Swine Leukocyte Antigen Class-II Region Is Associated with Variation in Porcine Circovirus 2b Susceptibility

Porcine circovirus type 2 (PCV2) alters innate and adaptive immune response, changes that could lead to susceptibility to Porcine Circovirus Associated Diseases (PCVAD). Crossbred pigs (n=974) experimentally infected with PCV2b were used to map genetic sources of variation in PCV2-susceptibility. A genome-wide association study including 56,433 SNPs uncovered two loci that explain 14% of the genetic variation for viral load. The position of the major locus is currently undetermined, predicted to be located on SSC12. The second locus explained 2.8% of the variation and mapped to SSC7 (29.3Mb), near swine leukocyte antigen class-II (SLAII). The favorable CC genotype was associated with lower viral load and viremia at 21 d and 28 d  (P < 0.05) compared to CT and TT genotypes and higher wk 3, wk 4 and overall ADG (P < 0.05) compared to CT genotype. The frequency of the unfavorable T allele varied from 0.08 to 0.37, with the TT genotype being rare across the genetic lines. Targeted sequencing of SLAII genes such as the polymorphic DQB1 uncovered nine class haplotypes and high proportion of non-synonymous polymorphic codons (16.2%). Thirty-five of these amino acid substitutions were located in the antigen recognition domain, with six of them having an effect on viral load (P < 0.05) in a subset of high and low viremic pigs (n = 274). These changes at the peptide level may affect the ability of the immune system to recognize and respond to specific pathogens such as PCV2 or have a broad role on immunity.