Spatial and temporal patterns of genentic variation of H1N1 influenza viruses in China in the 2009 pandemic

ii ACKNOWLEDGEMENTS Thank my advisor Margaret Carrel for her mentoring during these two years. Her intelligence and passion as a scholar and her kindness have influenced me so much, and I am truly blessed for having her as my advisor. Thank Professor Gerard Rushton for his mentoring and sincere words. Thank all my teachers through this program, you all make me even more passionate about public health, about science. Thank my dear friends who have been loving and supporting me through all the happy and frustrating periods. They are the best thing that happen to me during these two years. I could not be more thankful for all of their love and support. Thank my amazing family for their understanding and support. Thank my mom for always being there for me, for being so strong, supportive and open-minded. Thank Geography department for having me as a master student, I truly enjoyed being here and learned so much through the program. I am very grateful for being a part of this amazing department. iii ABSTRACT The 2009-2010 H1N1 influenza pandemic was caused by a novel strain, made up of genetic material from human, swine and avian influenza viruses. While the 2009 H1N1 strain originated in Mexico, Southeast Asia, and southern China in particular, remains the putative epicenter of new viral emergence. The aim of this study is to improve our understanding of the role of population, environmental, and cultural variables on the evolution of Influenza A viruses in China. Using genetic and epidemiological information from 433 H1N1 viral isolates taken during the 2009-2010 pandemic in China, we examined the spatial and temporal characteristics of viruses in concert with their genetic characteristics, identifying the spatial and temporal diffusion patterns. Then we applied Moran's I test to see if the gene distances of the H1N1 virus are spatially autocorrelated. We then explored the suspected factors driving the evolution of H1N1 viruses during the pandemic. Regression methods were applied to test the association of H1N1 virus's spatial and temporal patterns with environmental, social and biological variables. Variables considered in the regression included temperature and humidity, railway transportation, population density, morbidity of H1N1, population's accessibility to tap water, and sampled patient's age. We find that during the 2009-2010 pandemic H1N1 influenza viruses evolved more through time, that further evolved strains have a trend of spreading from Northern China to Southern China, and continued evolving in …