Objective  To assess the evolutionary rate of novel influenza A H7N9 virus based on the full length sequences and to provide a theoretical guidance for making prevention and control strategies.

  Methods  The sequences of the influenza A H7N9 virus from The Global Initiative on Sharing Avian Influenza Data (GISAID) were used to construct phylogenetic trees using programs BioEdit 7.0 and MEGA 6.06. Preliminary evolutionary rates were estimated with Path-o-gen; then using the preliminary rates as prior information, we further estimated the rates with BEAST 1.8.2 based on molecular clock and Monte Carlo Markov Chain (MCMC) model.

  Results  High evolutionary rates of the novel influenza A H7N9 virus were observed. The mean evolutionary rate for full-length genomic sequences is 4.60 × 10^–3 (95% highest probability density HPD: 3.94 × 10^–3, 5.40 × 10^–3) subs/site/year. The evolutionary rate of nucleotide substitution of haemagglutinin and neuraminidase (7.43 and 5.92 × 10^–3 subs/site/year) are higher than the evolutionary rate of the H7N9 and higher evolutionary rates of polymerase A (PA), polymerase B1 (PB1), and polymerase B2 (PB2) genes were also observed.

  Conclusion  The novel influenza A H7N9 virus evolves at a high rate, suggesting that effective and long-term surveillance should be carried out.