Advanced search
Publication Cover
Emerging Microbes & Infections Volume 8, 2019 - Issue 1
Submit an article Journal homepage
2,739
Views
26
CrossRef citations to date
0
Altmetric
Original Articles

Active surveillance and genetic evolution of avian influenza viruses in Egypt, 2016–2018

Ahmed Kandeila Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, National Research Centre, Giza, EgyptView further author information
,
Joseph T. Hicksb University of Texas Health Sciences Center, Houston, TX, USA;c Center for the Ecology of Infectious Diseases, University of Georgia, Athens, USAView further author information
,
Sean G. Youngd University of Arkansas for Medical Sciences, Little Rock, AR, USAORCID Iconhttps://orcid.org/0000-0002-0054-0627View further author information
ORCID Icon,
Ahmed N. El Taweela Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, National Research Centre, Giza, EgyptView further author information
,
Ahmed S. Kayeda Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, National Research Centre, Giza, EgyptView further author information
,
Yassmin Moatasima Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, National Research Centre, Giza, EgyptView further author information
,
Omnia Kutkata Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, National Research Centre, Giza, EgyptView further author information
,
Ola Bagatoa Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, National Research Centre, Giza, EgyptView further author information
,
Pamela P. McKenziee St. Jude Children’s Research Hospital, Memphis, TN, USAView further author information
,
Zhipeng Caif Georgia State University, Atlanta, GA, USAView further author information
,
Rebecca Badrag Human Link, Hazmieh, LebanonView further author information
,
Mohamed Kutkath Poultry Diseases Department, National Research Centre, Giza, EgyptView further author information
,
Justin Bahlb University of Texas Health Sciences Center, Houston, TX, USA;c Center for the Ecology of Infectious Diseases, University of Georgia, Athens, USAORCID Iconhttps://orcid.org/0000-0001-7572-4300View further author information
ORCID Icon,
Richard J. Webbye St. Jude Children’s Research Hospital, Memphis, TN, USAView further author information
,
Ghazi Kayalib University of Texas Health Sciences Center, Houston, TX, USA;g Human Link, Hazmieh, LebanonCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0002-5387-1622View further author information
ORCID Icon &
Mohamed A. Alia Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, National Research Centre, Giza, EgyptCorrespondence[email protected]
View further author information
 show all
Pages 1370-1382 | Received 13 Mar 2019, Accepted 22 Jul 2019, Published online: 17 Sep 2019

References

  • WHO/OIE/FAO. Continued evolution of highly pathogenic avian influenza A (H5N1): updated nomenclature; 2012.
  • de Vries E, Guo H, Dai M, et al. Rapid emergence of highly pathogenic avian influenza subtypes from a subtype H5N1 hemagglutinin Variant. Emerg Infect Dis. 2015 May;21(5):842–6. doi: 10.3201/eid2105.141927
  • Aly MM, Arafa A, Hassan MK. Epidemiological findings of outbreaks of disease caused by highly pathogenic H5N1 avian influenza virus in poultry in Egypt during 2006. Avian Dis. 2008 Jun;52(2):269–77. doi: 10.1637/8166-103007-Reg.1
  • El-Shesheny R, Kandeil A, Bagato O, et al. Molecular characterization of avian influenza H5N1 virus in Egypt and the emergence of a novel endemic subclade. J Gen Virol. 2014 Jul;95(Pt 7):1444–63. doi: 10.1099/vir.0.063495-0
  • Kayali G, Webby RJ, Ducatez MF, et al. The epidemiological and molecular aspects of influenza H5N1 viruses at the human-animal interface in Egypt. PLoS ONE. 2011;6(3):e17730. doi: 10.1371/journal.pone.0017730
  • Kandeil A, Kayed A, Moatasim Y, et al. Genetic characterization of highly pathogenic avian influenza A H5N8 viruses isolated from wild birds in Egypt. J Gen Virol. 2017 Jul 18.
  • Selim AA, Erfan AM, Hagag N, et al. Highly pathogenic avian influenza virus (H5N8) clade 2.3.4.4 infection in migratory birds, Egypt. Emerg Infect Dis. 2017 Jun;23(6):1048–51. doi: 10.3201/eid2306.162056
  • OIE. Update on avian influenza in animals. 2017. Available from: http://www.oie.int/wahis_2/public%5C..%5Ctemp%5Creports/en_fup_0000023232_20170314_163139.pdf.
  • Kandeil A, El-Shesheny R, Maatouq AM, et al. Genetic and antigenic evolution of H9N2 avian influenza viruses circulating in Egypt between 2011 and 2013. Arch Virol. 2014 Jul 3.
  • Kandeil A, El-Shesheny R, Maatouq A, et al. Novel reassortant H9N2 viruses in pigeons and evidence for antigenic diversity of H9N2 viruses isolated from quails in Egypt. J Gen Virol. 2017 Apr;98(4):548–62. doi: 10.1099/jgv.0.000657
  • Kayali G, Kandeil A, El-Shesheny R, et al. Active surveillance for avian influenza virus, Egypt, 2010–2012. Emerg Infect Dis. 2014 Apr;20(4):542–51. doi: 10.3201/eid2004.131295
  • Monne I, Yamage M, Dauphin G, et al. Reassortant avian influenza A(H5N1) viruses with H9N2-PB1 gene in poultry, Bangladesh. Emerg Infect Dis. 2013 Oct;19(10):1630–4. doi: 10.3201/eid1910.130534
  • Iqbal M, Yaqub T, Reddy K, et al. Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. PLoS ONE. 2009;4(6):e5788. doi: 10.1371/journal.pone.0005788
  • Kandeil A, El-Shesheny R, Maatouq A, et al. Novel reassortant H9N2 viruses in pigeons and evidence for antigenic diversity of H9N2 viruses isolated from quails in Egypt. J Gen Virol. 2016 Nov 11.
  • Kayali G, El-Shesheny R, Kutkat MA, et al. Continuing threat of influenza (H5N1) virus circulation in Egypt. Emerg Infect Dis. 2011 Dec;17(12):2306–8. doi: 10.3201/eid1712.110683
  • Kayali G, Kandeil A, El-Shesheny R, et al. Avian influenza A(H5N1) virus in Egypt. Emerg Infect Dis. 2016 Mar;22(3):379–88. doi: 10.3201/eid2203.150593
  • Kayed AS, Kandeil A, El Shesheny R, et al. Active surveillance of avian influenza viruses in Egyptian poultry, 2015. Eastern Mediterranean health journal=La revue de sante de la Mediterranee orientale=al-Majallah al-sihhiyah li-sharq al-mutawassit. 2016 Oct 2;22(7):557–61.
  • WHO. WHO Manual on Animal Influenza Diagnosis and Surveillance. 2002 [cited December 12, 2011]; 2nd Edition:[Available from: http://whqlibdoc.who.int/hq/2002/WHO_CDS_CSR_NCS_2002.5.pdf.
  • CDC. CDC realtime RTPCR protocol for detection and characterization of influenza. 2007.
  • Fereidouni SR, Starick E, Grund C, et al. Rapid molecular subtyping by reverse transcription polymerase chain reaction of the neuraminidase gene of avian influenza A viruses. Vet Microbiol. 2009 Mar 30;135(3-4):253–60. doi: 10.1016/j.vetmic.2008.09.077
  • Hoffmann E, Stech J, Guan Y, et al. Universal primer set for the full-length amplification of all influenza A viruses. Arch Virol. 2001 Dec;146(12):2275–89. doi: 10.1007/s007050170002
  • Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7. doi: 10.1093/nar/gkh340
  • Yang Z. Phylogenetic analysis using parsimony and likelihood methods. J Mol Evol. 1996 Feb;42(2):294–307. doi: 10.1007/BF02198856
  • Drummond AJ, Suchard MA, Xie D, et al. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012 Aug;29(8):1969–73. doi: 10.1093/molbev/mss075
  • WHO. WHO Manual on Animal Influenza Diagnosis and Surveillance. 2002. Available from: http://www.wpro.who.int/emerging_diseases/documents/docs/manualonanimalaidiagnosisandsurveillance.pdf?ua=1.
  • Cai Z, Zhang T, Wan XF. A computational framework for influenza antigenic cartography. PLoS Comput Biol. 2010;6(10):e1000949. doi: 10.1371/journal.pcbi.1000949
  • Cai Z, Zhang T, Wan XF. Concepts and applications for influenza antigenic cartography. Influenza Other Respir Viruses. 2011 May;5(Suppl 1):204–7.
  • Phillips SJ, Anderson RP, Schapire RE. Maximum entropy modeling of species geographic distributions. Ecol Model. 2006;190(3-4):231–59. doi: 10.1016/j.ecolmodel.2005.03.026
  • Phillips SJ, Dudik M, Schapire RE. MaxEnt. 2011 [cited 2018]. Available from: www.cs.princeton.edu/%7Eschapire/maxent.
  • Elith J, Graham C, Anderson RP, et al. Novel methods improve prediction of species’ distributions from occurrence data. Ecography. 2006;29:129–51. doi: 10.1111/j.2006.0906-7590.04596.x
  • Young SG, Carrel M, Malanson GP, et al. Predicting avian influenza Co-infection with H5N1 and H9N2 in northern Egypt. Int J Environ Res Public Health. 2016 Sep 6;13(9):886. doi: 10.3390/ijerph13090886
  • Li XH, Tian HD, Heiner M, et al. Global occurrence and spread of highly pathogenic avian influenza virus of the subtype H5N1. Avian Dis. 2011 Mar;55(1):21–8. doi: 10.1637/9306-031710-Reg.1
  • Agency DM. Digital Chart of the World. 1992 [cited 2018]. Available from: www.ngdc.noaa.gov/mgg/topo/report/s5/s5Avii.html.
  • Center for International Earth Science Information Network (CIESIN) CU. Gridded Population of the World (GPW), v4 | SEDAC. 2017 [cited 2018].; Available from: http://sedac.ciesin.columbia.edu/data/set/gpw-v4-population-density-rev10/docs.
  • Beaudoing H, Rodell M, NASA/GSFC/HSL. GLDAS Noah Land Surface Model L4 monthly 0.25 × 0.25 degree V2.0.; 2015.
  • Rodell M, Houser PR, Jambor U, et al. The Global land data Assimilation system. Bull Am Meteorol Soc. 2004;85(3):381–94. doi: 10.1175/BAMS-85-3-381
  • C H. phyloclim: Integrating phylogenetics and climatic niche modelling. 2009;R package version 0.0.1.
  • Warren DL, Glor RE, Turelli M. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution. 2008 Nov;62(11):2868–83. doi: 10.1111/j.1558-5646.2008.00482.x
  • Lemey P, Rambaut A, Drummond AJ, et al. Bayesian phylogeography finds its roots. PLoS Comput Biol. 2009 Sep;5(9):e1000520. doi: 10.1371/journal.pcbi.1000520
  • Bielejec F, Baele G, Vrancken B, et al. Spread3: Interactive Visualization of Spatiotemporal history and trait Evolutionary Processes. Mol Biol Evol. 2016 Aug;33(8):2167–9. doi: 10.1093/molbev/msw082
  • El-Shesheny R, Kayali G, Kandeil A, et al. Antigenic diversity and cross-reactivity of avian influenza H5N1 viruses in Egypt between 2006 and 2011. J Gen Virol. 2012 Dec;93(Pt 12):2564–74. doi: 10.1099/vir.0.043299-0
  • Lee MS, Jang EY, Cho J, et al. Development and comparison of two H5N8 influenza A vaccine candidate strains. Arch Virol. 2019 Jan;164(1):127–36. doi: 10.1007/s00705-018-4062-9
  • Bahl J, Pham TT, Hill NJ, et al. Ecosystem Interactions Underlie the spread of avian influenza A viruses with pandemic potential. PLoS Pathog. 2016 May;12(5):e1005620. doi: 10.1371/journal.ppat.1005620
  • Sun S, Wang Q, Zhao F, et al. Glycosylation site alteration in the evolution of influenza A (H1N1) viruses. PLoS ONE. 2011;6(7):e22844. doi: 10.1371/journal.pone.0022844
  • Adel A, Arafa A, Hussein HA, et al. Molecular and antigenic traits on hemagglutinin gene of avian influenza H9N2 viruses: evidence of a new escape mutant in Egypt adapted in quails. Res Vet Sci. 2017 Jun;112:132–40. doi: 10.1016/j.rvsc.2017.02.003
  • Ghazi K, Ahmed K, Rabeh E-S, et al. Avian influenza A(H5N1) virus in Egypt. Emerging Infectious Disease Journal. 2016;22(3.
  • Salaheldin AH, El-Hamid HS, Elbestawy AR, et al. Multiple Introductions of influenza A(H5N8) virus into poultry, Egypt, 2017. Emerging Infect. Dis. 2018 May;24(5). doi: 10.3201/eid2405.171935

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.