RT‐PCR/MALDI‐TOF mass spectrometry‐based detection of SARS‐CoV‐2 in saliva specimens

Abstract

As severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infections continue, there is a substantial need for cost‐effective and large‐scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS‐CoV‐2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT‐PCR/MALDI‐TOF mass spectrometry‐based assay (Agena MassARRAY®) to detect SARS‐CoV‐2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS‐CoV‐2 RNA in saliva by the cobas® 6800/8800 SARS‐CoV‐2 real‐time RT‐PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS‐CoV‐2 detection on the novel Agena system as well as on a conventional real‐time RT‐PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS‐CoV‐2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.

Application and Perspectives of MALDI–TOF Mass Spectrometry in Clinical Microbiology Laboratories

“…At present with the current COVID-19 pandemic, the need for a rapid diagnosis of SARS-CoV-2 has generated a rapid evolution and optimization of clinical methods, including MALDI–TOF MS. Because the gold standard and main diagnosis tool for SARS-CoV-2, the RT-PCR, is continuously producing false negatives, questions are being raised about whether MS-based technology, such as MassARRAY, which demonstrates superior sensitivity and discrimination of mutations within the viral genome, should overtake it [ 114 , 115 ]. MS-based methods using swab and saliva samples are reporting promising results.…”

MALDI MS-Based Investigations for SARS-CoV-2 Detection

“…MALDI-MS approaches used for SARS-CoV-2 detection are illustrated in Figure 2. As exemplified in Figure 2, current MALDI-MS approaches aimed at the detection of SARS-CoV-2 are based on "biotyping" [69,70] and "genotyping" [71][72][73] strategies. One study is based on "proteotyping" with high resolution MALDI-FTICR at the peptide level [74], while several studies used the "biomolecular host profiling" strategy to uncover biomarkers of diagnostic utility generated after SARS-CoV-2 infection [75][76][77][78][79].…”

“…The genotyping approaches exploiting the MS detection of PCR amplicons are very sensitive; consequently, enrichment methods such as cell culturing can be avoided. These approaches have been used successfully for the identification of several viruses and bacteria [71][72][73][87][88][89].…”

“…In this section, we report the MALDI-MS-based investigations which aimed to detect SARS-CoV-2 infection with the use of "proteotyping" [74], "biotyping" [69,70], "genotyping" [71][72][73], and biomolecular host profiling [75][76][77][78][79] approaches. Interestingly, two of these investigations used both biotyping and biomolecular host profiling strategies [69,70].…”

Investigation of MALDI-TOF Mass Spectrometry for Assessing the Molecular Diversity of Campylobacter jejuni and Comparison with MLST and cgMLST: A Luxembourg One-Health Study

“…On one hand, it has been successfully applied in routine for the identification of various microorganisms at the species level including aerobic and anaerobic bacteria, mycobacteria and yeasts including mycobacterium, and fungi in diagnostics [21][22][23]. On the other hand, researches in taxonomy usefulness extended to a wider range of organisms have suggested new perspectives, such as for helminths [24][25][26], for ectoparasites (e.g., ticks, fleas, mosquitoes), protozoa, and even more recently for the screening of the SARS-CoV-2 [27][28][29][30]. Further, MALDI-TOF MS has been used for other research proposes such as antimicrobial resistance screening [31][32][33].…”