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
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 duc...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-07-01
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| Series: | Veterinary Medicine and Science |
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| Online Access: | https://doi.org/10.1002/vms3.819 |
| _version_ | 1817970591800492032 |
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| author | Alireza Abtin Abdelhamid Shoushtari Mohammad Hossein Fallah Mehrabadi Aidin Molouki Seyed Ali Pourbakhsh Hadi Pourtaghi Fatemeh Eshratabadi |
| author_facet | Alireza Abtin Abdelhamid Shoushtari Mohammad Hossein Fallah Mehrabadi Aidin Molouki Seyed Ali Pourbakhsh Hadi Pourtaghi Fatemeh Eshratabadi |
| author_sort | Alireza Abtin |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T20:36:02Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2053-1095 |
| language | English |
| last_indexed | 2024-04-13T20:36:02Z |
| publishDate | 2022-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Veterinary Medicine and Science |
| spelling | doaj.art-68b93576e04f4b2d934122c44aacd6f42022-12-22T02:31:02ZengWileyVeterinary Medicine and Science2053-10952022-07-01841594160210.1002/vms3.819Characterisation, whole‐genome sequencing and phylogenetic analysis of three H3N2 avian influenza viruses isolated from domestic ducks at live poultry markets of Iran, 2017: First reportAlireza Abtin0Abdelhamid Shoushtari1Mohammad Hossein Fallah Mehrabadi2Aidin Molouki3Seyed Ali Pourbakhsh4Hadi Pourtaghi5Fatemeh Eshratabadi6Department of Avian Diseases Research and Diagnostics Razi Vaccine and Serum Research Institute Agricultural Research, Education and Extension Organization (AREEO) Karaj IranDepartment of Avian Diseases Research and Diagnostics Razi Vaccine and Serum Research Institute Agricultural Research, Education and Extension Organization (AREEO) Karaj IranDepartment of Avian Diseases Research and Diagnostics Razi Vaccine and Serum Research Institute Agricultural Research, Education and Extension Organization (AREEO) Karaj IranDepartment of Avian Diseases Research and Diagnostics Razi Vaccine and Serum Research Institute Agricultural Research, Education and Extension Organization (AREEO) Karaj IranDepartment of Avian Diseases Research and Diagnostics Razi Vaccine and Serum Research Institute Agricultural Research, Education and Extension Organization (AREEO) Karaj IranDepartment of Microbiology Karaj Branch Islamic Azad University Karaj IranDepartment of Avian Diseases Research and Diagnostics Razi Vaccine and Serum Research Institute Agricultural Research, Education and Extension Organization (AREEO) Karaj IranAbstract 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.https://doi.org/10.1002/vms3.819avian influenza virusdomestic ducksH3 subtypeIranlive poultry market |
| spellingShingle | Alireza Abtin Abdelhamid Shoushtari Mohammad Hossein Fallah Mehrabadi Aidin Molouki Seyed Ali Pourbakhsh Hadi Pourtaghi Fatemeh Eshratabadi 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 Veterinary Medicine and Science avian influenza virus domestic ducks H3 subtype Iran live poultry market |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | avian influenza virus domestic ducks H3 subtype Iran live poultry market |
| url | https://doi.org/10.1002/vms3.819 |
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