Genotyping by RT-PCR

Genotyping of Influenza A virus (H1 and H3), Influenza B virus, and Zoonotic Influenza A virus by *real-time RT-PCR and/or RT-PCR and sequencing  

• Influenza

Respiratory specimens (nasopharyngeal swab, throat swab, etc.) or viral isolates. Volume required: 1-2 mL.

For specimen collection, use sterile swabs and swab nasal cavity, throat, etc. Place swabs in 2-3 mL viral transport medium.

Keep samples refrigerated until shipped for testing. Ship on dry ice.

Shipping of specimens shall be done by a TDG certified individual in accordance with TDG regulations. For additional information regarding classification of specimens for the purposes of shipping, consult either Part 2 Appendix 3 of the TDG Regulations or section 3.6.2 of the IATA Dangerous Goods Regulations as applicable.

Suspected or confirmed influenza virus infection.

Completed requisition (current WHO Influenza Program – Antigenic Subtyping requisition form). Sender lab name, address, and telephone number must be provided for samples to be processed. Also include identifier (sender lab number), patient date of birth, patient gender, type of specimen, and date collected. Under additional information, please include if possible/applicable: passage history, patient travel history, extent of influenza activity, and date of collection relative to antiviral use.

Authorization must be obtained for genotyping by RT-PCR and sequencing on Influenza A virus (H1 and H3), Influenza B virus, and Zoonotic Influenza A virus.  Please contact the Influenza, Respiratory Viruses and Coronavirus Section before sending specimens.  Samples received three months after the collection date will not be tested unless prior arrangements have been made with the Section Chief. 

Nucleic acids are extracted from submitted specimens/isolates.  Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) is performed on extracted nucleic acids with real-time detection or visual confirmation (gel electrophoresis) of PCR products.  PCR generated amplicons may be sequenced and aligned with reference sequences to determine the genotype.

14 calendar days.

1. Real-Time RT-PCR (rRT-PCR) Protocol for Influenza. CDC. Revised, 2007.
2. Fouchier R. et al. Detection of Influenza A Viruses from Different Species by PCR Amplification of Conserved Sequences in the Matrix Gene. J. Clin. Microbiol. (2000) 38: 4096-4101

Pathogen Safety Data Sheets: Infectious Substances – Influenza virus (B and C)

Pathogen Safety Data Sheets: Infectious Substances – Influenza A virus subtypes H5, H7 and H9

Pathogen Safety Data Sheets: Infectious Substances – Influenza virus type A

Severe Acute Respiratory Infection (SARI) Case Definition

For health professionals: Avian influenza (H5N1)

Protocol for Microbiological Investigations of Severe Acute Respiratory Infections (SARI)

Canadian Pandemic Influenza Preparedness: Planning Guidance for the Health Sector

For health professionals: Avian influenza A(H7N9)

Flu (influenza): For health professionals

Laboratory-confirmed influenza (including novel influenza subtypes)

Flu (influenza): Symptoms and treatment

Emerging Respiratory Pathogens

Avian influenza A (H7N9)

Avian influenza (H5N1)