Sequence and phylogenetic analysis of surface protein genes of emerging H9N2 influenza viruses isolated from poultry in two geographical regions of China

Sequence characteristics and phylogenetic analysis of H9N2 subtype avian influenza A viruses detected from poultry and the environment in China, 2018

H9N2 subtype avian influenza A virus (AIV) is a causative agent that poses serious threats to both the poultry industry and global public health. In this study, we performed active surveillance to identify H9N2 AIVs from poultry (chicken, duck, and goose) and the environment of different regions in China, and we phylogenetically characterized the sequences. AIV subtype-specific reverse transcription polymerase chain reaction (RT-PCR) showed that 5.43% (83/1529) samples were AIV positive, and 87.02% (67/77) of which were H9N2 AIVs. Phylogenetic analysis revealed that all H9N2 field viruses belonged to the Y280-like lineage, exhibiting 93.9-100% and 94.6-100% of homology in the hemagglutinin (HA) gene and 94.4-100% and 96.3-100% in the neuraminidase (NA) gene, at the nucleotide (nt) and amino acid (aa) levels, respectively. All field viruses shared relatively lower identities with vaccine strains, ranging from 89.4% to 97.7%. The aa sequence at the cleavage site (aa 333-340) in HA of all the isolated H9N2 AIVs was PSRSSRG/L, which is a characteristic of low pathogenic avian influenza virus (LPAIV). Notably, all the H9N2 field viruses harbored eight glycosylation sites, whereas a glycosylation site 218 NRT was missing and a new site 313 NCS was inserted. All field viruses had NGLMR as their receptor binding sites (RBS) at aa position 224-229, showing high conservation with many recently-isolated H9N2 strains. All H9N2 field isolates at position 226 had the aa Leucine (L), indicating their ability to bind to sialic acid (SA) α, a 2-6 receptor of mammals that poses the potential risk of transmission to humans. Our results suggest that H9N2 AIVs circulating in poultry populations that have genetic variation and the potential of infecting mammalian species are of great significance when monitoring H9N2 AIVs in China.

Molecular characterization of H9N2 avian influenza viruses isolated from vaccinated broiler chickens in northeast Iran

Avian influenza is a highly contagious respiratory disease of poultry caused by influenza A viruses, family Orthomyxoviridae. H9N2 avian influenza outbreaks are a major problem of the poultry industry in Iran. To determine the genetic differences between field viruses and the vaccine strain, the genomes of four strains isolated in 2011 from vaccinated broiler flocks with a history of respiratory illness were sequenced. Genetic and serological comparisons were made. Sequence analysis of the hemagglutinin (HA) and neuraminidase (NA) genes indicated that the isolated strains shared nucleotide homologies of 91.6-93.9 and 90.2-91.7% with the vaccine strain, respectively. Phylogenetic analyses of HA and NA genes showed that all strains isolated in this study fell into the same group and belonged to the influenza A virus (A)/quail/Hong Kong/G1/97 H9N2 sublineage. Several amino acids have changed at the antigenic sites in HA in the field viruses. Extra potential glycosylation sites were observed in the HA and NA proteins expressed by the current isolates relative to those in the vaccine strain. The deduced amino acid sequence at the cleavage site of HA in recent isolates is the KSSR/GLF motif, whereas it is RSSR/GLF in the vaccine strain. A serological analysis revealed that the currently circulating strains are antigenically distinct from the vaccine strain. These results suggest that the commercial vaccine is insufficiently genetically and antigenically similar to the viruses currently circulating in the region. These findings confirm that it is important to monitor the genetic and antigenic variations in H9N2 influenza viruses when selecting a vaccine strain.