OBJECTIVES: Human severe infection with avian influenza A (H5N6) virus infection was identified firstly in 2014 in China. It was unknown or unclear on the disease or the pathogen by people. This study would illustrate the virological and clinical findings of a fatal human case with H5N6 virus infection.

METHODS: We obtained and analyzed the clinical, epidemiological and virological data from the patient. RT-PCR, viral culture and sequencing were conducted for determination of causative pathogen.

RESULTS: The patient who presented with fever, severe pneumonia, leucopenia and lymphopenia, developed septic shock and ARDS, and died on day 10 after illness onset. A novel reassortant avian-origin influenza A (H5N6) virus was isolated from the throat swab or trachea aspirate of the patient. The virus was reassorted with HA gene of Clade 2.3.4.4 H5, internal genes of Clade 2.3.2.1 H5 and NA gene of H6N6 avian viruses. The cleavage site of HA gene contained multiple basic amino acids indicating the novel H5N6 virus was highly pathogenic in chicken.

CONCLUSIONS: A novel highly pathogenic avian influenza H5N6 virus with the backbone of H5N1 virus acquired NA gene from H6N6 virus was first identified, and caused human infection with severe respiratory disease.