Genetic typing of classical swine fever virus

Three regions of the classical swine fever virus (CSFV) genome that have be en widely sequenced were compared with respect to their ability to discrimi nate between isolates and to segregate viruses into genetic groups. Sequenc e data-sets were assembled for 55 CSFVs comprising 150 nucleotides of the 5 ' non-translated region, 190 nucleotides of the E2 envelope glycoprotein ge ne and 409 nucleotides of the NS5B polymerase gene. Phylogenetic analysis o f 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 t he 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 ass ess 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 assignmen t, adapting rather than overturning the previous nomenclature divides CSF v iruses 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 sho uld improve the prospects of disease tracing in the future, and provide a b asis for a standardised approach to ensure that results from different labo ratories are comparable. (C) 2000 Elsevier Science B.V. All rights reserved .