Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing
1 Queensland Children’s Medical Research Institute, The University of Queensland, Brisbane, Qld, Australia
2 Queensland Paediatric Infectious Diseases Laboratory, The Royal Children’s Hospital, Brisbane, Qld, Australia
3 Murdoch Children’s Research Institute & Melbourne School of Population Health, The University of Melbourne, Parkville, Vic, Australia
4 Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
5 Sir Albert Sakzewski Virus Research Centre, Building C28, Back Rd, Herston, QLD 4029, Australia
BMC Infectious Diseases 2014, 14:275 doi:10.1186/1471-2334-14-275Published: 19 May 2014
Human Parainfluenza viruses are a common cause of both upper and lower respiratory tract infections, particularly in children. Of the four Parainfluenza virus serotypes, Parainfluenza 4 is least well characterised from both the clinical, epidemiological and genetic perspectives.
Flocked nose or throat swabs from a previous study investigating viral prevalence in community-based adults suffering from influenza like illness were used as the basis for this study. Samples in which no virus was detected using a 16 viral respiratory pathogen real-time PCR panel were barcoded and pyrosequenced using the Roche 454 GS FLX Titanium chemistry. The sequences were analysed using the VirusHunter bioinformatic pipeline. Sanger sequencing was used to complete the detected Parainfluenza 4 coding region.
A variant Parainfluenza 4 subtype b strain (QLD-01) was discovered in an otherwise healthy adult who presented with influenza like illness. Strain QLD-01 shared genomic similarities with both a and b subtypes. The extent of divergence of this genome from the 5 available whole Parainfluenza 4 genomes impacted the predicted binding efficiencies of the majority of published Parainfluenza 4 PCR assays.
These findings further support a possible role for Parainfluenza 4 in the aetiology of adult respiratory disease within the community setting, and highlight the caution needed to be used in designing PCR assays from limited sequence information or in using proprietary commercial PCR assays.