Test sensitivity is secondary to frequency and turnaround time for COVID-19 surveillance

Larremore, Daniel B.; Wilder, Bryan; Lester, Evan; Shehata, Soraya I.; Burke, James; Hay, James A.; Tambe, Milind; Mina, Michael J.; Parker, Roy

doi:10.1101/2020.06.22.20136309

Cited by 328 publications

(485 citation statements)

References 60 publications

(92 reference statements)

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“…Furthermore, more sensitive instrument and MS acquisition modes could be tested to gain further sensitivity. Importantly, because test sensitivity is considered as secondary to frequency and turnaround time for COVID-19 surveillance, 38 quick approaches such as the mass spectrometry methodology developed in this proof-of-concept may have direct application in clinical settings.…”

Section: Discussionmentioning

confidence: 99%

Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window

et al. 2020

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Rapid but yet sensitive, specific, and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostics that would not require specific reagents are worthy to investigate not only for fighting the COVID-19 pandemic but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC–MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry.

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Section: Discussionmentioning

confidence: 99%

Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window

et al. 2020

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“…Recent epidemiological models predict a key driver for containing infections within a community is frequent, weekly COVID-19 testing with a rapid reporting turnaround[2,3]. When combined with social distancing, frequent hand-sanitizing, and face mask requirements, these measures have the potential to eradicate transmission over time [4–6].…”

Section: Introductionmentioning

confidence: 99%

One-step RNA extraction for RT-qPCR detection of 2019-nCoV

Sentmanat

Kouranova

Cui

2020

Preprint

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The global outbreak of coronavirus disease 2019 has placed an unprecedented burden on healthcare systems as the virus spread from the initial 27 reported cases in the city of Wuhan, China to a global pandemic in under three months 1 . Resources essential to monitoring virus transmission have been challenged with a demand for expanded surveillance. The CDC 2019-nCoV Real-Time Diagnostic Panel uses a real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) consisting of two TaqMan probe and primer sets specific for the 2019-nCoV N gene, which codes for the nucleocapsid structural protein that encapsulates viral RNA, for the qualitative detection of 2019-nCoV viral RNA in respiratory samples. To isolate RNA from respiratory samples, the CDC lists RNA extraction kits from three manufacturers. In anticipation of a limited supply chain of RNA extraction kits and the need for test scalability, we sought to identify alternative RNA extraction methods. Here we show that direct lysis of respiratory samples can be used in place of RNA extraction kits to run the CDC 2019-nCoV Real-Time Diagnostic assay with the additional benefits of higher throughput, lower cost, faster turnaround and possibly higher senitivity and improved saftey.

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“…Interestingly, the majority of low viral load specimens are detected uniquely with the N gene by this assay. One possible explanation is a higher surveillance should favor accessibility and frequency while sensitivity should be secondary (13).…”

Section: Discussionmentioning

confidence: 99%

Efficient SARS-CoV-2 detection in unextracted oro-nasopharyngeal specimens by rRT-PCR with the Seegene AllplexTM 2019-nCoV assay

Freppel

Mérindol

Rallu

et al. 2020

Preprint

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The fight against the COVID-19 pandemic has created an urgent need to detect and isolate infected people. The challenge for clinical laboratories has been finding a high throughput, cheap, and efficient testing method in the context of extraction reagent shortages on a planetary scale. To answer this need, we studied SARS-CoV-2 detection in nasopharyngeal swabs stored in UTM (Universal Transport Media) or RNAse-free water by rRT-PCR with the Seegene Allplex TM 2019-nCoV assay without RNA extraction. Optimal results were obtained with 1/2 dilution for swabs in RNAse free water (30/30 detected) and 1/5 dilution for swabs in UTM (29/30 detected) followed by thermal lysis. In addition, a proteinase K (PK) treatment allows a significant reduction of invalid results and increases sensitivity for detection of low viral load specimens. In a panel of 90 known positives with all 3 viral genes present and N gene Ct values from 15 to 40, our detection rate was 98.9% with PK and 94.4% without. In a panel of 60 low positives with only the N gene detectable at Ct values > 30, the detection rate was 76.7% with PK vs 53.3% without it and the invalid rate fell off from 18.3% to 0%. Furthermore, we demonstrated that our method reliably detects specimens with Ct values up to 35, however false negatives become frequent above this range. Finally, we show that swabs should be stored at -70 o C rather than 4 o C when testing cannot be performed within 72 hours of collection when laboratories are overwhelmed.

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Test sensitivity is secondary to frequency and turnaround time for COVID-19 surveillance

Cited by 328 publications

References 60 publications

Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window

Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window

One-step RNA extraction for RT-qPCR detection of 2019-nCoV

Efficient SARS-CoV-2 detection in unextracted oro-nasopharyngeal specimens by rRT-PCR with the Seegene AllplexTM 2019-nCoV assay

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