Genotyping and phylogenetic analysis of bovine viral diarrhea virus isolates from BVDV infected alpacas in North America

Over a three-year period, 2004-2007, greater than 12,000 alpacas in the United States were screened by real-time RT-PCR to identify alpacas persistently infected (PI) with bovine viral diarrhea virus (BVDV). A total of 46 BVD viruses were isolated from PI alpacas or diagnostic samples from alpacas. Forty-three US alpaca BVDV isolates and 3 Canadian isolates were analyzed by comparison of nucleotide sequences of two viral genomic regions, the 5′-UTR and the N^pro gene to determine their genetic relatedness. All 46 alpaca BVDV isolates from 8 different states of the US and Canada were genotype 1b with ≥99% nt identity in the 290-base 5′-UTR region with the exception of one Canadian isolate. In contrast, 21 bovine BVDV isolates collected during the same period were grouped into the typical 3 genotypes, 1a, 1b, and 2, respectively. Forty five alpaca BVDV isolates formed a distinctive cluster separated from closely related bovine genotype 1b isolates by phylogenetic analysis of the 5′-UTR region. Comparison of the 504-base N^pro gene sequences of 32 alpaca isolates also assigned them all to type 1b in a similar fashion as observed with the 5′-UTR region. The results suggest that unique genotypes of bovine BVDV 1b may be maintained in the alpaca population even though camelids are susceptible to infection by other genotypes. Further studies are needed to address why alpacas were predominantly infected with genotype 1b BVDV isolates and how bovine BVD viruses evolved to infect alpacas.