Background: The genomes of several infectious pancreatic necrosis virus (IPNV) isolated in Chile were sequenced, by using a single amplification approach for both segments A and B. The obtained sequences were used to investigate how conserved were the primer binding regions used in PCR-based diagnosis methods described in literature. The analysis allowed us to study the robustness of each technique, which could be affected in the eventual case of further mutations within the primer binding sites.

Results: Analysis showed that most of the methods to detect Chilean IPNV varieties are currently adequate. However, the primers themselves were designed in function of specific genogroups, implying that most detection methods present some level of risk for detecting all strains present in the country, since genogroups 1 and 5 coexist.

Conclusions: Considering IPNV high genomic variability, negative results must be taken with caution. The use of detection techniques (qRT-PCR) based on degenerate primers should be considered to minimize possibilities of false negative detections.