Diagnosing COVID-19: The Disease and Tools for Detection

Udugama, Buddhisha; Kadhiresan, Pranav; Kozłowski, H; Malekjahani, Ayden; Osborne, Matthew; Li, Vanessa Y C; Chen, Hongmin; Mubareka, Samira; Gubbay, Jonathan B.; Chan, Warren C. W.

doi:10.1021/acsnano.0c02624

Cited by 1,592 publications

(1,853 citation statements)

References 106 publications

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“…Primers that anneal specifically to the SARS-COV-2 viral genome are included to prime amplification. The U.S. CDC protocol utilizes primers that target the viral N gene, while the China CDC uses primers matching both the N gene and the ORF1ab region and Charité Germany primers target the RdRp and E genes (Reviewed in Udugama et al 2020). For detection of amplification, qPCR can be performed using intercalating dyes like SybrGreen.…”

Section: Rt-pcrmentioning

confidence: 99%

Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection

Esbin

Whitney

Chong

et al. 2020

RNA

482

474

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The current COVID-19 pandemic presents a serious public health crisis, and a better understanding of the scope and spread of the virus would be aided by more widespread testing. Nucleicacid based tests currently offer the most sensitive and early detection of COVID-19. However, the "gold standard" test pioneered by the United States Center for Disease Control & Prevention, takes several hours to complete and requires extensive human labor, materials such as RNA extraction kits that could become in short supply and relatively scarce qPCR machines. It is clear that a huge effort needs to be made to scale up current COVID-19 testing by orders of magnitude. There is thus a pressing need to evaluate alternative protocols, reagents, and approaches to allow nucleic-acid testing to continue in the face of these potential shortages. There has been a tremendous explosion in the number of papers written within the first weeks of the pandemic evaluating potential advances, comparable reagents, and alternatives to the "gold-standard" CDC RT-PCR test. Here we present a collection of these recent advances in COVID-19 nucleic acid testing, including both peer-reviewed and preprint articles. Due to the rapid developments during this crisis, we have included as many publications as possible, but many of the cited sources have not yet been peer-reviewed, so we urge researchers to further validate results in their own labs. We hope that this review can urgently consolidate and disseminate information to aid researchers in designing and implementing optimized COVID-19 testing protocols to increase the availability, accuracy, and speed of widespread COVID-19 testing.

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Section: Rt-pcrmentioning

confidence: 99%

Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection

Esbin

Whitney

Chong

et al. 2020

RNA

482

474

View full text Add to dashboard Cite

show abstract

“…RT-PCR is a special version used when RNA is being detected and it is now being used as a test to detect SARS-CoV-2, the virus causing COVID-19. Nucleic acid amplification tests (NAAT) of respiratory secretions using the real-time reverse-transcriptase polymerase chain reaction have been proven to help identifying the virus in the early disease stages by detecting unique sequences of virus RNA [81]. Availability of different assays using the RT-PCR technology has helped in patient detection and efforts to contain the virus, since it detects presence of virus very early in the infection [82].…”

Section: Reverse-transcriptase Polymerase Chain Reaction (Rt-pcr) Testsmentioning

confidence: 99%

Elective, Non-urgent Procedures and Aesthetic Surgery in the Wake of SARS–COVID-19: Considerations Regarding Safety, Feasibility and Impact on Clinical Management

Kaye¹,

Paprottka²,

Escudero³

et al. 2020

Aesth Plast Surg

100

145

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Background The worldwide spread of a novel coronavirus disease has led to a near total stop of nonurgent, elective surgeries across all specialties in most affected countries. In the field of aesthetic surgery, the selfimposed moratorium for all aesthetic surgery procedures recommended by most international scientific societies has been adopted by many surgeons worldwide and resulted in a huge socioeconomic impact for most private practices and clinics. An important question still unanswered in most countries is when and how should elective/aesthetic procedures be scheduled again and what kind of organizational changes are necessary to protect patients and healthcare workers when clinics and practices reopen. Defining manageable, evidence-based protocols for testing, surgical/ procedural risk mitigation and clinical flow management/contamination management will be paramount for the safety of non-urgent surgical procedures. Methods We conducted a MEDLINE/PubMed research for all available publications on COVID-19 and surgery and COVID-19 and anesthesia. Articles and referenced literature describing possible procedural impact factors leading to exacerbation of the clinical evolution of COVID-19positive patients were identified to perform risk stratification for elective surgery. Based on these impact factors, considerations for patient selection, choice of procedural complexity, duration of procedure, type of anesthesia, etc., are discussed in this article and translated into algorithms for surgical/anesthesia risk management and clinical management. Current recommendations and published protocols on contamination control, avoidance of crosscontamination and procedural patient flow are reviewed. A COVID-19 testing guideline protocol for patients planning to undergo elective aesthetic surgery is presented and recommendations are made regarding adaptation of current patient information/informed consent forms and patient health questionnaires. Conclusion The COVID-19 crisis has led to unprecedented challenges in the acute management of the crisis, and the wave only recently seems to flatten out in some countries. The adaptation of surgical and procedural steps for a riskminimizing management of potential COVID-19-positive patients seeking to undergo elective aesthetic procedures in the wake of that wave will present the next big challenge for the aesthetic surgery community. We propose a clinical algorithm to enhance patient safety in elective surgery in the context of COVID-19 and to minimize cross-contamination between healthcare workers and patients. New evidence-based guidelines regarding surgical risk stratification, testing, and clinical flow management/contamination management are proposed. We believe that only the continuous development and broad implementation of guidelines like the ones proposed in this paper will allow an early reintegration of all aesthetic procedures into the scope of surgical care currently performed and to prepare

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“…Immunoassays, whole-genome sequencing (8) and mass spectrometry (MS) (9) technologies are commonly suggested alternatives to PCR-based assays. Among these, new generation MS offers a highly sensitive technology that allows the rapid identification of thousands of proteins present in a single sample.…”

Section: Introductionmentioning

confidence: 99%

Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window

Gouveia

Miotello

Gallais

et al. 2020

Preprint

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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 immunodiagnostic that would not require specific reagents are worth 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. 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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Diagnosing COVID-19: The Disease and Tools for Detection

Cited by 1,592 publications

References 106 publications

Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection

Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection

Elective, Non-urgent Procedures and Aesthetic Surgery in the Wake of SARS–COVID-19: Considerations Regarding Safety, Feasibility and Impact on Clinical Management

Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window

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