A One-Shot Assay for Flavivirus Identification

Proteomics expert Ruedi Aebersold discusses the use of multiplex targeted mass spectrometry for one-shot flavivirus diagnosis.

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Mass spectrometry (MS) is one of the most versatile, sensitive and quantitatively accurate analytical techniques and has been widely used for decades, primarily for the analysis of small molecules. More recently, it also has become the method of choice for the analysis of proteins and proteomes. Because it is the sequence and not the composition of amino acids that determines the identity of a peptide or protein, even highly accurate mass measurements of peptides are insufficient to determine their identity.

Confident peptide identification, therefore, requires tandem mass spectrometric techniques which determine not just the peptide mass, but also the amino acid sequence of peptides. Several tandem mass spectrometric methods have been developed, each with different performance profiles.

Among these, targeted MS is characterized by quantitative accuracy, high degree of reproducibility, relative insensitivity to the composition of the sample matrix, low limits of detection and by a wide dynamic range. Targeted MS was named method of the year in 2012 by Nature Methods and its favorable properties make it well suited for clinical applications, particularly for diagnostic tests which need to be highly precise, sensitive and reproducible.

A recently published, pioneering manuscript from the Gunaratne lab highlights the successful exploitation of targeted mass spectrometry for the diagnosis of flavivirus infections, a global healthcare threat. Flavivirus infections have no definitive treatment, making precise diagnosis pivotal for efficient disease management strategies.

The current gold standards, primarily based on immunoassays and viral RNA, have several limitations including cross-reactivity and limited extendibility to multiple flaviviruses without compromising sensitivity. The targeted-MS assay developed by the authors circumvents these shortcomings and enables an efficient response to newly emerging flavivirus outbreaks, with accurate diagnosis and virus typing possible shortly after the detection of a new virus.

Capitalizing on the power of MS to distinguish highly similar peptides, the authors selected viral non-structural protein 1 which is secreted and stably present in the patient blood for extended periods, to conclusively identify and distinguish different flavivirus infections down to the serotype level. The authors show that this single-shot, multiplexed assay can even diagnose secondary- and co-infections from a small amount of blood, a result that has been challenging to achieve with existing flavivirus diagnostics.

The present study is a powerful and well-constructed example of the application of advanced MS technology to an important clinical question. It promises a clear path for translation and broad utility. Further, the approach is readily extendible to new viruses or virus subtypes without the need for expensive and slow antibody development. The study therefore makes a unique contribution to the flavivirus field and points the way towards the conclusive detection of other types of virus.

In light of these advantages, various MS labs around the world are developing automated and simplified workflows to tailor this technology for diagnostics. It can therefore be expected that this outstanding work will make a contribution to public health.

The A*STAR-affiliated researchers contributing to the research featured in this article are from the Institute of Molecular and Cell Biology (IMCB).