Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by Mass Spectrometry

Abstract

Background: Amplification of viral ribonucleic acid (RNA) by real-time reverse transcriptase polymerase chain reaction (rRT-PCR) is the gold standard to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the initial outbreak, strategies to detect and isolate patients have been important to avoid uncontrolled viral spread. Although testing capacities have been upscaled, there is still a need for reliable high throughput test systems, specifically those that require alternative consumables. Therefore, we tested and compared two different methods for the detection of viral PCR products: rRT-PCR and mass spectrometry (MS). Methods: Viral RNA was isolated and amplified from oro- or nasopharyngeal swabs. A total of 22 samples that tested positive and 22 samples that tested negative for SARS-CoV-2 by rRT-PCR were analyzed by MS. Results of the rRT-PCR and the MS protocol were compared. Results: Results of rRT-PCR and the MS test system were in concordance in all samples. Time-to-results was faster for rRT-PCR. Hands-on-time was comparable in both assays. Conclusions: MS is a fast, reliable and cost-effective alternative for the detection of SARS-CoV-2 from oral and nasopharyngeal swabs.

‘The long tail of Covid-19’ - The detection of a prolonged inflammatory response after a SARS-CoV-2 infection in asymptomatic and mildly affected patients

“…This is ideal in addressing the need for evaluating less understood or defined immune response pathways. Novel assays for virus detection have been already developed using targeted mass spectrometry 4,5 but there are no assays available yet to look at the symptoms for the diagnosis or understanding of 'long Covid'.…”

‘The long tail of Covid-19’ - The detection of a prolonged inflammatory response after a SARS-CoV-2 infection in asymptomatic and mildly affected patients

“…Targeted proteomics using mass spectrometry to quantitate multiple diagnostic proteins can help address this. Novel assays for virus detection have been already developed using targeted mass spectrometry 3 , 4 but no assays are available to look at the symptoms for the diagnosis or understanding of ‘long Covid’.…”

Mass spectrometry analytical responses to the SARS-CoV2 coronavirus in review

“…In a more recent study, viral RNA was isolated and amplified from 44 nasopharyngeal or oropharyngeal swab specimens, that had tested either positive (22) or negative (22) for SARS-CoV-2 virus, were analysed by MALDI-TOF MS ( Figure 2 E) [ 31 ]. The assay was designed to detect the following SARS-CoV-2 targets: viral nucleocapsid genes (N1-3 across bases 28653-28760, 28880-28978, 28076-28190 respectively), and ORF1ab/nsp3 and ORF1ab/nsp10 across bases 3223-3335 and 13342-13432 respectively.…”

“…From this perspective, samples were identified as positive if two or more amplicon targets were detected and negative if less than two were detected. While the total run time for an exclusive RT-PCR analysis was considerably less than when combined with MS detection (some 80 versus 340 minutes), though both required a similar hands on intervention time [ 31 ]. The MS-based method also has a fast turnaround time from sample to diagnosis and therefore is suitable for routine use.…”