Статті в журналах: "RNA viruses Genetics"

1

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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2

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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3

Elena, Santiago F., Stéphanie Bedhomme, Purificación Carrasco, José M. Cuevas, Francisca de la Iglesia, Guillaume Lafforgue, Jasna Lalić, Àngels Pròsper, Nicolas Tromas, and Mark P. Zwart. "The Evolutionary Genetics of Emerging Plant RNA Viruses." Molecular Plant-Microbe Interactions® 24, no. 3 (March 2011): 287–93. http://dx.doi.org/10.1094/mpmi-09-10-0214.

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Over the years, agriculture across the world has been compromised by a succession of devastating epidemics caused by new viruses that spilled over from reservoir species or by new variants of classic viruses that acquired new virulence factors or changed their epidemiological patterns. Viral emergence is usually associated with ecological change or with agronomical practices bringing together reservoirs and crop species. The complete picture is, however, much more complex, and results from an evolutionary process in which the main players are ecological factors, viruses' genetic plasticity, and host factors required for virus replication, all mixed with a good measure of stochasticity. The present review puts emergence of plant RNA viruses into the framework of evolutionary genetics, stressing that viral emergence begins with a stochastic process that involves the transmission of a preexisting viral strain into a new host species, followed by adaptation to the new host.

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4

Aubry, Fabien, Antoine Nougairède, Lauriane de Fabritus, Gilles Querat, Ernest A. Gould, and Xavier de Lamballerie. "Single-stranded positive-sense RNA viruses generated in days using infectious subgenomic amplicons." Journal of General Virology 95, no. 11 (November 1, 2014): 2462–67. http://dx.doi.org/10.1099/vir.0.068023-0.

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Reverse genetics is a key methodology for producing genetically modified RNA viruses and deciphering cellular and viral biological properties, but methods based on the preparation of plasmid-based complete viral genomes are laborious and unpredictable. Here, both wild-type and genetically modified infectious RNA viruses were generated in days using the newly described ISA (infectious-subgenomic-amplicons) method. This new versatile and simple procedure may enhance our capacity to obtain infectious RNA viruses from PCR-amplified genetic material.

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5

Cuevas, Jose M., Pilar Domingo-Calap, Marianoel Pereira-Gomez, and Rafael Sanjuan. "Experimental Evolution and Population Genetics of RNA Viruses." Open Evolution Journal 3, no. 1 (May 11, 2009): 9–16. http://dx.doi.org/10.2174/1874404400903010009.

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6

Biacchesi, Stéphane. "The reverse genetics applied to fish RNA viruses." Veterinary Research 42, no. 1 (2011): 12. http://dx.doi.org/10.1186/1297-9716-42-12.

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7

Wickner, Reed B. "PRIONS AND RNA VIRUSES OFSACCHAROMYCES CEREVISIAE." Annual Review of Genetics 30, no. 1 (December 1996): 109–39. http://dx.doi.org/10.1146/annurev.genet.30.1.109.

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8

Froissart, Rémy, Claus O. Wilke, Rebecca Montville, Susanna K. Remold, Lin Chao, and Paul E. Turner. "Co-infection Weakens Selection Against Epistatic Mutations in RNA Viruses." Genetics 168, no. 1 (September 2004): 9–19. http://dx.doi.org/10.1534/genetics.104.030205.

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9

Turner, Paul E., та Lin Chao. "Sex and the Evolution of Intrahost Competition in RNA Virus φ6". Genetics 150, № 2 (1 жовтня 1998): 523–32. http://dx.doi.org/10.1093/genetics/150.2.523.

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Abstract Sex allows beneficial mutations that occur in separate lineages to be fixed in the same genome. For this reason, the Fisher-Muller model predicts that adaptation to the environment is more rapid in a large sexual population than in an equally large asexual population. Sexual reproduction occurs in populations of the RNA virus φ6 when multiple bacteriophages coinfect the same host cell. Here, we tested the model's predictions by determining whether sex favors more rapid adaptation of φ6 to a bacterial host, Pseudomonas phaseolicola. Replicate populations of φ6 were allowed to evolve in either the presence or absence of sex for 250 generations. All experimental populations showed a significant increase in fitness relative to the ancestor, but sex did not increase the rate of adaptation. Rather, we found that the sexual and asexual treatments also differ because intense intrahost competition between viruses occurs during coinfection. Results showed that the derived sexual viruses were selectively favored only when coinfection is common, indicating that within-host competition detracts from the ability of viruses to exploit the host. Thus, sex was not advantageous because the cost created by intrahost competition was too strong. Our findings indicate that high levels of coinfection exceed an optimum where sex may be beneficial to populations of φ6, and suggest that genetic conflicts can evolve in RNA viruses.

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10

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.

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11

Casais, Rosa, Volker Thiel, Stuart G. Siddell, David Cavanagh, and Paul Britton. "Reverse Genetics System for the Avian Coronavirus Infectious Bronchitis Virus." Journal of Virology 75, no. 24 (December 15, 2001): 12359–69. http://dx.doi.org/10.1128/jvi.75.24.12359-12369.2001.

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ABSTRACT Major advances in the study of the molecular biology of RNA viruses have resulted from the ability to generate and manipulate full-length genomic cDNAs of the viral genomes with the subsequent synthesis of infectious RNA for the generation of recombinant viruses. Coronaviruses have the largest RNA virus genomes and, together with genetic instability of some cDNA sequences in Escherichia coli, this has hampered the generation of a reverse-genetics system for this group of viruses. In this report, we describe the assembly of a full-length cDNA from the positive-sense genomic RNA of the avian coronavirus, infectious bronchitis virus (IBV), an important poultry pathogen. The IBV genomic cDNA was assembled immediately downstream of a T7 RNA polymerase promoter by in vitro ligation and cloned directly into the vaccinia virus genome. Infectious IBV RNA was generated in situ after the transfection of restricted recombinant vaccinia virus DNA into primary chick kidney cells previously infected with a recombinant fowlpox virus expressing T7 RNA polymerase. Recombinant IBV, containing two marker mutations, was recovered from the transfected cells. These results describe a reverse-genetics system for studying the molecular biology of IBV and establish a paradigm for generating genetically defined vaccines for IBV.

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12

Elena, Santiago F., Purificación Carrasco, José‐Antonio Daròs, and Rafael Sanjuán. "Mechanisms of genetic robustness in RNA viruses." EMBO reports 7, no. 2 (February 2006): 168–73. http://dx.doi.org/10.1038/sj.embor.7400636.

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13

Alejska, M., A. Kurzyńska-Kokorniak, M. Broda, R. Kierzek, and M. Figlerowicz. "How RNA viruses exchange their genetic material." Acta Biochimica Polonica 48, no. 2 (June 30, 2001): 391–407. http://dx.doi.org/10.18388/abp.2001_3924.

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One of the most unusual features of RNA viruses is their enormous genetic variability. Among the different processes contributing to the continuous generation of new viral variants RNA recombination is of special importance. This process has been observed for human, animal, plant and bacterial viruses. The collected data reveal a great susceptibility of RNA viruses to recombination. They also indicate that genetic RNA recombination (especially the nonhomologous one) is a major factor responsible for the emergence of new viral strains or species. Although the formation and accumulation of viral recombinants was observed in numerous RNA viruses, the molecular basis of this phenomenon was studied in only a few viral species. Among them, brome mosaic virus (BMV), a model (+)RNA virus offers the best opportunities to investigate various aspects of genetic RNA recombination in vivo. Unlike any other, the BMV-based system enables homologous and nonhomologous recombination studies at both the protein and RNA levels. As a consequence, BMV is the virus for which the structural requirements for genetic RNA recombination have been most precisely established. Nevertheless, the previously proposed model of genetic recombination in BMV still had one weakness: it could not really explain the role of RNA structure in nonhomologous recombination. Recent discoveries concerning the latter problem give us a chance to fill this gap. That is why in this review we present and thoroughly discuss all results concerning nonhomologous recombination in BMV that have been obtained until now.

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14

Domingo, Esteban, Carlos García-Crespo, Rebeca Lobo-Vega, and Celia Perales. "Mutation Rates, Mutation Frequencies, and Proofreading-Repair Activities in RNA Virus Genetics." Viruses 13, no. 9 (September 21, 2021): 1882. http://dx.doi.org/10.3390/v13091882.

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The error rate displayed during template copying to produce viral RNA progeny is a biologically relevant parameter of the replication complexes of viruses. It has consequences for virus–host interactions, and it represents the first step in the diversification of viruses in nature. Measurements during infections and with purified viral polymerases indicate that mutation rates for RNA viruses are in the range of 10−3 to 10−6 copying errors per nucleotide incorporated into the nascent RNA product. Although viruses are thought to exploit high error rates for adaptation to changing environments, some of them possess misincorporation correcting activities. One of them is a proofreading-repair 3′ to 5′ exonuclease present in coronaviruses that may decrease the error rate during replication. Here we review experimental evidence and models of information maintenance that explain why elevated mutation rates have been preserved during the evolution of RNA (and some DNA) viruses. The models also offer an interpretation of why error correction mechanisms have evolved to maintain the stability of genetic information carried out by large viral RNA genomes such as the coronaviruses.

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15

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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16

Cuevas, José M., Santiago F. Elena, and Andrés Moya. "Molecular Basis of Adaptive Convergence in Experimental Populations of RNA Viruses." Genetics 162, no. 2 (October 1, 2002): 533–42. http://dx.doi.org/10.1093/genetics/162.2.533.

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Abstract Characterizing the molecular basis of adaptation is one of the most important goals in modern evolutionary genetics. Here, we report a full-genome sequence analysis of 21 independent populations of vesicular stomatitis ribovirus evolved on the same cell type but under different demographic regimes. Each demographic regime differed in the effective viral population size. Evolutionary convergences are widespread both at synonymous and nonsynonymous replacements as well as in an intergenic region. We also found evidence for epistasis among sites of the same and different loci. We explain convergences as the consequence of four factors: (1) environmental homogeneity that supposes an identical challenge for each population, (2) structural constraints within the genome, (3) epistatic interactions among sites that create the observed pattern of covariation, and (4) the phenomenon of clonal interference among competing genotypes carrying different beneficial mutations. Using these convergences, we have been able to estimate the fitness contribution of the identified mutations and epistatic groups. Keeping in mind statistical uncertainties, these estimates suggest that along with several beneficial mutations of major effect, many other mutations got fixed as part of a group of epistatic mutations.

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17

Strauss, Ellen G., and James H. Strauss. "RNA viruses: genome structure and evolution." Current Opinion in Genetics & Development 1, no. 4 (December 1991): 485–93. http://dx.doi.org/10.1016/s0959-437x(05)80196-0.

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18

Félix, Marie-Anne, and David Wang. "Natural Viruses of Caenorhabditis Nematodes." Annual Review of Genetics 53, no. 1 (December 3, 2019): 313–26. http://dx.doi.org/10.1146/annurev-genet-112618-043756.

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Caenorhabditis elegans has long been a laboratory model organism with no known natural pathogens. In the past ten years, however, natural viruses have been isolated from wild-caught C. elegans (Orsay virus) and its relative Caenorhabditis briggsae (Santeuil virus, Le Blanc virus, and Melnik virus). All are RNA positive-sense viruses related to Nodaviridae; they infect intestinal cells and are horizontally transmitted. The Orsay virus capsid structure has been determined and the virus can be reconstituted by transgenesis of the host. Recent use of the Orsay virus has enabled researchers to identify evolutionarily conserved proviral and antiviral genes that function in nematodes and mammals. These pathways include endocytosis through SID-3 and WASP; a uridylyltransferase that destabilizes viral RNAs by uridylation of their 3′ end; ubiquitin protein modifications and turnover; and the RNA interference pathway, which recognizes and degrades viral RNA.

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19

Suzuki, Tatsuya, and Akatsuki Saito. "Advances in the reverse genetics system for RNA viruses." Folia Pharmacologica Japonica 157, no. 2 (2022): 134–38. http://dx.doi.org/10.1254/fpj.21072.

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20

Moya, Andrés, Edward C. Holmes, and Fernando González-Candelas. "The population genetics and evolutionary epidemiology of RNA viruses." Nature Reviews Microbiology 2, no. 4 (April 2004): 279–88. http://dx.doi.org/10.1038/nrmicro863.

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21

Moya, A., S. F. Elena, A. Bracho, R. Miralles, and E. Barrio. "The evolution of RNA viruses: A population genetics view." Proceedings of the National Academy of Sciences 97, no. 13 (June 20, 2000): 6967–73. http://dx.doi.org/10.1073/pnas.97.13.6967.

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22

Radecke, Frank, and Martin A. Billeter. "Reverse Genetics Meets the Nonsegmented Negative-Strand RNA Viruses." Reviews in Medical Virology 7, no. 1 (April 1997): 49–63. http://dx.doi.org/10.1002/(sici)1099-1654(199704)7:1<49::aid-rmv181>3.0.co;2-n.

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23

Dutta, Satyabrat, Ambika Arun, Richa Sarkar, Fulmali Devansh, Khushboo Panwar, Esha Sinha, Gorre Venu, and Arpita Sain. "APPLICATION OF REVERSE GENETICS IN RNA VIRUS VACCINE DEVELOPMENT: A BRIEF REVIEW." International Journal of Engineering Applied Sciences and Technology 7, no. 6 (October 1, 2022): 442–51. http://dx.doi.org/10.33564/ijeast.2022.v07i06.054.

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RNA viruses can quickly spread and cause serious, even fatal, illnesses in both humans and animals. Platforms for creating and refining viral mutants for vaccine development have been made available by the introduction of reverse genetics methods for manipulating and studying the genomes of RNA viruses. In this article, we review the effects of RNA virus reverse genetics systems on previous and ongoing initiatives to develop efficient and secure viral treatments and vaccines.

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24

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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25

Kojima, Shohei, Kohei Yoshikawa, Jumpei Ito, So Nakagawa, Nicholas F. Parrish, Masayuki Horie, Shuichi Kawano, and Keizo Tomonaga. "Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome." Proceedings of the National Academy of Sciences 118, no. 5 (January 25, 2021): e2010758118. http://dx.doi.org/10.1073/pnas.2010758118.

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Understanding the genetics and taxonomy of ancient viruses will give us great insights into not only the origin and evolution of viruses but also how viral infections played roles in our evolution. Endogenous viruses are remnants of ancient viral infections and are thought to retain the genetic characteristics of viruses from ancient times. In this study, we used machine learning of endogenous RNA virus sequence signatures to identify viruses in the human genome that have not been detected or are already extinct. Here, we show that the k-mer occurrence of ancient RNA viral sequences remains similar to that of extant RNA viral sequences and can be differentiated from that of other human genome sequences. Furthermore, using this characteristic, we screened RNA viral insertions in the human reference genome and found virus-like insertions with phylogenetic and evolutionary features indicative of an exogenous origin but lacking homology to previously identified sequences. Our analysis indicates that animal genomes still contain unknown virus-derived sequences and provides a glimpse into the diversity of the ancient virosphere.

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26

Gorbalenya, Alexander E., and Eugene V. Koonin. "Birnavirus RNA polymerase is related to polymerase of positive strand RNA viruses." Nucleic Acids Research 16, no. 15 (1988): 7735. http://dx.doi.org/10.1093/nar/16.15.7735.

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27

Mittelholzer, Christian, and Thomas Klimkait. "Advances in Molecular Genetics Enabling Studies of Highly Pathogenic RNA Viruses." Viruses 14, no. 12 (November 30, 2022): 2682. http://dx.doi.org/10.3390/v14122682.

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Experimental work with viruses that are highly pathogenic for humans and animals requires specialized Biosafety Level 3 or 4 facilities. Such pathogens include some spectacular but also rather seldomly studied examples such as Ebola virus (requiring BSL-4), more wide-spread and commonly studied viruses such as HIV, and the most recent example, SARS-CoV-2, which causes COVID-19. A common characteristic of these virus examples is that their genomes consist of single-stranded RNA, which requires the conversion of their genomes into a DNA copy for easy manipulation; this can be performed to study the viral life cycle in detail, develop novel therapies and vaccines, and monitor the disease course over time for chronic virus infections. We summarize the recent advances in such new genetic applications for RNA viruses in Switzerland over the last 25 years, from the early days of the HIV/AIDS epidemic to the most recent developments in research on the SARS-CoV-2 coronavirus. We highlight game-changing collaborative efforts between clinical and molecular disciplines in HIV research on the path to optimal clinical disease management. Moreover, we summarize how the modern technical evolution enabled the molecular studies of emerging RNA viruses, confirming that Switzerland is at the forefront of SARS-CoV-2 research and potentially other newly emerging viruses.

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28

Stram, Yehuda, and Larisa Kuzntzova. "Inhibition of Viruses by RNA Interference." Virus Genes 32, no. 3 (June 2006): 299–306. http://dx.doi.org/10.1007/s11262-005-6914-0.

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29

Huang, Henry V., Charles M. Rice, Cheng Xiong, and Sondra Schlesinger. "RNA viruses as gene expression vectors." Virus Genes 3, no. 1 (September 1989): 85–91. http://dx.doi.org/10.1007/bf00301989.

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30

Neumann, Gabriele, Michael A. Whitt, and Yoshihiro Kawaoka. "A decade after the generation of a negative-sense RNA virus from cloned cDNA – what have we learned?" Journal of General Virology 83, no. 11 (November 1, 2002): 2635–62. http://dx.doi.org/10.1099/0022-1317-83-11-2635.

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Since the first generation of a negative-sense RNA virus entirely from cloned cDNA in 1994, similar reverse genetics systems have been established for members of most genera of the Rhabdo- and Paramyxoviridae families, as well as for Ebola virus (Filoviridae). The generation of segmented negative-sense RNA viruses was technically more challenging and has lagged behind the recovery of nonsegmented viruses, primarily because of the difficulty of providing more than one genomic RNA segment. A member of the Bunyaviridae family (whose genome is composed of three RNA segments) was first generated from cloned cDNA in 1996, followed in 1999 by the production of influenza virus, which contains eight RNA segments. Thus, reverse genetics, or the de novo synthesis of negative-sense RNA viruses from cloned cDNA, has become a reliable laboratory method that can be used to study this large group of medically and economically important viruses. It provides a powerful tool for dissecting the virus life cycle, virus assembly, the role of viral proteins in pathogenicity and the interplay of viral proteins with components of the host cell immune response. Finally, reverse genetics has opened the way to develop live attenuated virus vaccines and vaccine vectors.

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31

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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32

Nagasaki, K., Y. Tomaru, Y. Shirai, Y. Takao, and H. Mizumoto. "Dinoflagellate-infecting viruses." Journal of the Marine Biological Association of the United Kingdom 86, no. 3 (April 10, 2006): 469–74. http://dx.doi.org/10.1017/s0025315406013361.

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Dinoflagellates (Dinophyceae) are considered to be one of the most abundant and diverse groups of phytoplankton; however, the viral impact on dinoflagellates was not studied until recently. This review shows the present information concerning the viruses infecting dinoflagellates and the ecology relationships between the host and the virus. So far, two viruses have been isolated and characterized: a large DNA virus (HcV: Heterocapsa circularisquama virus) and a small RNA virus (HcRNAV: H. circularisquama RNA virus); both of which are infectious to the harmful bloom-forming dinoflagellate H. circularisquama.In the present review, we mainly discuss the relationship between HcRNAV and H. circularisquama from the viewpoint of physiology, ecology and genetics. It will help clarify the viral impact on dinoflagellate populations in marine environments to understand the host/parasite ecology.

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33

Pekosz, A., B. He, and R. A. Lamb. "Reverse genetics of negative-strand RNA viruses: Closing the circle." Proceedings of the National Academy of Sciences 96, no. 16 (August 3, 1999): 8804–6. http://dx.doi.org/10.1073/pnas.96.16.8804.

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34

Walpita, Pramila, and Ramon Flick. "Reverse genetics of negative-stranded RNA viruses: A global perspective." FEMS Microbiology Letters 244, no. 1 (March 2005): 9–18. http://dx.doi.org/10.1016/j.femsle.2005.01.046.

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35

Shah, Het, and Andrews McEwan. "MECHANICAL PROPERTIES OF RNA NANOWIRES." International Journal of Advanced Research 9, no. 11 (November 30, 2021): 126–29. http://dx.doi.org/10.21474/ijar01/13721.

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RNA is a polymeric genetic bio-molecule found in all human beings. It is the main genetic material in many viruses. In this paper we test the mechanical properties of RNA NWs. We will find Youngs Modulus of RNA Nanowires (NWs) as a function of diameter with taking equilibrium strain, Poissons ratio and surface stress in consideration. As previously no study has been published regarding Youngs Modulus of RNA we take a theoretical approach towards it. We will predict the behavior of RNA NWs and see the resemblance to either semiconducting or metallic nature of NWs. This study extrapolates key factors in modelling RNA NWs for the creation of nanowires based aptasensors, genetics and other related applications.

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36

Stedman, Kenneth. "Mechanisms for RNA Capture by ssDNA Viruses: Grand Theft RNA." Journal of Molecular Evolution 76, no. 6 (June 2013): 359–64. http://dx.doi.org/10.1007/s00239-013-9569-9.

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37

Sanjuán, Rafael, José M. Cuevas, Victoria Furió, Edward C. Holmes, and Andrés Moya. "Selection for Robustness in Mutagenized RNA Viruses." PLoS Genetics 3, no. 6 (June 15, 2007): e93. http://dx.doi.org/10.1371/journal.pgen.0030093.

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38

Sanjuan, Rafael, Jose M. Cuevas, Victoria Furió, Edward C. Holmes, and Andres Moya. "Selection for Robustness in Mutagenized RNA Viruses." PLoS Genetics preprint, no. 2007 (2005): e93. http://dx.doi.org/10.1371/journal.pgen.0030093.eor.

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39

Wolf, Yuri I., Sukrit Silas, Yongjie Wang, Shuang Wu, Michael Bocek, Darius Kazlauskas, Mart Krupovic, Andrew Fire, Valerian V. Dolja, and Eugene V. Koonin. "Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome." Nature Microbiology 5, no. 10 (July 20, 2020): 1262–70. http://dx.doi.org/10.1038/s41564-020-0755-4.

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Abstract RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla.

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40

Flick, Ramon, Kirsten Flick, Heinz Feldmann, and Fredrik Elgh. "Reverse Genetics for Crimean-Congo Hemorrhagic Fever Virus." Journal of Virology 77, no. 10 (May 15, 2003): 5997–6006. http://dx.doi.org/10.1128/jvi.77.10.5997-6006.2003.

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ABSTRACT The widespread geographical distribution of Crimean-Congo hemorrhagic fever (CCHF) virus (more than 30 countries) and its ability to produce severe human disease with high mortality rates (up to 60%) make CCHF a major public health concern worldwide. We describe here the successful establishment of a reverse genetics technology for CCHF virus, a member of the genus Nairovirus, family Bunyaviridae. The RNA polymerase I (pol I) system was used to generate artificial viral RNA genome segments (minigenomes), which contained different reporter genes in antisense (virus RNA) or sense (virus-complementary RNA) orientation flanked by the noncoding regions of the CCHF virus S segment. Reporter gene expression was observed in different eukaryotic cell lines following transfection and subsequent superinfection with CCHF virus, confirming encapsidation, transcription, and replication of the pol I-derived minigenomes. The successful transfer of reporter gene activity to fresh cells demonstrated the generation of recombinant CCHF viruses, thereby confirming the packaging of the pol I-derived minigenomes into progeny viruses. The system offers a unique opportunity to study the biology of nairoviruses and to develop therapeutic and prophylactic measures against CCHF infections. In addition, we demonstrated for the first time that the human pol I system can be used to develop reverse genetics approaches for viruses in the family Bunyaviridae. This is important since it might facilitate the manipulation of bunyaviruses with cell and host tropisms restricted to primates.

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41

Chkuaseli, Tamari, and K. Andrew White. "Activation of viral transcription by stepwise largescale folding of an RNA virus genome." Nucleic Acids Research 48, no. 16 (August 12, 2020): 9285–300. http://dx.doi.org/10.1093/nar/gkaa675.

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Abstract The genomes of RNA viruses contain regulatory elements of varying complexity. Many plus-strand RNA viruses employ largescale intra-genomic RNA-RNA interactions as a means to control viral processes. Here, we describe an elaborate RNA structure formed by multiple distant regions in a tombusvirus genome that activates transcription of a viral subgenomic mRNA. The initial step in assembly of this intramolecular RNA complex involves the folding of a large viral RNA domain, which generates a discontinuous binding pocket. Next, a distally-located protracted stem-loop RNA structure docks, via base-pairing, into the binding site and acts as a linchpin that stabilizes the RNA complex and activates transcription. A multi-step RNA folding pathway is proposed in which rate-limiting steps contribute to a delay in transcription of the capsid protein-encoding viral subgenomic mRNA. This study provides an exceptional example of the complexity of genome-scale viral regulation and offers new insights into the assembly schemes utilized by large intra-genomic RNA structures.

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42

Strauss, Ellen G., and James H. Strauss. "RNA viruses: genome structure and evolution." Current Biology 2, no. 1 (January 1992): 33. http://dx.doi.org/10.1016/0960-9822(92)90425-a.

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43

Yamamoto, K., and H. Yoshikura. "Relation between genomic and capsid structures in RNA viruses." Nucleic Acids Research 14, no. 1 (1986): 389–96. http://dx.doi.org/10.1093/nar/14.1.389.

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44

Traina-Dorge, Vicki L., Jean K. Carr, Joan E. Bailey-Wilson, Robert C. Elston, Benjamin A. Taylor, and J. Craig Cohen. "CELLULAR GENES IN THE MOUSE REGULATE IN TRANS THE EXPRESSION OF ENDOGENOUS MOUSE MAMMARY TUMOR VIRUSES." Genetics 111, no. 3 (November 1, 1985): 597–615. http://dx.doi.org/10.1093/genetics/111.3.597.

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ABSTRACT The transcriptional activities of the eleven mouse mammary tumor virus (MMTV) proviruses endogenous to two sets of recombinant inbred (RI) mouse strains, BXD and BXH, were characterized. Comparison of the levels of virus-specific RNA quantitated in each strain showed no direct relationship between the presence of a particular endogenous provirus or with increasing numbers of proviruses. Association of specific genetic markers with the level of MMTV-specific RNA was examined by using multiple regression analysis. Several cellular loci as well as proviral loci were identified that were significantly associated with viral expression. Importantly, these cellular loci associated with MMTV expression segregated independently of viral sequences.

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45

Gao, Qinshan, Edward W. A. Brydon, and Peter Palese. "A Seven-Segmented Influenza A Virus Expressing the Influenza C Virus Glycoprotein HEF." Journal of Virology 82, no. 13 (April 30, 2008): 6419–26. http://dx.doi.org/10.1128/jvi.00514-08.

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ABSTRACT Influenza viruses are classified into three types: A, B, and C. The genomes of A- and B-type influenza viruses consist of eight RNA segments, whereas influenza C viruses only have seven RNAs. Both A and B influenza viruses contain two major surface glycoproteins: the hemagglutinin (HA) and the neuraminidase (NA). Influenza C viruses have only one major surface glycoprotein, HEF (hemagglutinin-esterase fusion). By using reverse genetics, we generated two seven-segmented chimeric influenza viruses. Each possesses six RNA segments from influenza virus A/Puerto Rico/8/34 (PB2, PB1, PA, NP, M, and NS); the seventh RNA segment encodes either the influenza virus C/Johannesburg/1/66 HEF full-length protein or a chimeric protein HEF-Ecto, which consists of the HEF ectodomain and the HA transmembrane and cytoplasmic regions. To facilitate packaging of the heterologous segment, both the HEF and HEF-Ecto coding regions are flanked by HA packaging sequences. When introduced as an eighth segment with the NA packaging sequences, both viruses are able to stably express a green fluorescent protein (GFP) gene, indicating a potential use for these viruses as vaccine vectors to carry foreign antigens. Finally, we show that incorporation of a GFP RNA segment enhances the growth of seven-segmented viruses, indicating that efficient influenza A viral RNA packaging requires the presence of eight RNA segments. These results support a selective mechanism of viral RNA recruitment to the budding site.

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46

Sanjuán, Rafael, and Katie Bradwell. "The Evolution and Emergence of RNA Viruses." Systematic Biology 59, no. 5 (August 19, 2010): 610–12. http://dx.doi.org/10.1093/sysbio/syq049.

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47

Zhang, Feifei, Margo Chase-Topping, Chuan-Guo Guo, Bram A. D. van Bunnik, Liam Brierley, and Mark E. J. Woolhouse. "Global discovery of human-infective RNA viruses: A modelling analysis." PLOS Pathogens 16, no. 11 (November 30, 2020): e1009079. http://dx.doi.org/10.1371/journal.ppat.1009079.

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RNA viruses are a leading cause of human infectious diseases and the prediction of where new RNA viruses are likely to be discovered is a significant public health concern. Here, we geocoded the first peer-reviewed reports of 223 human RNA viruses. Using a boosted regression tree model, we matched these virus data with 33 explanatory factors related to natural virus distribution and research effort to predict the probability of virus discovery across the globe in 2010–2019. Stratified analyses by virus transmissibility and transmission mode were also performed. The historical discovery of human RNA viruses has been concentrated in eastern North America, Europe, central Africa, eastern Australia, and north-eastern South America. The virus discovery can be predicted by a combination of socio-economic, land use, climate, and biodiversity variables. Remarkably, vector-borne viruses and strictly zoonotic viruses are more associated with climate and biodiversity whereas non-vector-borne viruses and human transmissible viruses are more associated with GDP and urbanization. The areas with the highest predicted probability for 2010–2019 include three new regions including East and Southeast Asia, India, and Central America, which likely reflect both increasing surveillance and diversity of their virome. Our findings can inform priority regions for investment in surveillance systems for new human RNA viruses.

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48

COENEN, ALEX, FERENC KEVEI, and ROLF F. HOEKSTRA. "Factors affecting the spread of double-stranded RNA viruses in Aspergillus nidulans." Genetical Research 69, no. 1 (February 1997): 1–10. http://dx.doi.org/10.1017/s001667239600256x.

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Viruses are common in asexual Aspergilli but not in sexual Aspergilli. We found no viruses in 112 isolates of the sexual Aspergillus nidulans. We have investigated factors that could play a role in preventing the spread of mycoviruses through populations of A. nidulans. Experiments were performed with A. nidulans strains infected with viruses originating from A. niger. Horizontal virus transmission was restricted but not prevented by somatic incompatibility. Viruses were transmitted vertically via conidiospores but not via ascospores. Competition experiments revealed no effect of virus infection on host fitness. Outcrossing was found to limit the spread of viruses significantly more than selfing. It is concluded that the exclusion of viruses from sexual Aspergilli could be due to the formation of new somatic incompatibility groups by sexual recombination.

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49

Lundstrom, Kenneth. "RNA Viruses as Tools in Gene Therapy and Vaccine Development." Genes 10, no. 3 (March 1, 2019): 189. http://dx.doi.org/10.3390/genes10030189.

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RNA viruses have been subjected to substantial engineering efforts to support gene therapy applications and vaccine development. Typically, retroviruses, lentiviruses, alphaviruses, flaviviruses rhabdoviruses, measles viruses, Newcastle disease viruses, and picornaviruses have been employed as expression vectors for treatment of various diseases including different types of cancers, hemophilia, and infectious diseases. Moreover, vaccination with viral vectors has evaluated immunogenicity against infectious agents and protection against challenges with pathogenic organisms. Several preclinical studies in animal models have confirmed both immune responses and protection against lethal challenges. Similarly, administration of RNA viral vectors in animals implanted with tumor xenografts resulted in tumor regression and prolonged survival, and in some cases complete tumor clearance. Based on preclinical results, clinical trials have been conducted to establish the safety of RNA virus delivery. Moreover, stem cell-based lentiviral therapy provided life-long production of factor VIII potentially generating a cure for hemophilia A. Several clinical trials on cancer patients have generated anti-tumor activity, prolonged survival, and even progression-free survival.

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50

Conzelmann, Karl-Klaus. "NONSEGMENTED NEGATIVE-STRAND RNA VIRUSES: Genetics and Manipulation of Viral Genomes." Annual Review of Genetics 32, no. 1 (December 1998): 123–62. http://dx.doi.org/10.1146/annurev.genet.32.1.123.

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