Bayesian coalescent analysis of pandemic H1N1 influenza A virus circulating in the South American region

► We have performed a Bayesian coalescent analysis of South American influenza viruses. ► The population dynamics is characterized by high evolutionary rates and fast growths. ► There is a significant contribution of first codon position to the evolutionary rate. ► Substitutions in all hemagglutinin epitope regions were found in a 178 days period. ► Analysis of neuraminidase proteins revealed epitope differences with vaccine strain.