scholarly journals Robust clinical detection of SARS‐CoV‐2 variants by RT‐PCR/MALDI‐TOF multi‐target approach

2021 ◽  
Author(s):  
Matthew M. Hernandez ◽  
Radhika Banu ◽  
Ana S. Gonzalez‐Reiche ◽  
Adriana Guchte ◽  
Zenab Khan ◽  
...  
Keyword(s):  
Rt Pcr ◽  
Maldi Tof ◽  
Clinical Detection

scholarly journals Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multi-target approach

2021 ◽  
Author(s):  
Matthew M. Hernandez ◽  
Radhika Banu ◽  
Ana S. Gonzalez-Reiche ◽  
Adriana van de Guchte ◽  
Zenab Khan ◽  
...  
Keyword(s):  
New York ◽  
Rapid Development ◽  
False Negative ◽  
Sequencing Data ◽  
Rt Pcr ◽  
Maldi Tof ◽  
Negative Results ◽  
False Negative Results ◽  
Clinical Detection ◽  
Target Design

The COVID-19 pandemic sparked rapid development of SARS-CoV-2 diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY SARS-CoV-2 Panel combines RT-PCR and MALDI-TOF mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified dataset of 1,262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 through April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly-specific for the alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.

scholarly journals Superiority of MALDI-TOF Mass Spectrometry over Real-Time PCR for SARS-CoV-2 RNA Detection

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 730
Author(s):  
Magda Rybicka ◽  
Ewa Miłosz ◽  
Krzysztof Piotr Bielawski
Keyword(s):  
Mass Spectrometry ◽  
Gold Standard ◽  
Viral Genome ◽  
False Negative ◽  
Rt Pcr ◽  
Rna Detection ◽  
Maldi Tof ◽  
Negative Results ◽  
False Negative Results ◽  
Pcr Test

At present, the RT-PCR test remains the gold standard for early diagnosis of SARS-CoV-2. Nevertheless, there is growing evidence demonstrating that this technique may generate false-negative results. Here, we aimed to compare the new mass spectrometry-based assay MassARRAY® SARS-CoV-2 Panel with the RT-PCR diagnostic test approved for clinical use. The study group consisted of 168 suspected patients with symptoms of a respiratory infection. After simultaneous analysis by RT-PCR and mass spectrometry methods, we obtained discordant results for 17 samples (10.12%). Within fifteen samples officially reported as presumptive positive, 13 were positive according to the MS-based assay. Moreover, four samples reported by the officially approved RT-PCR as negative were positive in at least one MS assay. We have successfully demonstrated superior sensitivity of the MS-based assay in SARS-CoV-2 detection, showing that MALDI-TOF MS seems to be ideal for the detection as well as discrimination of mutations within the viral genome.

Application of RT-PCR and MALDI-TOF MS for the detection of RNA luteovirus

2017 ◽  
Vol 539 ◽  
pp. 45-47 ◽  
Author(s):  
Hideyuki Kajiwara ◽  
Ritsuko Murakami
Keyword(s):  
Rt Pcr ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

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

2021 ◽  
Author(s):  
Matthew M. Hernandez ◽  
Radhika Banu ◽  
Paras Shrestha ◽  
Armi Patel ◽  
Feng Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Rt Pcr ◽  
Maldi Tof Mass Spectrometry ◽  
Maldi Tof

scholarly journals MALDI-ToF Protein Profiling as Potential Rapid Diagnostic Platform for COVID-19

2021 ◽  
Author(s):  
Prajkta Chivte ◽  
Zane LaCasse ◽  
Ventaka Devesh Reddy Seethi ◽  
Pratool Bharti ◽  
Elizabeth R. Gaillard
Keyword(s):  
Mass Spectrometry ◽  
High Specificity ◽  
Diagnostic Methods ◽  
Protein Profiling ◽  
Rt Pcr ◽  
High Demand ◽  
Non Invasive ◽  
Maldi Tof ◽  
Potential Biomarker ◽  
High Consistency

More than a year after the COVID-19 pandemic has been declared, the need still exists for accurate, rapid, inexpensive and non-invasive diagnostic methods that yield high specificity towards the current and newly emerging SARS-CoV-2 strains. Several studies have since established saliva as a more amenable specimen type in early detection and viral load quantitation as compared to the nasopharyngeal swabs. Considering the limitations and high demand for COVID-19 testing, we have employed MALDI-ToF mass spectrometry for the analysis of 60 gargle samples from human donors and compared the spectra with their respective RT-PCR results. Several standards including isolated human serum immunoglobulins and controls such as pre-COVID-19 saliva and heat inactivated SARS-CoV-2 virus were simultaneously analyzed to provide a relative view of the saliva and viral proteome as they would appear in this works methodology. Five potential biomarker peaks were established that demonstrated high consistency with PCR positive samples. Overall, the agreement of these results with RT-PCR testing was no less than 90% for the studied cohort, which consisted of young and largely asymptomatic student athletes. Further investigation of the potential biomarker peaks is necessary, however, from a clinical standpoint, these results are promising for a rapid and inexpensive COVID-19 assay.

scholarly journals Food for thought: Eating before saliva collection and interference with SARS-CoV-2 detection

2021 ◽  
Author(s):  
Matthew M. Hernandez ◽  
Mariawy Riollano-Cruz ◽  
Mary C. Boyle ◽  
Radhika Banu ◽  
Paras Shrestha ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Dietary Habits ◽  
Diagnostic Testing ◽  
Real Life ◽  
Oral Microbiota ◽  
Diagnostic Study ◽  
Healthy Children ◽  
Rt Pcr ◽  
Maldi Tof ◽  
Saliva Collection

AbstractBackgroundSaliva is an optimal specimen for detection of viruses that cause upper respiratory infections including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due to its cost-effectiveness and non-invasive collection. However, together with intrinsic enzymes and oral microbiota, children’s unique dietary habits may introduce substances that interfere with diagnostic testing.MethodsTo determine whether children’s dietary choices impact SARS-CoV-2 detection in saliva, we performed a diagnostic study that simulates testing of real-life specimens provided from healthy children (n=5) who self-collected saliva at home before and at 0, 20, and 60 minutes after eating from 20 foods they selected. Each of seventy-two specimens was split into two volumes and spiked with SARS-CoV-2-negative or -positive standards prior to side-by-side testing by reverse-transcription polymerase chain reaction matrix-assisted laser desorption ionization time-of-flight (RT-PCR/MALDI-TOF) assay.ResultsDetection of internal extraction control and SARS-CoV-2 nucleic acids was reduced in replicates of saliva collected at 0 minutes after eating 11 of 20 foods. Interference resolved at 20 and 60 minutes after eating all foods except hot dog in one participant. This represented a significant improvement in detection of nucleic acids compared to saliva collected at 0 minutes after eating (P=0.0005).ConclusionsWe demonstrate successful detection of viral nucleic acids in saliva self-collected by children before and after eating a variety of foods. Fasting is not required before saliva collection for SARS-CoV-2 testing by RT-PCR/MALDI-TOF, but waiting 20 minutes after eating is sufficient for accurate testing. These findings should be considered for SARS-CoV-2 testing and broader viral diagnostics in saliva specimens.

scholarly journals Assessment of 12 Quantitative RT-PCR Commercial Kits for the Detection of SARS-CoV-2

2020 ◽  
Author(s):  
Asmaa M. Altamimi ◽  
Dalia A. Obeid ◽  
Taghreed A. Alaifan ◽  
Moroje T. Taha ◽  
Marwa A. Alhothali ◽  
...  
Keyword(s):  
Clinical Samples ◽  
Rt Pcr ◽  
Gene Target ◽  
Global Response ◽  
Routine Diagnosis ◽  
Purification System ◽  
Clinical Detection ◽  
Public Emergency ◽  
Commercial Kits ◽  
Good Plan

Abstract BackgroundThe emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) in the final months of 2019 had the health officials declare a public emergency raising a global response. In response to the burden of the current pandemic, strict measurements were globally implemented to stop further transmission of the virus. These Measurements rely on an accurate diagnosis of individuals infected with the virus by using real-time reverse transcriptase PCR (RT-PCR). The goal of our study is to relate the fundamental clinical and analytical performance of chosen kits of RT-PCR from distinct manufacturers. Methods A total of 94 nasopharyngeal and oropharyngeal clinical samples were selected randomly, these samples were previously confirmed as 64 positives, and 30 negatives for SARS-COV-2. Generally, 400 µl of each respiratory specimen was subjected to extraction using ExiPrep 96 Viral RNA Kit with the ExiPrep 96 Lite Automated NA Purification System. All kits master mix preparation, cycling protocol, and results interpretation were carried out according to the manufactures’ instructions of use and recommendations. Results In our study, we were able to evaluate the performance of 12 commercial kits in detecting SARS-COV-2 using 5 different targets. The performance of the kits was comparable except for LYRA kit as it was less sensitive (F=67, P <0.001). Particularly, the performance of RealStar, BGI, DiaPlexQ, Genesig, LightMix, TaqPath, and RADI kits were the most sensitive. Moreover, the performance of these commercial kits by gene target showed no significant change in Ct values which indicates that kits disparities are mainly linked to the choice of the gene target (F=0.49, P=0.73).ConclusionWe believe that most of the commercially available RT-PCR kits included in this study can be used for routine diagnosis of SARS-COV-2 patients. Moreover, we recommend that regardless of the laboratory choice of diagnostic commercial kit for the clinical detection of COVID-19 patients the need a for good plan for validation and collaboration with exterior laboratories is essential in order to monitor the virus changes overtime, procedures, technicians, and the different kits performances.

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