Using mass spectrometer, researchers at the Delhi-based Institute of Genomics and Integrative Biology (IGIB) and the National Centre for Disease Control (NCDC) have been able to detect novel coronavirus with 95% sensitivity and 100% specificity with respect to RT-PCR (reverse transcription polymerase chain reaction). Detection of the virus takes less than three minutes; time from sample preparation to detection takes less than 30 minutes.
The new method can directly detect the virus without amplifying the RNA for detection, as is the case with RT-PCR. The new method relies on detecting the presence of two peptides which are unique to SARS-CoV-2 virus and not seen in any other coronavirus or other viruses. Though seven peptides were found to be unique to SARS-CoV-2 , only two peptides are used for quick virus detection. One of the peptides is the spike protein and the other is a replicase protein. The unique peptides were seen in over 54,000 genomic sequences of the SARS-CoV-2 virus deposited in a public database (GISAID) as on July 1.
“The sensitivity is 90.4% when compared to RT-PCR if we have very high stringency. By that we mean if the ratio of signal to noise is 10-fold. If we use the standard 3.3 times signal to noise ratio (where signal peak is 3.3 times higher than the noise) then the sensitivity is 95%,” says Dr. Shantanu Sengupta from IGIB, who led the team.
The results have been published in the Journal of Proteins and Proteomics . “We could detect the peptides of SARS-CoV-2 virus even in patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR. The peptides were present even after 14 days of initial infection. This highlights the sensitivity of the technique.”
The virus in the swab samples are inactivated using detergent and further processed before being used for virus detection.
The researchers initially tested the technique using 14 nasopharyngeal swab samples and then confirmed using 20 controls and 63 samples from COVID-19 patients who tested positive by RT-PCR and subsequently recovered.
“The mass spectrometer is expensive but it would cost only about ₹100 per test, and so cheaper than RT-PCR. Many research labs have the mass spectrometer,” Dr. Sengupta says. “Since it takes less than 30 minutes to detect the virus and is also highly sensitive and specific, it can be used for screening and diagnostic purposes. It can either complement RT-PCR or be used as an alternative to RT-PCR.”