Detecting RNA virus in saliva samples using Raman Spectroscopy

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Researchers at the Mumbai-based Tata Memorial Centre have used Raman Spectroscopy to detect RNA viruses present in saliva samples. It is a proof-of-concept study to analyse non-infectious RNA viruses using conventional Raman Spectroscopy without using any additional reagent to enhance the signal.

If Israel developed a spectroscopy-based one-minute breathe analyser to detect coronavirus, a team led by Dr. Amit Dutt from the Mumbai-based Tata Memorial Centre has turned to Raman Spectroscopy to detect RNA viruses present in saliva samples. It is a proof-of-concept study to analyse non-infectious RNA viruses using conventional Raman Spectroscopy without using any additional reagent to enhance the signal.

Novel coronavirus has been reported to be found in sufficient numbers in human saliva. For the study, the researchers spiked saliva samples with non-infectious RNA viruses and analysed it with Raman Spectroscopy.

The researchers analysed the raw data obtained from Raman Spectroscopy and compared the signals with both viral positive and negative samples. Based on statistical analysis of all the 1,400 spectra obtained for each sample, they found a set of 65 Raman spectral features was adequate to identify the viral positive signal. “Interestingly, most of these spectra were specific for the RNA molecule,” says Dr. Dutt.

“We confirmed our finding by adding enzyme that specifically degrades RNA molecule — the RNase — in presence of which the 65 spectra-based features was completely abrogated that though didn’t happen in presence of DNase or proteinase. We thus confirmed that the signal was coming from the RNA contributed by the intact virions,” says Dr. Dutt.

The signal set has 92.5% sensitivity and 88.8% specificity. The results are published in the Journal of Biophotonics. Dr. Sudeep Gupta, Director of TMC is a co-author of the paper.

To minimise variability and automate the analysis of the Raman spectra for RNA viruses, they developed an automated tool — RNA Virus Detector — using a graphical user interface. The tool can be used for detecting RNA virus from an individual or a group of samples in an unambiguous and reproducible manner. This tool is freely downloadable.

“This tool, the first of its kind, takes raw data from a Raman Spectrometer analysis based on the 65 spectra signature and provides an objective output if viral RNA is present or absent in the sample,” says Dr. Duttt.

“This conceptual framework to detect RNA viruses in saliva could form the basis for field application of Raman Spectroscopy in managing viral outbreaks, such as the ongoing COVID-19 pandemic,” they write.

Since the tool can only identify RNA viruses without being able to identify which specific RNA virus is, it can be used only for screening. “The RNA virus detected could be a common cold virus as well or any other RNA virus such as HIV. It doesn’t look for COVID-19 viral-specific signature,” he explains. The advantage is that the tool can be taken to the field and people who test positive for RNA virus can be quarantined while another sample may be sent for validation using RT-PCR.

“This whole process of data acquisition and analysis can be performed within a minute. Since no additional reagent is needed there is no recurring cost. A portable (benchtop or handheld) Raman spectrophotometer installed at the port of entry such as airports or at any point of care (in the field) can quickly screen passengers within minutes,” he adds.

Published in The Hindu on July 4, 2020