الفهرس 
Introduction
Historic emergence of AIOnly 14 pages are availabe for public view
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Abstract
ThisthesiswascarriedoutfordetectionandmolecularcharacterizationofAIVs inwaterfowlsinUpperEgypt(Assiut,El-MinyaandSohag)duringtheyearof
2014.AtotalNo.of80cloacalswabsampleswerecollectedfrom waterfowls (ducksandgeese) fromthe backyard. Thecollectedswabsweretestedusingavian influenza virusrapidantigentestkitthatrevealed8positive samplesout of 80 collectedoneswith 10%ofpositivity.
With theonestepRealTimeReverseTranscriptase-PCR(rRT-PCR)technique weexamined 50 samples(42 havenegativeresultswiththeAIVrapiddirectkit andthe8positivesamplesthatwere determinedpreviously withtherapidantigen kit)fordetectionanddeterminationoftheH5andH9subtypesofAIV.Theresults showed18positivesamples(14H5-AIV,3H9-AIVandonesampleshowedmixed infectionof bothH5andH9subtypes)outof 50examinedsamples(36%).
Haemagglutinin(HA) gene sequencingwere conductedfor sevenH5 isolates and oneH9 isolate.The analysis results of thededuced amino acids of the haemagglutinin(HA)genecleavagesitefortheobtainedH5sequencesshowedthat allthesevenisolateshadmultibasicamino acidsequence“324EKRRKKR/GLF333 motif” atthe proteolytic cleavage site (PCS) whichindicated thatthe isolatesare HPAIbelongedtosubclade2.2.1/C.Analysisof theaminoacids ofthe haemagglutinin(HA) generevealed differentaminoacid substitutionsatthe proteolyticcleavagesiteaswellastheentireHAgene.Phylogeneticanalysisbased ontheHA nucleotide sequence of theisolatesshowedthatallthe isolatedstrains wereclusteredwiththeclassicalsubclade2.2.1(2.2.1/C).ComparingtheHAgene of theisolateswiththeHAgeneofsomethe vaccinalstrainscommonly usedin EgyptshowedthatthetestedH5isolatesweregeneticallydistantfromthevaccinal
strainscommonlyusedinEgyptwhichislowestwithA/chicken/Mexico/232/94 vaccinalstrains.
Haemagglutinincleavagemotifaminoacidsequenceofthe H9isolatewas foundtobe335RSSR/GLF341suggestedthatitwasoflowpathogenic nature.The phylogeneticanalysisof theHAgeneoftheobtainedisolateshowedthatthe isolatedstrainwasclosetotheH9virusesisolatedinEgyptandMiddleEastwhich formeda characteristic groupamongstG1likeviruses.