Dan Janies, Department of Bioinformatics and Genomics
Influenza A subtype H7 is a transboundary viral disease that includes highly pathogenic strains. Traditionally two clusters of related viruses have been observed, one in the Americas and another in Eurasia. H7 subtype viruses have infected Aves throughout Asia, Australia, Europe, and North America and Equidae in Brazil. H7 periodically infects humans - including the events of Spring 2013 in China. Here we develop and use phylogenetics and interactive visualization techniques to study the spread of H7 viruses over time, space, and various, hosts. We focus on historical data ranging from 1902 to January 2013 and on the Spring 2013 emergence of H7N9 in Eastern China. We find multiple occurrences of transboundary and transcontinental spread, both within and between the previously observed American and Eurasian clusters. Our results indicate that H7 influenza virus transboundary spread has occurred multiple times that patterns of spread differ by gene, indicating viral reassortment. Case in point is the China-Taiwan H7N9 outbreak, which was caused by a virus made of genetic segments previously circulating in chickens in China and ducks in Korea. Some segments have international connections to and from China-Taiwan to neighboring countries. H7N9 has reemerged in late 2013 in Southern China and Hong Kong. As a means to understand the trajectory of this outbreak we examine the historical globaltransmission of H7 viruses across time space and various hosts. Based on the global spread of genes that have been part of H7 we conclude that there is a high probability that H7N9 willspread beyond China, Taiwan, and Hong Kong. Historically, genes from H7 viruses have spread from China to at least 16 countries. Spread of H7 from China has been common for Australia, Czech Republic, Japan Netherlands, Pakistan,Hong Kong, Vietnam, and South Africa.