Proteotyping to Type the Parainfluenza Virus and Subtype the Influenza Type A Neuraminidase using High Resolution Mass Spectrometry

The human parainfluenza virus (HPIV) and the influenza virus commonly cause respiratory tract infections. HPIV is the second most common cause of acute lower respiratory tract infections in infants and young children, and accounts for approximately 75% of all croup cases. The influenza virus causes millions of severe respiratory tract infections each year and is responsible for approximately 250,000 – 500,000 deaths annually. In order to minimise the morbidity and mortality rate of these respiratory viruses, it is essential to maintain regular surveillance of these viruses and characterise them at the molecular level. The conventional method used to characterise the viruses employs reverse transcriptase-polymerase chain reaction (RT-PCR). Despite its sensitivity, this approach may fail if mutations in the viral genome prevent primers binding to the generated cDNA. Proteotyping is a novel method that can detect and characterise viruses based on the identification of signature peptides, peptides that are conserved in sequence within particular types and/or subtypes, by high resolution mass spectrometry. Proteotyping has previously been applied to type and subtype human influenza viruses, establish the lineage of influenza strains, and distinguish seasonal from pandemic H1N1 influenza strains. In this thesis, proteotyping was successfully applied to differentiate parainfluenza type 1, type 2, and type 3, and distinguish them from the influenza virus. This is the first application of the proteotyping approach to a virus other than influenza. In addition, proteotyping has also been applied to characterise all nine subtypes of the influenza type A neuraminidase, the viral protein targeted by current anti-viral inhibitors. The results from both these studies provide support for the development of proteotyping as a method for viral surveillance