Differentiation between vaccine strain and field isolates of classical swine fever virus using polymerase chain reaction and restriction test.

The CS vaccine strain of Classical Swine Fever Virus is a derivative from the LK parental strain that has been used in Russia for more than 30 years. A 10697 nucleotide fragment of the CS strain's genome has been sequenced. Sixteen unique restriction markers have been found in the CS genome comparing to the following strains: Alfort187, Alfort Tubingen, Brescia, CAP, Glentorf, ALD, GPE-, Chinese, C-strain, Riems, P97. Fourteen of these sites (AflII, AvaI, CfoI, Eco47II, HaeII, KpnI, MunI, NspI, PstI, ScaI, SmaI, SpeI, StyI, VspI) are only present in the CS strain genome. The 2 sites (BgII, NdeI) are present in all other genomes except for the genome of vaccine strain. A PCR/restriction test has been developed based on these findings in order to distinguish the vaccine strain from field isolates. Two pairs of nested primers and a criteria of analysis have been designed for each restriction marker site. The tests have been conducted first on the reference strains resulting in predicted restriction patterns. Finally, the tests have been applied to a number of field isolates obtained at different locations in Russia in different years. These results give further evidence that PCR/restriction tests can identify the LK and CS vaccines helping to avoid confusion with field strains.