New influenza A virus reassortments have been found in Danish swine in 2011

In 2011 a passive surveillance for influenza A virus was conducted in Danish swine. Tested samples were clinical samples from affected pigs submitted to the Danish National Veterinary Institute for swine influenza virus detection. In total 713 samples from 276 herds were analysed and about 24% of the samples were positive for swine influenza virus. All influenza positive samples were tested for the H1N1pdm09 virus by a real time RT-PCR assay specific for the pandemic HA gene and 26% of the samples were positive. Subtyping of 90 samples by sequencing revealed the presence of; i) H1N1 “avian like” viruses which have been circulating in Danish pigs since it was found for the first time in 1981. ii) H1N2 reassortant viruses which comprise HA from “avian like” H1N1 and NA from swine H3N2. The reassortant H1N2 virus was discovered in Danish pig for the first time in 2003 and is now well established in the Danish pig population. iii) H1N1pdm09 viruses which were found the first time in Danish pigs in January 2010. iv) Three new subtype variants comprising H1 “avian like” together with N2 “human like”, H1 pandemic with N2 “human like” and finally H1 pandemic with N2 from swine H3N2. The presence of N2 “human like” gene in Danish swine is new and genetic analysis indicate that it is most closely related to NA of human H3N2 viruses. In addition, full genome characterization of 40 viruses from the surveillance revealed the presence of additional new reassortments of which some have internal genes from the pandemic H1N1 virus.
This study contribute significantly to our knowledge of the epidemiology of swine influenza A virus circulating in Danish swine and the potential role of swine in the emergence of novel reassortant viruses.