Cleavage site stability of Egyptian highly pathogenic avian influenza viruses in backyard chickens during 2009–2011

PurposeTwo distinguishable subclades of H5N1 (classic and variant strains) are cocirculating among the poultry populations in Egypt despite the intensive vaccination programs. A study to investigate the genetic relationship between avian influenza virus (AIV) isolates from backyard chickens in Sharkia (2009–2011), subclades, and commercially available vaccines was carried out.MethodsForty-eight suspected AIV infected birds were clinically examined and used for virus isolation followed by reverse transcription-polymerase chain reaction. Four H5N1 virus isolates were sequenced and analyzed. The intravenous pathogenicity index (IVPI) of three AIV isolates was determined.ResultsThirty-four hemagglutinating viral agents (30 AIV subtype H5N1 and 4 Newcastle disease virus) were detected. Both the nucleotide and amino acid sequence identities of four H5N1 virus isolates (SHZA-0412/2009, SHZA-0801/2010, SHMK-1903/2010, and SHAH-1403/2011) were high—98.4–99.7% and 100%, respectively—indicative of their genetic homogeneity. The hemagglutinin cleavage site characterization revealed the presence of multiple basic amino acids (–PQRERRRKKR/GL–) of the highly pathogenic phenotype. These results were supported by IVPI in chickens of 2.69–2.90. The similarity of our isolates with H5N1 AIV vaccine strains (93.9–95.1%) was higher than that with H5N2 strains (77.8–91.9%). The divergence of four sequences with classic and variant lineages is 2–2.7% and 2.3–3%, respectively, with two amino acid substitutions (A249P and N251Y).ConclusionGenetic characterization and IVPI data of backyard H5N1 isolates are indicative of a highly pathogenic avian influenza virus with hemagglutinin cleavage site constancy and two amino acids substitutions with Egyptian classic and variant lineages, suggesting a beginning of antigenic drift.