Genetic subtyping of influenza A viruses using RT-PCR with a single set of primers based on conserved sequences within the HA2 coding region

• Published in: Journal of virological methods Vol. 122; no. 1; pp. 119 - 122
• Main Authors: Phipps, L.P., Essen, S.C., Brown, I.H.
• Format: Journal Article
• Language: English
• Published: London Elsevier B.V 01.12.2004; Amsterdam Elsevier; New York, NY
• Subjects: Biological and medical sciences; DNA Primers; Fundamental and applied biological sciences. Psychology; Genotype; Haemagglutinin; Hemagglutinin Glycoproteins, Influenza Virus - genetics; Influenza A virus; Influenza A virus - classification; Influenza A virus - genetics; Influenza virus; Microbiology; Reverse Transcriptase Polymerase Chain Reaction; Reverse transcription-polymerase chain reaction (RT-PCR); Subtype; Techniques used in virology; Virology; Haemagglutinin; Reverse transcription-polymerase chain reaction (RT-PCR); Influenza A virus; Subtype; Microbiology; Hemagglutinin; Orthomyxoviridae; Method; Virology; Infection; Virus; Conserved sequence; Influenzavirus A; Viral disease; Influenza A; Genetics; Reverse transcription polymerase chain reaction
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2004.08.008

Influenza A viruses are subtyped conventionally according to the antigenic characteristics of the external glycoproteins, haemagglutinin (HA) and neuraminidase (NA). To date 15 HA and 9 NA subtypes have been described. There is a need to develop fast, accurate and reliable methods to identify influenza virus subtypes, which may be associated with disease outbreaks. An RT-PCR is described using a single primer pair based on a conserved region of the HA2 gene that can detect all 15 HA influenza A subtypes. The assay was validated initially using a panel of 12 known standard prototype strains of influenza virus representing 6 HA subtypes and subsequently in a blind study using a panel of 30 strains. Selected viruses represented all known HA subtypes derived from avian, swine and human hosts separated both geographically and with time Sequence analysis of RT-PCR product showed complete correlation with results obtained using conventional serological methods. It is concluded that this RT-PCR is a reliable, robust and reproducible tool for the rapid identification of a wide range of all the HA subtypes of influenza A viruses.