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Background  Influenza H7N9 has become an endemic pathogen in China where circulating virus is found extensively in wild birds and domestic poultry. Two epidemic waves of Human H7N9 infections have taken place in Eastern and South Central China during the years of 2013 and 2014. In this study, we report on the first four human cases of influenza H7N9 in Shantou, Guangdong province, which occurred during the second H7N9 wave, and the subsequent analysis of the viral isolates.    Methods  Viral genomes were subjected to multisegment amplification and sequenced in an Illumina MiSeq. Later, phylogenetic analyses of influenza H7N9 viruses were performed to establish the evolutionary context of the disease in humans.    Results  The sequences of the isolates from Shantou have closer evolutionary proximity to the predominant Eastern H7N9 cluster (similar to A/Shanghai/1/2013 (H7N9)) than to the Southern H7N9 cluster (similar to A/Guangdong/1/2013 (H7N9)).    Conclusions  Two distinct phylogenetic groups of influenza H7N9 circulate currently in China and cause infections in humans as a consequence of cross-species spillover from the avian disease. The Eastern cluster, which includes the four isolates from Shantou, presents a wide geographic distribution and overlaps with the more restricted area of circulation of the Southern cluster. Continued monitoring of the avian disease is of critical importance to better understand and predict the epidemiological behaviour of the human cases.    Electronic supplementary material  The online version of this article (doi:10.1186/s12879-015-0829-8) contains supplementary material, which is available to authorized users.

Genetic diversity of the 2013–14 human isolates of influenza H7N9 in China