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Near-Complete Genome Sequence of an H5N1 Avian Influenza Virus Strain Isolated from a Swan in Southwest Kazakhstan in 2006.

ABSTRACT: We report the near-complete genome sequence of an influenza H5N1 virus strain isolated from a dead swan on the southeastern Caspian seashore in 2006. The results of the surface protein HA phylogenetic analysis showed that the A/swan/Mangystau/3/2006 virus belongs to the EA-nonGsGD clade.

SUBMITTER: Burashev Y

PROVIDER: S-EPMC7098892 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Near-Complete Genome Sequence of an H5N1 Avian Influenza Virus Strain Isolated from a Swan in Southwest Kazakhstan in 2006.

Burashev Yerbol Y Strochkov Vitaliy V Sultankulova Kulyaisan K Orynbayev Mukhit M Kassenov Markhabat M Kozhabergenov Nurlan N Shorayeva Kamshat K Sadikaliyeva Sandugash S Issabek Aisha A Almezhanova Meirym M Nakhanov Aziz A Savitskaya Irina I Zakarya Kunsulu K

Microbiology resource announcements 20200326 13

We report the near-complete genome sequence of an influenza H5N1 virus strain isolated from a dead swan on the southeastern Caspian seashore in 2006. The results of the surface protein HA phylogenetic analysis showed that the A/swan/Mangystau/3/2006 virus belongs to the EA-nonGsGD clade. ...[more]

PMID: 32217669

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Project description:BACKGROUND: The analysis of the nonstructural (NS) gene of the highly pathogenic (HP) H5N1 avian influenza viruses (AIV) isolated in Sweden early 2006 indicated the co-circulation of two sub-lineages of these viruses at that time. In order to complete the information on their genetic features and relation to other HP H5N1 AIVs the seven additional genes of twelve Swedish isolates were amplified in full length, sequenced, and characterized. RESULTS: The presence of two sub-lineages of HP H5N1 AIVs in Sweden in 2006 was further confirmed by the phylogenetic analysis of approximately the 95% of the genome of twelve isolates that were selected on the base of differences in geographic location, timing and animal species of origin. Ten of the analyzed viruses belonged to sub-clade 2.2.2. and grouped together with German and Danish isolates, while two 2.2.1. sub-clade viruses formed a cluster with isolates of Egyptian, Italian, Slovenian, and Nigerian origin. The revealed amino acid differences between the two sub-groups of Swedish viruses affected the predicted antigenicity of the surface glycoproteins, haemagglutinin and neuraminidase, rather than the nucleoprotein, polymerase basic protein 2, and polymerase acidic protein, the main targets of the cellular immune responses. The distinctive characteristics between members of the two subgroups were identified and described. CONCLUSION: The comprehensive genetic characterization of HP H5N1 AIVs isolated in Sweden during the spring of 2006 is reported. Our data support previous findings on the coincidental spread of multiple sub-lineage H5N1 HPAIVs via migrating aquatic birds to large distance from their origin. The detection of 2.2.1. sub-clade viruses in Sweden adds further data regarding their spread in the North of Europe in 2006. The close genetic relationship of Swedish isolates sub-clade 2.2.2. to the contemporary German and Danish isolates supports the proposition of the introduction and spread of a single variant of 2.2.2. sub-clade H5N1 avian influenza viruses in the Baltic region. The presented findings underline the importance of whole genome analysis.

Project description:BACKGROUND: Since the first outbreak recorded in northern areas of Pakistan in early 2006, highly pathogenic avian influenza H5N1 viruses were isolated from commercial poultry and wild/domestic birds from different areas of Pakistan up to July 2008. Different isolates of H5N1 were sequenced to explore the genetic diversity of these viruses. RESULTS: Phylogenetic analysis revealed close clustering and highest sequence identity in all 8 genes to HPAI H5N1 isolates belonging to unified H5 clade 2.2, sub-lineage EMA-3 recovered from Afghanistan during the same time period. Two subgroups within Pakistani H5N1 viruses, from domestic and wild birds, were observed on the basis of their sequence homology and mutations. HPAI motif, preferred receptor specificity for ?-(2, 3) linkages, potential N-linked glycosylation sites and an additional glycosylation site at the globular head of HA protein of four Pakistani H5N1 isolates. While, the amino acids associated with sensitivities to various antiviral drugs (Oseltamivir, Zanamivir, Amantadine) were found conserved for the Pakistani H5N1 isolates. Conspicuously, some important mutations observed at critical positions of antigenic sites (S141P, D155S, R162I & P181S) and at receptor binding pocket (A185T, R189K & S217P) of HA-1. A high sequence similarity between Pakistani HP H5N1 and LP H9N2 viruses was also observed. Avian like host specific markers with the exception of E627K in PB2, K356R in PA, V33I in NP, I28V in M2 and L107F in NS2 proteins were also observed. CONCLUSIONS: Various point mutations in different genes of H5 viruses from Pakistan were observed during its circulation in the field. The outbreaks started in Khyber Pakhtoon Khawa (North West) province in 2006 and spread to the Southern regions over a period of time. Though migratory birds may have a role for this continued endemicity of clade 2.2 H5N1 viruses during 2006-2008 in Pakistan, the possibility of their transmission through legal or illegal poultry trade across the borders cannot be ignored.

Dataset Information

Near-Complete Genome Sequence of an H5N1 Avian Influenza Virus Strain Isolated from a Swan in Southwest Kazakhstan in 2006.

Publications

Near-Complete Genome Sequence of an H5N1 Avian Influenza Virus Strain Isolated from a Swan in Southwest Kazakhstan in 2006.

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