Genotyping and reassortment analysis of highly pathogenic avian influenza viruses H5N8 and H5N2 from Egypt reveals successive annual replacement of genotypes

Highly pathogenic (HP) H5N1, clade 2.2.1, and low pathogenic avian influenza (LPAI) H9N2 viruses, G1-B lineage, are endemic in poultry in Egypt and have co-circulated for almost a decade. Surprisingly, no inter-subtypic reassortment events have been reported from the field during that time. After th...

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Published in:Infection, genetics and evolution genetics and evolution, 2020-10, Vol.84, p.104375-104375, Article 104375
Main Authors: Hassan, Kareem E., Saad, Noha, Abozeid, Hassanein H., Shany, Salama, El-Kady, Magdy F., Arafa, Abdelsatar, EL-Sawah, Azza A.A., Pfaff, Florian, Hafez, Hafez M., Beer, Martin, Harder, Timm
Format: Article
Language:English
Subjects:
Beast analysis
Egypt
Genotyping
H5N2
H9N2
Highly pathogenic avian influenza
Phylogenetic analysis
Reassortment
Subtype H5N8
Tanglegram
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Summary:Highly pathogenic (HP) H5N1, clade 2.2.1, and low pathogenic avian influenza (LPAI) H9N2 viruses, G1-B lineage, are endemic in poultry in Egypt and have co-circulated for almost a decade. Surprisingly, no inter-subtypic reassortment events have been reported from the field during that time. After the introduction of HPAIV H5N8, clade 2.3.4.4b, in Egyptian poultry in 2016, suddenly HP H5N2 reassortants with H9N2 viruses emerged. The current analyses focussed on studying 32 duck flocks, 4 broiler chicken flocks, and 1 turkey flock, suffering from respiratory manifestations with moderate to high mortality reared in two Egyptian governorates during 2019. Real-time RT-PCR substantiated the presence of HP H5N8 in 21 of the 37 investigated flocks with mixed infection of H9N2 in two of them. HP H5N1 was not detected. Full hemagglutinin (HA) sequencing of 10 samples with full-genome sequencing of three of them revealed presence of a single genotype. Very few substituting mutations in the HA protein were detected versus previous Egyptian HA sequences of that clade. Interestingly, amino acid substitutions in the Matrix (M2) and the Neuraminidase (NA) proteins associated with conferring both Amantadine and Oseltamivir resistance were present. Systematic reassortment analysis of all publicly available Egyptian whole genome sequences of HP H5N8 (n = 23), reassortant HP H5N2 (n = 2) and LP H9N2 (n = 53) viruses revealed presence of at least seven different genotypes of HPAI H5Nx viruses of clade 2.3.4.4b in Egypt since 2016. For H9N2 viruses, at least three genotypes were distinguishable. Heat mapping and tanglegram analyses suggested that several internal gene segments in both HP H5Nx and H9N2 viruses originated from avian influenza viruses circulating in wild bird species in Egypt. Based on the limited set of whole genome sequences available, annual replacement patterns of HP H5Nx genotypes emerged and suggested selective advantages of certain genotypes since 2016. •At least seven different genotypes of HPAI H5Nx viruses of clade 2.3.4.4b have been circulating in Egypt.•Several internal gene segments in HP H5Nx and H9N2 viruses originated from AI viruses circulating in wild birds in Egypt.•Presence of mutations associated with resistance against both Amantadine and Oseltamivir were detected.
ISSN:1567-1348
1567-7257
DOI:10.1016/j.meegid.2020.104375