Cellular insertions in the NS2-3 genome region of cytopathic bovine viral diarrhoea virus (BVDV) isolates

When compared to noncytopathic (ncp) bovine viral diarrhoea virus (BVDV), s ome cytopathic (cp) BVDV contain additional sequences in the NS2-3 genomic region. One of these insertions, which is 270 nucleotides long and of host origin (cINS), was first described for strain NADL. To find out how frequen tly this type of insertion occurs in other cp BVDV, 32 cp BVDV field isolat es and the BVDV reference cp strain Indiana were screened using RT-PCR whic h detected cINS in NADL. For most cp viruses an RT-PCR product of 402 bp in dicated the presence of NS2-3 genes without insertions. In addition, one or two DNA fragments, around 600-850 bp in size, were amplified from the geno mes of 13 cp viruses indicating the presence of insertions. Sequencing of t he PCR products, i.e. 402 bp DNA fragment (with no insertion) and longer fr agments (with insertion) revealed the location of the insertions in the NS2 -3 coding region of eight cp BVDV genomes. All of the insertions were confi rmed to be of the cINS type and were located in a very similar position to that found previously in the NADL genome. They were in the same reading fra me as the viral polypeptide and they encoded 90-140 amino acids. The 5' and 3' ends of the insertions were different in most of the cp isolates studie d. Interestingly, a 14-amino-acid stretch at the 5'-end of the insertion in the cp 5569 isolate as well as 15 amino acids at the 3'-end of the inserti on in the cp 5.19516 isolate were not homologous to the cINS sequence. No s ignificant matches for these stretches were found in the EMBL and Swissprot databases. (C) 2000 Elsevier Science B.V. All rights reserved.