Abstract: Objective To investigate the origin and the recombinant model of H7N9 virus prevailing in China by sequence
analysis. Methods The sequences of H7N9 virus were collected and analyzed with the software BLAST and MEGA 5.0. The
phylogenetic trees were constructed after multiple sequences alignment. The homologous sequences of H7N9 segments were
determined and the model was inferred according to the origin of H7N9 segments. Results The most relevant sequences of
HA, NA, NS and PB2 segments were located at one branch of the phylogenetic tree, while the closest relevant sequences of
PB1, PA, NP and MP contained two H9N2 virus origins. According to the analysis of sequence origin, H7N9 viruses might be
divided into 5 genotypes: namely A, B, A/Shanghai/1/2013-H7N9, A/Pigeon/Shanghai/S1069-H7N9 and A/Zhejiang/HZ1/
2013-H7N9, and the genotype A consisted of A1 and A2 subtypes. Conclusion The prevailing H7N9 virus might be derived
from 5 different viruses after 4 times of recombination, which resulted in the two major types of A and B. The subtypes of A1
and A2 were two different derivatives from one reassortant. The A/Pigeon/Shanghai/S1069-H7N9 strain might be the
recombinant of type A H7N9 virus with a local H9N2 virus during the H7N9 epidemics. The A/Zhejiang/HZ1/2013-H7N9
strain could be the re-arrangement of subtype A2 with type B H7N9 virus.