Phylogenetic visualization of the spread of H7 influenza A viruses

Official URL: http://dx.doi.org/10.1111/cla.12107

Viruses of influenza A subtype H7 can be highly pathogenic and periodically infect humans. For example, there have been numerous outbreaks of H7 in the Americas and Europe since 1996. More recently, a reassortant H7N9 has emerged among humans and birds during 2013–2014 in China, Taiwan and Hong Kong. This H7N9 genome consists of genetic segments that assort with H7 and H9 viruses previously circulating in chickens and wild birds in China and ducks in Korea. Epidemic risk modellers have used agricultural, climatic and demographic data to predict that the virus will spread to northern Vietnam via poultry. To shed light on the traffic of H7 viruses in general, we examine genetic segments of influenza that have assorted with many strains of H7 viruses dating back to 1902. We focus on use cases from the United States, Italy and China. We apply a novel metric, betweenness, an associated phylogenetic visualization technique, transmission networks, and compare these with another technique, route mapping. In contrast to traditional views, our results illustrate that segments that assort with H7 viruses are spread frequently between the Americas and Eurasia. In summary, genetic segments that historically assort with H7 influenza viruses have been spread from China to: Australia, Czech Republic, Denmark, Egypt, Germany, Hong Kong, Italy, Japan, Mongolia, the Netherlands, New Zealand, Pakistan, South Africa, South Korea, Spain, Sweden, the UK, the US, and Vietnam.