Genomic molecular characterization of a highly pathogenic avian influenza A (H5N1) virus

Abstract:

[Background] H5N1 influenza virus can cause severe respiratory infection in human with high fatality. [Objective] To analyze the virus A/Nanjing/1/2015, a human infected highly pathogenic avian influenza virus H5N1 confirmed in our laboratory, and to investigate its possible origins and genomic molecular characterization. [Methods] Whole genome sequencing was performed on the samples of patient?s sputum. CLC Genomics Workbench 9.0 was used for sequence assembly. Genome homology and genetic molecular characterization were analyzed by BLAST and MEGA 5.22 software. [Results] The virus belonged to H5 subtype clade 2.3.2.1c. The 8 segments were highly homologous with those viruses isolated from domestic poultry in Jiangsu and Zhejiang area and no re-assortment was observed. Molecular characterization analysis revealed that the amino acid sequences of hemagglutinin (HA) protein cleavage site were PQRERRRR/G. The Receptor Binding Sites (RBS) was in avian type, however, D94N, S133A and T188I substitutions enhanced the affinity to human receptors. A 20 amino acid deletion at position 49?68 in neuraminidase (NA) stalk, and a deletion at position 80?84 together with a P42S mutation in the non-structural protein 1 (NS1) were observed. Several amino acid mutations enhancing virulence and affinity to human cells in other proteins were also found in the present strain. Analysis on drug resistance sites revealed the presence of oseltamivir resistant mutation H274Y, and the virus remained sensitive to amantadine. [Conclusion] The human infected highly pathogenic avian influenza A (H5N1) virus A/Nanjing/1/2015 belonged to clade 2.3.2.1c and was avian in origin. The key sites in the present strain were relatively conservative; however, there were still several amino acid evolution and mutations to make it more favorable for infecting human. H5N1 avian influenza virus is evolving actively and continued surveillance is warranted.