Determination and analysis of the complete genome sequences of a vaccine strain and field isolate of Lumpy Skin Disease Virus (LSDV)

Abstract

In this study, the genomes of both the attenuated South African lumpy skin disease virus (LSDV) Neethling vaccine strain (LW) and a virulent field isolate from a recent outbreak namely the South African lumpy skin disease virus (LSDV) Neethling Warmbaths isolate (LD) have been cloned, sequenced and analysed. The genomic sequences of the South African LSDV Neethling Warmbaths isolate (LD) and the South African LSDV Neethling vaccine strain (LW), were compared to each other. The virulent South African isolate, LD was also compared to the previously sequenced virulent LSDV Neethling strain 2490 (LK), to determine molecular differences. The LSDV genome is approximately 150 kbp in size and consists of 156 putative genes. Of the 156 potential encoded proteins of the virulent LSDV field isolates, the South African LSDV Neethling Warmbaths isolate (LD) and the LSDV Kenyan Neethling strain 2490 (LK), 120 were identical, 21 showed differences of a single amino acid, 7 showed two amino acid differences, while only one showed three amino acid differences. These were mostly found in the variable terminal regions. The LSDV Kenyan Neethling strain 2490 (LK) was isolated in Kenya in 1958 and than re-isolated in 1987 from lesions of an experimentally infected cow (Tulmanet al. 2001). The South African LSDV Neethling Warmbaths isolate (LD) was isolated from lesions of a severely infected calf in the Northern Province of the Republic of South Africa, on the farm Bothasvlei in 2001 (David Wallace, Biotechnology Division, Onderstepoort Veterinary Institute, Republic of South Africa; Personal communication, 2001). Considering the geographically distant African regions of the isolates, namely South Africa (LD) and Kenya (LK) as well as the time when these viruses were isolated, minimal genetic variation was observed thereby suggesting that lumpy skin disease virus is genetically stable. When the attenuated vaccine strain (L W) was compared with the South African field isolate LD, a total of 480 amino acid differences were observed in 121 of the 156 potential encoded proteins. These were again mainly in genes of the terminal regions and a number of these led to frameshifts that caused truncated open reading frames (ORFs) as well as deletions of up to nine amino acids and insertions of up to 42 amino acids. These modified open reading frames (ORFs) encode proteins that are involved in various aspects, such as the regulation of host immune responses [a soluble interferon (IFN)-gamma receptor, and an interleukin-l (IL-l) receptor-like protein], gene expression (mutT motif proteins), DNA repair (superoxide dismutase), host-range specificity (ankyrin-repeat protein, kelch-like proteins) including proteins with unassigned functions. These differences could lead to a reduction in immuno evasive mechanisms and virulence factors present in attenuated LSDV strains. At this stage, it is not possible to define which amino acid differences in particular are responsible for dramatic alterations in viral virulence. A good indication, however are differences occurring in functional domains. A mutation in a trans-membrane region, for example, could alter the levels of secretion of a protein involved in the regulation of the host immune response. We conclude that the attenuated effect is likely to be the sum of the altered phenotypes of the expressed proteins, although it is also likely that a few specific proteins carry more weight. Further studies to determine the functions of the relevant encoded gene products will hopefully confirm this. The molecular design of an effective vaccine is likely to be based on the strategic manipulation of such genes.