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The matrix gene of influenza A H5N1 in Egypt, 2006–2016: molecular insights and distribution of amantadine-resistant variants

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Abstract

Large-scale sequence analysis of Matrix (M) gene and its coding proteins M1 and M2 was performed for 274 highly pathogenic avian influenza viruses H5N1 circulated in Egypt from 2006 to 2016. The aim is to study the amantadine-resistant markers distribution and to estimate the evolutionary rate. 246 viruses were obtained from the Global Initiative on Sharing All Influenza Data base, and 28 additional viruses were sequenced. Maximum clade credibility (MCC) phylogenetic tree revealed that the M gene has evolved into two different lineages. Estimated Evolutionary analysis showed that the M2 protein possessed higher evolutionary rates (3.45 × 10−3) than the M1 protein (2.73 × 10−3). M gene encoding proteins revealed significant markers described to be associated with host tropism and increase in virulence: V15I, N30D, and T121A in M1 and L55F in M2 protein. Site analysis focusing attention on the temporal and host distribution of the amantadine-resistant markers was carried out and showed that vast majority of the M2 amantadine-resistant variants of clade 2.2.1.1 (n = 90) is N31 marker, in addition to G27 (n = 7), A27 (n = 5), I27 (n = 1), and S30 (n = 1). In 2010–2011, amantadine resistant frequency increased considerably resembling more than half of the resistant variants. Notably, all viruses of clade 2.2.1.1 possessed amantadine-resistant marker. However, almost all current circulating viruses in Egypt of clade 2.2.1.2 from 2014 to 2016 did not carry any amantadine-resistant markers.

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Acknowledgments

The authors gratefully acknowledge Prof. Dr. Timm Harder, Friedrich Loeffler Institute, Germany for his excellent support. The authors thank colleagues and co-workers in FAO-ECTAD, Egypt for their co-operation. The authors acknowledge the colleagues who made the data available on the GISAID platform (Table S2).

Author information

Authors and Affiliations

  1. Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493, Greifswald Insel-Riems, Germany

    Mahmoud M. Naguib

  2. National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza, 12618, Egypt

    Mahmoud M. Naguib, Naglaa Hagag & Abdel-Satar Arafa

  3. Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt

    Ahmed A. El-Sanousi & Hussein Ali Hussein

Authors
  1. Mahmoud M. Naguib
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  2. Naglaa Hagag
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  3. Ahmed A. El-Sanousi
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  4. Hussein Ali Hussein
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  5. Abdel-Satar Arafa
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Corresponding author

Correspondence to Mahmoud M. Naguib.

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Samples collection by veterinarians was achieved from poultry sectors in Egypt. Obtaining swab samples from the trachea of poultry is minimally invasive and does not require any anesthesia for the animal; minimal restrainment is used for a very short time.

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All the authors declare that they have no conflict of interest.

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Edited by Keizo Tomonaga.

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Naguib, M.M., Hagag, N., El-Sanousi, A.A. et al. The matrix gene of influenza A H5N1 in Egypt, 2006–2016: molecular insights and distribution of amantadine-resistant variants. Virus Genes 52, 872–876 (2016). https://doi.org/10.1007/s11262-016-1373-3

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  • DOI: https://doi.org/10.1007/s11262-016-1373-3

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