Spatiotemporal analysis of the genetic diversity of seal influenza A(H10N7) virus, Northwestern Europe

Influenza A viruses are major pathogens for humans, domestic animals and wildlife that cross the species barrier occasionally. In spring 2014, increased mortality of harbor seals (Phoca vitulina) was reported in Sweden and Denmark, associated with infection with an influenza A(H10N7) virus. Within a few months, this virus spread to seals of the coastal waters of Germany and the Netherlands, causing the death of thousands of animals. Genetic analysis of the hemagglutinin (HA) and neuraminidase (NA) genes of this seal influenza A(H10N7) virus revealed that it was most closely related to various avian influenza A(H10N7) viruses. The collection of samples from infected seals during the course of the outbreak provided an unique opportunity to follow the adaptation of this avian virus to its new seal host. Sequence data was obtained from samples collected from 41 different seals from four different countries between April 2014 and January 2015 using Sanger sequencing and next-generation sequencing to describe the molecular epidemiology of the seal influenza A(H10N7) virus. The majority of sequence variation occurred in the HA gene, and some mutations corresponded with amino acid changes not found in H10 viruses isolated from Eurasian birds. Also, sequence variation in the HA gene was greater at the beginning than at the end of the epidemic, when a number of the mutations observed earlier had been fixed. These results imply that when an avian influenza virus jumps the species barrier from birds to seals, amino acid changes in the HA may occur rapidly and are important for virus adaptation to its new mammalian host. Importance Influenza A viruses are major pathogens for humans, domestic animals and wildlife. In addition to the continuous circulation of influenza A viruses among various host species, cross-species transmission of influenza A viruses occurs occasionally. Wild waterfowl and shorebirds are the main reservoir for most influenza A virus subtypes, and spillover of influenza A viruses from birds to humans or other mammalian species may result in major outbreaks. In the present study, various sequencing methods were used to elucidate the genetic changes that occurred after the introduction and subsequent spread of an avian influenza A(H10N7) among harbor seals of Northwestern Europe using various samples collected during the outbreak. Such detailed knowledge of genetic changes necessary for introduction and adaptation of avian influenza A viruses to mammalian hosts is important for a rapid risk assessment of such viruses soon after they cross the species barrier.