Bovine viral diarrhea virus resistance in the bovine kidney CRIB cell line is not from disruption of PTPN12, GRID2, and RABGAP1L genes

Bovine viral diarrhea virus (BVDV) entry into bovine cells involves attachment of virions to cellular receptors, internalization, and pH-dependent fusion with endosomal membranes. The primary host receptor for BVDV is CD46; however, the complete set of host factors required for virus entry is unknown. The bovine Madin-Darby bovine kidney (MDBK) cell line is susceptible to BVDV infection, while a derivative cell line (CRIB) is resistant at the level of virus entry. We performed complete genome sequencing of these two cell lines to determine genomic variation underlying the change to the resistant phenotype with the aim of identifying host factors essential for BVDV entry. Comparative genome analyses identified three large compound deletions in the BVDV-resistant CRIB cell line that were predicted to disrupt the expression or function of the genes PTPN12, GRID2, and RABGAP1L. However, CRISPR/Cas9 mediated knockout of these genes, individually or in combination, in the parental MDBK cell line did not impact virus entry or replication. Therefore, resistance to BVDV in the CRIB cell line is not due to the apparent loss of PTPN12, GRID2, or RABGAP1L gene function. Identifying the functional cause of BVDV resistance in the CRIB cell line may require more detailed comparisons of the genomes and epigenomes.