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. 2023 Dec;12(2):2225645.
doi: 10.1080/22221751.2023.2225645.

Genetic characterization of a new candidate hemagglutinin subtype of influenza A viruses

Sasan Fereidouni  1 , Elke Starick  2 , Kobey Karamendin  3 , Cecilia Di Genova  4 , Simon D Scott  4 , Yelizaveta Khan  3 , Timm Harder  2 , Aidyn Kydyrmanov  3
Affiliations

Genetic characterization of a new candidate hemagglutinin subtype of influenza A viruses

Sasan Fereidouni et al. Emerg Microbes Infect. 2023 Dec.

Abstract

ABSTRACTAvian influenza viruses (AIV) have been classified on the basis of 16 subtypes of hemagglutinin (HA) and 9 subtypes of neuraminidase. Here we describe genomic evidence for a new candidate HA subtype, nominally H19, with a large genetic distance to all previously described AIV subtypes, derived from a cloacal swab sample of a Common Pochard (Aythya ferina) in Kazakhstan, in 2008. Avian influenza monitoring in wild birds especially in migratory hotspots such as central Asia is an important approach to gain information about the circulation of known and novel influenza viruses. Genetically, the novel HA coding sequence exhibits only 68.2% nucleotide and 68.5% amino acid identity with its nearest relation in the H9 (N2) subtype. The new HA sequence should be considered in current genomic diagnostic AI assays to facilitate its detection and eventual isolation enabling further study and antigenic classification.

Keywords: Influenza A viruses; Kazakhstan; influenza subtypes; one-health; wild birds.

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Conflict of interest statement

No potential conflict of interest was reported by the author(s).

Figures

Figure 1.
Figure 1.
The complete open reading frame (ORF) of the HA gene of A/ Common Pochard/Kazakhstan/Kz52/2008 influenza virus (new subtype), compared to closely related H9 subtype isolates. Representative isolates for each lineage included: H9-bat: A/Bat/Egypt/381OP/2017(H9N2), H9-Y280: A/Chicken/Beijing/1/97(H9N2), H9-G1: A/quail/Hong Kong/G1/97(H9N2), H9-Y439: A/Duck/Hong Kong/Y439/97(H9N2), H9-N. America: A/Mallard/California/D1713634/2017(H9N2), H9-Korea: A/chicken/Korea/GH2/2007(H9N2).
Figure 2.
Figure 2.
Phylogenetic analysis of Kz52 HA coding region nucleotide sequences and the representative sequences of other influenza subtypes using obtained from publicly available sequence datasets (GenBank). (a) The distances and (b) the corresponding bootstrap values. Analysis was based on full-length coding sequence of the HA gene. Only bootstrap values >80 are shown. Bar represents 0.01 nt substitutions.
Figure 2.
Figure 2.
Phylogenetic analysis of Kz52 HA coding region nucleotide sequences and the representative sequences of other influenza subtypes using obtained from publicly available sequence datasets (GenBank). (a) The distances and (b) the corresponding bootstrap values. Analysis was based on full-length coding sequence of the HA gene. Only bootstrap values >80 are shown. Bar represents 0.01 nt substitutions.
Figure 3.
Figure 3.
Schematics showing predicted 3D models of the Kz52 HA Ribbon (right) and surface (left) formats generated using Phyre2 software. The images show the HA1 and HA2 subunits (green and yellow respectively), the cleavage site (red), and receptor-binding sites (blue).
See this image and copyright information in PMC

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Grants and funding

This work was supported by grants from the Ministry of Science and Higher Education of the Republic of Kazakhstan: “Molecular evolution and ecology of influenza A viruses circulating among wild birds in Kazakhstan and revealing a novel subtype (AP09258993).”
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