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Relevant bibliographies by topics / RNA viruses

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Academic literature on the topic 'RNA viruses'

Author: Grafiati

Published: 4 June 2021

Last updated: 31 July 2024

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Journal articles on the topic "RNA viruses"

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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.

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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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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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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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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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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.

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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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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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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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Dissertations / Theses on the topic "RNA viruses"

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Chare, Elizabeth R. "Recombination in RNA viruses and plant virus evolution." Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.433381.

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Olabode, Abayomi. "The evolution of RNA viruses." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/the-evolution-of-rna-viruses(ac87e71c-e9ce-44c6-8dc1-6adbb01e5efb).html.

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This thesis analyzes the evolutionary trajectories that drive the evolution of several RNA viruses. These viruses have been identified to be the leading causes of viral outbreaks and deaths in humans. Studying the mechanisms influencing their evolution could therefore produce vital information for controlling the spread of these viruses or for their eradication. The availability of huge sequence repositories and advancement in computing and sequencing technologies allows for the development of novel methods for understanding the evolution of viruses even during an on-going outbreak, epidemic or pandemic. In this study, I developed a method that incorporates phylogenetic and structural based techniques to study the evolution of drug resistance in (A) HIV-1 Pol proteins, (B) the evolutionary dynamics of the 2013 - 2016 EBOV outbreak and (C) the evolution of the A(H1N1) influenza virus amongst human, avian and swine species. Findings from this thesis show that though HIV-1 evolves differently in the presence and absence of drug selection pressure, the virus is generally constrained by the need to maintain viral protein structure stability. The virus achieves this by accumulating enabling mutations early in its evolutionary history in order to accommodate the emergence of drug resistance associated mutations, which are mostly destabilizing. I also show that although the 2013 - 2016 EBOV was evolving rapidly, early data indicated that it was not changing at the functional level and not adapting to the human host. This is because most of the mutations occur in either inter genic or intrinsically disordered regions, which are less constrained, while the structured bits are characterized by neutral impact mutations. This again suggests that the virus needs to maintain a stable protein structure in order to remain functional. I show that EBOV is relatively stably evolving and the major force driving its evolution is more of an epidemiologic rather than a molecular factor whereas HIV-1 is evolving adaptively and its evolution is driven by molecular processes. However, one residue change, A82V seems to have altered the ability of the virus to bind its human receptor. This suggests that adaptive or functional mutations (which are mostly destabilizing in nature) work hand in hand with enabling mutations in such a way that a virus can acquire a mutation that confers drug resistance or leads to a gain of function without compromising its fitness while also retaining its functions such as infectivity and transmissibility. This indicates that the mechanisms described above may be a general way through which viruses evolve. The methods developed in the study can easily be applied to studying the evolution of other viruses and other systems e.g. microorganisms and cancer cells. Even if selection analysis does not show positive selection or any mutations in functional site, my thesis has demonstrated that structural analysis will be very useful for identifying and also predicting mutations that could facilitate adaptation of viruses. Also the influenza study shows that though the A(H1N1) is evolving somewhat differently in the humans, avian and swine species, one thing they seem to have in common is that stability constrains their evolution. I also show that my findings based on the human A(H1N1) influenza virus is consistent with the other human viruses (HIV and EBOV) analyzed in this project work.

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Choudhury, Md Abu Hasnat Zamil. "Population Dynamics of RNA viruses." Thesis, Queensland University of Technology, 2013. https://eprints.qut.edu.au/60866/1/Md._Choudhury_Thesis.pdf.

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Between 50 and 100 million people are infected with dengue viruses each year and more than 100,000 of these die. Dr Choudhury has demonstrated that populations of dengue viruses in individual patients are genetically and functionally very diverse and that this diversity changes significantly at the time of major outbreaks of disease. The results of his studies may inform strategies which will make dengue vaccines far more effective.

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Bakker, Saskia. "RNA packaging and uncoating in simple single-stranded RNA viruses." Thesis, University of Leeds, 2012. http://etheses.whiterose.ac.uk/2801/.

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Simple (non-enveloped) small, positive-sense single-stranded RNA viruses infect hosts from all kingdoms of life. However, their assembly and uncoating processes remain poorly understood. For turnip crinkle virus (TCV), 3D reconstructions by cryoelectron microscopy (cryo-EM) are shown for the native and the expanded form. The expanded form is a putative disassembly intermediate and exhibits pores that are large enough to allow exit of single-stranded RNA. Biochemical experiments revealed the expanded form is protease-sensitive, although the RNA genome remains protected from ribonuclease. Virus particles complexed with ribosomes are shown by negative stain EM. Proteolysis causes release of some coat protein from the capsid, while the capsid remains largely intact. Proteolysed particles have lost their icosahedral symmetry and show a protuberance in negative stain EM. Taken together, these results suggest expansion and subsequent proteolysis are essential steps in the uncoating process of TCV, and that the capsid plays multiple roles consistent with ribosome-mediated genome uncoating to avoid host anti-viral activity. Similarly, 3D cryo-EM reconstructions are presented for native equine rhinitis A virus (ERAV) an expanded particle containing no RNA. The native virus fits well with the ERAV crystal structure. The empty particle is a putative disassembly intermediate representing a stage after the release of the RNA genome. A mechanism is suggested that is consistent with the RNA release from the endosome without exposure to the endosomal contents. A crystal structure is presented of satellite tobacco necrosis virus (STNV) virus-like particles containing a small RNA fragment. The coat protein structure is identical to that of native STNV. Although density internal to the coat protein shell has been observed in the experiment that corresponds to earlier experiments, no unambiguous RNA structure can be built into the density. Together, the results presented here shed some light on the life cycle of three of these viruses.

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Wain, Louise V. "Origins of diversity of RNA viruses." Thesis, University of Nottingham, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.440123.

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Willcocks, Margaret Mary. "Small RNA viruses associated with diarrhoea." Thesis, University of Newcastle Upon Tyne, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.287271.

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Boz, Mustafa Burak. "Modeling and simulations of single stranded rna viruses." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/44815.

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The presented work is the application of recent methodologies on modeling and simulation of single stranded RNA viruses. We first present the methods of modeling RNA molecules using the coarse-grained modeling package, YUP. Coarse-grained models simplify complex structures such as viruses and let us study general behavior of the complex biological systems that otherwise cannot be studied with all-atom details. Second, we modeled the first all-atom T=3, icosahedral, single stranded RNA virus, Pariacoto virus (PaV). The x-ray structure of PaV shows only 35% of the total RNA genome and 88% of the capsid. We modeled both missing portions of RNA and protein. The final model of the PaV demonstrated that the positively charged protein N- terminus was located deep inside the RNA. We propose that the positively charged N- terminal tails make contact with the RNA genome and neutralize the negative charges in RNA and subsequently collapse the RNA/protein complex into an icosahedral virus. Third, we simulated T=1 empty capsids using a coarse-grained model of three capsid proteins as a wedge-shaped triangular capsid unit. We varied the edge angle and the potentials of the capsid units to perform empty capsid assembly simulations. The final model and the potential are further improved for the whole virus assembly simulations. Finally, we performed stability and assembly simulations of the whole virus using coarse-grained models. We tested various strengths of RNA-protein tail and capsid protein-capsid protein attractions in our stability simulations and narrowed our search for optimal potentials for assembly. The assembly simulations were carried out with two different protocols: co-transcriptional and post-transcriptional. The co-transcriptional assembly protocol mimics the assembly occurring during the replication of the new RNA. Proteins bind the partly transcribed RNA in this protocol. The post-transcriptional assembly protocol assumes that the RNA is completely transcribed in the absence of proteins. Proteins later bind to the fully transcribed RNA. We found that both protocols can assemble viruses, when the RNA structure is compact enough to yield a successful virus particle. The post-transcriptional protocol depends more on the compactness of the RNA structure compared to the co-transcriptional assembly protocol. Viruses can exploit both assembly protocols based on the location of RNA replication and the compactness of the final structure of the RNA.

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Li, Tin-wai Olive. "Influenza polymerase subunit compatibility between human H1 and H5 viruses." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B41896890.

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Keese, Paul Konrad. "Structures of viroids and virusoids and their functional significance." Title page, contents and summary only, 1986. http://web4.library.adelaide.edu.au/theses/09PH/09phk268.pdf.

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Afsharifar, Alireza. "Characterisation of minor RNAs associated with plants infected with cucumber mosaic virus." Title page, table of contents and abstract only, 1997. http://web4.library.adelaide.edu.au/theses/09PH/09pha2584.pdf.

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Bibliography: leaves 127-138. This thesis studies the minor double stranded RNAs (dsRNA) and single stranded RNAs (ssRNA) which are consistently associated with plants infected with Q strain of cucumber mosaic virus (Q-CMV). The investigations are focused on the structural elucidation of new RNAs which have been observed in single stranded and double stranded RNA profiles of Q strain of CMV.

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Books on the topic "RNA viruses"

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A, Brinton Margo, Calisher Charles H, Rueckert Roland R, and International Symposium on Positive Strand RNA Viruses (3rd : 1992 : Clearwater, Fla.), eds. Positive-strand RNA viruses. Wien: Springer-Verlag, 1994.

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Luo, Ming. Negative strand RNA virus. Singapore: World Scientific, 2011.

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A, Brinton Margo, and Heinz Franz X, eds. New aspects of positive-strand RNA viruses. Washington, D.C: American Society for Microbiology, 1990.

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Brinton, Margo A., Charles H. Calisher, and Roland Rueckert, eds. Positive-Strand RNA Viruses. Vienna: Springer Vienna, 1994. http://dx.doi.org/10.1007/978-3-7091-9326-6.

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F, Murant A., and Harrison B. D, eds. The plant viruses. New York: Plenum Press, 1996.

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D, Harrison B., and Murant A. F, eds. Poly hedral virions and bipartite RNA genomes. New York: Plenum Press, 1996.

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Luo, Ming. Negative strand RNA virus. Singapore: World Scientific, 2011.

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Holmes, Edward C. The evolution and emergence of RNA viruses. Oxford: Oxford University Press, 2009.

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Holland, John J., ed. Genetic Diversity of RNA Viruses. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-77011-1.

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Perez, Daniel R., ed. Reverse Genetics of RNA Viruses. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6964-7.

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Book chapters on the topic "RNA viruses"

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Fusaki, Noemi. "Nonintegrating RNA Viruses." In Primary and Stem Cells, 103–18. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118147177.ch6.

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Hodinka, Richard L. "Respiratory RNA Viruses." In Diagnostic Microbiology of the Immunocompromised Host, 233–71. Washington, DC: ASM Press, 2016. http://dx.doi.org/10.1128/9781555819040.ch11.

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Ball, Jonathan. "Analysis of RNA virus quasispecies." In RNA Viruses, 105–40. Oxford University PressOxford, 2000. http://dx.doi.org/10.1093/oso/9780199637171.003.0006.

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Abstract A virus quasispecies can be thought of as a complex population of genetically related yet distinct variants (1). The term has been used to describe populations of a number of RNA viruses, e.g. human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV). Although this definition of a quasispecies appears simple in theory, in practice it can be rather ambiguous (2). For example, the term has been applied to describe unrelated viruses present in different individuals, unrelated viruses arising from multiple infections within the same individual, and to genetically related but distinct variants co-circulating within the same individual and arising from a single infection. It is probably less confusing to use the term to describe the virus population co-existing within a single individual.

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Bridgen, A., and R. M. Elliott. "Reverse genetics of RNA viruses." In RNA Viruses, 201–28. Oxford University PressOxford, 2000. http://dx.doi.org/10.1093/oso/9780199637171.003.0009.

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Abstract RNA viruses comprise many of the most serious human pathogens. There are now possibly 500 million carriers of hepatitis C virus world-wide (1). Rotavirus infections are responsible for around 18 million cases of severe diarrhoea and nearly 1 million deaths in young children in developing countries annually (2). Measles is still also one of the leading causes of infant death in developing countries, and can induce the rare, but fatal, neurodegenerative disease subacute sclerosing panencephalitis (3). Many human respiratoiy infections are caused by RNA viruses such as influenza, human respiratoiy syncytial virus, coronaviruses, enteroviruses and, one of the most frequent virus pathogens of humans, the rhinoviruses (4). Hantaviruses, members of the Bunyaviridae family, are responsible for haemorrhagic diseases and form one of a number of virus groups whose incidence has increased greatly over the last few years, the so-called ‘emerging viruses’ (5). Perhaps the most frightening of all virus diseases, because of their high mortality and lack of effective prophylaxis and treatment, are those caused by the filoviruses Marburg and Ebola (6).

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Makino, S. "Analysis of transcriptional control in RNA virus infection." In RNA Viruses, 43–68. Oxford University PressOxford, 2000. http://dx.doi.org/10.1093/oso/9780199637171.003.0003.

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Abstract This chapter will illustrate several commonly used methods for the analysis of mRNAs and their transcriptional control by RNA viruses. I will first describe the conventional methods for characterizing mRNAs in virus-infected cells. Subsequently, methods utilizing genetically engineered virus RNA or cDNA with or without reporter genes will be described. These methods enable the analysis of cis- and trans-acting RNA sequences to be determined.

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Montano, Monty, and Paola Sebastiani. "Efforts to Characterize Host Response to HIV-1 Infection." In RNA Viruses, 3–29. WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789812833808_0001.

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Gee, Katrina, Sasmita Mishra, Wei Ma, Marko Kryworuchko, and Ashok Kumar. "Signaling Pathways Activated by HIV and Their Impact on Immune Responses." In RNA Viruses, 31–58. WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789812833808_0002.

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Allison, Robert D., and Shyam Kottilil. "Host Immune Responses in HIV Infection." In RNA Viruses, 59–82. WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789812833808_0003.

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Klase, Zachary A., Kuan-Teh Jeang, and Fatah Kashanchi. "HIV-1 and RNA Interference — Examining a Complex System." In RNA Viruses, 83–105. WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789812833808_0004.

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Pleschka, Stephan, Stephan Ludwig, Oliver Planz, and Thorsten Wolff. "Signaling Pathways Induced by Influenza Viruses." In RNA Viruses, 109–29. WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789812833808_0005.

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Conference papers on the topic "RNA viruses"

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Belov, George. "COUPLING POLIOVIRUS RNA REPLICATION TO CELLULAR MEMBRANES." In Viruses: Discovering Big in Small. TORUS PRESS, 2019. http://dx.doi.org/10.30826/viruses-2019-12.

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Aleshina, Yu A., A. V. Orlov, and A. N. Lukashev. "RECOMBINATION AND MODULAR EVOLUTION OF POSITIVE-STRAND RNA VIRUSES." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-227.

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Recombination is one of the major forces generating genetic diversity in positive-strand RNA viruses. We systematically analyzed patterns of natural recombination in four (+)RNA virus families — Astroviridae, Caliciviridae, Picornaviridae and Coronaviridae, using both classical recombination detection methods and by comparing correspondence of genetic distances in different genome regions.

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Evseev, Peter, Sergey Potapov, Galina Podlesnaya, Andrei Krasnopeev, Anna Gorshkova, and Olga Belykh. "Horizontal Gene Transfer Involving RNA Viruses and DNA Viruses." In 2022 Ural-Siberian Conference on Computational Technologies in Cognitive Science, Genomics and Biomedicine (CSGB). IEEE, 2022. http://dx.doi.org/10.1109/csgb56354.2022.9865651.

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Alipanah, Morteza, Carlos Manzanas, John A. Lednicky, Chang-Yu Wu, and Z. Hugh Fan. "Integration of Minivalves With RNA Amplification Device for Simultaneous Detection of SARS-CoV-2 and Influenza Viruses." In ASME 2022 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2022. http://dx.doi.org/10.1115/imece2022-96831.

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Abstract We report a point-of-care (POC) device for simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A viruses. The device carries out sample preparation using ball-based valves for sequential delivery of reagents. A microfluidic paper-based analytical device (μPAD) in the detection unit enables RNA isolation and enrichment, followed by reverse transcription loop-mediated isothermal amplification (RT-LAMP) and colorimetric detection. The device integrates all the necessary steps for the sample preparation, including virus lysis, RNA enrichment and purification of two virus samples. The device enabled simultaneous detection of SARS-CoV-2 and Influenza A N1H1 viruses in 50 min., with limit of detection of 2 and 6 genome equivalents (GEs), respectively. The device was also capable of detecting environmental sample of the two viruses.

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Alipanah, Morteza, John A. Lednicky, J. Glenn Morris, and Z. Hugh Fan. "A Point-Of-Care Device Integrating Sample Preparation With Isothermal Amplification for Detection of Mayaro Virus." In ASME 2023 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2023. http://dx.doi.org/10.1115/imece2023-114292.

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Abstract Mayaro virus (MAYV) is an emerging mosquito-borne alphavirus that causes clinical symptoms similar to those caused by Chikungunya virus (CHIKV), Dengue virus (DENV), and Zika virus (ZIKV). To differentiate MAYV from these viruses diagnostically, we have developed the first reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of MAYV. We designed six LAMP primers targeting MAYV’s non-structural protein (NS1) gene and determined the visual limit of detection of at least 10 viral genome equivalents (GEs) per reaction. The assay was specific for MAYV, without cross-reactions with CHIKV, DENV, or ZIKV. A 30 min. RT-LAMP assay was integrated with valve-enabled sample preparation device wherein virus lysis and RNA enrichment/purification were carried out on the spot, without requiring pipetting. Colorimetric detection was achieved by naked eye or a smartphone. The functions of our platform were demonstrated using purified RNA and cultured viruses for their potential usage. We have used the device for detection of cultured MAYV in 50 min.

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Sivov, I. G., and I. S. Firsov. "FLECK QUANTIFICATION OF THE NUMBER OF INFECTIOUS SARS-COV-2 CORONAVIRUS PARTICLES." In Molecular Diagnostics and Biosafety. Federal Budget Institute of Science 'Central Research Institute for Epidemiology', 2020. http://dx.doi.org/10.36233/978-5-9900432-9-9-173.

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The principle of obtaining sensors for detecting infectious particles of RNA viruses in samples was proposed for the diagnosis of infectious particles SARS-CoV-2. Previously, the similar sensor pattern was successfully applied in relation to the hepatitis C virus. It was founded that the ratio of the RNA titer, determined in the RT-PCR reaction in Real Time mode, refers to the number of infectious («shine») centers formed on the cell sensor culture, approximately as 100: 1, in the «coronavirus-positive» sample.

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Benslimane, Fatiha M., Hebah Al Khatib, Dana Albatesh, Ola Al-Jamal, Sonia Boughattas, Asmaa A. Althani, and Hadi M. Yassine. "Nanopore Sequencing SARS-CoV-2 Genome in Qatar." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0289.

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Background: The current pandemic, COVID-19, is cause by an RNA Coronavirus that was recently identified as SARS-CoV-2. RNA viruses tend to have a high mutation rate; the rate is around a million times greater than that of their hosts. The mutagenic potential of the virus depends on many factors, including the fidelity of nucleic acid-replicating viral enzymes, such as SARSCoV-2 RNA dependent RNA polymerase (RdRp). The rate of mutation drives viral evolution and genome variability, consequently allowing viruses to escape the immunity of the host and develop resistance to drugs. Therefore, the characterization of SARS-CoV-2 variants might lead to implement better therapeutics treatments, vaccines design and identify new diagnostics approaches. Aim: The aim of this study was to establish a fast sequencing method to identify SARS-CoV-2 mutations in Qatar. This will help to assess if there are new viral variants that are spreading in country. Methods: RNA was isolated from samples collected from Qatar COVID-19 positive patients. The Artic Network V3 primer scheme and Oxford Nanopore ligation sequencing kit were used to prepare the sequencing libraries. Libraries were loaded on to R9.4.1 flow cells and ran on a GridION. Bioinformatics analysis was done following the Artic Network SARA-CoV-2 bioinformatics tools. Results: Genome coverage of sequenced samples was >80% and the depth was average at 200x. The coverage was highly dependable on sample viral load; samples of CT value lower than 30 resulted in better sequence coverage. The sequenced genomes were deposited in GISAID and were mainly clustering with genomes deposited from the UK. Sequences were compared to Illumina and sanger sequences and they showed compatible results. Conclusion: The use of ONT to sequence SARA-CoV-2 is a quick, affordable, and reliable technique to determine viral mutation. Using this technique, the first sequences from Qatar were deposited in to GISAID. Up to date, 700 genomes have been sequenced from Qatari samples.

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Okhezin, E. V., A. G. Litov, and G. G. Karganova. "RESISTANCE OF VIRAL RNA STRUCTURES OF FLAVI-LIKE VIRUSES WITH SEGMENTED GENOME TO XRN1 EXONUCLEASE." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-258.

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Subgenomic orthoflaviviral RNA is a product of incomplete degradation of genomic orthoflavivirus RNA by 5’-3’ cell exoribonuclease XRN1. Resistance to complete hydrolysis is determined by conserved secondary structure motifs localized at the 3’ end of the genomic RNA. In this research, we study the exonuclease resistance of genomic RNA segments Alonghan virus in an in vitro assay

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Al Khatib, Heba, Muna Al Maslamani, Peter Coyle, Sameer Pathan, Asmaa Al Thani, and Hadi Mohamad Yassine. "Molecular Characterization of Influenza Virus in Intestines and its Effect on Intestinal Microbiota." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0165.

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Background: Influenza predominantly causes respiratory diseases; however, gastrointestinal symptoms are not uncommonly reported, particularly among high-risk groups. Influenza virus RNA has been also detected in stools of patients infected with pandemic and seasonal influenza, however, the role and the clinical significance of intestinal infection has not been clearly demonstrated. Methods: Here, we used NGS technology to investigate molecular characterization of viral RNA shedding in feces of adults with active influenza infection. Paired nasal and fecal samples were collected from 295 patients showing to emergency department at Hamad Medical Corporation with flu-like symptoms during January 2018 and April 2019. Results: Among these, 90 nasal samples were positive for influenza, of which, 26 fecal samples were positive for influenza in real-time PCR and only five showed virus growth in both monolayer and 3D cell culture. Full genome sequencing of isolated viruses revealed some unique mutations that we are currently in the process of studying their effect on virus kinetics. Then, we investigated the potential impact of respiratory influenza infection on intestinal microbiota diversity and composition. Microbiome analysis results suggest that changes in gut microbiota composition in influenza-infected patients are significantly associated with (1) influenza virus type, and (2) the presence of viral RNA in intestines of infected patients. We also identified bacterial taxa for which relative abundance was significantly higher in the patients with severe respiratory symptoms. Conclusion: Altogether, our findings suggest that influenza viruses can affect intestinal environment either by direct intestinal infection or indirectly by modulating intestinal microbiota.

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Korneenko, E. V., А. E. Samoilov, I. V. Artyushin, M. V. Safonova, V. G. Dedkov, K. F. Khafizov, A. A. Deviatkin, V. V. Kaptelova, E. V. Pimkina, and A. S. Speranskaya. "DETECTION OF ALFACORONAVIRUSES, BETACORONAVIRUSES AND ASTROVIRUSES IN BAT FECAL SAMPLES FROM MOSCOW REGION." In Molecular Diagnostics and Biosafety. Federal Budget Institute of Science 'Central Research Institute for Epidemiology', 2020. http://dx.doi.org/10.36233/978-5-9900432-9-9-42.

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In our study we analyzed viral RNA in bat fecal samples from Moscow region (Zvenigorod district) collected in 2015. To detect various virus families and genera in bat fecal samples we used PCR amplification of viral genome fragments, followed by high-throughput sequencing. Blastn search of unassembled reads revealed the presence of viruses from families Astroviridae, Coronaviridae and Herpesviridae. Assembly using SPAdes 3.14 yields contigs of length 460–530 b.p. which correspond to genome fragments of Coronaviridae and Astroviridae. The taxonomy of coronaviruses has been determined to the genus level. We also showed that one bat can be a reservoir of several virus genuses. Thus, the bats in the Moscow region were confirmed as reservoir hosts for potentially zoonotic viruses.

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Reports on the topic "RNA viruses"

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Davison, Michelle, Ruonan Wu, Vincent Danna, and Iobani Godinez. Uncovering novel RNA viruses in permafrost. Office of Scientific and Technical Information (OSTI), October 2020. http://dx.doi.org/10.2172/1776877.

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Morris, T. J., and A. O. Jackson. Characterization of defective interfering RNAs associated with RNA plant viruses. Office of Scientific and Technical Information (OSTI), January 1993. http://dx.doi.org/10.2172/6880107.

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Gal-On, Amit, Shou-Wei Ding, Victor P. Gaba, and Harry S. Paris. role of RNA-dependent RNA polymerase 1 in plant virus defense. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597919.bard.

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Objectives: Our BARD proposal on the impact of RNA-dependent RNA polymerase 1 (RDR1) in plant defense against viruses was divided into four original objectives. 1. To examine whether a high level of dsRNA expression can stimulate RDR1 transcription independent of salicylic acid (SA) concentration. 2. To determine whether the high or low level of RDR1 transcript accumulation observed in virus resistant and susceptible cultivars is associated with viral resistance and susceptibility. 3. To define the biogenesis and function of RDR1-dependent endogenous siRNAs. 4. To understand why Cucumber mosaic virus (CMV) can overcome RDR1-dependent resistance. The objectives were slightly changed due to the unique finding that cucumber has four different RDR1 genes. Background to the topic: RDR1 is a key plant defense against viruses. RDR1 is induced by virus infection and produces viral and plant dsRNAs which are processed by DICERs to siRNAs. siRNAs guide specific viral and plant RNA cleavage or serve as primers for secondary amplification of viral-dsRNA by RDR. The proposal is based on our preliminary results that a. the association of siRNA and RDR1 accumulation with multiple virus resistance, and b. that virus infection induced the RDR1-dependent production of a new class of endogenous siRNAs. However, the precise mechanisms underlying RDR1 induction and siRNA biogenesis due to virus infection remain to be discovered in plants. Major conclusions, solutions and achievements: We found that in the cucurbit family (cucumber, melon, squash, watermelon) there are 3-4 RDR1 genes not documented in other plant families. This important finding required a change in the emphasis of our objectives. We characterized 4 RDR1s in cucumber and 3 in melon. We demonstrated that in cucumber RDR1b is apparently a new broad spectrum virus resistance gene, independent of SA. In melon RDR1b is truncated, and therefore is assumed to be the reason that melon is highly susceptible to many viruses. RDR1c is dramatically induced due to DNA and RNA virus infection, and inhibition of RDR1c expression led to increased virus accumulation which suggested its important on gene silencing/defense mechanism. We show that induction of antiviral RNAi in Arabidopsis is associated with production of a genetically distinct class of virus-activated siRNAs (vasiRNAs) by RNA dependent RNA polymerase-1 targeting hundreds of host genes for RNA silencing by Argonaute-2. Production of vasiRNAs is induced by viruses from two different super groups of RNA virus families, targeted for inhibition by CMV, and correlated with virus resistance independently of viral siRNAs. We propose that antiviral RNAi activate broad-spectrum antiviral activity via widespread silencing of host genes directed by vasiRNAs, in addition to specific antiviral defense Implications both scientific and agricultural: The RDR1b (resistance) gene can now be used as a transcription marker for broad virus resistance. The discovery of vasiRNAs expands the repertoire of siRNAs and suggests that the siRNA-processing activity of Dicer proteins may play a more important role in the regulation of plant and animal gene expression than is currently known. We assume that precise screening of the vasiRNA host targets will lead in the near future for identification of plant genes associate with virus diseases and perhaps other pathogens.

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Morris, T. J., and A. O. Jackson. Characterization of defective interfering RNAs associated with RNA plant viruses. Progress report. Office of Scientific and Technical Information (OSTI), April 1993. http://dx.doi.org/10.2172/10139870.

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Mawassi, Munir, and Valerian Dolja. Role of RNA Silencing Suppression in the Pathogenicity and Host Specificity of the Grapevine Virus A. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592114.bard.

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RNA silencing is a defense mechanism that functions against virus infection and involves sequence-specific degradation of viral RNA. Diverse RNA and DNA viruses of plants encode RNA silencing suppressors (RSSs), which, in addition to their role in viral counterdefense, were implicated in the efficient accumulation of viral RNAs, virus transport, pathogenesis, and determination of the virus host range. Despite rapidly growing understanding of the mechanisms of RNA silencing suppression, systematic analysis of the roles played by diverse RSSs in virus biology and pathology is yet to be completed. Our research was aimed at conducting such analysis for two grapevine viruses, Grapevine virus A (GVA) and Grapevine leafroll-associated virus-2 (GLRaV- 2). Our major achievements on the previous cycle of BARD funding are as follows. 1. GVA and GLRaV-2 were engineered into efficient gene expression and silencing vectors for grapevine. The efficient techniques for grapevine infection resulting in systemic expression or silencing of the recombinant genes were developed. Therefore, GVA and GLRaV-2 were rendered into powerful tools of grapevine virology and functional genomics. 2. The GVA and GLRaV-2 RSSs, p10 and p24, respectively, were identified, and their roles in viral pathogenesis were determined. In particular, we found that p10 functions in suppression and pathogenesis are genetically separable. 3. We revealed that p10 is a self-interactive protein that is targeted to the nucleus. In contrast, p24 mechanism involves binding small interfering RNAs in the cytoplasm. We have also demonstrated that p10 is relatively weak, whereas p24 is extremely strong enhancer of the viral agroinfection. 4. We found that, in addition to the dedicated RSSs, GVA and GLRaV-2 counterdefenses involve ORF1 product and leader proteases, respectively. 5. We have teamed up with Dr. Koonin and Dr. Falnes groups to study the evolution and function of the AlkB domain presents in GVA and many other plant viruses. It was demonstrated that viral AlkBs are RNA-specific demethylases thus providing critical support for the biological relevance of the novel process of AlkB-mediated RNA repair.

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Mawassi, Munir, and Valerian V. Dolja. Role of the viral AlkB homologs in RNA repair. United States Department of Agriculture, June 2014. http://dx.doi.org/10.32747/2014.7594396.bard.

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AlkB proteins that repair DNA via reversing methylation damage are conserved in a broad range of prokaryotes and eukaryotes including plants. Surprisingly, AlkB-domains were discovered in the genomes of numerous plant positive-strand RNA viruses, majority of which belong to the family Flexiviridae. The major goal of this research was to reveal the AlkB functions in the viral infection cycle using a range of complementary genetic and biochemical approaches. Our hypotheses was that AlkB is required for efficient replication and genetic stability of viral RNA genomes The major objectives of the research were to identify the functions of GVA AlkB domain throughout the virus infection cycle in N. benthamiana and grapevine, to investigate possible RNA silencing suppression activity of the viral AlkBs, and to characterize the RNA demethylation activity of the mutated GVA AlkBs in vitro and in vivo to determine methylation status of the viral RNA. Over the duration of project, we have made a very substantial progress with the first two objectives. Because of the extreme low titer of the virus particles in plants infected with the AlkB mutant viruses, we were unable to analyze RNA demethylation activity and therefore had to abandon third objective. The major achievements with our objectives were demonstration of the AlkB function in virus spread and accumulation in both experimental and natural hosts of GVA, discovery of the functional cooperation and physical interaction between AlkB and p10 AlkB in suppression of plant RNA silencing response, developing a powerful virus vector technology for grapevine using GLRaV-2-derived vectors for functional genomics and pathogen control in grapevine, and in addition we used massive parallel sequencing of siRNAs to conduct comparative analysis of the siRNA populations in grape plants infected with AlkB-containing GLRaV-3 versus GLRaV-2 that does not encode AlkB. This analysis revealed dramatically reduced levels of virus-specific siRNAs in plants infected with GLRaV-3 compared to that in GLRaV-2 infection implicating AlkB in suppression of siRNA formation. We are pleased to report that BARD funding resulted in 5 publications directly supported by BARD, one US patent, and 9 more publications also relevant to project. Moreover, two joint manuscripts that summarize work on GVA AlkB (led by Israeli PI) and on viral siRNAs in grapevine (led by US PI in collaboration with University of Basel) are in preparation.

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Sette, Alesandro, Bjoern Peters, and Martin Blythe. Predicting the Interplay of Epitope Recognition and Evolution in RNA Viruses Under Immune Pressure. Fort Belvoir, VA: Defense Technical Information Center, April 2008. http://dx.doi.org/10.21236/ada500852.

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ARIZONA STATE UNIV TEMPE CANCER RESEARCH INST. Discovery and Development of Therapeutic Drugs Against Lethal Human RNA Viruses: A Multidisciplinary Assault. Fort Belvoir, VA: Defense Technical Information Center, March 1992. http://dx.doi.org/10.21236/ada251561.

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Pettit, George R. Discovery and Development of Therapeutic Drugs against Lethal Human RNA Viruses: a Multidisciplinary Assault. Fort Belvoir, VA: Defense Technical Information Center, July 1991. http://dx.doi.org/10.21236/ada239742.

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Pettit, George R. Discovery and Development of Therapeutic Drugs against Lethal Human RNA- Viruses: A Multidisciplinary Assault. Fort Belvoir, VA: Defense Technical Information Center, February 1990. http://dx.doi.org/10.21236/ada219393.

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