Improved confirmatory diagnosis of SARS-CoV-2 infection using protein mass spectrometry

Project summary This research project aims to develop a new test to detect viral proteins in patient samples. Virus will be extracted from nasopharyngeal swabs and processed for analysis via liquid chromatography and mass spectrometry (LC-MS) to measure the viral proteins. These results can be used together with the gene tests to evaluate infection status and provide more definitive diagnosis in the case of ambiguous results from current testing methods. This methodology could be adapted for other viruses including influenza and may be used to detect emerging viral mutations. What is the issue for NSW? A significant proportion of patients who have tested positive for SARS-CoV-2 infection using the current testing methodology continue to return positive results well after the typical window of infection has passed and symptoms have cleared, causing social and economic burdens. These patients and their families must isolate and cannot return to work. Continued re-testing of these patients places additional workload on the NSW HP Virology department and reduces the capacity of the lab to test new specimens. What does the research aim to do and how? The team will develop a liquid chromatography-tandem mass spectrometry (LC-MS/MS) viral protein assay that could offer a major paradigm shift in diagnosis: lower assay testing turnaround time (TAT) and cost, and reduce need for molecular test consumables of short supply allow confirmation of infection by detection of a different analyte (viral proteins) rather than RNA estimate a patient's viral load provide data on whether replication competent (i.e. infectious and transmissible) virus is present.