Detecting RNA virus in saliva samples using Raman spectroscopy

Essential lines: Analysis of 1,400 spectra from each sample, showed that 65 Raman spectral features were adequate to identify the viral positive signal.

Essential lines: Analysis of 1,400 spectra from each sample, showed that 65 Raman spectral features were adequate to identify the viral positive signal.   | Photo Credit: Special Arrangement

If Israel developed a spectroscopy-based one-minute breath-analyser to detect coronavirus, a team led by 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.

It has been reported that novel coronavirus is 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. They analysed the raw Raman Spectroscopy data and compared the signals with both viral positive and negative samples. Statistical analysis of all the 1,400 spectra obtained for each sample, showed a set of 65 Raman spectral features was adequate to identify the viral positive signal. “Interestingly, most of the spectra were specific for the RNA molecule,” says Dr. Dutt. “We confirmed our finding by adding an enzyme that specifically degrades RNA molecule — the RNase — in presence of which the 65 spectra–based feature was completely abrogated that didn’t happen in presence of DNase or proteinase. We thus confirmed that the signal came 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.

Free downloads

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, and 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. Dutt.

“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 and not identify the specific one, 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 any point of care (in the field) can quickly screen passengers within minutes,” he adds.

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Printable version | Sep 24, 2020 4:17:48 PM |

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