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A single nucleotide polymorphism within EHV-1 gene ORF 30, which encodes for the viral DNA polymerase, allows the differentiation of the neuropathogenic (G2254) from non-neuropathogenic genotype (A2254). The aim of our study was to investigate the distribution of the neuropathogenic and non-neuropathogenic genotype of EHV-1 isolates associated with abortions in Germany. To determine the nucleotide sequence at the polymorphic site the amplification product of ORF 30 gene specific nested PCR was digested with restriction enzyme SalI and sequenced. Thirty-two EHV-1 isolates from six abortion outbreaks and 34 archived isolates from individual cases were obtained between 1987 and 2009 from stud farms in different regions of Germany. 89.4% (59/66) of the EHV-1 abortion isolates was of non-neuropathogenic genotype (N752/A2254) and 10.6% (7/66) contained the neuropathogenic marker (D752/G2254). Two out of seven EHV-1 abortion isolates with the mutation (G2254) came from the same outbreak and were derived from mares with neurological signs. Interestingly, the semen of a stallion from the same stud was tested positive for the neuropathogenic genotype (G2254) too. The other five EHV-1 strains came from individual abortion cases with no neurological signs. In addition to the A2254 to G2254 substitution, two EHV-1 reference strains (Ab4 and RacH) and one field isolate from an individual abortion case showed an exchange of adenine to cytosine at position 2258. In sum, we confirmed coherence between the occurrence of abortions and the non-neuropathogenic EHV-1 (A2254), but 10.6% of the abortion strains carried the mutation (G2254). The relevance of this finding as well as the role of the additional mutation and of stallions as carriers should be further investigated.