Molecular analysis of bovine viral diarrhoea virus isolates from South Africa.

The presence of bovine viral diarrhoea virus in South Africa has been confirmed by several serological surveys. However, little is known about its biological properties. Twenty five isolates obtained by isolation in tissue culture and detected by means of the antigen capture ELISA from clinically sick cattle and from foetal calf serum in South Africa were characterized on the basis of analysis of the 5' non-translated (NTR) region of the genome. A reverse-transcription polymerase chain reaction (RT-PCR) was used to amplify specific sequences from the 5'NTR of the genome. The oligonucleotide primers corresponding to positions 105-125 and 399-378, respectively, in the sequence of BVDV strain NADL were used to generate the PCR products. Both strands were sequenced directly with these primers and fluorescence-labelled dideoxynucleotides in an automated nucleic acid sequencer. Reference strains of pestiviruses [(BVDV type I, BVDV type II, border disease virus (BDV) and hog cholera virus (HCV)] and isolates from a previous investigation on BVDV in southern Africa were included for comparative purposes. All the BVDV strains obtained during this study belong to subgroups of BVDV genotype I. No association could be demonstrated between the geographic origin of the isolates. A number of isolates formed another branch separate from the existing branches Ia, Ib and Ic. These findings suggest that extensive genetic diversity can be found within BVDV type I isolates from southern Africa. Isolates that group with the classical BVDV type I strains, particularly of American origin, coexist with variants that appear to represent a local genetic pool and or variants evolving from the classical strains.