Intra- and inter-genotypic size variation in the central variable region of the 9RL open reading frame of diverse African swine fever viruses

Abstract

African swine fever (ASF) viruses are characterised by numerous p72 genotypes, but by low levels of intra-genotypic variation, particularly in domestic pig associated genotypes. As it is precisely these viral lineages that are involved in outbreaks of the disease it is imperative that alternative, more informative gene regions be identified which are suitable for intra-genotypic resolution of relationships. To this end, the central variable region (CVR) of the 9RL open reading frame of diverse ASF viruses was amplified and product sizes scored and compared within and between genotypes. Results indicate that although product sizes are not genotype restricted, there is a high degree of intra-genotypic size variation particularly within the homogeneous p72 genotypes. Within one such genotype, the ESACWA virus genotype, 12 size-discrete CVR products were identified, four corresponding to viruses of west African origin and eight to viruses from countries where the disease is exotic, namely Europe, South America and the Caribbean. The high degree of size heterogeneity in the CVR of this genotype is significant and attests to the usefulness of the CVR gene marker in elucidating the epidemiology of African swine fever.