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A high diversity of Eurasian lineage low pathogenicity avian influenza A viruses circulate among wild birds sampled in Egypt.

ABSTRACT: Surveillance for influenza A viruses in wild birds has increased substantially as part of efforts to control the global movement of highly pathogenic avian influenza A (H5N1) virus. Studies conducted in Egypt from 2003 to 2007 to monitor birds for H5N1 identified multiple subtypes of low pathogenicity avian influenza A viruses isolated primarily from migratory waterfowl collected in the Nile Delta. Phylogenetic analysis of 28 viral genomes was performed to estimate their nearest ancestors and identify possible reassortants. Migratory flyway patterns were included in the analysis to assess gene flow between overlapping flyways. Overall, the viruses were most closely related to Eurasian, African and/or Central Asian lineage low pathogenicity viruses and belonged to 15 different subtypes. A subset of the internal genes seemed to originate from specific flyways (Black Sea-Mediterranean, East African-West Asian). The remaining genes were derived from a mixture of viruses broadly distributed across as many as 4 different flyways suggesting the importance of the Nile Delta for virus dispersal. Molecular clock date estimates suggested that the time to the nearest common ancestor of all viruses analyzed ranged from 5 to 10 years, indicating frequent genetic exchange with viruses sampled elsewhere. The intersection of multiple migratory bird flyways and the resulting diversity of influenza virus gene lineages in the Nile Delta create conditions favoring reassortment, as evident from the gene constellations identified by this study. In conclusion, we present for the first time a comprehensive phylogenetic analysis of full genome sequences from low pathogenic avian influenza viruses circulating in Egypt, underscoring the significance of the region for viral reassortment and the potential emergence of novel avian influenza A viruses, as well as representing a highly diverse influenza A virus gene pool that merits continued monitoring.

SUBMITTER: Gerloff NA

PROVIDER: S-EPMC3710070 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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A high diversity of Eurasian lineage low pathogenicity avian influenza A viruses circulate among wild birds sampled in Egypt.

Gerloff Nancy A NA Jones Joyce J Simpson Natosha N Balish Amanda A Elbadry Maha Adel MA Baghat Verina V Rusev Ivan I de Mattos Cecilia C CC de Mattos Carlos A CA Zonkle Luay Elsayed Ahmed LE Kis Zoltan Z Davis C Todd CT Yingst Sam S Cornelius Claire C Soliman Atef A Mohareb Emad E Klimov Alexander A Donis Ruben O RO

PloS one 20130712 7

Surveillance for influenza A viruses in wild birds has increased substantially as part of efforts to control the global movement of highly pathogenic avian influenza A (H5N1) virus. Studies conducted in Egypt from 2003 to 2007 to monitor birds for H5N1 identified multiple subtypes of low pathogenicity avian influenza A viruses isolated primarily from migratory waterfowl collected in the Nile Delta. Phylogenetic analysis of 28 viral genomes was performed to estimate their nearest ancestors and id ...[more]

PMID: 23874653

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Project description:BACKGROUND: Since the emergence of H5N1 high pathogenicity (HP) avian influenza virus (AIV) in Asia, numerous efforts worldwide have focused on elucidating the relative roles of wild birds and domestic poultry movement in virus dissemination. In accordance with this a surveillance program for AIV in wild birds was conducted in Mongolia from 2005-2007. An important feature of Mongolia is that there is little domestic poultry production in the country, therefore AIV detection in wild birds would not likely be from spill-over from domestic poultry. RESULTS: During 2005-2007 2,139 specimens representing 4,077 individual birds of 45 species were tested for AIV by real time RT-PCR (rRT-PCR) and/or virus isolation. Bird age and health status were recorded. Ninety rRT-PCR AIV positive samples representing 89 individual birds of 19 species including 9 low pathogenicity (LP) AIVs were isolated from 6 species. A Bar-headed goose (Anser indicus), a Whooper swan (Cygnus cygnus) and 2 Ruddy shelducks (Tadorna ferruginea) were positive for H12N3 LP AIV. H16N3 and H13N6 viruses were isolated from Black-headed gulls (Larus ridibundus). A Red-crested pochard (Rhodonessa rufina) and 2 Mongolian gulls (Larus vagae mongolicus) were positive for H3N6 and H16N6 LP AIV, respectively. Full genomes of each virus isolate were sequenced and analyzed phylogenetically and were most closely related to recent European and Asian wild bird lineage AIVs and individual genes loosely grouped by year. Reassortment occurred within and among different years and subtypes. CONCLUSION: Detection and/or isolation of AIV infection in numerous wild bird species, including 2 which have not been previously described as hosts, reinforces the wide host range of AIV within avian species. Reassortment complexity within the genomes indicate the introduction of new AIV strains into wild bird populations annually, however there is enough over-lap of infection for reassortment to occur. Further work is needed to clarify how AIV is maintained in these wild bird reservoirs.

Project description:A total of 50 poultry farms of commercial broilers (N = 39) and commercial layers (N = 11) suffered from respiratory problems and mortality during the period from January 2016 to December 2017 were investigated. Also, samples were collected from quail (N = 4), Bluebird (Sialis, N = 1), and Greenfinch (Chloris chloris, N = 1) for analysis. Respiratory viral pathogens were screened by PCR and positive samples were subjected to virus isolation and genetic identification. Antigenic relatedness of isolated avian influenza (AI) H5 subtype was evaluated using cross-hemagglutination inhibition. Results revealed that the incidence of single virus infections in commercial broilers was 64.1% (25/39), with the highest incidence for ND (33.3%) and H9N2 (20.5%), followed by H5N1 (7.7%) and H5N8 (2.7). Meanwhile, H9N2/ND mixed infection was the most observed case (7.7%). Other mixed infections H5N1/ND, H5N1/H9N2/ND, H5N1/H9N2/ND/IB, H9N2/IB, and H9N2/ILT were also observed (2.6% each). In commercial layers, H5N1 and ILT were the only detected single infections (18.1% each). Mixed H9N2/ND was the most predominant infection in layers (27.3%). Other mixed infections of H9N2/IB, H5N1/H5N8/H9N2, and H9N2/ND/IB were observed in 3 separate farms (9.1% each). The H5N8 virus was detected in one quail farm and 2 out of 3 wild bird's samples. Partial HA gene sequence analysis showed the clustering of the selected AI H5N8 within the 2.3.4.4 clade, while H5N1 clustered with the clade 2.2.1.2. Interestingly, the H5N8 isolated from chickens possessed 6 amino acids substitutions at HA1 compared to those isolated from wild birds with low antigenic relatedness to AI H5N1 clades 2.2.1 or 2.2.1.2. In conclusion, mixed viral infections were observed in both broiler and layer chickens in Egypt. The detected triple H5N1, H9N2, and H5N8 influenza co-infection raises the concern of potential AI epidemic strain emergence. The low genetic and antigenic relatedness between AI H5N1 and H5N8 viruses suggest the need for modification of vaccination strategies of avian influenza in Egypt along with strict biosecurity measures.

Dataset Information

A high diversity of Eurasian lineage low pathogenicity avian influenza A viruses circulate among wild birds sampled in Egypt.

Publications

A high diversity of Eurasian lineage low pathogenicity avian influenza A viruses circulate among wild birds sampled in Egypt.

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