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Parthiban S, Kowsalya B, Parthiban M, Ramesh A, Raja P, Gopal K, Jaisree S, Thangathurai R, Senthilkumar K. Molecular Analysis of Classical Swine Fever Virus Associated Field Infections Evidence Novel CSFV Sub Genotype in Tamil Nadu, Southern India. Indian J Microbiol 2024; 64:1347-1354. [PMID: 39282161 PMCID: PMC11399502 DOI: 10.1007/s12088-024-01345-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/19/2024] [Indexed: 09/18/2024] Open
Abstract
Classical swine fever (CSF) is an endemic and major viral infection of Indian swine husbandry, contributing to great economic losses with multiple genotypes associated with vast clinical and subclinical outcomes. Molecular detection and genotyping of CSF virus directly from field samples has great application in disease monitoring and control measures hence this study aimed to isolate and characterize CSFV genotypes circulating in southern states of India. Fifty-seven porcine post-mortem tissues (lymph nodes, spleens, livers, lungs, and kidneys) collected from pigs suspected of systemic infections and sudden death with the history of live attenuated CSF vaccination from different regions of Tamil Nadu were used in this study. An NS5B gene based CSFV specific RT-PCR screening confirmed CSFV positivity in 7% (4/57) of samples with a specific amplicon of 449 bp. Further molecular screening for other viral co-infections such as PCV2, PPV and PRRSV done by specific individual PCR assays to all the samples. Non-involvement of above screened three viral pathogens in all four field samples which showed positivity for CSFV confirming CSFV as primary pathogen. Two RT-PCR positive samples (TNI-4 and CHNL-2) selected randomly and sequenced. Aligned contig sequences of both samples were subjected to BLAST homology search and phylogentic characterization. BLAST study of TNI-4 sequence revealed 99% sequence identity with Indian CSFV sequences of genotype 1 and CHNL-2 showed 98% sequence identity with Indian CSFV sequences of genotype 2. Phylogenetic analysis of the TNI-4 and CHNL-2 sequences obtained in this study along with 38 published CSFV sequences consisting of all 5 new genotypes and 14 sub genotypes through the Maximum Likelihood tree method in MEGA 11 revealed that TNI-4 clustering together with 1.7 sub genotypes and CHNL-2 clustering together with 2.2 sub genotypes. TNI-4 and CHNL-2 partial NS5B gene sequences obtained in this study deposited in the GenBank database under accession numbers of MW822568 and MW822569 respectively. The study is the first to report CSF infections associated with the newer 1.7 sub genotype in Tamil Nadu, southern India. It is possible that vaccination could affect the genetic diversity of the CSFV through recombination and point mutations for immune evasion.
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Affiliation(s)
- S Parthiban
- Department of Animal Biotechnology, Faculty of Basic Sciences, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, 600007 India
| | - B Kowsalya
- Department of Animal Biotechnology, Faculty of Basic Sciences, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, 600007 India
| | - M Parthiban
- Department of Animal Biotechnology, Faculty of Basic Sciences, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, 600007 India
| | - A Ramesh
- Department of Veterinary Microbiology, Madras Veterinary College, Chennai, 600007 India
| | - P Raja
- Department of Animal Biotechnology, Faculty of Basic Sciences, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, 600007 India
| | - K Gopal
- Department of Veterinary Pathology, VCRI, Namakkal, 637002 India
| | - S Jaisree
- Central University Laboratory, MMC, TANUVAS, Chennai, 600051 India
| | - R Thangathurai
- Department of Veterinary Pathology, VCRI, Tirunelveli, 627358 India
| | - K Senthilkumar
- Post Graduate Research Institute in Animal Sciences, Kattupakkam, India
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Johnston CM, Olesen AS, Lohse L, le Maire Madsen A, Bøtner A, Belsham GJ, Rasmussen TB. A Deep Sequencing Strategy for Investigation of Virus Variants within African Swine Fever Virus-Infected Pigs. Pathogens 2024; 13:154. [PMID: 38392892 PMCID: PMC10893071 DOI: 10.3390/pathogens13020154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
African swine fever virus (ASFV) is the causative agent of African swine fever, an economically important disease of pigs, often with a high case fatality rate. ASFV has demonstrated low genetic diversity among isolates collected within Eurasia. To explore the influence of viral variants on clinical outcomes and infection dynamics in pigs experimentally infected with ASFV, we have designed a deep sequencing strategy. The variant analysis revealed unique SNPs at <10% frequency in several infected pigs as well as some SNPs that were found in more than one pig. In addition, a deletion of 10,487 bp (resulting in the complete loss of 21 genes) was present at a nearly 100% frequency in the ASFV DNA from one pig at position 6362-16849. This deletion was also found to be present at low levels in the virus inoculum and in two other infected pigs. The current methodology can be used for the currently circulating Eurasian ASFVs and also adapted to other ASFV strains and genotypes. Comprehensive deep sequencing is critical for following ASFV molecular evolution, especially for the identification of modifications that affect virus virulence.
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Affiliation(s)
- Camille Melissa Johnston
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark; (C.M.J.); (A.S.O.); (L.L.); (A.l.M.M.)
| | - Ann Sofie Olesen
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark; (C.M.J.); (A.S.O.); (L.L.); (A.l.M.M.)
| | - Louise Lohse
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark; (C.M.J.); (A.S.O.); (L.L.); (A.l.M.M.)
| | - Agnete le Maire Madsen
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark; (C.M.J.); (A.S.O.); (L.L.); (A.l.M.M.)
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, DK-1353 København, Denmark
| | - Anette Bøtner
- Section for Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Denmark; (A.B.); (G.J.B.)
| | - Graham J. Belsham
- Section for Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Denmark; (A.B.); (G.J.B.)
| | - Thomas Bruun Rasmussen
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark; (C.M.J.); (A.S.O.); (L.L.); (A.l.M.M.)
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E-2 Glycoprotein Structural Variations Analysed within the CSFV 2.2. Genogroup in a “Closed Grid” Sampling Study from Meghalaya, India. MICROBIOLOGY RESEARCH 2023. [DOI: 10.3390/microbiolres14010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
CSF is enzootic in most of pig-producing states, particularly in the NorthEastern (NE) region of India. In this study, a total of 249 sera and 190 tissue samples were collected from different parts of Meghalaya. Samples were processed by ELISA and RT-PCR for serological and molecular diagnosis. Representative positive samples from the Khasi Hills region were selected for sequencing and “close grid” phylogenetic relationship using partial genomic regions of 5′UTR and E2. High seroprevalence (74.7%) of CSFV was recorded. Detection of the CSFV genome in serologically positive serum samples and tissue samples was 61.29% and 18.94%, respectively. BLAST and phylogenetic analyses indicate the clustering of all the field samples in subgroup 2.2, with high identity with EF014334 from China. Molecular structural modelling of the E2 partial sequence using representative sequences MG563797 from Meghalaya and EF014334 from China indicate potential changes in the protein motif and its conformation, which may explain the emergence of subgroup 2.2 CSFV replacing the predominant subgroup 1.1 viruses in NorthEast India. The epidemiological information presented in this study may be helpful for determination of disease incidence in this region, whereas the virus profile may be useful for framing disease control programs.
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Fan D, Hu C, Yang X, Yang X, Chen Y, Lin J. Generation of a DNA-launched classical swine fever virus infectious clone packaged in bacterial artificial chromosome. Virus Res 2023; 323:198961. [PMID: 36209918 PMCID: PMC10194133 DOI: 10.1016/j.virusres.2022.198961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/12/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022]
Abstract
Reverse genetics system offers powerful tool for the research of RNA viruses. The infectious clones of classical swine fever virus (CSFV) were commonly constructed either in high- or low-copy number plasmids and transcribed to infectious RNA using phage RNA-polymerases. Herein, the full-length genome of CSFV Shimen strain, flanked by cytomegalovirus immediate-early (CMV) promoter (a eukaryotic RNA polymerase II promoter) sequence at the 5'-end and the hepatitis delta virus ribozyme along with the bovine growth hormone termination and polyadenylation signal sequences at the 3'-end, was packaged in bacterial artificial chromosome vector to establish a CSFV infectious clone pBAC-smCSFV. This infectious cDNA clone maintained stability after passaged 20 times in bacteria. Transfection of PK15 cells with this cDNA clone facilitated recovery of infectious progeny virus which was identical to parent virus as characterized by RT-qPCR, western blotting, indirect immunofluorescence assay, one-step growth kinetics analysis and nucleotide sequencing. Based on this CSFV infectious cDNA clone, the mCherry was inserted between viral Npro and C protein to develop reporter virus CSFV-mCherry. The mCherry was stably expressed after CSFV-mCherry was passaged 10 times in PK15 cells. Taken together, this present study develops a concise and efficient CSFV infectious cDNA clone and a reporter virus CSFV-mCherry. To the best of our knowledge, this is the first combination of CMV promoter and BAC system in construction of CSFV reverse genetics system. The CSFV infectious cDNA clone and the reporter virus will be useful in the study of CSFV virus biology, virulence determinants, molecular pathogenesis, vaccine development and virus-host interaction.
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Affiliation(s)
- Dinglin Fan
- School of Nursing, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Congxia Hu
- School of Nursing, Southwest Medical University, Luzhou, Sichuan 646000, China; Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xidan Yang
- School of Nursing, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xuetao Yang
- School of Nursing, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yanhua Chen
- School of Nursing, Southwest Medical University, Luzhou, Sichuan 646000, China.
| | - Jihui Lin
- School of Nursing, Southwest Medical University, Luzhou, Sichuan 646000, China.
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Fahnøe U, Deng Y, Davids NA, Lohse L, Bukh J, Belsham GJ, Rasmussen TB. Identification of specific amino acid residues in the border disease virus glycoprotein E2 that modify virus growth in pig cells but not in sheep cells. J Gen Virol 2021; 101:1170-1181. [PMID: 32857690 DOI: 10.1099/jgv.0.001483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Border disease virus (BDV) envelope glycoprotein E2 is required for entry into cells and is a determinant of host tropism for sheep and pig cells. Here, we describe adaptive changes in the BDV E2 protein that modify virus replication in pig cells. To achieve this, two BDV isolates, initially collected from a pig and a sheep on the same farm, were passaged in primary sheep and pig cells in parallel with a rescued variant of the pig virus derived from a cloned full-length BDV cDNA. The pig isolate and the rescued virus shared the same amino acid sequence, but the sheep isolate differed at ten residues, including two substitutions in E2 (K771E and Y925H). During serial passage in cells, the viruses displayed clear selectivity for growth in sheep cells; only the cDNA-derived virus adapted to grow in pig cells. Sequencing revealed an amino acid substitution (Q739R) in the E2 domain DA of this rescued virus. Adaptation at the same residue (Q739K/Q739R) was also observed after passaging of the pig isolate in sheep cells. Use of reverse genetics confirmed that changing residue Q739 to R or K (each positively charged) was sufficient to achieve adaptation to pig cells. Furthermore, this change in host tropism was suppressed if Q739R was combined with K771E. Another substitution (Q728R), conferring an additional positive charge, acquired during passaging, restored the growth of the Q739R/K771E variant. Overall, this study provided evidence that specific, positively charged, residues in the E2 domain DA are crucial for pig-cell tropism of BDV.
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Affiliation(s)
- Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark.,DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Yu Deng
- School of Animal Science, Xichang College, Xichang 615013, PR China.,DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Nana A Davids
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.,DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Louise Lohse
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.,DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Graham J Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, DK-1870 Frederiksberg C, Denmark.,DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Thomas Bruun Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark.,Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
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Analysis of Virus Population Profiles within Pigs Infected with Virulent Classical Swine Fever Viruses: Evidence for Bottlenecks in Transmission but Absence of Tissue-Specific Virus Variants. J Virol 2020; 94:JVI.01119-20. [PMID: 32699086 DOI: 10.1128/jvi.01119-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/14/2020] [Indexed: 11/20/2022] Open
Abstract
Classical swine fever virus (CSFV) contains a specific motif within the E2 glycoprotein that differs between strains of different virulence. In the highly virulent CSFV strain Koslov, this motif comprises residues S763/L764 in the polyprotein. However, L763/P764 represent the predominant alleles in published CSFV genomes. In this study, changes were introduced into the CSFV strain Koslov (here called vKos_SL) to generate modified CSFVs with substitutions at residues 763 and/or 764 (vKos_LL, vKos_SP, and vKos_LP). The properties of these mutant viruses, in comparison to those of vKos_SL, were determined in pigs. Each of the viruses was virulent and induced typical clinical signs of CSF, but the vKos_LP strain produced them significantly earlier. Full-length CSFV cDNA amplicons (12.3 kb) derived from sera of infected pigs were deep sequenced and cloned to reveal the individual haplotypes that contributed to the single-nucleotide polymorphism (SNP) profiles observed in the virus population. The SNP profiles for vKos_SL and vKos_LL displayed low-level heterogeneity across the entire genome, whereas vKos_SP and vKos_LP displayed limited diversity with a few high-frequency SNPs. This indicated that vKos_SL and vKos_LL exhibited a higher level of fitness in the host and more stability at the consensus level, whereas several consensus changes were observed in the vKos_SP and vKos_LP sequences, pointing to adaptation. For each virus, only a subset of the variants present within the virus inoculums were maintained in the infected pigs. No clear tissue-dependent quasispecies differentiation occurred within inoculated pigs; however, clear evidence for transmission bottlenecks to contact animals was observed, with subsequent loss of sequence diversity.IMPORTANCE The surface-exposed E2 protein of classical swine fever virus is required for its interaction with host cells. A short motif within this protein varies between strains of different virulence. The importance of two particular amino acid residues in determining the properties of a highly virulent strain of the virus has been analyzed. Each of the different viruses tested proved highly virulent, but one of them produced earlier, but not more severe, disease. By analyzing the virus genomes present within infected pigs, it was found that the viruses which replicated within inoculated animals were only a subset of those within the virus inoculum. Furthermore, following contact transmission, it was shown that a very restricted set of viruses had transferred between animals. There were no significant differences in the virus populations present in various tissues of the infected animals. These results indicate mechanisms of virus population change during transmission between animals.
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7
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Dalmann A, Wernike K, Snijder EJ, Oreshkova N, Reimann I, Beer M. Single-Round Infectious Particle Production by DNA-Launched Infectious Clones of Bungowannah Pestivirus. Viruses 2020; 12:v12080847. [PMID: 32759644 PMCID: PMC7472241 DOI: 10.3390/v12080847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 11/24/2022] Open
Abstract
Reverse genetics systems are powerful tools for functional studies of viral genes or for vaccine development. Here, we established DNA-launched reverse genetics for the pestivirus Bungowannah virus (BuPV), where cDNA flanked by a hammerhead ribozyme sequence at the 5′ end and the hepatitis delta ribozyme at the 3′ end was placed under the control of the CMV RNA polymerase II promoter. Infectious recombinant BuPV could be rescued from pBuPV-DNA-transfected SK-6 cells and it had very similar growth characteristics to BuPV generated by conventional RNA-based reverse genetics and wild type BuPV. Subsequently, DNA-based ERNS deleted BuPV split genomes (pBuPV∆ERNS/ERNS)—co-expressing the ERNS protein from a separate synthetic CAG promoter—were constructed and characterized in vitro. Overall, DNA-launched BuPV genomes enable a rapid and cost-effective generation of recombinant BuPV and virus mutants, however, the protein expression efficiency of the DNA-launched systems after transfection is very low and needs further optimization in the future to allow the use e.g., as vaccine platform.
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Affiliation(s)
- Anja Dalmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (A.D.); (K.W.)
| | - Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (A.D.); (K.W.)
| | - Eric J. Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (E.J.S.); (N.O.)
| | - Nadia Oreshkova
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (E.J.S.); (N.O.)
| | - Ilona Reimann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (A.D.); (K.W.)
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (A.D.); (K.W.)
- Correspondence:
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8
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Virus Adaptation and Selection Following Challenge of Animals Vaccinated against Classical Swine Fever Virus. Viruses 2019; 11:v11100932. [PMID: 31658773 PMCID: PMC6833067 DOI: 10.3390/v11100932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/30/2019] [Accepted: 10/09/2019] [Indexed: 01/15/2023] Open
Abstract
Vaccines against classical swine fever have proven very effective in protecting pigs from this deadly disease. However, little is known about how vaccination impacts the selective pressures acting on the classical swine fever virus (CSFV). Here we use high-throughput sequencing of viral genomes to investigate evolutionary changes in virus populations following the challenge of naïve and vaccinated pigs with the highly virulent CSFV strain “Koslov”. The challenge inoculum contained an ensemble of closely related viral sequences, with three major haplotypes being present, termed A, B, and C. After the challenge, the viral haplotype A was preferentially located within the tonsils of naïve animals but was highly prevalent in the sera of all vaccinated animals. We find that the viral population structure in naïve pigs after infection is very similar to that in the original inoculum. In contrast, the viral population in vaccinated pigs, which only underwent transient low-level viremia, displayed several distinct changes including the emergence of 16 unique non-synonymous single nucleotide polymorphisms (SNPs) that were not detectable in the challenge inoculum. Further analysis showed a significant loss of heterogeneity and an increasing positive selection acting on the virus populations in the vaccinated pigs. We conclude that vaccination imposes a strong selective pressure on viruses that subsequently replicate within the vaccinated animal.
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Characterization of internal ribosome entry sites according to secondary structure analysis to classify border disease virus strains. J Virol Methods 2019; 275:113704. [PMID: 31518634 DOI: 10.1016/j.jviromet.2019.113704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/18/2019] [Accepted: 07/18/2019] [Indexed: 11/24/2022]
Abstract
Applying palindromic nucleotide substitutions (PNS) method, variable loci of the internal ribosome entry site (IRES) secondary structure in the 5' untranslated region (UTR) of Border disease virus sequences were analysed allowing their allocation into ten IRES classes within the species. Sequence characteristics of Turkish and Chinese strains were highly divergent from other genogroups, indicating geographic segregation and micro-evolutive steps within the species. Observed heterogeneity in the BDV species has to be considered for potential implications on diagnostic tests, control and preventive measures.
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Giangaspero M, Zhang SQ, Apicella C. Heterogeneity of <i>Pestivirus</i> Species in Asia. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/aim.2019.93019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Grierson SS, McGowan S, Cook C, Steinbach F, Choudhury B. Molecular and in vitro characterisation of hepatitis E virus from UK pigs. Virology 2018; 527:116-121. [PMID: 30496912 DOI: 10.1016/j.virol.2018.10.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 02/08/2023]
Abstract
Hepatitis E virus (HEV) infection is widespread in the global pig population. Although clinically inapparent in pigs, HEV infection is the cause of Hepatitis E in humans and transmission via the food chain has been established. Following a 2013 study that investigated prevalence of HEV infection in UK slaughter-age pigs samples indicating highest viral load were selected for further characterisation. High throughput sequencing was used to obtain the complete coding sequence from five samples. An in-frame insertion was observed within the HEV hypervariable region in two samples. To interrogate whether this mutation may be the cause of high-level viraemia and faecal shedding as observed in the sampled pigs virus isolation and culture was conducted. Based on viral growth kinetics there was no evidence that these insertions affected replication efficiency in vitro, suggesting as yet undetermined host factors may affect the course of infection and consequently the risk of foodborne transmission.
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Affiliation(s)
- Sylvia S Grierson
- Animal and Plant Health Agency, Department of Virology, Addlestone, Surrey, UK.
| | - Sarah McGowan
- Animal and Plant Health Agency, Department of Virology, Addlestone, Surrey, UK
| | - Charlotte Cook
- Animal and Plant Health Agency, Department of Epidemiological Sciences, Addlestone, Surrey, UK
| | - Falko Steinbach
- Animal and Plant Health Agency, Department of Virology, Addlestone, Surrey, UK
| | - Bhudipa Choudhury
- Animal and Plant Health Agency, Department of Virology, Addlestone, Surrey, UK
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12
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Cui T, Bin Y, Yan J, Mei P, Li Z, Zhou C, Song Z. Development of Infectious cDNA Clones of Citrus Yellow Vein Clearing Virus Using a Novel and Rapid Strategy. PHYTOPATHOLOGY 2018; 108:1212-1218. [PMID: 29726761 DOI: 10.1094/phyto-02-18-0029-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Yellow vein clearing disease (YVCD) causes significant economic losses in lemon and other species of citrus. Usually, citrus yellow vein clearing virus (CYVCV) is considered to be the causal agent of YVCD. However, mixed infection of CYVCV and Indian citrus ringspot virus (ICRSV) or other pathogens is often detected in citrus plants with YVCD. In this study, we re-examined the causal agent of YVCD to fulfill Koch's postulates. First, the full-length genome of CYVCV isolate AY (CYVCV-AY) was amplified by long-distance RT-PCR from a Eureka lemon (Citrus limon) tree with typical YVCD symptoms. The genomic cDNAs were then cloned into a ternary Yeast-Escherichia coli-Agrobacterium tumefaciens shuttle vector, pCY, using transformation-associated recombination (TAR) strategy, and 15 full-length cDNA clones of CYVCV-AY were obtained. Subsequently, four of these clones were selected randomly and inoculated on Jincheng (C. sinensis) seedlings through Agrobacterium-mediated vacuum-infiltration, and it was found that 80 to 100% of inoculated plants were infected with CYVCV by RT-PCR at 20 to 40 days postinoculation (dpi) and by direct tissue blot immunoassay at 60 dpi. The progeny of CYVCV-AY from cDNA clones caused typical symptoms of YVCD such as yellow vein clearing, leaf distortion, and chlorosis, which were the same as that elicited by wild-type virus. Finally, the regeneration of CYVCV-AY genome was confirmed by long-distance RT-PCR in lemon trees inoculated with the infectious cDNA clone. These results proved that CYVCV was the primary causal agent of YVCD. This is the first report on the development of infectious cDNA clones of CYVCV, which lays the foundation for further studies on viral gene functions and virus-host interactions.
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Affiliation(s)
- Tiantian Cui
- All authors: Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Yu Bin
- All authors: Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Jianhong Yan
- All authors: Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Pengying Mei
- All authors: Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Zhongan Li
- All authors: Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Changyong Zhou
- All authors: Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Zhen Song
- All authors: Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
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Johnston CM, Fahnøe U, Belsham GJ, Rasmussen TB. Strategy for efficient generation of numerous full-length cDNA clones of classical swine fever virus for haplotyping. BMC Genomics 2018; 19:600. [PMID: 30092775 PMCID: PMC6085635 DOI: 10.1186/s12864-018-4971-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/31/2018] [Indexed: 01/15/2023] Open
Abstract
Background Direct molecular cloning of full-length cDNAs derived from viral RNA is an approach to identify the individual viral genomes within a virus population. This enables characterization of distinct viral haplotypes present during infection. Results In this study, we recover individual genomes of classical swine fever virus (CSFV), present in a pig infected with vKos that was rescued from a cDNA clone corresponding to the highly virulent CSFV Koslov strain. Full-length cDNA amplicons (ca. 12.3 kb) were made by long RT-PCR, using RNA extracted from serum, and inserted directly into a cloning vector prior to detailed characterization of the individual viral genome sequences. The amplicons used for cloning were deep sequenced, which revealed low level sequence variation (< 5%) scattered across the genome consistent with the clone-derived origin of vKos. Numerous full-length cDNA clones were generated using these amplicons and full-genome sequencing of individual cDNA clones revealed insights into the virus diversity and the haplotypes present during infection. Most cDNA clones were unique, containing several single-nucleotide polymorphisms, and phylogenetic reconstruction revealed a low degree of order. Conclusions This optimized methodology enables highly efficient construction of full-length cDNA clones corresponding to individual viral genomes present within RNA virus populations. Electronic supplementary material The online version of this article (10.1186/s12864-018-4971-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Camille Melissa Johnston
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771, Kalvehave, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Graham J Belsham
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771, Kalvehave, Denmark
| | - Thomas Bruun Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771, Kalvehave, Denmark.
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14
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Willcocks MM, Zaini S, Chamond N, Ulryck N, Allouche D, Rajagopalan N, Davids NA, Fahnøe U, Hadsbjerg J, Rasmussen TB, Roberts LO, Sargueil B, Belsham GJ, Locker N. Distinct roles for the IIId2 sub-domain in pestivirus and picornavirus internal ribosome entry sites. Nucleic Acids Res 2018; 45:13016-13028. [PMID: 29069411 PMCID: PMC5727462 DOI: 10.1093/nar/gkx991] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 10/12/2017] [Indexed: 01/23/2023] Open
Abstract
Viral internal ribosomes entry site (IRES) elements coordinate the recruitment of the host translation machinery to direct the initiation of viral protein synthesis. Within hepatitis C virus (HCV)-like IRES elements, the sub-domain IIId(1) is crucial for recruiting the 40S ribosomal subunit. However, some HCV-like IRES elements possess an additional sub-domain, termed IIId2, whose function remains unclear. Herein, we show that IIId2 sub-domains from divergent viruses have different functions. The IIId2 sub-domain present in Seneca valley virus (SVV), a picornavirus, is dispensable for IRES activity, while the IIId2 sub-domains of two pestiviruses, classical swine fever virus (CSFV) and border disease virus (BDV), are required for 80S ribosomes assembly and IRES activity. Unlike in SVV, the deletion of IIId2 from the CSFV and BDV IRES elements impairs initiation of translation by inhibiting the assembly of 80S ribosomes. Consequently, this negatively affects the replication of CSFV and BDV. Finally, we show that the SVV IIId2 sub-domain is required for efficient viral RNA synthesis and growth of SVV, but not for IRES function. This study sheds light on the molecular evolution of viruses by clearly demonstrating that conserved RNA structures, within distantly related RNA viruses, have acquired different roles in the virus life cycles.
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Affiliation(s)
- Margaret M Willcocks
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Salmah Zaini
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Nathalie Chamond
- Faculté des Sciences Pharmaceutiques et Biologiques, UMR8015, Université Paris Descartes, Paris, France
| | - Nathalie Ulryck
- Faculté des Sciences Pharmaceutiques et Biologiques, UMR8015, Université Paris Descartes, Paris, France
| | - Delphine Allouche
- Faculté des Sciences Pharmaceutiques et Biologiques, UMR8015, Université Paris Descartes, Paris, France
| | - Noemie Rajagopalan
- Faculté des Sciences Pharmaceutiques et Biologiques, UMR8015, Université Paris Descartes, Paris, France
| | - Nana A Davids
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Ulrik Fahnøe
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Johanne Hadsbjerg
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Thomas Bruun Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Lisa O Roberts
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Bruno Sargueil
- Faculté des Sciences Pharmaceutiques et Biologiques, UMR8015, Université Paris Descartes, Paris, France
| | - Graham J Belsham
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
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15
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Tuo D, Fu L, Shen W, Li X, Zhou P, Yan P. Generation of stable infectious clones of plant viruses by using Rhizobium radiobacter for both cloning and inoculation. Virology 2017; 510:99-103. [PMID: 28715654 PMCID: PMC7173343 DOI: 10.1016/j.virol.2017.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/07/2017] [Accepted: 07/08/2017] [Indexed: 01/08/2023]
Abstract
A novel Rhizobium radiobacter (synonym Agrobacterium tumefaciens)-mediated approach was developed to generate stable infectious clones of plant viruses. This method uses R. radiobacter for both cloning and inoculation of infectious clones, bypassing the requirement of cloning in E. coli to avoid the instability. Only three steps are included in this method: (i) construct viral genome-encoding plasmids in vitro by one-step Gibson assembly; (ii) transform the assembled DNA products into R. radiobacter; (iii) inoculate plants with the R. radiobacter clones containing the viral genome. Stable infectious clones were obtained from two potyviruses papaya ringspot virus (PRSV) and papaya leaf distortion mosaic virus (PLDMV) using this method, whereas attempts utilizing "classical" E. coli cloning system failed repeatedly. This method is simple and efficient, and is promising for a wide application in generation of infectious clones of plant virus, especially for those which are instable in E. coli. A novel approach was developed to generate infectious clones of plant viruses. It uses R. radiobacter for both cloning and inoculation of infectious clones. It bypasses the requirement of cloning in E. coli to avoid the instability. Stable infectious clones of PRSV and PLDMV were obtained using this method.
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Affiliation(s)
- Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Lanlan Fu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaoying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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16
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Use of homologous recombination in yeast to create chimeric bovine viral diarrhea virus cDNA clones. Braz J Microbiol 2016; 47:993-999. [PMID: 27522929 PMCID: PMC5052387 DOI: 10.1016/j.bjm.2016.07.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/25/2016] [Indexed: 01/11/2023] Open
Abstract
The open reading frame of a Brazilian bovine viral diarrhea virus (BVDV) strain, IBSP4ncp, was recombined with the untranslated regions of the reference NADL strain by homologous recombination in Saccharomyces cerevisiae, resulting in chimeric full-length cDNA clones of BVDV (chi-NADL/IBSP4ncp#2 and chi-NADL/IBSP4ncp#3). The recombinant clones were successfully recovered, resulting in viable viruses, having the kinetics of replication, focus size, and morphology similar to those of the parental virus, IBSP4ncp. In addition, the chimeric viruses remained stable for at least 10 passages in cell culture, maintaining their replication efficiency unaltered. Nucleotide sequencing revealed a few point mutations; nevertheless, the phenotype of the rescued viruses was nearly identical to that of the parental virus in all experiments. Thus, genetic stability of the chimeric clones and their phenotypic similarity to the parental virus confirm the ability of the yeast-based homologous recombination to maintain characteristics of the parental virus from which the recombinant viruses were derived. The data also support possible use of the yeast system for the manipulation of the BVDV genome.
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17
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Hadsbjerg J, Friis MB, Fahnøe U, Nielsen J, Belsham GJ, Rasmussen TB. Sequence adaptations during growth of rescued classical swine fever viruses in cell culture and within infected pigs. Vet Microbiol 2016; 192:123-134. [PMID: 27527774 DOI: 10.1016/j.vetmic.2016.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/24/2016] [Accepted: 07/06/2016] [Indexed: 02/05/2023]
Abstract
Classical swine fever virus (CSFV) causes an economically important disease of swine. Four different viruses were rescued from full-length cloned cDNAs derived from the Paderborn strain of CSFV. Three of these viruses had been modified by mutagenesis (with 7 or 8 nt changes) within stem 2 of the subdomain IIIf of the internal ribosome entry site (IRES) that directs the initiation of protein synthesis. Rescued viruses were inoculated into pigs. The rescued vPader10 virus, without modifications in the IRES, induced clinical disease in pigs that was very similar to that observed previously with the parental field strain and transmission to in-contact pigs occurred. Two sequence reversions, in the NS2 and NS5B coding regions, became dominant within the virus populations in these infected pigs. Rescued viruses, with mutant IRES elements, did not induce disease and only very limited circulation of viral RNA could be detected. However, the animals inoculated with these mutant viruses seroconverted against CSFV. Thus, these mutant viruses were highly attenuated in vivo. All 4 rescued viruses were also passaged up to 20 times in cell culture. Using full genome sequencing, the same two adaptations within each of four independent virus populations were observed that restored the coding sequence to that of the parental field strain. These adaptations occurred with different kinetics. The combination of reverse genetics and in depth, full genome sequencing provides a powerful approach to analyse virus adaptation and to identify key determinants of viral replication efficiency in cells and within host animals.
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Affiliation(s)
- Johanne Hadsbjerg
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark
| | - Martin B Friis
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark
| | - Ulrik Fahnøe
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark
| | - Jens Nielsen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark
| | - Graham J Belsham
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark.
| | - Thomas Bruun Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark
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18
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Yun SI, Song BH, Kim JK, Lee YM. Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses. J Vis Exp 2015:e53164. [PMID: 26780115 PMCID: PMC4780872 DOI: 10.3791/53164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Reverse genetics, an approach to rescue infectious virus entirely from a cloned cDNA, has revolutionized the field of positive-strand RNA viruses, whose genomes have the same polarity as cellular mRNA. The cDNA-based reverse genetics system is a seminal method that enables direct manipulation of the viral genomic RNA, thereby generating recombinant viruses for molecular and genetic studies of both viral RNA elements and gene products in viral replication and pathogenesis. It also provides a valuable platform that allows the development of genetically defined vaccines and viral vectors for the delivery of foreign genes. For many positive-strand RNA viruses such as Japanese encephalitis virus (JEV), however, the cloned cDNAs are unstable, posing a major obstacle to the construction and propagation of the functional cDNA. Here, the present report describes the strategic considerations in creating and amplifying a genetically stable full-length infectious JEV cDNA as a bacterial artificial chromosome (BAC) using the following general experimental procedures: viral RNA isolation, cDNA synthesis, cDNA subcloning and modification, assembly of a full-length cDNA, cDNA linearization, in vitro RNA synthesis, and virus recovery. This protocol provides a general methodology applicable to cloning full-length cDNA for a range of positive-strand RNA viruses, particularly those with a genome of >10 kb in length, into a BAC vector, from which infectious RNAs can be transcribed in vitro with a bacteriophage RNA polymerase.
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Affiliation(s)
- Sang-Im Yun
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University
| | - Byung-Hak Song
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University
| | - Jin-Kyoung Kim
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University
| | - Young-Min Lee
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University;
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19
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Construction of infectious cDNA clone derived from a classical swine fever virus field isolate in BAC vector using in vitro overlap extension PCR and recombination. J Virol Methods 2015; 226:60-6. [DOI: 10.1016/j.jviromet.2015.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/26/2015] [Accepted: 10/13/2015] [Indexed: 11/19/2022]
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20
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Fahnøe U, Pedersen AG, Dräger C, Orton RJ, Blome S, Höper D, Beer M, Rasmussen TB. Creation of Functional Viruses from Non-Functional cDNA Clones Obtained from an RNA Virus Population by the Use of Ancestral Reconstruction. PLoS One 2015; 10:e0140912. [PMID: 26485566 PMCID: PMC4613144 DOI: 10.1371/journal.pone.0140912] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/01/2015] [Indexed: 02/05/2023] Open
Abstract
RNA viruses have the highest known mutation rates. Consequently it is likely that a high proportion of individual RNA virus genomes, isolated from an infected host, will contain lethal mutations and be non-functional. This is problematic if the aim is to clone and investigate high-fitness, functional cDNAs and may also pose problems for sequence-based analysis of viral evolution. To address these challenges we have performed a study of the evolution of classical swine fever virus (CSFV) using deep sequencing and analysis of 84 full-length cDNA clones, each representing individual genomes from a moderately virulent isolate. In addition to here being used as a model for RNA viruses generally, CSFV has high socioeconomic importance and remains a threat to animal welfare and pig production. We find that the majority of the investigated genomes are non-functional and only 12% produced infectious RNA transcripts. Full length sequencing of cDNA clones and deep sequencing of the parental population identified substitutions important for the observed phenotypes. The investigated cDNA clones were furthermore used as the basis for inferring the sequence of functional viruses. Since each unique clone must necessarily be the descendant of a functional ancestor, we hypothesized that it should be possible to produce functional clones by reconstructing ancestral sequences. To test this we used phylogenetic methods to infer two ancestral sequences, which were then reconstructed as cDNA clones. Viruses rescued from the reconstructed cDNAs were tested in cell culture and pigs. Both reconstructed ancestral genomes proved functional, and displayed distinct phenotypes in vitro and in vivo. We suggest that reconstruction of ancestral viruses is a useful tool for experimental and computational investigations of virulence and viral evolution. Importantly, ancestral reconstruction can be done even on the basis of a set of sequences that all correspond to non-functional variants.
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Affiliation(s)
- Ulrik Fahnøe
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
- Center for Biological Sequence Analysis, DTU Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Anders Gorm Pedersen
- Center for Biological Sequence Analysis, DTU Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Carolin Dräger
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Richard J Orton
- Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- MRC–University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Thomas Bruun Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
- * E-mail:
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21
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Abstract
Classical swine fever (CSF) is one of the most devastating epizootic diseases of pigs, causing high morbidity and mortality worldwide. The diversity of clinical signs and similarity in disease manifestations to other diseases make CSF difficult to diagnose with certainty. The disease is further complicated by the presence of a number of different strains belonging to three phylogenetic groups. Advanced diagnostic techniques allow detection of antigens or antibodies in clinical samples, leading to implementation of proper and effective control programs. Polymerase chain reaction (PCR)-based methods, including portable real-time PCR, provide diagnosis in a few hours with precision and accuracy, even at the point of care. The disease is controlled by following a stamping out policy in countries where vaccination is not practiced, whereas immunization with live attenuated vaccines containing the 'C' strain is effectively used to control the disease in endemic countries. To overcome the problem of differentiation of infected from vaccinated animals, different types of marker vaccines, with variable degrees of efficacy, along with companion diagnostic assays have been developed and may be useful in controlling and even eradicating the disease in the foreseeable future. The present review aims to provide an overview and status of CSF as a whole with special reference to swine husbandry in India.
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22
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Kozasa T, Abe Y, Mitsuhashi K, Tamura T, Aoki H, Ishimaru M, Nakamura S, Okamatsu M, Kida H, Sakoda Y. Analysis of a pair of END+ and END- viruses derived from the same bovine viral diarrhea virus stock reveals the amino acid determinants in Npro responsible for inhibition of type I interferon production. J Vet Med Sci 2014; 77:511-8. [PMID: 25648277 PMCID: PMC4478729 DOI: 10.1292/jvms.14-0420] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Exaltation of Newcastle disease virus (END) phenomenon is induced by the
inhibition of type I interferon in pestivirus-infected cells in vitro,
via proteasomal degradation of cellular interferon regulatory factor (IRF)-3 with the
property of the viral autoprotease protein Npro. Reportedly, the amino acid
residues in the zinc-binding TRASH motif of Npro determine the difference in
characteristics between END-phenomenon-positive (END+) and
END-phenomenon-negative (END−) classical swine fever viruses (CSFVs). However,
the basic mechanism underlying this function in bovine viral diarrhea virus (BVDV) has not
been elucidated from the genomic differences between END+ and END−
viruses using reverse genetics till date. In the present study, comparison of complete
genome sequences of a pair of END+ and END− viruses isolated from
the same virus stock revealed that there were only four amino acid substitutions (D136G,
I2623V, D3148G and D3502Y) between two viruses. Based on these differences, viruses with
and without mutations at these positions were generated using reverse genetics. The END
assay, measurements of induced type I interferon and IRF-3 detection in cells infected
with these viruses revealed that the aspartic acid at position 136 in the zinc-binding
TRASH motif of Npro was required to inhibit the production of type I interferon
via the degradation of cellular IRF-3, consistently with CSFV.
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Affiliation(s)
- Takashi Kozasa
- Food Safety and Consumer Affairs Bureau, Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo 100-8950, Japan
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Steinbach F, Westcott DG, McGowan SL, Grierson SS, Frossard JP, Choudhury B. Re-emergence of a genetic outlier strain of equine arteritis virus: Impact on phylogeny. Virus Res 2014; 202:144-50. [PMID: 25527462 PMCID: PMC7172687 DOI: 10.1016/j.virusres.2014.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/05/2014] [Accepted: 12/09/2014] [Indexed: 12/24/2022]
Abstract
Re-emergence of a “historical” EAV strain. An updated EAV phylogeny scheme. Measures to improve EAV phylogenetic analysis through harmonization.
Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory and reproductive disease of equids, which is notifiable in some countries including the Great Britain (GB) and to the OIE. Herein, we present the case of a persistently infected stallion and the phylogenetic tracing of the virus strain isolated. Discussing EAV occurrence and phylogenetic analysis we review features, which may aid to harmonise and enhance the classification of EAV.
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Affiliation(s)
- F Steinbach
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom
| | - D G Westcott
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom
| | - S L McGowan
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom
| | - S S Grierson
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom
| | - J P Frossard
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom
| | - B Choudhury
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom.
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24
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Mokhtar H, Eck M, Morgan SB, Essler SE, Frossard JP, Ruggli N, Graham SP. Proteome-wide screening of the European porcine reproductive and respiratory syndrome virus reveals a broad range of T cell antigen reactivity. Vaccine 2014; 32:6828-37. [DOI: 10.1016/j.vaccine.2014.04.054] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/11/2014] [Accepted: 04/17/2014] [Indexed: 01/06/2023]
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25
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Rescue of the highly virulent classical swine fever virus strain “Koslov” from cloned cDNA and first insights into genome variations relevant for virulence. Virology 2014; 468-470:379-387. [DOI: 10.1016/j.virol.2014.08.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 07/07/2014] [Accepted: 08/21/2014] [Indexed: 11/18/2022]
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26
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Arenhart S, Flores EF, Weiblen R, Gil LHVG. Insertion and stable expression of Gaussia luciferase gene by the genome of bovine viral diarrhea virus. Res Vet Sci 2014; 97:439-48. [PMID: 25108838 DOI: 10.1016/j.rvsc.2014.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 06/29/2014] [Accepted: 07/08/2014] [Indexed: 11/16/2022]
Abstract
As a tool to address selected issues of virus biology, we constructed a recombinant cDNA clone of bovine viral diarrhea virus (BVDV) expressing Gaussia luciferase (Gluc) reporter gene. A full-length genomic cDNA clone of a non-cytopathic BVDV isolate was assembled by recombination in yeast Saccharomyces cerevisiae. The Gluc gene was inserted between the N(pro) and Core protein coding regions by recombination. The cDNA transcribed in vitro was infectious upon transfection of MDBK cells, resulting in reporter gene expression and productive virus replication. The rescued viruses were stable for 15 passages in cell culture, maintaining the replication kinetics, focus size and morphology similar to those of the parental virus. Expression and correct processing of the reporter protein were also maintained, as demonstrated by Gluc activity. These results demonstrate that genes up to 555 bp are simply assembled by a single step in yeast recombination and are stably expressed by this cDNA clone.
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Affiliation(s)
- S Arenhart
- Laboratório de Virologia e Terapia Experimental (LaViTE), Departamento de Virologia e Terapia Experimental, Centro de Pesquisas Aggeu Magalhães (CPqAM), Fundação Oswaldo Cruz (Fiocruz), Recife, PE 50670-420, Brasil; Setor de Virologia (SV), Departamento de Medicina Veterinária Preventiva (DMVP), Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria, Santa Maria, RS 97105-900, Brasil
| | - E F Flores
- Setor de Virologia (SV), Departamento de Medicina Veterinária Preventiva (DMVP), Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria, Santa Maria, RS 97105-900, Brasil
| | - R Weiblen
- Setor de Virologia (SV), Departamento de Medicina Veterinária Preventiva (DMVP), Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria, Santa Maria, RS 97105-900, Brasil
| | - L H V G Gil
- Laboratório de Virologia e Terapia Experimental (LaViTE), Departamento de Virologia e Terapia Experimental, Centro de Pesquisas Aggeu Magalhães (CPqAM), Fundação Oswaldo Cruz (Fiocruz), Recife, PE 50670-420, Brasil.
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27
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RNA virus reverse genetics and vaccine design. Viruses 2014; 6:2531-50. [PMID: 24967693 PMCID: PMC4113782 DOI: 10.3390/v6072531] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/18/2014] [Accepted: 06/19/2014] [Indexed: 12/22/2022] Open
Abstract
RNA viruses are capable of rapid spread and severe or potentially lethal disease in both animals and humans. The development of reverse genetics systems for manipulation and study of RNA virus genomes has provided platforms for designing and optimizing viral mutants for vaccine development. Here, we review the impact of RNA virus reverse genetics systems on past and current efforts to design effective and safe viral therapeutics and vaccines.
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Complete genome sequence of classical Swine Fever virus genotype 2.2 strain bergen. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00483-14. [PMID: 24874676 PMCID: PMC4038881 DOI: 10.1128/genomea.00483-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete genome sequence of the genotype 2.2 classical swine fever virus strain Bergen has been determined; this strain was originally isolated from persistently infected domestic pigs in the Netherlands and is characterized to be of low virulence.
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Vilcek S, Leskova V, Meyer D, Postel A, Becher P. Molecular characterization of border disease virus strain Aveyron. Vet Microbiol 2014; 171:87-92. [PMID: 24742950 DOI: 10.1016/j.vetmic.2014.03.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/21/2014] [Accepted: 03/22/2014] [Indexed: 11/17/2022]
Abstract
For the pestivirus border disease virus (BDV) at least seven major genotypes have been described (BDV-1-BDV-7). So far, complete genomic sequences have been reported for four BDV genotypes (BDV-1-BDV-4). In this study we report the entire genomic sequence of the noncytopathogenic (ncp) BDV-5 reference strain Aveyron. The viral genome encompasses 12,284 nucleotides (nt) and contains one large open reading frame (11,700 nt) flanked by a 370 nt long 5'-untranslated region (UTR) and a 214 nt long 3'-UTR. The genome organization as well as the lengths of the viral polyprotein (3899 amino acids) and the 5'-UTR are very similar to the ones of other BDV strains, while the 3'-UTR of BDV Aveyron is considerably shorter when compared to other BDV strains. Comparative analysis of complete coding sequences revealed that BDV Aveyron shares nucleotide sequence identities of 76.9% to 79.0% with the other BDV strains, and less than 72% identity with other pestiviruses. In contrast to other BDV strains, a unique insertion of four amino acids (KAPD) of unknown origin is present in the C-terminal part of the viral autoprotease NS2 encoded by BDV Aveyron. Immunoblot analysis revealed that infection of cells with the ncp BDV strain Aveyron comprising this unique insertion in NS2 resulted in the expression of high amounts of NS3 and thereby showed that BDV Aveyron significantly differs from other ncp BDV strains in terms of NS2-3 processing and production of NS3.
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Affiliation(s)
- Stefan Vilcek
- University of Veterinary Medicine and Pharmacy, SK 041 81 Kosice, Slovakia
| | - Valeria Leskova
- University of Veterinary Medicine and Pharmacy, SK 041 81 Kosice, Slovakia
| | - Denise Meyer
- Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine, D-30559 Hannover, Germany
| | - Alexander Postel
- Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine, D-30559 Hannover, Germany
| | - Paul Becher
- Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine, D-30559 Hannover, Germany.
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Complete genome sequence of border disease virus genotype 3 strain gifhorn. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01142-13. [PMID: 24435861 PMCID: PMC3894275 DOI: 10.1128/genomea.01142-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete genome sequence of the genotype 3 border disease virus strain Gifhorn has been determined; this strain was originally isolated from pigs. This represents the consensus sequence for the virus used to produce the bacterial artificial chromosome (BAC) cDNA clone pBeloGif3, which yields a virus that is severely attenuated in cell culture.
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Siridechadilok B, Gomutsukhavadee M, Sawaengpol T, Sangiambut S, Puttikhunt C, Chin-inmanu K, Suriyaphol P, Malasit P, Screaton G, Mongkolsapaya J. A simplified positive-sense-RNA virus construction approach that enhances analysis throughput. J Virol 2013; 87:12667-74. [PMID: 24049164 PMCID: PMC3838137 DOI: 10.1128/jvi.02261-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 09/09/2013] [Indexed: 11/20/2022] Open
Abstract
Here we present an approach that advances the throughput of a genetic analysis of a positive-sense RNA virus by simplifying virus construction. It enabled comprehensive dissection of a complex, multigene phenotype through rapid derivation of a large number of chimeric viruses and construction of a mutant library directly from a virus pool. The versatility of the approach described here expands the applicability of diverse genetic approaches to study these viruses.
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Affiliation(s)
- Bunpote Siridechadilok
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Methee Gomutsukhavadee
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Thunyarat Sawaengpol
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Sutha Sangiambut
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Chunya Puttikhunt
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Kwanrutai Chin-inmanu
- Bioinformatics and Data Management for Research Unit, Office of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prapat Suriyaphol
- Bioinformatics and Data Management for Research Unit, Office of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prida Malasit
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
- Dengue Hemorrhagic Fever Unit, Office of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Gavin Screaton
- Molecular Immunology Unit, Hammersmith Campus, Department of Medicine, Imperial College London, London, United Kingdom
| | - Juthathip Mongkolsapaya
- Dengue Hemorrhagic Fever Unit, Office of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Molecular Immunology Unit, Hammersmith Campus, Department of Medicine, Imperial College London, London, United Kingdom
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Rasmussen TB, Risager PC, Fahnøe U, Friis MB, Belsham GJ, Höper D, Reimann I, Beer M. Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA. BMC Genomics 2013; 14:819. [PMID: 24262008 PMCID: PMC3840674 DOI: 10.1186/1471-2164-14-819] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/14/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infectious cDNA clones are a prerequisite for directed genetic manipulation of RNA viruses. Here, a strategy to facilitate manipulation and rescue of classical swine fever viruses (CSFVs) from full-length cDNAs present within bacterial artificial chromosomes (BACs) is described. This strategy allows manipulation of viral cDNA by targeted recombination-mediated mutagenesis within bacteria. RESULTS A new CSFV-BAC (pBeloR26) derived from the Riems vaccine strain has been constructed and subsequently modified in the E2 coding sequence, using the targeted recombination strategy to enable rescue of chimeric pestiviruses (vR26_E2gif and vR26_TAV) with potential as new marker vaccine candidates. Sequencing of the BACs revealed a high genetic stability during passages within bacteria. The complete genome sequences of rescued viruses, after extensive passages in mammalian cells showed that modifications in the E2 protein coding sequence were stably maintained. A single amino acid substitution (D3431G) in the RNA dependent RNA polymerase was observed in the rescued viruses vR26_E2gif and vR26, which was reversion to the parental Riems sequence. CONCLUSIONS These results show that targeted recombination-mediated mutagenesis provides a powerful tool for expediting the construction of novel RNA genomes and should be applicable to the manipulation of other RNA viruses.
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Affiliation(s)
- Thomas Bruun Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771, Kalvehave, Denmark.
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Wescott DG, Mildenberg Z, Bellaiche M, McGowan SL, Grierson SS, Choudhury B, Steinbach F. Evidence for the circulation of equine encephalosis virus in Israel since 2001. PLoS One 2013; 8:e70532. [PMID: 23950952 PMCID: PMC3741287 DOI: 10.1371/journal.pone.0070532] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 06/24/2013] [Indexed: 11/19/2022] Open
Abstract
Equine encephalosis virus (EEV) distribution was thought to be limited to southern Africa until 2008 when we reported EEV in Israel. It was then assumed that the clinical presentation resembled the initial incursion in Israel. To investigate further we conducted a retrospective analysis of equine sera, which had been collected for diagnosis of other suspected diseases, via serum neutralisation test. The data demonstrated that EEV was circulating as early as 2001 with incidence ranging from 20–100% for time period 2001–2008. As the symptoms of EEV can be similar to other equine notifiable diseases this is a significant finding which highlights the need for vigilance and education to accurately diagnose new and emerging diseases.
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Affiliation(s)
- David G. Wescott
- Department of Virology, Animal Health and Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom
| | | | | | - Sarah L. McGowan
- Department of Virology, Animal Health and Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom
| | - Sylvia S. Grierson
- Department of Virology, Animal Health and Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom
| | - Bhudipa Choudhury
- Department of Virology, Animal Health and Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom
- * E-mail:
| | - Falko Steinbach
- Department of Virology, Animal Health and Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom
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A fast and robust method for full genome sequencing of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Type 1 and Type 2. J Virol Methods 2013; 193:697-705. [PMID: 23891870 DOI: 10.1016/j.jviromet.2013.07.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/03/2013] [Accepted: 07/12/2013] [Indexed: 11/21/2022]
Abstract
PRRSV is a positive-sense RNA virus with a high degree of genetic variability among isolates. For diagnostic sensitivity and vaccine design it is essential to monitor PRRSV genetic diversity. However, to date only a few full genome sequences of PRRSV isolates have been made publicly available. In the present study, fast and robust methods for long range RT-PCR amplification and subsequent next generation sequencing (NGS) were developed and validated on nine Type 1 and nine Type 2 PRRSV viruses. The methods generated robust and reliable sequences both on primary material and cell culture adapted viruses and the protocols performed well on all three NGS platforms tested (Roche 454 FLX, Illumina HiSeq2000, and Ion Torrent PGM™ Sequencer). These methods will greatly facilitate the generation of more full genome PRRSV sequences globally.
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Risager PC, Fahnøe U, Gullberg M, Rasmussen TB, Belsham GJ. Analysis of classical swine fever virus RNA replication determinants using replicons. J Gen Virol 2013; 94:1739-1748. [PMID: 23580431 DOI: 10.1099/vir.0.052688-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Self-replicating RNAs (replicons), with or without reporter gene sequences, derived from the genome of the Paderborn strain of classical swine fever virus (CSFV) have been produced. The full-length viral cDNA, propagated within a bacterial artificial chromosome, was modified by targeted recombination within Escherichia coli. RNA transcripts were produced in vitro and introduced into cells by electroporation. The translation and replication of the replicon RNAs could be followed by the accumulation of luciferase (from Renilla reniformis or Gaussia princeps) protein expression (where appropriate), as well as by detection of CSFV NS3 protein production within the cells. Inclusion of the viral E2 coding region within the replicon was advantageous for replication efficiency. Production of chimeric RNAs, substituting the NS2 and NS3 coding regions (as a unit) from the Paderborn strain with the equivalent sequences from the highly virulent Koslov strain or the vaccine strain Riems, blocked replication. However, replacing the Paderborn NS5B coding sequence with the RNA polymerase coding sequence from the Koslov strain greatly enhanced expression of the reporter protein from the replicon. In contrast, replacement with the Riems NS5B sequence significantly impaired replication efficiency. Thus, these replicons provide a system for determining specific regions of the CSFV genome required for genome replication without the constraints of maintaining infectivity.
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Affiliation(s)
- Peter Christian Risager
- National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark
| | - Ulrik Fahnøe
- National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark
| | - Maria Gullberg
- National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark
| | - Thomas Bruun Rasmussen
- National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark
| | - Graham J Belsham
- National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark
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Töpfer A, Höper D, Blome S, Beer M, Beerenwinkel N, Ruggli N, Leifer I. Sequencing approach to analyze the role of quasispecies for classical swine fever. Virology 2013; 438:14-9. [PMID: 23415390 DOI: 10.1016/j.virol.2012.11.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
Abstract
Classical swine fever virus (CSFV) is a positive-sense RNA virus with a high degree of genetic variability among isolates. High diversity is also found in virulence, with strains covering the complete spectrum from avirulent to highly virulent. The underlying genetic determinants are far from being understood. Since RNA polymerases of RNA viruses lack any proof-reading activity, different genome variations called haplotypes, occur during replication. A set of haplotypes is referred to as a viral quasispecies. Genetic variability can be a fitness advantage through facilitating of a more effective escape from the host immune response. In order to investigate the correlation of quasispecies composition and virulence in vivo, we analyzed next-generation sequencing data of CSFV isolates of varying virulence. Viral samples from pigs infected with the highly virulent isolates "Koslov" and "Brescia" showed higher quasispecies diversity and more nucleotide variability, compared to samples of pigs infected with low and moderately virulent isolates.
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Affiliation(s)
- Armin Töpfer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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Abstract
Modulation of translation initiation efficiency on classical swine fever virus (CSFV) RNA can be achieved by targeted mutations within the internal ribosome entry site (IRES). In this study, cDNAs corresponding to the wild-type (wt) or mutant forms of the IRES of CSFV strain Paderborn were amplified and inserted into dicistronic reporter plasmids encoding Fluc and Rluc under the control of a T7 promoter. The mutations were within domains II, IIId(1), and IIIf of the IRES. The plasmids were transfected into baby hamster kidney (BHK) cells infected with recombinant vaccinia virus vTF7-3, which expresses the T7 RNA polymerase. IRES mutants with different levels of IRES activity were identified and then introduced by homologous recombination into bacterial artificial chromosomes (BACs) containing CSFV Paderborn cDNA downstream of a T7 promoter. From the wt and mutant BACs, full-length CSFV RNA transcripts were produced in vitro and electroporated into porcine PK15 cells. Rescued mutant viruses were obtained from RNAs that contained mutations within domain IIIf which retained more than 75% of the wt translation efficiency. Sequencing of cDNA generated from these rescued viruses verified the maintenance of the introduced changes within the IRES. The growth characteristics of each rescued mutant virus were compared to those of the wt virus. It was shown that viable mutant viruses with reduced translation initiation efficiency can be designed and generated and that viruses containing mutations within domain IIIf of the IRES have reduced growth in cell culture compared to the wt virus.
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Viral bacterial artificial chromosomes: generation, mutagenesis, and removal of mini-F sequences. J Biomed Biotechnol 2012; 2012:472537. [PMID: 22496607 PMCID: PMC3303620 DOI: 10.1155/2012/472537] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/21/2011] [Accepted: 10/27/2011] [Indexed: 12/29/2022] Open
Abstract
Maintenance and manipulation of large DNA and RNA virus genomes had presented an obstacle for virological research. BAC vectors provided a solution to both problems as they can harbor large DNA sequences and can efficiently be modified using well-established mutagenesis techniques in Escherichia coli. Numerous DNA virus genomes of herpesvirus and pox virus were cloned into mini-F vectors. In addition, several reverse genetic systems for RNA viruses such as members of Coronaviridae and Flaviviridae could be established based on BAC constructs. Transfection into susceptible eukaryotic cells of virus DNA cloned as a BAC allows reconstitution of recombinant viruses. In this paper, we provide an overview on the strategies that can be used for the generation of virus BAC vectors and also on systems that are currently available for various virus species. Furthermore, we address common mutagenesis techniques that allow modification of BACs from single-nucleotide substitutions to deletion of viral genes or insertion of foreign sequences. Finally, we review the reconstitution of viruses from BAC vectors and the removal of the bacterial sequences from the virus genome during this process.
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Leifer I, Hoeper D, Blome S, Beer M, Ruggli N. Clustering of classical swine fever virus isolates by codon pair bias. BMC Res Notes 2011; 4:521. [PMID: 22126254 PMCID: PMC3341591 DOI: 10.1186/1756-0500-4-521] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 11/29/2011] [Indexed: 11/29/2022] Open
Abstract
Background The genetic code consists of non-random usage of synonymous codons for the same amino acids, termed codon bias or codon usage. Codon juxtaposition is also non-random, referred to as codon context bias or codon pair bias. The codon and codon pair bias vary among different organisms, as well as with viruses. Reasons for these differences are not completely understood. For classical swine fever virus (CSFV), it was suggested that the synonymous codon usage does not significantly influence virulence, but the relationship between variations in codon pair usage and CSFV virulence is unknown. Virulence can be related to the fitness of a virus: Differences in codon pair usage influence genome translation efficiency, which may in turn relate to the fitness of a virus. Accordingly, the potential of the codon pair bias for clustering CSFV isolates into classes of different virulence was investigated. Results The complete genomic sequences encoding the viral polyprotein of 52 different CSFV isolates were analyzed. This included 49 sequences from the GenBank database (NCBI) and three newly sequenced genomes. The codon usage did not differ among isolates of different virulence or genotype. In contrast, a clustering of isolates based on their codon pair bias was observed, clearly discriminating highly virulent isolates and vaccine strains on one side from moderately virulent strains on the other side. However, phylogenetic trees based on the codon pair bias and on the primary nucleotide sequence resulted in a very similar genotype distribution. Conclusion Clustering of CSFV genomes based on their codon pair bias correlate with the genotype rather than with the virulence of the isolates.
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Affiliation(s)
- Immanuel Leifer
- Institute of Virology and Immunoprophylaxis (IVI), Sensemattstrasse 293, CH-3147 Mittelhäusern, Switzerland.
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Leifer I, Hoffmann B, Höper D, Bruun Rasmussen T, Blome S, Strebelow G, Höreth-Böntgen D, Staubach C, Beer M. Molecular epidemiology of current classical swine fever virus isolates of wild boar in Germany. J Gen Virol 2010; 91:2687-97. [PMID: 20660149 DOI: 10.1099/vir.0.023200-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Classical swine fever (CSF) has caused significant economic losses in industrialized pig production, and is still present in some European countries. Recent CSF outbreaks in Europe were mainly associated with strains of genogroup 2 (subgroup 2.3). Although there are extensive datasets regarding 2.3 strains, there is very little information available on longer fragments or whole classical swine fever virus (CSFV) genomes. Furthermore, there are no detailed analyses of the molecular epidemiology of CSFV wild boar isolates available. Nevertheless, complete genome sequences are supportive in phylogenetic analyses, especially in affected wild boar populations. Here, German CSFV strains of subgroup 2.3 were fully sequenced using two different approaches: (i) a universal panel of CSFV primers that were developed to amplify the complete genome in overlapping fragments for chain-terminator sequencing; and (ii) generation of a single full-length amplicon of the CSFV genome obtained by long-range RT-PCR for deep sequencing with next-generation sequencing technology. In total, five different strains of CSFV subgroup 2.3 were completely sequenced using these newly developed protocols. The approach was used to study virus spread and evolutionary history in German wild boar. For the first time, the results of our study clearly argue for the possibility of a long-term persistence of genotype 2.3 CSFV strains in affected regions at an almost undetectable level, even after long-term oral vaccination campaigns with intensive monitoring. Hence, regional persistence in wild boar populations has to be taken into account as an important factor in the continual outbreaks in affected areas.
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Affiliation(s)
- Immanuel Leifer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
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