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. 2022 Jul;8(4):1594-1602.
doi: 10.1002/vms3.819. Epub 2022 Jun 2.

Characterisation, whole-genome sequencing and phylogenetic analysis of three H3N2 avian influenza viruses isolated from domestic ducks at live poultry markets of Iran, 2017: First report

Alireza Abtin  1 , Abdelhamid Shoushtari  1 , Mohammad Hossein Fallah Mehrabadi  1 , Aidin Molouki  1 , Seyed Ali Pourbakhsh  1 , Hadi Pourtaghi  2 , Fatemeh Eshratabadi  1
Affiliations

Characterisation, whole-genome sequencing and phylogenetic analysis of three H3N2 avian influenza viruses isolated from domestic ducks at live poultry markets of Iran, 2017: First report

Alireza Abtin et al. Vet Med Sci. 2022 Jul.

Abstract

Background: Avian influenza type A viruses (AIV) can infect a broad range of hosts including human and birds, making them an important viral pathogen with zoonotic potential. Ducks are a known reservoir for many avian viruses including the AIV.

Objectives: To sequence the entire genome of duck-derived H3N2 and ran comprehensive phylogenetic analysis on them to study their origin.

Methods: In this study, 962 cloacal swabs were collected from domestic ducks at several live poultry markets (LPMs) of Gilan, Mazandaran and Golestan provinces of Iran in the year 2017.

Results: Preliminary assays such as haemagglutination inhibition assay (HI), Neuraminidase Inhibition assay(NI) and RT-qPCR suggested that 0.5% of the birds were infected by H3 low pathogenic influenza viruses (LPAI). Three isolates were selected for whole genome sequencing. The cleavage site of the HA genes showed a PEKQTR/GLF motif, an indicator of LPAI. Furthermore, BLAST and phylogenetic analyses of the HA gene showed high homology to the Eurasian lineage of H3N8 AIV (95.5%-97.1% to several European and East Asian isolates). However, the NA genes showed high homology (at most 96.5-96.9%) to those belonging to AIV N2 subtype. Furthermore, internal genes showed high homology (96%-98%) to a variety of duck-origin subtypes and glycoprotein combinations, which were different for each segment. This showed a complex reassortment between different subtypes.

Discussion: This report is the first whole genome sequencing and complete characterisation of H3N2 AIV from Iran.

Conclusion: Such surveillance should continue to study the evolution and possible emergence of viruses with pandemic potential.

Keywords: H3 subtype; Iran; avian influenza virus; domestic ducks; live poultry market.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

FIGURE 1
FIGURE 1
Geographical map of the swab collection locations of the current study
FIGURE 2
FIGURE 2
Phylogenetic tree of HA. The isolates of the current study clustered to a group including mostly AIV H3N8 subtype belonging to Eurasian lineage. The isolates are indicated with black circle
FIGURE 3
FIGURE 3
Phylogenetic tree of NA of the isolates of the currents study showed that they belong to the Eurasian lineage. The isolates are indicated with black circle
See this image and copyright information in PMC

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