Bovine viral diarrhea virus’s (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 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 each to identify genomic variation underlying the resistant phenotype with the aim of identifying host factors essential for BVDV entry. Three large compound deletions in the BVDV-resistant CRIB cell line were identified and predicted to disrupt the function or expression 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 spontaneous 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.
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Funding for this research was provided by the USDA, ARS appropriated project 3040-32000-034-00D.
The datasets produced during this study are available in the NCBI BioProject repository under accession PRJNA761701 (MDBK, CRIB, and MDBK knockout clone WGS and MDBK and CRIB RNASeq).
The following are available online at https://www.mdpi.com/article/10.3390/v13112147/s1, Table S1. Gene names and ARS-UCD1.2 coordinates for the top three homozygous deletions in MDBK-CRIB cell line comparison. Figure S1. Integrative Genomics Viewer session showing MDBK+_CRIB- BED file. The materials are also available for download as the additional file listed at the end of this record.
Workman, Aspen M.; Heaton, Michael P.; Webster, Dennis A.; Harhay, Gregory P.; Kalbfleisch, Theodore S.; Smith, Timothy P. L.; Falkenberg, Shollie M.; Carlson, Daniel F.; and Sonstegard, Tad S., "Evaluating Large Spontaneous Deletions in a Bovine Cell Line Selected for Bovine Viral Diarrhea Virus Resistance" (2021). Maxwell H. Gluck Equine Research Center Faculty Publications. 62.