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Respiratory PCR detects influenza after intranasal live-attenuated influenza vaccination
  1. S Lumley,
  2. C Atkinson,
  3. T Haque
  1. UCL Department of Virology, Royal Free London NHS Foundation Trust, London, UK
  1. Correspondence to Dr S Lumley, UCL Department of Virology, Royal Free London NHS Foundation Trust, Pond Street, London NW3 2QG, UK; sheila.lumley{at}

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From 2013 an annual nasal live-attenuated influenza vaccine (LAIV—Fluenz) is available for all children in the UK aged 2 and 3 years and other ‘at-risk’ children, as part of the National Health Service (NHS) childhood vaccination programme.1 ,2 The vaccine contains reassortant influenza viruses; two influenza A viruses (H1N1 and H3N2) and one influenza B virus,3 and has previously been used in children in the USA.

A 2-year-old child presented with respiratory symptoms. PCR assay of nasopharyngeal swab was strongly positive for Rhinovirus (Cycle Threshold, CT 21) and weakly positive for Influenza B (CT 37.6). Further questioning revealed that the child had received the intranasal influenza vaccine 10 days previously. Due to the difference in CT values and detection of an alternative virus (Rhinovirus), a diagnosis of Rhinovirus bronchiolitis was made and the weak Influenza B positivity was attributed to the intranasal vaccine.

Immunocompetent children vaccinated with LAIV can shed vaccine viruses for up to 3 weeks (mean duration: 7.6 days); maximal shedding occurs within 2 days of vaccination. Shedding is in lower amounts than with wild-type influenza viruses. Rarely, shed vaccine viruses can be transmitted from vaccine recipients to unvaccinated persons; however, serious illness has not been reported.4

Both wild-type and live-attenuated vaccine virus strains are detected by laboratory respiratory PCR assay. Wild-type and vaccine virus strains could be distinguished by genome sequencing; however, the low copy number of shed vaccine virus precludes this approach. In this case, a clinical decision must be made as to whether the influenza virus is the cause of disease or a consequence of vaccination. This will influence decisions about treating with antivirals.

As LAIV is introduced into UK clinical practice, this is a useful reminder to take care in interpreting respiratory PCR results in recently vaccinated children, highlighting the need for a precise vaccination history.



  • Contributors SL and CA prepared the manuscript and TH reviewed.

  • Competing interests None.

  • Provenance and peer review Not commissioned; internally peer reviewed.