Molecular epidemiology study of swine influenza virus revealing a reassorted virus H1N1 in swine farms in Cuba

•We describe the emergence of a novel H1N1 swine influenza virus in pigs.•The virus was originated from a reassortment event between the H1N1 pandemic influenza virus and classical swine influenza virus.•The gene constellation of the isolate is novel and unique.•The establishment of H1N1 pandemic influenza virus in swine is suggested to occur.

In this report, we describe the emergence of reassorted H1N1 swine influenza virus, originated from a reassortment event between the H1N1 pandemic influenza virus (H1N1p/2009) and endemic swine influenza virus in Cuban swine population. In November 2010, a clinical respiratory outbreak was reported on a pig fattening farm in Cuba. Phylogenetic analysis showed that all the genes of one of the isolate obtained, with the exception of neuraminidase, belonged to the H1N1p/2009 cluster. This finding suggests that H1N1pdm has been established in swine and has become a reservoir of reassortment that may produce new viruses with both animal and public health risks.