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Fajardo T, Sung PY, Roy P. Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity. PLoS Pathog 2015; 11:e1005321. [PMID: 26646790 PMCID: PMC4672896 DOI: 10.1371/journal.ppat.1005321] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/11/2015] [Indexed: 11/18/2022] Open
Abstract
Bluetongue virus (BTV) causes hemorrhagic disease in economically important livestock. The BTV genome is organized into ten discrete double-stranded RNA molecules (S1-S10) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly. To substantiate and extend these studies, we have investigated the RNA sorting and packaging mechanisms with a new experimental approach using inhibitory oligonucleotides. Putative packaging signals present in the 3’untranslated regions of BTV segments were targeted by a number of nuclease resistant oligoribonucleotides (ORNs) and their effects on virus replication in cell culture were assessed. ORNs complementary to the 3’ UTR of BTV RNAs significantly inhibited virus replication without affecting protein synthesis. Same ORNs were found to inhibit complex formation when added to a novel RNA-RNA interaction assay which measured the formation of supramolecular complexes between and among different RNA segments. ORNs targeting the 3’UTR of BTV segment 10, the smallest RNA segment, were shown to be the most potent and deletions or substitution mutations of the targeted sequences diminished the RNA complexes and abolished the recovery of viable viruses using reverse genetics. Cell-free capsid assembly/RNA packaging assay also confirmed that the inhibitory ORNs could interfere with RNA packaging and further substitution mutations within the putative RNA packaging sequence have identified the recognition sequence concerned. Exchange of 3’UTR between segments have further demonstrated that RNA recognition was segment specific, most likely acting as part of the secondary structure of the entire genomic segment. Our data confirm that genome packaging in this segmented dsRNA virus occurs via the formation of supramolecular complexes formed by the interaction of specific sequences located in the 3’ UTRs. Additionally, the inhibition of packaging in-trans with inhibitory ORNs suggests this that interaction is a bona fide target for the design of compounds with antiviral activity. Bluetongue virus (BTV) is an economically important pathogen of ruminants that belongs to a group of viruses whose genome consists of multiple segments of double-stranded RNA. In order for the virus to synthesize viable and infectious progeny, a precise set of the 10 newly replicated BTV segments must be selected for packaging into each new virus particle. How the virus is able to select its own genomic strands from the vast array of cellular RNAs is not clearly understood. One possibility is that that BTV segments harbours an interaction signal that allows them to be sorted and packaged as a set. Correct identification of these signals has basic and applied implications for a possible target of antiviral therapeutics through inhibition of genome sorting and packaging process. Here we showed that a series of short oligonucleotides (ORNs) complementary to multiple sites on the BTV RNA prevented the growth of viable virus in infected cells. ORNs positive for inhibition in virus growth also prevented the genomic RNA to be packaged in an in vitro packaging assay. Moreover, when these same targeted sequences were deleted or mutated in viral genome, viable virus recovery was abolished. Exchanging the terminal sequences between segments failed to recover virus confirming that such changes are deleterious to virus viability. These studies have identified specific regions and sequences key to genome packaging in dsRNA viruses and viability. The specific genome packaging sequences targeted by inhibitory activities of ORNs are bona fide drug target which, as a mechanism common amongst all serotypes, may represent an Achilles’ heel for the development of virus therapeutics.
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Affiliation(s)
- Teodoro Fajardo
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Po-Yu Sung
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Polly Roy
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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Umeshappa CS, Singh KP, Ahmed KA, Pandey AB, Nanjundappa RH. The measurement of three cytokine transcripts in naïve and sensitized ovine peripheral blood mononuclear cells following in vitro stimulation with bluetongue virus serotype-23. Res Vet Sci 2011; 90:212-4. [DOI: 10.1016/j.rvsc.2010.05.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 05/04/2010] [Accepted: 05/25/2010] [Indexed: 10/19/2022]
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Cell-mediated immune response and cross-protective efficacy of binary ethylenimine-inactivated bluetongue virus serotype-1 vaccine in sheep. Vaccine 2010; 28:2522-31. [DOI: 10.1016/j.vaccine.2010.01.039] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Revised: 01/14/2010] [Accepted: 01/16/2010] [Indexed: 11/22/2022]
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Balumahendiran M, Sreenivasulu D, Kumar CA, Suryanarayana VVS, Byregowda SM. Characterization of VP2 gene of an Indian Bluetongue virus serotype 2 and its close phylogenetic relationship to the Taiwan isolate. Res Vet Sci 2008; 86:332-8. [PMID: 18649903 DOI: 10.1016/j.rvsc.2008.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 04/17/2008] [Accepted: 05/22/2008] [Indexed: 11/17/2022]
Abstract
In this study we present the first report on partial amplification, sequencing and phylogenetic relationship of VP2 of the Indian isolate BTV-2. A PCR product of 1135 bp was amplified, cloned and sequenced. About 1063 bp of partial VP2 gene (1792-2854 bp region) of the Indian isolate was subjected to sequence analysis with already published sequences available in the genome database. The percent similarity of 85.2 was observed with Taiwan isolate and 59% with other isolates of BTV-2. However, 46.2% similarity with Australian BTV-1 and no significant similarity were noted with other serotypes. In-silico analysis and restriction enzyme digestion confirmed the presence of conserved SalI site at 2380 bp position in both Indian and Taiwan isolates. Phylogenetic analysis showed that all BTV-2 isolates formed one distinct group in which BTV-2 Indian and Taiwan isolate is more closely related and further demonstrated that BTV's of the same serotype from different geographical regions were closely related at nucleotide and amino acid level, respectively.
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Affiliation(s)
- M Balumahendiran
- Project Directorate on Animal Disease Monitoring and Surveillance (PD_ADMAS), I.V.R.I. Campus, Hebbal, Bangalore 560024, Karnataka, India.
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Maan S, Maan NS, Samuel AR, Rao S, Attoui H, Mertens PPC. Analysis and phylogenetic comparisons of full-length VP2 genes of the 24 bluetongue virus serotypes. J Gen Virol 2007; 88:621-630. [PMID: 17251581 DOI: 10.1099/vir.0.82456-0] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The outer capsid protein VP2 of Bluetongue virus (BTV) is a target for the protective immune response generated by the mammalian host. VP2 contains the majority of epitopes that are recognized by neutralizing antibodies and is therefore also the primary determinant of BTV serotype. Full-length cDNA copies of genome segment 2 (Seg-2, which encodes VP2) from the reference strains of each of the 24 BTV serotypes were synthesized, cloned and sequenced. This represents the first complete set of full-length BTV VP2 genes (from the 24 serotypes) that has been analysed. Each Seg-2 has a single open reading frame, with short inverted repeats adjacent to conserved terminal hexanucleotide sequences. These data demonstrated overall inter-serotype variations in Seg-2 of 29 % (BTV-8 and BTV-18) to 59 % (BTV-16 and BTV-22), while the deduced amino acid sequence of VP2 varied from 22.4 % (BTV-4 and BTV-20) to 73 % (BTV-6 and BTV-22). Ten distinct Seg-2 lineages (nucleotypes) were detected, with greatest sequence similarities between those serotypes that had previously been reported as serologically ‘related’. Fewer similarities were observed between different serotypes in regions of VP2 that have been reported as antigenically important, suggesting that they may play a role in the neutralizing antibody response. The data presented form an initial basis for BTV serotype identification by sequence analyses and comparison of Seg-2, and for development of molecular diagnostic assays for individual BTV serotypes (by RT-PCR).
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Affiliation(s)
- S Maan
- Department of Arbovirology, Institute for Animal Health, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | - N S Maan
- Department of Arbovirology, Institute for Animal Health, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | - A R Samuel
- Department of Arbovirology, Institute for Animal Health, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | - S Rao
- Department of Arbovirology, Institute for Animal Health, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | - H Attoui
- Department of Arbovirology, Institute for Animal Health, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | - P P C Mertens
- Department of Arbovirology, Institute for Animal Health, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
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Kataria RS, Desai GS, Tiwari AK, Nagaleekar VK, Bandyopadhyay SK. Sequence analysis of VP7 gene of Indian bluetongue virus serotype-23 shows its close phylogenetic relationship to Australian and Chinese serotypes. ACTA ACUST UNITED AC 2006; 17:65-73. [PMID: 16753819 DOI: 10.1080/10425170500511198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Bluetongue, an arthropod borne viral disease of wild and domestic ruminants, causes heavy economic losses throughout the world. In the present study, full-length VP7 gene of Indian bluetongue virus (BTV) serotype 23 was sequenced and compared with prototype strains of BTV reported from different countries. Nucleotide sequence analysis of VP7 gene revealed Indian BTV serotype 23 to have 1154 nucleotides with the deletion of two nucleotides at 3' non-coding region and a unique amino acid change 211S-N. The Indian virus also demonstrated a maximum similarity of 94.2% with Australian serotype 1 and a minimum similarity of 67.4% with Australian serotype 15. However, at deduced amino acid level, it had maximum similarity of 99.7% and a minimum of 82.5% with Chinese serotypes 1, 2 and 4 and Australian serotype 15, respectively. Deduced amino acid sequence analysis of putative receptor binding domain (121-249) revealed all the nine hydrophilic domains to be conserved across the serotypes. Functional motifs present in VP7 protein were also conserved in almost all the BTV serotypes including Indian serotype 23. Phylogenetic analysis based on VP7 gene sequence revealed Indian BTV serotype 23 segregating into a monophyletic group along with Australian serotype 1 and Chinese serotypes 1, 2 and 4, indicating its close evolutionary relationship with these Australian and Chinese serotypes.
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Affiliation(s)
- R S Kataria
- DNA Fingerprinting Unit, National Bureau of Animal Genetic Resources, GT Road By-Pass, P. Box 129, Karnal, Haryana 132 001, India.
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Zientara S, Sailleau C, Dauphin G, Roquier C, Rémond EM, Lebreton F, Hammoumi S, Dubois E, Agier C, Merle G, Bréard E. Identification of bluetongue virus serotype 2 (Corsican strain) by reverse-transcriptase PCR reaction analysis of segment 2 of the genome. Vet Rec 2002; 150:598-601. [PMID: 12036242 DOI: 10.1136/vr.150.19.598] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In October 2000, bluetongue virus was detected on the French island of Corsica. The disease was also reported in Sardinia, Calabria, Sicily and on the Spanish islands of Majorca and Minorca. This paper describes the use of molecular techniques for a rapid identification and serotype determination of serotype 2 of the virus. The nucleotide sequences of segments 2 and 7 of the genome of the Corsican strain were determined and its phylogenetic relationships are described.
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Affiliation(s)
- S Zientara
- Agence Française de Sécurité Sanitaire des Aliments-Alfort, France
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DeMaula CD, Bonneau KR, MacLachlan NJ. Changes in the outer capsid proteins of bluetongue virus serotype ten that abrogate neutralization by monoclonal antibodies. Virus Res 2000; 67:59-66. [PMID: 10773319 DOI: 10.1016/s0168-1702(00)00130-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Six neutralizing monoclonal antibodies (Mabs) and nine neutralization resistant viral variants (escape-mutant viruses (EMVs)) were used to further characterize the neutralization determinants of bluetongue virus serotype 10 (BTV10). The EMVs were produced by sequential passage of a highly cell culture adapted United States prototype strain of BTV10 in the presence of individual neutralizing Mabs. Mabs were characterized by neutralization and immune precipitation assays, and phenotypic properties of EMVs were characterized by neutralization assay. Sequencing of the gene segments encoding outer capsid proteins VP2 and VP5 identified mutations responsible for the altered phenotypic properties exhibited by individual EMVs. Amino acid substitutions in VP2 were responsible for neutralization resistance in most EMVs, whereas an amino acid substitution in VP5, without any change in VP2, was responsible for the neutralization resistance of one EMV. The data confirm that VP2 contains the major neutralization determinants of BTV, and that VP5 also can influence neutralization of the virus. The considerable plasticity of the neutralization determinants of BTV has significant implications for future development of non-replicating vaccines.
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Affiliation(s)
- C D DeMaula
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, 1126 Haring Hall, Davis, CA 95616, USA
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