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      Genome Sequence of Classical Swine Fever Virus Genotype 1.1 with a Genetic Marker of Attenuation Detected in a Continuous Porcine Cell Line

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          Abstract

          The complete genome sequencing and analysis of a classical swine fever virus (CSFV) detected in a porcine kidney cell line revealed a close relationship with genotype 1.1 viruses circulating in India and China. The presence of consecutive T insertions in the 3′ untranslated region (UTR), as seen in vaccine strains of CSFV, suggested some degree of attenuation.

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          Genetic typing of classical swine fever virus.

          D.J. Paton, A McGoldrick, I Greiser-Wilke … (2000)
          Three regions of the classical swine fever virus (CSFV) genome that have been widely sequenced were compared with respect to their ability to discriminate between isolates and to segregate viruses into genetic groups. Sequence data-sets were assembled for 55 CSFVs comprising 150 nucleotides of the 5' non-translated region, 190 nucleotides of the E2 envelope glycoprotein gene and 409 nucleotides of the NS5B polymerase gene. Phylogenetic analysis of each data-set revealed similar groups and subgroups. For closely related viruses, the more variable or larger data-sets gave better discrimination, and the most reliable classification was obtained with sequence data from the NS5B region. No evidence was found for intertypic recombination between CSFVs. A larger data-set was also analysed comprising 190 nucleotides of E2 sequence from 100 CSFVs from different parts of the world, in order to assess the extent and global distribution of CSFV diversity. Additional groups of CSFV are evident from Asia and the nomenclature of Lowings et al. (1996) [Lowings, P., Ibata, G., Needham, J., Paton, D., 1996. J. Gen. Virol. 77, 1311-1321] needs to be updated to accommodate these. A tentative assignment, adapting rather than overturning the previous nomenclature divides CSF viruses into three groups with three or four subgroups: 1.1, 1.2, 1.3; 2.1, 2.2, 2.3; 3.1, 3.2, 3.3, 3.4. The expanding data-base of CSFV sequences should improve the prospects of disease tracing in the future, and provide a basis for a standardised approach to ensure that results from different laboratories are comparable.
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            Molecular characterization of pestiviruses.

            Abby G Meyers, William Thiel (1995)
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              Attenuated lapinized chinese strain of classical swine fever virus: complete nucleotide sequence and character of 3'-noncoding region.

              H Wu, J. Wang, C. Zhang … (2001)
              The complete nucleotide sequence including precise 5'- and 3'-terminal non-coding regions (NCRs) of the attenuated lapinized Chinese strain (HCLV) of Classical Swine Fever Virus (CSFV) was determined from overlapping cDNA clones constructed by separated RT-PCR and rapid amplification of cDNA ends (RACE) methods. The genomic RNA of the HCLV strain consists of 12.310 nucleotides (nts) including 374 nts and 242nts in the 5'- and 3'-NCRs, respectively. It contains one large open reading frame (ORF) encoding a polyprotein of 3,898 amino acids with a calculated molecular weight of 437.6 kDa. There is one notable insertion of 12 continuous nts, CTTTTTTCTTTT in the 3'-NCR of HCLV genomic cDNA when compared with its parental virulent Shimen strain. Sequence alignment of partial 3'-NCR reveals two groups of CSFV vaccine strains carrying similar T-rich insertions at different positions in this region. Computer-predicted secondary structures suggest that T-rich insertion greatly change the structures and thus decrease the promoter functions of 3'-NCRs during the replications of these two groups of CSFV vaccine strains.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 30 April 2015
                Publication date Collection: Mar-Apr 2015
                Volume: 3
                Issue: 2
                Electronic Location Identifier: e00375-15
                Affiliations
                [a ]Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
                [b ]Department of Veterinary Pathology, College of Veterinary Science, CAU, Aizawl, Mizoram, India
                [c ]Department of Bioscience & Biotechnology, Banasthali University, Rajasthan, India
                Author notes
                Address correspondence to G. Saikumar, saikumarivri@ 123456gmail.com .
                Article
                Publisher ID: genomeA00375-15
                DOI: 10.1128/genomeA.00375-15
                PMC ID: 4417697
                PubMed ID: 25931601
                SO-VID: a107ede0-96f5-4246-983b-5ee097631fcf
                Copyright © Copyright © 2015 Tomar et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                Date received : 17 March 2015
                Date accepted : 19 March 2015
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 4, Pages: 1, Words: 925
                Categories
                Subject: Viruses
                Custom metadata
                cover-date March/April 2015
                access-type free

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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