Genetic characterization of a novel reassortant H5N6 avian influenza virus identified from a 10-year-old girl

Abstract

A 10-year-old girl was confirmed, by laboratory tests, to be infected with the H5N6 subtype of the highly pathogenic avian influenza virus in Suzhou city in November, 2018 (JSSZ01). The hemagglutinin (HA) gene of this H5N6 virus belonged to the 2.3.4.4 H5 clade, and the HA linkage peptide of the JSSZ01 strain was RERRRKR↓GLF with multiple basic amino acids. Q226L and G228S mutations were not observed, but S128P, S137A, and T160A substitutions were identified in the receptor binding sites. The resistance mutation D198N in the neuraminidase (NA) protein was also identified in this strain. Additionally, an 11 amino acid (AA positions 59–69) deletion was identified in the NA stalk region. Most genes of JSSZ01 exhibited highest identity with previously characterized H5N6 viruses, but its PA segment sequence was highly similar to previously identified avian H3 viruses (Accession Number: EPI596567 or EPI590058), indicating that JSSZ01 may be created by gene reassortment.