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Diagnosis of Influenza by PCR Assay

(July 2005)

(Download  Diagnosis of Influenza by PCR Assay.pdf)

The influenza season has now commenced and will usually continue into October. It is important to diagnose influenza early in admitted patients in order to explain clinical presentations, outbreaks and prevent cross transmission to other patients. Early diagnosis (<72 hours) also allows anti-viral therapy to be considered. Previous laboratory diagnostic methods (eg viral immunofluoresence (IF) and culture) are not very sensitive and are slow. Polymerase chain reaction (PCR) influenza testing enables early identification of influenza A, B and pathogenic avian strains. It is now available through HAPS Microbiology.

Paediatricians, please note that only RSV antigen and influenza PCR will be done on nasopharyngeal aspirates (NPA) from infants, not the extended IF panel. If diagnosis of other respiratory viruses by IF is required in a child with severe illness, then contact the Duty Clinical Microbiologist (telephone 49214398). Alternatively, request extended respiratory virus PCR.

Test request name: Influenza PCR
Preferred sample types:

Samples are best collected early in the illness (preferably within 72 hours of onset, maximum up to 7 days)

Infants <2 years: nasopharyngeal aspirate or nose/throat swab, also request RSV antigen testing if appropriate.

Other children and adults: combined nose/throat swab sample - see collection instructions below; must use correct swab type (green viral culture transport swab). Assay can also be performed on sputum.

Do not use a nasopharyngeal swab - this is reserved for pertussis PCR testing

Assay frequency: Daily during influenza outbreak but normally twice weekly in absence of outbreak
Results: In a situation where daily testing is occurring, specimens should reach the John Hunter laboratory by 10 am for urgent (next day) results. PCR positive samples will also undergo viral culture to attempt isolation and characterisation of influenza strains. A later report will be issued if culture is successful.
Interpretation note: Detection of influenza nucleic acids by PCR is approximately 100 times more sensitive than either viral IF or culture. This enables detection of virus out to 7 days after onset of symptoms in a majority of patients.

Influenza illness is most usually characterised by an abrupt onset of fever, most usually associated with cough, nasal congestion, sore throat and anorexia. Myalgia is a feature in around 60%. Note that fever with myalgia without cough is less likely to present influenza.

Collection Procedure: Nasal/Throat Swab for Influenza PCR

Equipment

  • Viral swabs (green top viral transport swab) x 2 (must be correct swab type)
  • Normal saline (0.9%) 10 mL disposable plastic ampule
  • Wooden or plastic disposable tongue depressor
  • Personal protective equipment (surgical mask, eye goggles)
  • Alcohol hand gel (Aqium)

To obtain supplies, contact HAPS Stores, 49214096

Procedure

HAPS Collectors are trained in this procedure and can be requested to obtain patient samples.

  1. Explain the procedure to the patient
  2. Clean hands with alcohol gel (Aqium) and put on PPE (protective glasses and mask)
  3. Take viral culture nasal swab
    Moisten swab with sterile normal salineSample the anterior nostril by gently abrading the nasal mucosa on both sidesInsert swab into transport medium
  4. Take viral culture throat swab
    Take the other swab and moisten in sterile normal salineSample both tonsils and the posterior oropharynx with the swab. Avoid touching the swab on the tongue or other parts of the mouth.Insert swab into transport medium
  5. Forward the labelled specimens to HAPS ASAP
  6. Discard PPE and clean hands with alcohol gel or hand wash

About the Author

Dr John Ferguson, Clinical Microbiologist, wrote this Communique. If you have any questions regarding this topic he can be contact as follows:

Microbiology Contacts

Dr Stephen Graves (Clinical Microbiologist & Director) - 49214420
Dr John Ferguson (Clinical Microbiologist & Infectious Diseases Physician) - 49214422
Microbiology Laboratories - 49214000 or 1800 801 949