H7N9 virus has caused five infection waves since it emerged in 2013. The highest number of human cases was seen in Wave Five; however, the underlying reasons have not been thoroughly elucidated. In this study, the geographical distribution, phylogeny and genetic evolution of 240 H7N9 viruses in Wave Five, including 35 new isolates from patients and poultry in nine provinces, were comprehensively analyzed together with strains from first four waves. Geographical distribution analysis displayed the newly-emerging highly pathogenic (HP) and low pathogenic (LP) H7N9 viruses were co-circulating, causing human and poultry infections across China. Genetic analysis indicated that dynamic reassortment of the internal genes among LP-H7N9/H9N2/H6Ny and HP-H7N9, as well as the surface genes between Yangtze and Pearl River Delta lineages resulted in at least 36 genotypes, with three major genotypes (G1, A/chicken/Jiangsu/SC537/2013-like, G3, A/Chicken/Zhongshan/ZS/2017-like and G11, A/Anhui/40094/2015-like). The HP-H7N9 likely evolved from G1 LP-H7N9 by the insertion of a “KRTA” motif at the cleavage site (CS), then evolved into fifteen genotypes with four different CS motifs including PKGKRTAR/G, PKGKRIAR/G, PKRKRAAR/G and PKRKRTAR/G. Approximately 46% (28/61) of HP strains belonged to G3. Importantly, neuraminidase (NA) inhibitor resistance (R292K in NA) and mammalian adaptation (eg. E627K and A588V in PB2) mutations were found in a few non-human-derived HP-H7N9 strains. In summary, the enhanced prevalence and diverse genetic characteristics with mammalian-adapted and NAI-resistant mutations may have contributed towards increased numbers of human infections in Wave Five.
IMPORTANCE The highest numbers of human H7N9 infections were observed during Wave Five from October 2016 to September 2017. Our results showed that HP-H7N9 and LP-H7N9 has spread virtually throughout China and underwent dynamic reassortment with different subtypes (H7N9/H9N2 and H6Ny) and lineages (Yangtze and Pearl River Delta lineages), resulting in a total of 36 and three major genotypes. Notably, the NAI drug-resistant (R292K in NA) and mammalian-adapted (eg. E627K in PB2) mutations were found in HP-H7N9 not only from humans, but also from poultry and environmental isolates, indicating increased risks for human infections. The broad dissemination of LP- and HP-H7N9 with high genetic diversity, host adaptation and drug-resistant mutations likely accounted for the sharp increases in the number of human infections during Wave Five. Therefore, more strategies are needed against the further spread and damage of H7N9 in the world.