title: Evolutionary trajectories and diagnostic challenges of potentially zoonotic avian influenza viruses H5N1 and H9N2 co-circulating in Egypt.
abstract: In Egypt, since 2006, descendants of the highly pathogenic avian influenza virus (HP AIV) H5N1 of clade 2.2 continue to cause sharp losses in poultry production and seriously threaten public health. Potentially zoonotic H9N2 viruses established an endemic status in poultry in Egypt as well and co-circulate with HP AIV H5N1 rising concerns of reassortments between H9N2 and H5N1 viruses along with an increase of mixed infections of poultry. Nucleotide sequences of whole genomes of 15 different isolates (H5N1: 7; H9N2: 8), and of the hemagglutinin (HA) and neuraminidase (NA) encoding segments of nine further clinical samples (H5N1: 2; H9N2: 7) from 2013 and 2014 were generated and analysed. The HA of H5N1 viruses clustered with clade 2.2.1 while the H9 HA formed three distinguishable subgroups within cluster B viruses. BEAST analysis revealed that H9N2 viruses are likely present in Egypt since 2009. Several previously undescribed substituting mutations putatively associated with host tropism and virulence modulation were detected in different proteins of the analysed H9N2 and H5N1 viruses. Reassortment between HP AIV H5N1 and H9N2 is anticipated in Egypt, and timely detection of such events is of public health concern. As a rapid tool for detection of such reassortants discriminative SYBR-Green reverse transcription real-time PCR assays (SG-RT-qPCR), targeting the internal genes of the Egyptian H5N1 and H9N2 viruses were developed for the rapid screening of viral RNAs from both virus isolates and clinical samples. However, in accordance to Sanger sequencing, no reassortants were found by SG-RT-qPCR. Nevertheless, the complex epidemiology of avian influenza in poultry in Egypt will require sustained close observation. Further development and continuing adaptation of rapid and cost-effective screening assays such as the SG-RT-qPCR protocol developed here are at the basis of efforts for improvement the currently critical situation.
authors.affiliation: Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald-Insel Riems, Germany; National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, P.O. Box 246, Giza 12618, Egypt.
authors.forename: Mahmoud M
authors.initials: MM
authors.lastname: Naguib
authors.affiliation: National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, P.O. Box 246, Giza 12618, Egypt.
authors.forename: Abdel-Satar A
authors.initials: AS
authors.lastname: Arafa
authors.affiliation: Poultry Disease Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt.
authors.forename: Magdy F
authors.initials: MF
authors.lastname: El-Kady
authors.affiliation: National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, P.O. Box 246, Giza 12618, Egypt.
authors.forename: Abdullah A
authors.initials: AA
authors.lastname: Selim
authors.affiliation: Bioinformatics Institute, Agency for Science, Technology and Research, 138671 Singapore, Singapore.
authors.forename: Vithiagaran
authors.initials: V
authors.lastname: Gunalan
authors.affiliation: Bioinformatics Institute, Agency for Science, Technology and Research, 138671 Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore; National Public Health Laboratory, Ministry of Health, 169854 Singapore, Singapore.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Maurer-Stroh
authors.affiliation: Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald-Insel Riems, Germany.
authors.forename: Katja V
authors.initials: KV
authors.lastname: Goller
authors.affiliation: National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, P.O. Box 246, Giza 12618, Egypt.
authors.forename: Mohamed K
authors.initials: MK
authors.lastname: Hassan
authors.affiliation: Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald-Insel Riems, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Beer
authors.affiliation: Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald-Insel Riems, Germany.
authors.forename: E M
authors.initials: EM
authors.lastname: Abdelwhab
authors.affiliation: Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald-Insel Riems, Germany. Electronic address: timm.harder@fli.bund.de.
authors.forename: Timm C
authors.initials: TC
authors.lastname: Harder
mesh_terms: D000818:Animals; D002642:Chick Embryo; D004285:Dogs; D004534:Egypt; D019143:Evolution, Molecular; D005814:Genes, Viral; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics* / Q000472:pathogenicity; D053127:Influenza A Virus, H9N2 Subtype / Q000235:genetics* / Q000472:pathogenicity; D005585:Influenza in Birds / Q000821:virology*; D061985:Madin Darby Canine Kidney Cells; D010802:Phylogeny; D011200:Poultry / Q000821:virology; D011201:Poultry Diseases / Q000821:virology*; D012641:Selection, Genetic; D014764:Viral Proteins / Q000235:genetics; D014774:Virulence
chemical_list: D014764:Viral Proteins
keywords: Egypt; Evolution; H5N1; H9N2; Pandemic; Poultry; Reassortment; SYBR-Green RT-qPCR