New real-time reverse transcriptase polymerase chain reactions facilitate detection and differentiation of novel A/H1N1 influenza virus in porcine and human samples

Influenza A viruses are maintained as a quasispecies cloud in several natural host reservoirs of avian as well as mammalian species. Accidental host exposure, selection and further adaptation of individual influenza A viruses during sporadic trans-species transmission may eventually lead to the establishment of new, stably circulating lineages in a new, possibly mammalian, host species. Given a high transmissibility of such a virus and a susceptible, immunologically naive population, pandemic spread of such viruses within a short time may ensue. In April 2009, a novel multi-reassortant influenza A virus of subtype H1N1 has emerged and regionally spread in humans in Mexico and the United States causing flu-like symptoms. Until June 2009 increasing levels of a multiregional, global spread of this virus prompted the WHO to raise the pandemic alert to the highest level. Data from experimental infections in pigs as well as experience from natural outbreaks in swine farms world-wide have shown that porcine populations are fully susceptible to the new virus and are able to sustain uninterrupted transmission chains. A broad front incursion of the new human pandemic virus into the porcine population would have a significant negative impact on measures to restrict further spread of the virus in the human population. Therefore, sensitive tools for monitoring and detection of such an incursion in a timely manner are mandatory. We have developed two real-time RI PCRs which are specific for the hemagglutinin gene of the novel A/H1N1 virus and which allow detection of infected pigs with high sensitivity. These PCRs may become useful tools in future surveillance programmes.