title: The rapid molecular subtyping and pathotyping of avian influenza viruses.
abstract: Highly conserved nucleotide stretches flanking the cleavage site of the haemagglutinin (HA) gene of influenza type A viruses were utilised for generating PCR amplicons from a broad range of avian influenza viruses (AIV) in a one-step real-time SYBR Green RT-PCR assay. The nucleotide sequencing of the amplified PCR products simultaneously reveals both the HA subtype and the pathotype of the AIV isolates, as we demonstrated in case of H5 subtype viruses. The specificity of the assay was confirmed by investigating 66 strains of AIV and nine heterologous pathogens, including influenza B, C and various avian pathogenic viruses. This assay enables a general HA subtype identification and pathotype determination of AIV isolates providing a useful alternative tool for avian influenza diagnosis.
authors.affiliation: The National Veterinary Institute and The Swedish University of Agricultural Sciences, OIE Collaborating Centre for the Biotechnology-Based Diagnosis of Infectious Diseases in Veterinary Medicine, Ulls väg 2B, SE 751 89 Uppsala, Sweden. alia.yacoub@sva.se
authors.forename: A
authors.initials: A
authors.lastname: Yacoub
authors.forename: I
authors.initials: I
authors.lastname: Kiss
authors.forename: S
authors.initials: S
authors.lastname: Zohari
authors.forename: M
authors.initials: M
authors.lastname: Hakhverdyan
authors.forename: G
authors.initials: G
authors.lastname: Czifra
authors.forename: N
authors.initials: N
authors.lastname: Mohamed
authors.forename: P
authors.initials: P
authors.lastname: Gyarmati
authors.forename: J
authors.initials: J
authors.lastname: Blomberg
authors.forename: S
authors.initials: S
authors.lastname: Belák
mesh_terms: D000818:Animals; D001717:Birds / Q000821:virology*; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics*; D009980:Influenza A virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D005585:Influenza in Birds / Q000175:diagnosis* / Q000821:virology; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; D012367:RNA, Viral