ARS | Publication request: Emerging Pestiviruses

Submitted to: UJNR Food & Agricultural Panel Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: December 18, 2009
Publication Date: January 20, 2010
Citation: Ridpath, J.F., Bayles, D.O., Neill, J.D., Kirkland, P.D., Finlaison, D.S., Frost, M.J. 2010. Emerging Pestiviruses [abstract]. UJNR Food & Agricultural Panel. p. 114-115.

Technical Abstract: Currently four species of pestiviruses are recognized by the International Committee on Viral Taxonomy (ICTV). They are bovine viral diarrhea virus genotype 1 (BVDV1), bovine viral diarrhea virus genotype 2 (BVDV2), border disease virus (BDV), and classical swine fever virus (CSFV). A tentative species, pestivirus of giraffe (giraffe), has also been recognized. The ICTV’s basis for recognition of species is at least a 25% difference in sequence identity. The goal of this study was to look at conserved and variable domains among recognized and emerging pestiviruses and determine differences if a pestivirus isolated in the U.S. from pronghorn antelope (Antilocopra americana) (pronghorn) and a pestivirus isolated from pigs in Australia (bungowannah) would qualify as members of two new pestivirus species. Full length sequences of pronghorn and bungowannah were generated. These sequences were compared with published sequences derived from BVDV1 strains, BVDV2 strains, BDV strains, CSFV strains, and giraffe. Polyclonal antisera against BVDV1, BVDV2, BDV, and pronghorn were produced in goats. Phylogenetic trees constructed using the unrooted geometric means analysis method (UPGMA) revealed that pronghorn and bungowannah were relatively distant (> 60% difference in sequence identity) from the recognized pestivirus species. The highest conservation among the viruses compared, within the open reading frame, was in regions coding for the Npro, capsid, Erns, NS3 and NS5b proteins. The most highly conserved domains were those coding for the Npro endopeptidase, the NS3 serine protease, the NS3 helicase ,and NS5b RNA-dependent RNA polymerase. While the region coding for the NS2 was highly variable, predicted transmembrane regions in the NS2 were highly conserved. The cleavage sites within the polyprotein that are targets for viral proteases Npro (Npro/capsid) and NS2-3 (NS2-3/NS4a, NS4a/NS4b, NS4b/NS5a, NS5a/NS5b) were highly conserved among all viruses examined. A high degree of similarity was seen both among the NS2-3 cleavage sites within a viral genome and between the genomes of different viruses. In contrast, the cleavage sites that theoretically are cleaved by host supplied proteases (capsid/Erns, Erns/E1, E1/E2) were poorly conserved. Sequence variation in the 5’ UTR resulted in the failure of published “pan-pestivirus” PCR primers to amplify bungowannah virus. Attempts to design new “pan-pestivirus” PCR primers based on conserved sequences in the NS3 region yielded several promising primer sets. Very limited antigenic cross reactivity (= 1:4) was observed between pronghorn and bungowannah and the recognized pestiviruses. Based on the criteria for pestivirus speciation set by the ICVT pronghorn and bungowannah represent two new species of pestivirus. These two new species are distant from the recognized pestivirus species of BVDV1, BVDV2, BDV and CSFV, and each other. Further, cross neutralization revealed very limited cross reactivity. Higher conservation observed in some coding regions may exploited in the design of antivirals and diagnostics.