruses continue to highlight the need to further understand the virus–host interactions that govern disease severity and infection outcome. As part of the early host antiviral defense, the innate immune system mediates pathogen recognition and initiation of potent antiviral programs that serve to limit virus replication, limit virus spread and activate adaptive immune responses. Concordantly, viral pathogens have evolved several strategies to counteract pathogen recognition and cell-intrinsic antiviral responses. In this review, we highlight the major mechanisms of innate immune evasion by emerging and re-emerging RNA Viruses, focusing on pathogens that pose significant risk to public health.
Xi Zhou - One of the best experts on this subject based on the ideXlab platform.
-
cucurbit 7 uril as a broad spectrum antiviral agent against diverse RNA Viruses
Virologica Sinica, 2021Co-Authors: Jia Quan, Xiangjun Zhang, Yuanfu Ding, Yang Qiu, Ruibing Wang, Xi ZhouAbstract:The emergence and re-emergence of RNA virus outbreaks highlight the urgent need for the development of broad-spectrum antivirals. Polyamines are positively-charged small molecules required for the infectivity of a wide range of RNA Viruses, therefore may become good antiviral targets. Cucurbit[7]uril (CB[7]), a synthetic macrocyclic molecule, which can bind with amine-based organic compounds with high affinity, has been shown to regulate bioactive molecules through competitive binding. In this study, we tested the antiviral activity of CB[7] against diverse RNA Viruses, including a panel of enteroViruses (i.e. human enterovirus A71, coxsackievirus A16, coxsackievirus B3, and echovirus 11), some flaviViruses (i.e. dengue virus and Zika virus), and an alphavirus representative Semliki forest virus. CB[7] can inhibit virus replications in a variety of cell lines, and its mechanism of action is through the competitive binding with polyamines. Our findings not only for the first time provide evidence that CB[7] can be a promising broad-spectrum antiviral agent, but more importantly, offer a novel therapeutic strategy to fight against RNA Viruses by supramolecular sequestration of polyamines.
