Propidium Monoazide Integrated with qPCR Enables the Detection and Enumeration of Infectious Enteric RNA and DNA Viruses in Clam and Fermented Sausages

Abstract Background Sterile alpha motif and HD domain 1 (SAMHD1) is a deoxynucleotide triphosphohydrolase (dNTPase) that restricts the infection of a variety of RNA and DNA viruses, including herpesviruses. The anti-viral function of SAMHD1 is associated with its dNTPase activity, which is regulated by several post-translational modifications, including phosphorylation, acetylation and ubiquitination. Our recent studies also demonstrated that the E3 SUMO ligase PIAS1 functions as an Epstein-Barr virus (EBV) restriction factor. However, whether SAMHD1 is regulated by PIAS1 to restrict EBV replication remains unknown. Results In this study, we showed that PIAS1 interacts with SAMHD1 and promotes its SUMOylation. We identified three lysine residues (K469, K595 and K622) located on the surface of SAMHD1 as the major SUMOylation sites. We demonstrated that phosphorylated SAMHD1 can be SUMOylated by PIAS1 and SUMOylated SAMHD1 can also be phosphorylated by viral protein kinases. We showed that SUMOylation-deficient SAMHD1 loses its anti-EBV activity. Furthermore, we demonstrated that SAMHD1 is associated with EBV genome in a PIAS1-dependent manner. Conclusion Our study reveals that PIAS1 synergizes with SAMHD1 to inhibit EBV lytic replication through protein–protein interaction and SUMOylation.

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Phenoxazine nucleoside derivatives with a multiple activity against RNA and DNA viruses

European Journal of Medicinal Chemistry ◽

10.1016/j.ejmech.2021.113467 ◽

2021 ◽

Vol 220 ◽

pp. 113467

Author(s):

Liubov I. Kozlovskaya ◽

Viktor P. Volok ◽

Anna A. Shtro ◽

Yulia V. Nikolaeva ◽

Alexey A. Chistov ◽

...

Keyword(s):

Dna Viruses ◽

Rna And Dna

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Identification of Hepatitis C Virus NS5A Inhibitors

Journal of Virology ◽

10.1128/jvi.01360-09 ◽

2009 ◽

Vol 84 (1) ◽

pp. 482-491 ◽

Cited By ~ 137

Author(s):

Julie A. Lemm ◽

Donald O'Boyle ◽

Mengping Liu ◽

Peter T. Nower ◽

Richard Colonno ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Amino Acid ◽

Therapeutic Index ◽

Dna Viruses ◽

Genotype 1A ◽

A Cell ◽

Ns3 Protease ◽

Derivatives Of ◽

Rna And Dna

ABSTRACT Using a cell-based replicon screen, we identified a class of compounds with a thiazolidinone core structure as inhibitors of hepatitis C virus (HCV) replication. The concentration of one such compound, BMS-824, that resulted in a 50% inhibition of HCV replicon replication was ∼5 nM, with a therapeutic index of >10,000. The compound showed good specificity for HCV, as it was not active against several other RNA and DNA viruses. Replicon cells resistant to BMS-824 were isolated, and mutations were identified. A combination of amino acid substitutions of leucine to valine at residue 31 (L31V) and glutamine to leucine at residue 54 (Q54L) in NS5A conferred resistance to this chemotype, as did a single substitution of tyrosine to histidine at amino acid 93 (Y93H) in NS5A. To further explore the region(s) of NS5A involved in inhibitor sensitivity, genotype-specific NS5A inhibitors were used to evaluate a series of genotype 1a/1b hybrid replicons. Our results showed that, consistent with resistance mapping, the inhibitor sensitivity domain also mapped to the N terminus of NS5A, but it could be distinguished from the key resistance sites. In addition, we demonstrated that NS5A inhibitors, as well as an active-site inhibitor that specifically binds NS3 protease, could block the hyperphosphorylation of NS5A, which is believed to play an essential role in the viral life cycle. Clinical proof of concept has recently been achieved with derivatives of these NS5A inhibitors, indicating that small molecules targeting a nontraditional viral protein like NS5A, without any known enzymatic activity, can also have profound antiviral effects on HCV-infected subjects.

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Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination

Advances in Experimental Medicine and Biology - Respiratory Treatment and Prevention ◽

10.1007/5584_2016_42 ◽

2016 ◽

pp. 53-62 ◽

Cited By ~ 17

Author(s):

Iwona Bukowska-Ośko ◽

Karol Perlejewski ◽

Shota Nakamura ◽

Daisuke Motooka ◽

Tomasz Stokowy ◽

...

Keyword(s):

Cerebrospinal Fluid ◽

Next Generation Sequencing ◽

Metagenomic Analysis ◽

Next Generation ◽

Confounding Effect ◽

Dna Viruses ◽

Generation Sequencing ◽

Rna And Dna

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A Simplified Quantitative Real-Time PCR Assay for Monitoring SARS-CoV-2 Growth in Cell Culture

mSphere ◽

10.1128/msphere.00658-20 ◽

2020 ◽

Vol 5 (5) ◽

Author(s):

Christian Shema Mugisha ◽

Hung R. Vuong ◽

Maritza Puray-Chavez ◽

Adam L. Bailey ◽

Julie M. Fox ◽

...

Keyword(s):

Cell Culture ◽

Real Time ◽

Real Time Pcr ◽

Rna Extraction ◽

Quantitative Real Time Pcr ◽

Pcr Assay ◽

Dna Viruses ◽

Culture Supernatants ◽

Hiv 1 ◽

Rna And Dna

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions within just a few months, causing severe respiratory disease and mortality. Assays to monitor SARS-CoV-2 growth in vitro depend on time-consuming and costly RNA extraction steps, hampering progress in basic research and drug development efforts. Here, we developed a simplified quantitative real-time PCR assay that bypasses viral RNA extraction steps and can monitor SARS-CoV-2 growth from a small amount of cell culture supernatants. In addition, we show that this approach is easily adaptable to numerous other RNA and DNA viruses. Using this assay, we screened the activities of a number of compounds that were predicted to alter SARS-CoV-2 entry and replication as well as HIV-1-specific drugs in a proof-of-concept study. We found that E64D (inhibitor of endosomal proteases cathepsin B and L) and apilimod (endosomal trafficking inhibitor) potently decreased the amount of SARS-CoV-2 RNA in cell culture supernatants with minimal cytotoxicity. Surprisingly, we found that the macropinocytosis inhibitor ethylisopropylamiloride (EIPA) similarly decreased SARS-CoV-2 RNA levels in supernatants, suggesting that entry may additionally be mediated by an alternative pathway. HIV-1-specific inhibitors nevirapine (a nonnucleoside reverse transcriptase inhibitor [NNRTI]), amprenavir (a protease inhibitor), and allosteric integrase inhibitor 2 (ALLINI-2) modestly inhibited SARS-CoV-2 replication, albeit the 50% inhibitory concentration (IC50) values were much higher than that required for HIV-1. Taking the data together, this simplified assay will expedite basic SARS-CoV-2 research, be amenable to mid-throughput screening assays (i.e., drug, CRISPR, small interfering RNA [siRNA], etc.), and be applicable to a broad number of RNA and DNA viruses. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 (COVID-19) pandemic, is continuing to cause immense respiratory disease and social and economic disruptions. Conventional assays that monitor SARS-CoV-2 growth in cell culture rely on costly and time-consuming RNA extraction procedures, hampering progress in basic SARS-CoV-2 research and development of effective therapeutics. Here, we developed a simple quantitative real-time PCR assay to monitor SARS-CoV-2 growth in cell culture supernatants that does not necessitate RNA extraction and that is as accurate and sensitive as existing methods. In a proof-of-concept screen, we found that E64D, apilimod, EIPA, and remdesivir can substantially impede SARS-Cov-2 replication, providing novel insight into viral entry and replication mechanisms. In addition, we show that this approach is easily adaptable to numerous other RNA and DNA viruses. This simplified assay will undoubtedly expedite basic SARS-CoV-2 and virology research and be amenable to use in drug screening platforms to identify therapeutics against SARS-CoV-2.

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ChemInform Abstract: ANTIVIRAL ACTIVITY OF SOME β-DIKETONES. 1. ARYL ALKYL DIKETONES. IN VITRO ACTIVITY AGAINST BOTH RNA AND DNA VIRUSES

Chemischer Informationsdienst ◽

10.1002/chin.197742143 ◽

1977 ◽

Vol 8 (42) ◽

pp. no-no

Author(s):

G. D. DIANA ◽

U. J. SALVADOR ◽

E. S. ZALAY ◽

R. E. JOHNSON ◽

J. C. COLLINS ◽

...

Keyword(s):

Antiviral Activity ◽

Vitro Activity ◽

In Vitro Activity ◽

Dna Viruses ◽

Rna And Dna

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Properties and abundance of overlapping genes in viruses

Virus Evolution ◽

10.1093/ve/veaa009 ◽

2020 ◽

Vol 6 (1) ◽

Cited By ~ 6

Author(s):

Timothy E Schlub ◽

Edward C Holmes

Keyword(s):

Genome Structure ◽

Virus Genome ◽

Overlapping Genes ◽

Genome Database ◽

Dna Viruses ◽

Virus Family ◽

Flexible Genome ◽

Gene Overlap ◽

Reference Genomes ◽

Rna And Dna

Abstract Overlapping genes are commonplace in viruses and play an important role in their function and evolution. However, aside from studies on specific groups of viruses, relatively little is known about the extent and nature of gene overlap and its determinants in viruses as a whole. Here, we present an extensive characterisation of gene overlap in viruses through an analysis of reference genomes present in the NCBI virus genome database. We find that over half the instances of gene overlap are very small, covering <10 nt, and 84 per cent are <50 nt in length. Despite this, 53 per cent of all viruses still contained a gene overlap of 50 nt or larger. We also investigate several predictors of gene overlap such as genome structure (single- and double-stranded RNA and DNA), virus family, genome length, and genome segmentation. This revealed that gene overlap occurs more frequently in DNA viruses than in RNA viruses, and more frequently in single-stranded viruses than in double-stranded viruses. Genome segmentation is also associated with gene overlap, particularly in single-stranded DNA viruses. Notably, we observed a large range of overlap frequencies across families of all genome types, suggesting that it is a common evolutionary trait that provides flexible genome structures in all virus families.

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Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients

Journal of Molecular Diagnostics ◽

10.1016/j.jmoldx.2019.10.007 ◽

2020 ◽

Vol 22 (2) ◽

pp. 196-207 ◽

Cited By ~ 5

Author(s):

Sander van Boheemen ◽

Anneloes L. van Rijn ◽

Nikos Pappas ◽

Ellen C. Carbo ◽

Ruben H.P. Vorderman ◽

...

Keyword(s):

Pediatric Patients ◽

Metagenomic Sequencing ◽

Dna Viruses ◽

Combined Detection ◽

Rna And Dna

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Artificial Small RNA-Based Silencing Tools for Antiviral Resistance in Plants

Plants ◽

10.3390/plants9060669 ◽

2020 ◽

Vol 9 (6) ◽

pp. 669 ◽

Cited By ~ 1

Author(s):

Adriana E. Cisneros ◽

Alberto Carbonell

Keyword(s):

Small Rnas ◽

Rational Design ◽

High Specificity ◽

Plant Viruses ◽

Antiviral Resistance ◽

Small Interfering Rnas ◽

Crop Species ◽

Dna Viruses ◽

Induce Resistance ◽

Rna And Dna

Artificial small RNAs (art-sRNAs), such as artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs), are highly specific 21-nucleotide small RNAs designed to recognize and silence complementary target RNAs. Art-sRNAs are extensively used in gene function studies or for improving crops, particularly to protect plants against viruses. Typically, antiviral art-sRNAs are computationally designed to target one or multiple sites in viral RNAs with high specificity, and art-sRNA constructs are generated and introduced into plants that are subsequently challenged with the target virus(es). Numerous studies have reported the successful application of art-sRNAs to induce resistance against a large number of RNA and DNA viruses in model and crop species. However, the application of art-sRNAs as an antiviral tool has limitations, such as the difficulty to predict the efficacy of a particular art-sRNA or the emergence of virus variants with mutated target sites escaping to art-sRNA-mediated degradation. Here, we review the different classes, features, and uses of art-sRNA-based tools to induce antiviral resistance in plants. We also provide strategies for the rational design of antiviral art-sRNAs and discuss the latest advances in developing art-sRNA-based methodologies for enhanced resistance to plant viruses.

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