Dating the emergence of Influenza A (H5N1) Virus

Abstract

Since the first detection of highly pathogenic avian influenza (H5N1) virus in geese in Guangdong, China, H5N1 viruses have transmitted to poultry throughout southern China. In late 2003 the first transmission wave spread the virus to multiple Southeast Asian countries. In May 2005, the second transmission wave of H5N1 virus westwards to Europe and Africa was initiated following a major outbreak in migratory birds at Qinghai Lake, China, while a third transmission wave has been initiated since mid-2005. Those viruses are now endemic in poultry populations in some affected regions and cause repeated outbreaks in poultry and increasing human infection cases, creating persistent pandemic concerns. Genetic data from systematic surveillance of H5N1 for the past seven years in marketing poultry, along with sequence data from outbreaks throughout the region, provide us with a unique opportunity to estimate the most recent common ancestor (MRCA) and postulate the dates of introduction of H5N1 variants into different affected countries. In this study, we estimated the time of emergence of those three transmission waves …