The infectious pancreatic necrosis virus (IPNV; genus Aquabirnavirus) affects salmon and trout, causing high mortality in first-feeding fry. The classification of this virus includes nine serotypes and seven genogroups. In Mexico, two different isolates were identified in 2000 and 2008, respectively. Both isolates were classified into genogroup I according to the RNA genome of this virus. As Mexico is importing rainbow trout Oncorhynchus mykiss eggs from different countries, the aim of this study was to genotype IPNV isolates obtained from four rainbow trout producer regions within the state of Mexico. We utilized a fragment of the VP2* (outer capsid protein) gene sequence of Mexican IPNV isolates as a molecular marker to determine the genogroup to which they belong. Although all Mexican IPNV isolates were grouped into genogroup I, we identified genetic diversity among these isolates, and 14 unique nucleotide sequence types were associated with the four producer regions in Mexico State.

The infectious pancreatic necrosis virus (IPNV) affects several species of freshwater and marine fish. In Mexico, IPNV has an important impact on farming of rainbow trout Oncorhynchus mykiss; however, IPNV distribution in Mexico is unclear. The diagnosis of IPNV is laborious; usually it is based on isolation tests in cell culture followed by immunological identification using techniques of serum neutralization, immunofluorescence, or enzyme-linked immunosorbent assay. It has recently been demonstrated that reverse transcriptase polymerase chain reaction (RT-PCR) is an adequate method for the detection of aquatic birnaviruses. However, its diagnostic use is still limited because very low titers of viable virus cannot be easily detected. In this study, a combination of short-time cell culture and multiplex RT-PCR was established for the diagnosis of IPNV in rainbow trout obtained from farms in the state of Mexico. Three primer sets were used in a single reaction in the multiplex RT-PCR to increase the probability of identifying all serotypes of IPNV serogroup A as well as to help prevent a false-negative result. This approach was able to identify samples with an IPNV concentration of just 0.01 tissue culture infective dose with 50% endpoint (TCID50)/mL, and it identified more infected fish than RT-PCR alone or first-passage cell culture alone. Moreover, this technique made the same identifications as second-passage cell culture but in approximately 30% of the time needed for second-passage cell culture. Consequently, the time and cost efficiency of IPNV diagnosis were greatly reduced.