Journal articles: 'RNA viruses'

1

Shi, Rui-Zhu, Yuan-Qing Pan, and Li Xing. "RNA Helicase A Regulates the Replication of RNA Viruses." Viruses 13, no. 3 (February 25, 2021): 361. http://dx.doi.org/10.3390/v13030361.

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The RNA helicase A (RHA) is a member of DExH-box helicases and characterized by two double-stranded RNA binding domains at the N-terminus. RHA unwinds double-stranded RNA in vitro and is involved in RNA metabolisms in the cell. RHA is also hijacked by a variety of RNA viruses to facilitate virus replication. Herein, this review will provide an overview of the role of RHA in the replication of RNA viruses.

2

Ahlquist, Paul. "Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses." Nature Reviews Microbiology 4, no. 5 (April 3, 2006): 371–82. http://dx.doi.org/10.1038/nrmicro1389.

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Sokoloski, Kevin J., Carol J. Wilusz, and Jeffrey Wilusz. "Viruses: Overturning RNA Turnover." RNA Biology 3, no. 4 (October 2006): 140–44. http://dx.doi.org/10.4161/rna.3.4.4076.

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4

Yang, Jie, Hongjie Xia, Qi Qian, and Xi Zhou. "RNA chaperones encoded by RNA viruses." Virologica Sinica 30, no. 6 (December 2015): 401–9. http://dx.doi.org/10.1007/s12250-015-3676-2.

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5

Enami, Masayoshi. "Negative-strand RNA viruses. Reverse genetics of negative-strand RNA viruses." Uirusu 45, no. 2 (1995): 145–57. http://dx.doi.org/10.2222/jsv.45.145.

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6

Ahlquist, P. "RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing." Science 296, no. 5571 (May 17, 2002): 1270–73. http://dx.doi.org/10.1126/science.1069132.

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7

Newburn, Laura R., and K. Andrew White. "Trans-Acting RNA–RNA Interactions in Segmented RNA Viruses." Viruses 11, no. 8 (August 14, 2019): 751. http://dx.doi.org/10.3390/v11080751.

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RNA viruses represent a large and important group of pathogens that infect a broad range of hosts. Segmented RNA viruses are a subclass of this group that encode their genomes in two or more molecules and package all of their RNA segments in a single virus particle. These divided genomes come in different forms, including double-stranded RNA, coding-sense single-stranded RNA, and noncoding single-stranded RNA. Genera that possess these genome types include, respectively, Orbivirus (e.g., Bluetongue virus), Dianthovirus (e.g., Red clover necrotic mosaic virus) and Alphainfluenzavirus (e.g., Influenza A virus). Despite their distinct genomic features and diverse host ranges (i.e., animals, plants, and humans, respectively) each of these viruses uses trans-acting RNA–RNA interactions (tRRIs) to facilitate co-packaging of their segmented genome. The tRRIs occur between different viral genome segments and direct the selective packaging of a complete genome complement. Here we explore the current state of understanding of tRRI-mediated co-packaging in the abovementioned viruses and examine other known and potential functions for this class of RNA–RNA interaction.

8

SATO, Hironori, and Masaru YOKOYAMA. "RNA viruses and mutations." Uirusu 55, no. 2 (2005): 221–29. http://dx.doi.org/10.2222/jsv.55.221.

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9

MINE, Akira, and Tetsuro OKUNO. "Viruses and RNA silencing." Uirusu 58, no. 1 (2008): 61–68. http://dx.doi.org/10.2222/jsv.58.61.

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10

Strauss, J. H., and E. G. Strauss. "Evolution of RNA Viruses." Annual Review of Microbiology 42, no. 1 (October 1988): 657–83. http://dx.doi.org/10.1146/annurev.mi.42.100188.003301.

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11

Carmichael, Gordon G. "Silencing viruses with RNA." Nature 418, no. 6896 (July 2002): 379–80. http://dx.doi.org/10.1038/418379a.

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12

King, Andrew M. Q. "RNA viruses do it." Trends in Genetics 3 (January 1987): 60–61. http://dx.doi.org/10.1016/0168-9525(87)90173-9.

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13

Billiau, A. "Double-stranded RNA viruses." Antiviral Research 5, no. 3 (June 1985): 191–92. http://dx.doi.org/10.1016/0166-3542(85)90052-x.

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14

Saiz, Juan-Carlos. "Vaccines against RNA Viruses." Vaccines 8, no. 3 (August 27, 2020): 479. http://dx.doi.org/10.3390/vaccines8030479.

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15

Slamon, Dennis J., and Irvin S. Y. Chen. "RNA viruses and cancer." Infectious Diseases Newsletter 5, no. 4 (April 1986): 28–30. http://dx.doi.org/10.1016/0278-2316(86)90068-x.

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16

Hammarskjöld, Marie-Louise. "RNA and lessons from viruses." RNA 21, no. 4 (March 16, 2015): 632–33. http://dx.doi.org/10.1261/rna.050310.115.

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17

Lundstrom, Kenneth. "Self-Replicating RNA Viruses for RNA Therapeutics." Molecules 23, no. 12 (December 13, 2018): 3310. http://dx.doi.org/10.3390/molecules23123310.

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Self-replicating single-stranded RNA viruses such as alphaviruses, flaviviruses, measles viruses, and rhabdoviruses provide efficient delivery and high-level expression of therapeutic genes due to their high capacity of RNA replication. This has contributed to novel approaches for therapeutic applications including vaccine development and gene therapy-based immunotherapy. Numerous studies in animal tumor models have demonstrated that self-replicating RNA viral vectors can generate antibody responses against infectious agents and tumor cells. Moreover, protection against challenges with pathogenic Ebola virus was obtained in primates immunized with alphaviruses and flaviviruses. Similarly, vaccinated animals have been demonstrated to withstand challenges with lethal doses of tumor cells. Furthermore, clinical trials have been conducted for several indications with self-amplifying RNA viruses. In this context, alphaviruses have been subjected to phase I clinical trials for a cytomegalovirus vaccine generating neutralizing antibodies in healthy volunteers, and for antigen delivery to dendritic cells providing clinically relevant antibody responses in cancer patients, respectively. Likewise, rhabdovirus particles have been subjected to phase I/II clinical trials showing good safety and immunogenicity against Ebola virus. Rhabdoviruses have generated promising results in phase III trials against Ebola virus. The purpose of this review is to summarize the achievements of using self-replicating RNA viruses for RNA therapy based on preclinical animal studies and clinical trials in humans.

18

Lundstrom, Kenneth. "Self-Amplifying RNA Viruses as RNA Vaccines." International Journal of Molecular Sciences 21, no. 14 (July 20, 2020): 5130. http://dx.doi.org/10.3390/ijms21145130.

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Single-stranded RNA viruses such as alphaviruses, flaviviruses, measles viruses and rhabdoviruses are characterized by their capacity of highly efficient self-amplification of RNA in host cells, which make them attractive vehicles for vaccine development. Particularly, alphaviruses and flaviviruses can be administered as recombinant particles, layered DNA/RNA plasmid vectors carrying the RNA replicon and even RNA replicon molecules. Self-amplifying RNA viral vectors have been used for high level expression of viral and tumor antigens, which in immunization studies have elicited strong cellular and humoral immune responses in animal models. Vaccination has provided protection against challenges with lethal doses of viral pathogens and tumor cells. Moreover, clinical trials have demonstrated safe application of RNA viral vectors and even promising results in rhabdovirus-based phase III trials on an Ebola virus vaccine. Preclinical and clinical applications of self-amplifying RNA viral vectors have proven efficient for vaccine development and due to the presence of RNA replicons, amplification of RNA in host cells will generate superior immune responses with significantly reduced amounts of RNA delivered. The need for novel and efficient vaccines has become even more evident due to the global COVID-19 pandemic, which has further highlighted the urgency in challenging emerging diseases.

19

Raj, Pushker. "Classification of medically important viruses II: RNA viruses." Clinical Microbiology Newsletter 16, no. 17 (September 1994): 129–34. http://dx.doi.org/10.1016/0196-4399(94)90005-1.

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20

Fisher, Susie. "Are RNA Viruses Vestiges of an RNA World?" Journal for General Philosophy of Science 41, no. 1 (May 25, 2010): 121–41. http://dx.doi.org/10.1007/s10838-010-9119-8.

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21

Geng, Guowei, Deya Wang, Zhifei Liu, Yalan Wang, Mingjing Zhu, Xinran Cao, Chengming Yu, and Xuefeng Yuan. "Translation of Plant RNA Viruses." Viruses 13, no. 12 (December 13, 2021): 2499. http://dx.doi.org/10.3390/v13122499.

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Plant RNA viruses encode essential viral proteins that depend on the host translation machinery for their expression. However, genomic RNAs of most plant RNA viruses lack the classical characteristics of eukaryotic cellular mRNAs, such as mono-cistron, 5′ cap structure, and 3′ polyadenylation. To adapt and utilize the eukaryotic translation machinery, plant RNA viruses have evolved a variety of translation strategies such as cap-independent translation, translation recoding on initiation and termination sites, and post-translation processes. This review focuses on advances in cap-independent translation and translation recoding in plant viruses.

22

Silva-Júnior, Edeildo F. da. "Entry Inhibitors of RNA Viruses." Current Medicinal Chemistry 29, no. 4 (February 2022): 609–11. http://dx.doi.org/10.2174/092986732904220207113503.

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23

Pompei, Simone, Vittorio Loreto, and Francesca Tria. "Phylogenetic Properties of RNA Viruses." PLoS ONE 7, no. 9 (September 20, 2012): e44849. http://dx.doi.org/10.1371/journal.pone.0044849.

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24

Simon-Loriere, Etienne, and Edward C. Holmes. "Why do RNA viruses recombine?" Nature Reviews Microbiology 9, no. 8 (July 4, 2011): 617–26. http://dx.doi.org/10.1038/nrmicro2614.

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25

Steinhauer, D. A., and J. J. Holland. "Rapid Evolution of RNA Viruses." Annual Review of Microbiology 41, no. 1 (October 1987): 409–31. http://dx.doi.org/10.1146/annurev.mi.41.100187.002205.

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26

Gillespie, J. H. "Episodic evolution of RNA viruses." Proceedings of the National Academy of Sciences 90, no. 22 (November 15, 1993): 10411–12. http://dx.doi.org/10.1073/pnas.90.22.10411.

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27

Zeller, Mark, and Kristian G. Andersen. "Backbone of RNA viruses uncovered." Nature 556, no. 7700 (April 2018): 182–83. http://dx.doi.org/10.1038/d41586-018-03923-w.

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28

Said, Elias A., Felipe Diaz-Griffero, Dorine Bonte, Daniel Lamarre, and Ali A. Al-Jabri. "Immune Responses to RNA Viruses." Journal of Immunology Research 2018 (June 12, 2018): 1–2. http://dx.doi.org/10.1155/2018/5473678.

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29

Russell, Stephen J. "RNA viruses as virotherapy agents." Cancer Gene Therapy 9, no. 12 (November 22, 2002): 961–66. http://dx.doi.org/10.1038/sj.cgt.7700535.

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30

Woodland, David L. "A Focus on RNA Viruses." Viral Immunology 24, no. 2 (April 2011): 67–68. http://dx.doi.org/10.1089/vim.2011.ed.24.2.

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31

Rima, B. K. "Viruses in the RNA World." Biochemical Society Transactions 24, no. 1 (February 1, 1996): 1–13. http://dx.doi.org/10.1042/bst0240001.

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32

BHUVANESHWARI, M., H. SUBRAMANYA, M. MURTHY, K. GOPINATH, and H. SAVITHRI. "Architecture of small RNA viruses." Progress in Crystal Growth and Characterization of Materials 34, no. 1-4 (1997): 1–10. http://dx.doi.org/10.1016/s0960-8974(97)00001-6.

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33

Michalakis, Y. "EVOLUTION: Epistasis in RNA Viruses." Science 306, no. 5701 (November 26, 2004): 1492–93. http://dx.doi.org/10.1126/science.1106677.

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34

Colbère-Garapin, Florence, Bruno Blondel, Aure Saulnier, Isabelle Pelletier, and Karine Labadie. "Silencing viruses by RNA interference." Microbes and Infection 7, no. 4 (April 2005): 767–75. http://dx.doi.org/10.1016/j.micinf.2005.02.003.

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35

Ruigrok, R. W. H. "Assembly of enveloped RNA viruses." FEBS Letters 202, no. 1 (June 23, 1986): 159. http://dx.doi.org/10.1016/0014-5793(86)80670-6.

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36

Lang, Andrew S., Matthew L. Rise, Alexander I. Culley, and Grieg F. Steward. "RNA viruses in the sea." FEMS Microbiology Reviews 33, no. 2 (March 2009): 295–323. http://dx.doi.org/10.1111/j.1574-6976.2008.00132.x.

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37

Drake, J. W., and J. J. Holland. "Mutation rates among RNA viruses." Proceedings of the National Academy of Sciences 96, no. 24 (November 23, 1999): 13910–13. http://dx.doi.org/10.1073/pnas.96.24.13910.

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38

Dadley-Moore, Davina. "RNA viruses: all bases covered?" Nature Reviews Immunology 6, no. 5 (May 2006): 341. http://dx.doi.org/10.1038/nri1856.

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39

Rossmann, Michael G. "The evolution of RNA viruses." BioEssays 7, no. 3 (September 1987): 99–103. http://dx.doi.org/10.1002/bies.950070302.

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40

Weber, Friedemann, Valentina Wagner, Simon B. Rasmussen, Rune Hartmann, and Søren R. Paludan. "Double-Stranded RNA Is Produced by Positive-Strand RNA Viruses and DNA Viruses but Not in Detectable Amounts by Negative-Strand RNA Viruses." Journal of Virology 80, no. 10 (May 15, 2006): 5059–64. http://dx.doi.org/10.1128/jvi.80.10.5059-5064.2006.

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ABSTRACT Double-stranded RNA (dsRNA) longer than 30 bp is a key activator of the innate immune response against viral infections. It is widely assumed that the generation of dsRNA during genome replication is a trait shared by all viruses. However, to our knowledge, no study exists in which the production of dsRNA by different viruses is systematically investigated. Here, we investigated the presence and localization of dsRNA in cells infected with a range of viruses, employing a dsRNA-specific antibody for immunofluorescence analysis. Our data revealed that, as predicted, significant amounts of dsRNA can be detected for viruses with a genome consisting of positive-strand RNA, dsRNA, or DNA. Surprisingly, however, no dsRNA signals were detected for negative-strand RNA viruses. Thus, dsRNA is indeed a general feature of most virus groups, but negative-strand RNA viruses appear to be an exception to that rule.

41

Richaud, Aurélien, Lise Frézal, Stephen Tahan, Hongbing Jiang, Joshua A. Blatter, Guoyan Zhao, Taniya Kaur, David Wang, and Marie-Anne Félix. "Vertical transmission in Caenorhabditis nematodes of RNA molecules encoding a viral RNA-dependent RNA polymerase." Proceedings of the National Academy of Sciences 116, no. 49 (November 18, 2019): 24738–47. http://dx.doi.org/10.1073/pnas.1903903116.

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Here, we report on the discovery in Caenorhabditis nematodes of multiple vertically transmitted RNAs coding for putative RNA-dependent RNA polymerases. Their sequences share similarity to distinct RNA viruses, including bunyaviruses, narnaviruses, and sobemoviruses. The sequences are present exclusively as RNA and are not found in DNA form. The RNAs persist in progeny after bleach treatment of adult animals, indicating vertical transmission of the RNAs. We tested one of the infected strains for transmission to an uninfected strain and found that mating of infected animals with uninfected animals resulted in infected progeny. By in situ hybridization, we detected several of these RNAs in the cytoplasm of the male and female germline of the nematode host. The Caenorhabditis hosts were found defective in degrading exogenous double-stranded RNAs, which may explain retention of viral-like RNAs. Strikingly, one strain, QG551, harbored three distinct virus-like RNA elements. Specific patterns of small RNAs complementary to the different viral-like RNAs were observed, suggesting that the different RNAs are differentially recognized by the RNA interference (RNAi) machinery. While vertical transmission of viruses in the family Narnaviridae, which are known as capsidless viruses, has been described in fungi, these observations provide evidence that multicellular animal cells harbor similar viruses.

42

Chao, Shufen, Haoran Wang, Shu Zhang, Guoqing Chen, Chonghui Mao, Yang Hu, Fengquan Yu, et al. "Novel RNA Viruses Discovered in Weeds in Rice Fields." Viruses 14, no. 11 (November 10, 2022): 2489. http://dx.doi.org/10.3390/v14112489.

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Weeds often grow alongside crop plants. In addition to competing with crops for nutrients, water and space, weeds host insect vectors or act as reservoirs for viral diversity. However, little is known about viruses infecting rice weeds. In this work, we used metatranscriptomic deep sequencing to identify RNA viruses from 29 weed samples representing 23 weed species. A total of 224 RNA viruses were identified: 39 newly identified viruses are sufficiently divergent to comprise new families and genera. The newly identified RNA viruses clustered within 18 viral families. Of the identified viruses, 196 are positive-sense single-stranded RNA viruses, 24 are negative-sense single-stranded RNA viruses and 4 are double-stranded RNA viruses. We found that some novel RNA viruses clustered within the families or genera of several plant virus species and have the potential to infect plants. Collectively, these results expand our understanding of viral diversity in rice weeds. Our work will contribute to developing effective strategies with which to manage the spread and epidemiology of plant viruses.

43

Yang, Siwy Ling, Riccardo Delli Ponti, Yue Wan, and Roland G. Huber. "Computational and Experimental Approaches to Study the RNA Secondary Structures of RNA Viruses." Viruses 14, no. 8 (August 16, 2022): 1795. http://dx.doi.org/10.3390/v14081795.

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Most pandemics of recent decades can be traced to RNA viruses, including HIV, SARS, influenza, dengue, Zika, and SARS-CoV-2. These RNA viruses impose considerable social and economic burdens on our society, resulting in a high number of deaths and high treatment costs. As these RNA viruses utilize an RNA genome, which is important for different stages of the viral life cycle, including replication, translation, and packaging, studying how the genome folds is important to understand virus function. In this review, we summarize recent advances in computational and high-throughput RNA structure-mapping approaches and their use in understanding structures within RNA virus genomes. In particular, we focus on the genome structures of the dengue, Zika, and SARS-CoV-2 viruses due to recent significant outbreaks of these viruses around the world.

44

Boonrod, Kajohn, and Gabriele Krczal. "Inhibitions of Positive-Sense (ss) RNA Viruses RNA-Dependent RNA Polymerases." Current Enzyme Inhibition 5, no. 4 (December 1, 2009): 234–44. http://dx.doi.org/10.2174/157340809789630262.

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45

Nicholson, Beth L., and K. Andrew White. "Functional long-range RNA–RNA interactions in positive-strand RNA viruses." Nature Reviews Microbiology 12, no. 7 (June 16, 2014): 493–504. http://dx.doi.org/10.1038/nrmicro3288.

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46

Swaminathan, Gokul, Julio Martin-Garcia, and Sonia Navas-Martin. "RNA viruses and microRNAs: challenging discoveries for the 21st century." Physiological Genomics 45, no. 22 (November 15, 2013): 1035–48. http://dx.doi.org/10.1152/physiolgenomics.00112.2013.

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RNA viruses represent the predominant cause of many clinically relevant viral diseases in humans. Among several evolutionary advantages acquired by RNA viruses, the ability to usurp host cellular machinery and evade antiviral immune responses is imperative. During the past decade, RNA interference mechanisms, especially microRNA (miRNA)-mediated regulation of cellular protein expression, have revolutionized our understanding of host-viral interactions. Although it is well established that several DNA viruses express miRNAs that play crucial roles in their pathogenesis, expression of miRNAs by RNA viruses remains controversial. However, modulation of the miRNA machinery by RNA viruses may confer multiple benefits for enhanced viral replication and survival in host cells. In this review, we discuss the current literature on RNA viruses that may encode miRNAs and the varied advantages of engineering RNA viruses to express miRNAs as potential vectors for gene therapy. In addition, we review how different families of RNA viruses can alter miRNA machinery for productive replication, evasion of antiviral immune responses, and prolonged survival. We underscore the need to further explore the complex interactions of RNA viruses with host miRNAs to augment our understanding of host-virus interplay.

47

Kolakofsky, Daniel. "A short biased history of RNA viruses." RNA 21, no. 4 (March 16, 2015): 667–69. http://dx.doi.org/10.1261/rna.049916.115.

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48

Ortín, Juan, and Jaime Martín-Benito. "The RNA synthesis machinery of negative-stranded RNA viruses." Virology 479-480 (May 2015): 532–44. http://dx.doi.org/10.1016/j.virol.2015.03.018.

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49

Wang, Wenqing, Xianhong Wang, Chunyan Tu, Mengmeng Yang, Jun Xiang, Liping Wang, Ni Hong, Lifeng Zhai, and Guoping Wang. "Novel Mycoviruses Discovered from a Metatranscriptomics Survey of the Phytopathogenic Alternaria Fungus." Viruses 14, no. 11 (November 18, 2022): 2552. http://dx.doi.org/10.3390/v14112552.

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Alternaria fungus can cause notable diseases in cereals, ornamental plants, vegetables, and fruits around the world. To date, an increasing number of mycoviruses have been accurately and successfully identified in this fungus. In this study, we discovered mycoviruses from 78 strains in 6 species of the genus Alternaria, which were collected from 10 pear production areas using high-throughput sequencing technology. Using the total RNA-seq, we detected the RNA-dependent RNA polymerase of 19 potential viruses and the coat protein of two potential viruses. We successfully confirmed these viruses using reverse transcription polymerase chain reaction with RNA as the template. We identified 12 mycoviruses that were positive-sense single-stranded RNA (+ssRNA) viruses, 5 double-strand RNA (dsRNA) viruses, and 4 negative single-stranded RNA (−ssRNA) viruses. In these viruses, five +ssRNA and four −ssRNA viruses were novel mycoviruses classified into diverse the families Botourmiaviridae, Deltaflexivirus, Mymonaviridea, and Discoviridae. We identified a novel −ssRNA mycovirus isolated from an A. tenuissima strain HB-15 as Alternaria tenuissima negative-stranded RNA virus 2 (AtNSRV2). Additionally, we characterized a novel +ssRNA mycovirus isolated from an A. tenuissima strain SC-8 as Alternaria tenuissima deltaflexivirus 1 (AtDFV1). According to phylogenetic and sequence analyses, we determined that AtNSRV2 was related to the viruses of the genus Sclerotimonavirus in the family Mymonaviridae. We also found that AtDFV1 was related to the virus family Deltaflexivirus. This study is the first to use total RNA sequencing to characterize viruses in Alternaria spp. These results expand the number of Alternaria viruses and demonstrate the diversity of these mycoviruses.

50

Bwalya, John, and Kook-Hyung Kim. "The Crucial Role of Chloroplast-Related Proteins in Viral Genome Replication and Host Defense against Positive-Sense Single-Stranded RNA Viruses." Plant Pathology Journal 39, no. 1 (February 1, 2023): 28–38. http://dx.doi.org/10.5423/ppj.rw.10.2022.0139.

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Plant viruses are responsible for worldwide production losses of numerous economically important crops. The most common plant RNA viruses are positivesense single-stranded RNA viruses [(+)ss RNA viruses]. These viruses have small genomes that encode a limited number of proteins. The viruses depend on their host’s machinery for the replication of their RNA genome, assembly, movement, and attraction to the vectors for dispersal. Recently researchers have reported that chloroplast proteins are crucial for replicating (+)ss plant RNA viruses. Some chloroplast proteins, including translation initiation factor [eIF(iso)4E] and 75 DEAD-box RNA helicase RH8, help viruses fulfill their infection cycle in plants. In contrast, other chloroplast proteins such as PAP2.1, PSaC, and ATPsyn-α play active roles in plant defense against viruses. This is also consistent with the idea that reactive oxygen species, salicylic acid, jasmonic acid, and abscisic acid are produced in chloroplast. However, knowledge of molecular mechanisms and functions underlying these chloroplast host factors during the virus infection is still scarce and remains largely unknown. Our review briefly summarizes the latest knowledge regarding the possible role of chloroplast in plant virus replication, emphasizing chloroplast-related proteins. We have highlighted current advances regarding chloroplast-related proteins’ role in replicating plant (+)ss RNA viruses.

Journal articles on the topic 'RNA viruses'

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