Strategy for RT-PCR and nucleotide sequencing. The 5´-terminal portion of the classical swine fever virus genome encompassing parts of the 5´ nontranslated region (NTR) and the region encoding the N-terminal autoprotease Npro and the structural proteins C, Erns, E1, and E2 was amplified by RT-PCR in three overlapping amplicons (PCR1, PCR2 and PCR3). The analyzed regions include the commonly used 5´NTR fragment (150 nt) and E2 fragment (190 nt) sequences. Location of primers (indicated by arrows) and sequence length of the 5´NTR-E2 region (3508–3510 nt) correspond to the sequence of CSFV strain Alfort187 [GenBank: X87939] and can differ between the isolates due to presence or absence of nucleotides in the 5´NTR. Further information on all primers is given in Table 3.