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SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2022)

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Summary: In this study, the 3D structure of the SARS-CoV-2 membrane protein was modeled using template-free modeling approaches. The trRosetta server provided the most accurate model compared to other methods. Molecular dynamics simulations and analysis were performed to study the protein's behavior in a membrane environment. The study identified interacting residues and predicted potential drug and peptide binding sites.

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Functionalized Co2FeAl Nanoparticles for Detection of SARS CoV-2 Based on Reverse Transcriptase Loop-Mediated Isothermal Amplification

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Secondary structure of the SARS-CoV-2 5'-UTR

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Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy

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CELL (2021)

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Practical challenges to the clinical implementation of saliva for SARS-CoV-2 detection

Nancy Matic et al.

Summary: Amid the global shortage of flocked nasopharyngeal swabs and viral transport media, alternative diagnostic specimens for SARS-CoV-2 detection, such as saliva samples, are being sought. Saliva samples showed good agreement with nasopharyngeal swabs in detecting SARS-CoV-2, with some barriers observed in collecting saliva from long-term care residents and outbreak settings. Additionally, the study indicated that SARS-CoV-2 RNA remains stable in human saliva at room temperature for up to 48 hours after collection.

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Pooled Saliva Specimens for SARS-CoV-2 Testing

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Summary: Saliva testing showed high positive and negative agreement compared to nasopharyngeal swabs, especially for samples with moderate to high viral load. Pooling saliva specimens for testing exhibited decreased sensitivity compared to individual testing, but could still detect individuals with higher viral loads in an asymptomatic screening program. This method eliminates the need for swabs or viral transport medium and may improve screening compliance among individuals averse to nasal collections.

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Saliva Is a Promising Alternative Specimen for the Detection of SARS-CoV-2 in Children and Adults

Rebecca Yee et al.

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Zhe Wang et al.

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SARS-CoV-2: Comparative analysis of different RNA extraction methods

Cecilia Ambrosi et al.

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Lauren K. Clark et al.

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Development of a reverse transcription recombinase polymerase amplification assay for rapid and direct visual detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Yee Ling Lau et al.

Summary: RT-RPA is a rapid and accurate detection method for SARS-CoV-2, with a clinical sensitivity of 98% and specificity of 100%, proving to be a viable alternative to RT-qPCR.

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PLOS ONE (2021)

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Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein

Thomas G. Flower et al.

Summary: The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04-angstrom resolution by X-ray crystallography, revealing unique dimerization interfaces that may allow the protein to form large-scale assemblies, potentially mediating immune suppression and evasion activities.

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Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples

Alisa Alekseenko et al.

Summary: The study optimized the RT-LAMP detection method to make it more cost-effective and applicable for expanding the scale of COVID-19 diagnostics; it explored the compatibility between different DNA polymerases and reverse transcriptases, and validated the effectiveness of the method in clinical samples; the optimized RT-LAMP method is expected to facilitate the global expansion of SARS-CoV-2 testing, particularly in places where commercial alternatives cannot meet the demand.

SCIENTIFIC REPORTS (2021)

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Summary: A low-cost, highly specific method for SARS-CoV-2 detection has been successfully developed using the SYBR Green RT-PCR method, with the ability to screen out negative cases and high safety and efficacy. Optimization of experimental parameters achieved high specificity of PCR products, providing technical support for large-scale screening.

SCIENTIFIC REPORTS (2021)

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Development and comparison of novel multiple cross displacement amplification (MCDA) assays with other nucleic acid amplification methods for SARS-CoV-2 detection

Laurence Don Wai Luu et al.

Summary: The development of alternative isothermal amplification assays, such as multiple cross displacement amplification (MCDA), may overcome the speed and portability limitations of real-time PCR (rt-PCR) methods for SARS-CoV-2 detection. MCDA was found to be the fastest nucleic acid amplification method for SARS-CoV-2, while rt-PCR exhibited the highest sensitivity. Different nucleic acid amplification methods offer distinct advantages, which should be taken into consideration when selecting the most suitable method for specific applications.

SCIENTIFIC REPORTS (2021)

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Digital droplet PCR accurately quantifies SARS-CoV-2 viral load from crude lysate without nucleic acid purification

Harish N. Vasudevan et al.

Summary: The study demonstrates the accurate and consistent measurement of SARS-CoV-2 viral load using digital droplet PCR (ddPCR) directly from crude lysate without nucleic acid purification. ddPCR performs well in nasopharyngeal swab specimens with low input viral copy numbers, showing higher sensitivity and robustness compared to qPCR when using crude lysate.

SCIENTIFIC REPORTS (2021)

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Structural Insight Into the SARS-CoV-2 Nucleocapsid Protein C-Terminal Domain Reveals a Novel Recognition Mechanism for Viral Transcriptional Regulatory Sequences

Mei Yang et al.

Summary: The study reveals that the nucleocapsid protein C-terminal domain (CTD) of SARS-CoV-2 may play a crucial role in viral transcriptional regulation by recognizing different patterns of viral genomic intergenic transcriptional regulatory sequences (TRSs), leading to discontinuous viral transcription.

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Aubin Samacoits et al.

Summary: The paper introduces a cost-effective smartphone-based device combined with machine learning software for CRISPR diagnosis of SARS-CoV-2. The device has a detection limit of 6.25 RNA copies/μL in laboratory samples, with a test accuracy of 95% and sensitivity of 97% on nasopharyngeal swab samples with transmissible viral loads.

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Rapid One-Pot Detection of SARS-CoV-2 Based on a Lateral Flow Assay in Clinical Samples

Chao Zhang et al.

Summary: This study developed a rapid detection method for SARS-CoV-2, with the entire sample-to-result workflow taking less than 40 minutes. The method achieved 100% accuracy compared to PCR-based assays, offering a potential universal platform for rapid and point-of-care detection of emerging infectious diseases.

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Virus-Like Particles as Positive Controls for COVID-19 RT-LAMP Diagnostic Assays

Soo Khim Chan et al.

Summary: Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid and inexpensive method for detecting SARS-CoV-2, but lacks proper internal and external positive controls as well as stability in detection RNA. By using virus-like particles (VLPs) to encapsidate target RNA, the reliability of RT-LAMP assays is improved, showing promise as positive controls for molecular testing.

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Comparison of real-time and droplet digital PCR to detect and quantify SARS-CoV-2 RNA in plasma

Ana P. Tedim et al.

Summary: In this study, the detection of SARS-CoV-2 RNA in plasma from different severity groups of COVID-19 patients was compared using RT-qPCR and ddPCR. The results showed similar prevalence of RNAemia between groups, with ICU patients showing the highest positivity rates. RT-qPCR was demonstrated to be as effective as ddPCR in detecting and quantifying SARS-CoV-2 RNAemia in plasma.

EUROPEAN JOURNAL OF CLINICAL INVESTIGATION (2021)

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Article Infectious Diseases

Collection of lower respiratory specimen by bronchoscopy for the diagnosis of COVID-19

Joyce K. C. Ng et al.

Summary: Bronchoscopy, a procedure that generates aerosols, is not routinely performed in high-risk COVID-19 patients due to the risk of transmission to healthcare workers. However, obtaining lower respiratory specimens via bronchoscopy with bronchoalveolar lavage (BAL) is necessary for confirming COVID-19 or other diagnoses that could change clinical management. This report describes a case where the final diagnosis of COVID-19 was confirmed by BAL after five negative SARS-CoV-2 RT-PCR tests in upper respiratory tract and stool samples. Special precautions should be taken when performing bronchoscopy in high-risk non-intubated patients.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2021)

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Editorial Material Biochemistry & Molecular Biology

COVID-19 and Diagnostic Testing for SARS-CoV-2 by RT-qPCR-Facts and Fallacies

Stephen Bustin et al.

Summary: This commentary aims to clarify the true strengths and limitations of molecular testing technology, especially RT-qPCR, and to address and help stop the unfounded speculation surrounding its use.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Editorial Material Medicine, General & Internal

SARS-CoV-2 Viral Variants-Tackling a Moving Target

John R. Mascola et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2021)

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Article Microbiology

Self-Collected Saline Gargle Samples as an Alternative to Health Care Worker-Collected Nasopharyngeal Swabs for COVID-19 Diagnosis in Outpatients

David M. Goldfarb et al.

Summary: This study evaluated the performance, stability, and user acceptability of different self-collected sample types for detecting SARS-CoV-2. Saline mouth rinse/gargle samples showed excellent sensitivity and stability, as well as the highest acceptability scores, making them a promising option for outpatient self-collection in adults and school-aged children.

JOURNAL OF CLINICAL MICROBIOLOGY (2021)

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Article Microbiology

Copan eNAT Transport System To Address Challenges in COVID-19 Diagnostics in Regions with Limited Testing Access

Melissa Richard-Greenblatt et al.

Summary: By evaluating eNAT as an alternative transport system, the study found that it can support COVID-19 diagnostics while ensuring viral inactivation, expanding testing to remote areas. The stability of SARS-CoV-2 molecular detection was not affected by storage temperature changes over two weeks in eNAT or PBS, in contrast to other transport media.

JOURNAL OF CLINICAL MICROBIOLOGY (2021)

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SARS-CoV-2 detection by fluorescence loop-mediated isothermal amplification with and without RNA extraction

Keisuke Taki et al.

Summary: Rapid and simple point-of-care detection of SARS-CoV-2 is crucial to control the pandemic. RT-LAMP can detect the virus faster than RT-PCR, with saliva being a suitable non-invasive specimen for mass screening. However, the need for RNA extraction for optimal detection by RT-fLAMP suggests its critical role in virus detection.

JOURNAL OF INFECTION AND CHEMOTHERAPY (2021)

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Editorial Material Virology

Will the emergent SARS-CoV2 B.1.1.7 lineage affect molecular diagnosis of COVID-19?

Juan D. Ramirez et al.

Summary: As the COVID-19 pandemic continues to affect global public health systems, mutations in the SARS-CoV2 genome are being observed. The emergence of the B.1.1.7 lineage in the UK has raised concerns among global authorities due to potential challenges it may pose to diagnostic testing. Efforts must be made to closely monitor SARS-CoV-2 genomes for variants that could impact testing accuracy and lead to false negative results.

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One-tube SARS-CoV-2 detection platform based on RT-RPA and CRISPR/Cas12a

Yangyang Sun et al.

Summary: The OR-DETECTR platform for detecting COVID-19 is rapid, accurate, and can be completed in one tube, with a low detection limit and 100% consistency with rRT-PCR results. Additionally, a lateral flow assay based on OR-DETECTR has been developed for COVID-19 detection.

JOURNAL OF TRANSLATIONAL MEDICINE (2021)

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Article Biochemical Research Methods

End-point RT-PCR: A potential alternative for diagnosing coronavirus disease 2019 (COVID-19)

Jose Valter Joaquim Silva Junior et al.

Summary: Real-time reverse transcription-polymerase chain reaction (RT-qPCR) is considered the gold standard for diagnosing SARS-CoV-2 infections, but its limitations in many laboratories have led to the development of an alternative, sensitive RT-PCR platform with comparable specificity and sensitivity in a smaller reaction volume. This platform may provide a viable option for SARS-CoV-2 diagnosis in laboratories where RT-qPCR is not available, offering cost efficiency and reliable results.

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A nanoscale genosensor for early detection of COVID-19 by voltammetric determination of RNA-dependent RNA polymerase (RdRP) sequence of SARS-CoV-2 virus

Leila Farzin et al.

Summary: The developed voltammetric genosensor can accurately detect SARS-CoV-2 RdRP sequence in sputum samples, showing a good linear response and low detection limit. The sensor also demonstrated a good recovery rate in real sample analysis.

MICROCHIMICA ACTA (2021)

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Article Multidisciplinary Sciences

Development of a multiplex Loop-Mediated Isothermal Amplification (LAMP) assay for on-site diagnosis of SARS CoV-2

Woong Sik Jang et al.

Summary: In this study, three RT-LAMP primer sets were designed for detecting different genes of SARS CoV-2. It was found that the detection limits of two primer sets were low, showing comparable sensitivity to other widely used detection methods.

PLOS ONE (2021)

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Article Multidisciplinary Sciences

Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: Comparison with automated systems

Henrik Dimke et al.

Summary: Our study reveals that conventional RNA purification is a comparable alternative to modern automated systems for detecting SARS-CoV-2 with similar sensitivity and specificity. It is easily scalable, cost-effective, and suitable for conventional laboratories as a replacement for automated systems.

PLOS ONE (2021)

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Article Multidisciplinary Sciences

Evaluation of two automated low-cost RNA extraction protocols for SARS-CoV-2 detection

Fernando Lazaro-Perona et al.

Summary: Two automatable in-house protocols for high-throughput RNA extraction from nasopharyngeal swabs for SARS-CoV-2 detection have been evaluated. The study found that both protocols are suitable for SARS-CoV-2 detection in high-throughput facilities and can save costs compared to commercial kits.

PLOS ONE (2021)

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Article Multidisciplinary Sciences

Extraction-free protocol combining proteinase K and heat inactivation for detection of SARS-CoV-2 by RT-qPCR

Valeria Genoud et al.

Summary: The PK+HID method is an extraction-free RT-qPCR technique for SARS-CoV-2 detection, showing improved performance compared to traditional heat-inactivation procedures. It can be combined with multiplexing RT-qPCR kits, demonstrating high sensitivity and specificity in clinical sample analysis.

PLOS ONE (2021)

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Article Multidisciplinary Sciences

Rapid processing of SARS-CoV-2 containing specimens for direct RT-PCR

Piotr Chomczynski et al.

Summary: Widespread diagnostic testing is crucial in reducing the transmission of COVID-19. The AG processing method simplifies and increases the sensitivity of viral RNA detection, providing a reliable and scalable diagnostic test that can be integrated into various workflows.

PLOS ONE (2021)

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Article Multidisciplinary Sciences

Open-source RNA extraction and RT-qPCR methods for SARS-CoV-2 detection

Thomas G. W. Graham et al.

Summary: Re-opening of communities during the COVID-19 pandemic has led to new waves of infections, necessitating widespread testing for SARS-CoV-2. This study evaluates simpler and cheaper protocols for RNA extraction and RT-qPCR, with the potential to reduce the time and cost of COVID-19 testing.

PLOS ONE (2021)

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Article Virology

Optimal preparation of SARS-CoV-2 viral transport medium for culture

Julie McAuley et al.

Summary: The sudden outbreak of COVID-19 placed significant stresses on supply chains, including the need for viral transport medium (VTM). This study describes the preparation and validation testing of VTM for expanding diagnostic testing, with results showing that filter and autoclave-based sterilization methods yield the best outcomes. The storage time and temperature of VTM have an impact on diagnostic analyses.

VIROLOGY JOURNAL (2021)

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Article Virology

Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week

Paloma Troyano-Hernaez et al.

Summary: Monitoring the genetic diversity and mutations of SARS-CoV-2 is crucial for understanding its evolution and ensuring the effectiveness of diagnostic tests, vaccines, and therapies against COVID-19. This study analyzed over 100,000 worldwide SARS-CoV-2 sequences and found significant amino acid changes in the structural proteins, highlighting the importance of ongoing surveillance and research on emerging mutations.

VIRUSES-BASEL (2021)

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Article Virology

Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications

Jasdeep B. Singh et al.

Summary: The SARS-CoV-2 virus has undergone multiple mutations during its global circulation, leading to the emergence of three new lineages in the UK, South Africa, and Brazil. These mutations impact crucial proteins such as spike, ORF8, and nucleocapsid, potentially affecting host receptor affinity and antibody resistance.

VIRUSES-BASEL (2021)

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Article Multidisciplinary Sciences

Point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP

Lukas Bokelmann et al.

Summary: Cap-iLAMP combines RNA extraction with improved RT-LAMP color scoring to detect SARS-CoV-2 positive samples in less than an hour, reducing reagent costs per test.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Rapid electrochemical detection of coronavirus SARS-CoV-2

Thanyarat Chaibun et al.

Summary: The researchers developed an ultrasensitive electrochemical biosensor based on isothermal rolling circle amplification for rapid detection of SARS-CoV-2, capable of detecting as low as 1 copy/mu L of N and S genes in clinical samples. The sensor showed a 100% concordance with qRT-PCR results in clinical sample evaluation.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)

Thanh Thi Nguyen et al.

Summary: This study analyzed genomic mutations in the coding regions of SARS-CoV-2 and their impact on protein secondary structure and solvent accessibility, indicating the establishment of a mutation dataset beneficial for virus tracking, as well as identifying stable coding genes suitable for vaccine and drug development.

SCIENTIFIC REPORTS (2021)

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Article Multidisciplinary Sciences

Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests

Bindu Swapna Madala et al.

Summary: DNA synthesis in vitro allows rapid production of reference standards for use as controls in diagnostic tests, improving accuracy and quality. Incorporating both positive and negative controls into diagnostic testing helps evaluate test specificity, while cross-validating these controls in the same reaction distinguishes control and test failures.

SCIENTIFIC REPORTS (2021)

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Article Multidisciplinary Sciences

Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2

Yajuan Dong et al.

Summary: This study compared the performance of 19 sets of primers in COVID-19 detection and identified 6 sets of primers with faster amplification. Among them, the Set-4 primer set had the highest positive detection rate of SARS-CoV-2.

SCIENTIFIC REPORTS (2021)

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Article Multidisciplinary Sciences

Digital PCR for high sensitivity viral detection in false-negative SARS-CoV-2 patients

Paolo Poggio et al.

Summary: False negatives remain a challenge in COVID-19 diagnostic testing, but the use of digital PCR can help to address this issue by accurately detecting infections in samples with low viral loads.

SCIENTIFIC REPORTS (2021)

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Article Medicine, General & Internal

Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study

Robert Challen et al.

Summary: The study found that the mortality hazard ratio associated with infection with VOC-202012/1 compared with previously circulating variants was 1.64, indicating an increase in deaths from 2.5 to 4.1 per 1000 detected cases in comparatively low risk group of covid-19 patients in the community. This suggests that infection with VOC-202012/1 may lead to substantial additional mortality compared with previously circulating variants, impacting healthcare capacity planning and control policies.

BMJ-BRITISH MEDICAL JOURNAL (2021)

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Review Immunology

Lessons learned 1 year after SARS-CoV-2 emergence leading to COVID-19 pandemic

Kelvin Kai-Wang To et al.

Summary: The lack of modern medical management and vaccines could lead to the COVID-19 pandemic reaching the levels of past deadly outbreaks like the 1894 plague and 1918-A(H1N1) influenza pandemic. The presence of multiple coronaviruses with pandemic potential in animals, coupled with environmental factors like the mixing and selling of wild mammals with poor hygiene practices in urban markets, pose a significant threat to global health. The emergence of new viruses and the challenges of mass testing, contact tracing, treatment, and potential development of vaccine-resistant virus variants highlight the importance of global preparedness in combating infectious diseases.

EMERGING MICROBES & INFECTIONS (2021)

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Article Chemistry, Multidisciplinary

Rapid, Ultrasensitive, and Highly Specific Diagnosis of COVID-19 by CRISPR-Based Detection

Xiong Zhu et al.

Summary: The study developed a novel diagnostic test for COVID-19, called COVID-19 MCCD, by combining MCDA with CRISPR-Cas12a technology, which is sensitive, rapid, and reliable for the diagnosis of SARS-CoV-2 infection.

ACS SENSORS (2021)

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Article Multidisciplinary Sciences

INSIGHT: A population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing

Qianxin Wu et al.

Summary: INSIGHT is a two-stage COVID-19 testing strategy that combines point-of-care diagnosis with next-generation sequencing to achieve population-scale testing; the first stage provides quick decentralized readout, aiming for early isolation of asymptomatic patients and gives results within 1 to 2 hours; the second stage confirms near-patient testing results and facilitates centralized data collection.

SCIENCE ADVANCES (2021)

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Article Medicine, General & Internal

Simpler and faster Covid-19 testing: Strategies to streamline SARS-CoV-2 molecular assays

Nuttada Panpradist et al.

Summary: A low-cost RT-PCR kit was developed for faster detection of SARS-CoV-2 infections, with high sensitivity and specificity demonstrated in both laboratory and clinical settings. The assay showed promising performance and could potentially expand access to Covid-19 testing.

EBIOMEDICINE (2021)

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Article Medicine, General & Internal

A Simple, Affordable, Rapid, Stabilized, Colorimetric, Versatile RT-LAMP Assay to Detect SARS-CoV-2

Juan Garcia-Bernalt Diego et al.

Summary: The global SARS-CoV-2 pandemic has brought about a need for widespread testing for COVID-19, with RT-qPCR as the gold standard method, but facing challenges. A novel RT-LAMP method has been developed, showing promise for cost-effective, rapid, and stable detection of SARS-CoV-2.

DIAGNOSTICS (2021)

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Review Medicine, General & Internal

Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis

Vania M. Moreira et al.

Summary: This study critically appraised and compared the clinical performance of various specimens for SARS-CoV-2 detection, with saliva showing the highest accuracy and being identified as the best alternative to the current standard swab samples.

DIAGNOSTICS (2021)

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Article Biochemistry & Molecular Biology

Rapid and Sensitive Detection of SARS-CoV-2 Using Clustered Regularly Interspaced Short Palindromic Repeats

Jen-Hui Tsou et al.

Summary: This study developed a rapid CRISPR test for sensitive detection of SARS-CoV-2 without the need for RNA extraction, allowing for completion within one hour. The test is simple to operate, requiring minimal equipment, and results can be visualized immediately using a UV light illuminator or paper strips.

BIOMEDICINES (2021)

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Article Biophysics

Emulsion-based isothermal nucleic acid amplification for rapid SARS-CoV-2 detection via angle-dependent light scatter analysis

Alexander S. Day et al.

Summary: The SARS-CoV-2 pandemic has highlighted the need for new technologies with faster detection capabilities. The eLAMP platform developed allows for faster detection time by compartmentalizing LAMP reactions and utilizing light scatter intensity to monitor amplification reactions. This technology can differentiate between different initial target concentrations and can be integrated into a smartphone-based platform for real-time monitoring.

BIOSENSORS & BIOELECTRONICS (2021)

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Article Biophysics

A rapid diagnosis of SARS-CoV-2 using DNA hydrogel formation on microfluidic pores

Hwang-soo Kim et al.

Summary: The study proposes an innovative method for detecting the new coronavirus using isothermal amplification of nucleic acids on a mesh with multiple microfluidic pores, with a detection limit of 0.7 aM. This approach offers rapid, easy, and effective detection of the target pathogen without the need for sophisticated equipment.

BIOSENSORS & BIOELECTRONICS (2021)

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Article Biochemical Research Methods

Rapid visual detection of SARS-CoV-2 by colorimetric loop-mediated isothermal amplification

Barbara Reynes et al.

Summary: The study evaluated the performance of a new set of primers defined from the ORF1ab sequence and its combination with a previously published set of primers from the N sequence for detecting SARS-CoV-2 RNA using loop-mediated isothermal amplification technique. The results showed that the ORF1ab primer set enabled visual detection of SARS-CoV-2 RNA in 16 minutes, and a simultaneous reaction with both ORF1ab and N primers allowed for higher sensitivity of detection, particularly when low numbers of copies were present (250 viral RNA copies). Additionally, the protocol was able to detect viral RNA in saliva samples, demonstrating the potential for developing a new and sensitive rapid point-of-care device for visual detection of SARS-CoV-2 RNA.

BIOTECHNIQUES (2021)

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Article Medical Laboratory Technology

A Highly Automated Mobile Laboratory for On-site Molecular Diagnostics in the COVID-19 Pandemic

Wanli Xing et al.

Summary: The study introduced a highly automated and fully integrated mobile laboratory for rapid deployment during infectious disease outbreaks, enabling on-site specimen collection, inactivation, analysis, and reporting. This provides a promising solution for fast deployment of medical diagnostic resources in critical situations and helps facilitate local containment of SARS-CoV-2 transmission.

CLINICAL CHEMISTRY (2021)

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Article Infectious Diseases

Diagnostic accuracy of loop-mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations

Anetta Ptasinska et al.

Summary: LamPORE is a highly accurate methodology for detecting SARS-CoV-2 in both symptomatic and asymptomatic populations, showing high sensitivity and specificity compared to the reference RT-qPCR test, especially in asymptomatic samples. It can be used as an alternative to RT-qPCR for effective diagnostics in population settings.

CLINICAL MICROBIOLOGY AND INFECTION (2021)

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Editorial Material Infectious Diseases

How the European in vitro diagnostic regulation could negatively impact the European response to the next pandemic: an urgent call for action before May 2022

Pieter Vermeersch et al.

CLINICAL MICROBIOLOGY AND INFECTION (2021)

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Article Microbiology

Comparative effects of viral-transport-medium heat inactivation upon downstream SARS-CoV-2 detection in patient samples

Jamie L. Thompson et al.

Summary: The study evaluated alternative commercially available kits for SARS-CoV-2 genome detection and found that using heat inactivation in an extraction-free protocol could reduce the time from sample receipt to test outcome. The results demonstrate that sample treatment can significantly impact the performance of diagnostic kits, with different effects depending on the kit used.

JOURNAL OF MEDICAL MICROBIOLOGY (2021)

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Article Pathology

Prolonged Unfrozen Storage and Repeated Freeze-Thawing of SARS-CoV-2 Patient Samples Have Minor Effects on SARS-CoV-2 Detectability by RT-PCR

Andreas Dzung et al.

Summary: This study shows that viral RNA levels are relatively stable at higher temperatures and after repetitive freeze-thawing, but storage conditions can have an impact on RT-PCR detection results.

JOURNAL OF MOLECULAR DIAGNOSTICS (2021)

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Article Biochemical Research Methods

The effect of heat-treatment on SARS-CoV-2 viability and detection

Jane Burton et al.

Summary: Heat treatment can effectively reduce the viability of SARS-CoV-2, but the outcome varies significantly depending on the temperature and duration. Local validation is crucial for assessing the efficacy of heat-inactivation in molecular testing.

JOURNAL OF VIROLOGICAL METHODS (2021)

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Article Biochemical Research Methods

RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19

Maha Alafeef et al.

Summary: This protocol presents a novel approach for rapid detection of COVID-19 without the need for RNA extraction, using nucleic acid amplification and plasmonic sensing technology. The test demonstrates high accuracy, sensitivity (>98.4%), specificity (>96.6%) and a detection limit of 10 copies/mu L.

NATURE PROTOCOLS (2021)

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Article Multidisciplinary Sciences

Versatile and flexible microfluidic qPCR test for high-throughput SARS-CoV-2 and cellular response detection in nasopharyngeal swab samples

Julien Fassy et al.

Summary: The emergence and fast spread of SARS-CoV-2 has highlighted the insufficient testing capacity in many countries due to limitations in resources, technology, and personnel. While traditional RT-qPCR diagnostic tests remain the standard method, a quantitative nanofluidic assay based on the Biomark™ instrument from Fluidigm offers a more efficient and cost-effective approach to testing, overcoming some of the limitations of traditional methods. This advanced system allows for high-throughput testing, monitoring of specific SARS-CoV-2 variants, and detection of other pathogens and host cellular responses.

PLOS ONE (2021)

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Article Virology

Accessible LAMP-Enabled Rapid Test (ALERT) for Detecting SARS-CoV-2

Ali Bektas et al.

Summary: The COVID-19 pandemic has highlighted the challenges in large-scale testing, leading to the development of a DIY workflow for rapid and accurate detection of viral RNA with high sensitivity and specificity. This method improves efficiency and accuracy of testing through various techniques, allowing for quick testing at home or in healthcare settings.

VIRUSES-BASEL (2021)

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Article Virology

Effect of Inactivation Methods on SARS-CoV-2 Virion Protein and Structure

Emma K. Loveday et al.

Summary: Research has shown that heat treatment for 15 minutes at 65 degrees Celsius or UV irradiation at 70,000 mu J/cm(2) can completely inactivate SARS-CoV-2, offering efficient options for research purposes. It has also been observed that UV irradiation results in a 2-log reduction of detectable viral genomes compared to heat inactivation, indicating differences in effectiveness between the two methods.

VIRUSES-BASEL (2021)

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Article Medicine, General & Internal

Detection of SARS-CoV-2 Infection in Human Nasopharyngeal Samples by Combining MALDI-TOF MS and Artificial Intelligence

Meritxell Deulofeu et al.

Summary: The study developed a rapid and accurate diagnostic test for COVID-19 by combining MALDI-TOF MS analysis of NP samples with machine learning techniques. The best model showed high performance with accuracy, sensitivity, and specificity values exceeding 90%, making it a reliable method for early detection of the disease.

FRONTIERS IN MEDICINE (2021)

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Article Chemistry, Analytical

Point-of-Care PCR Assays for COVID-19 Detection

Niharika Gupta et al.

Summary: Molecular diagnostics, including RT-PCR and qRT-PCR, have been vital in the global response to the COVID-19 pandemic. In addition to these gold standards, faster antigen tests and other point-of-care devices have also played a crucial role in containing the spread of the virus. The development of miniaturized, high-throughput PCR systems, digital PCR, electrochemical PCR, and CRISPR/Cas technology for POC diagnostics are areas of increasing interest and research focus. Commercial RT-PCR POC systems approved for COVID-19 detection by various agencies have also been discussed.

BIOSENSORS-BASEL (2021)

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Article Pediatrics

Understanding Laboratory Testing for SARS-CoV-2

Ritu Cheema et al.

Summary: The global impact of the COVID-19 pandemic has affected millions of lives, prompting the FDA to approve molecular assays and serological tests under emergency use authorization. These tests are crucial for clinical diagnosis and therapeutic decision-making, as well as for understanding the epidemiology of the pandemic. Limited experience with available tests and variations among them, even with similar technology, highlight the importance of improving clinicians' understanding of SARS-CoV-2 test procedures and their limitations.

CHILDREN-BASEL (2021)

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Article Chemistry, Analytical

Single- and Two-Stage, Closed-Tube, Point-of-Care, Molecular Detection of SARS-CoV-2

Jinzhao Song et al.

Summary: This study reports on single-stage and two-stage molecular diagnostic tests that can be conducted with simple or no instrumentation, effectively detecting the COVID-19 virus. The tests have high sensitivity, low sample processing requirements, and are suitable for screening at home, at the point of need, and in resource-poor settings.

ANALYTICAL CHEMISTRY (2021)

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Article Biophysics

Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis

Mohd Azhar et al.

Summary: FELUDA is a new rapid detection method for DNA/RNA pathogenic sequences or variants, which can accurately detect single nucleotide variants (SNVs) including heterozygous carriers with 100% accuracy. It is semi-quantitative, adaptable to multiple signal detection platforms, and can be used for various applications such as molecular diagnosis during infectious disease outbreaks like COVID-19.

BIOSENSORS & BIOELECTRONICS (2021)

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Article Biochemistry & Molecular Biology

Detection of SARS-CoV-2 RNA by a Multiplex Reverse-Transcription Loop-Mediated Isothermal Amplification Coupled with Melting Curves Analysis

Igor P. Oscorbin et al.

Summary: Loop-mediated isothermal amplification (LAMP) is a stable nucleic acid amplification method that is resistant to DNA amplification inhibitors, allowing for multiplexing and suitable for SARS-CoV-2 viral RNA detection with high accuracy and short analysis time.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Biotechnology & Applied Microbiology

LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding

Kerstin U. Ludwig et al.

Summary: Frequent and fast testing with high sensitivity and specificity, low cost, and easy deployment make LAMP-Seq a promising tool for integrated public health surveillance programs in containing COVID-19 outbreaks.

NATURE BIOTECHNOLOGY (2021)

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Article Virology

Resource-efficient internally controlled in-house real-time PCR detection of SARS-CoV-2

Janine Michel et al.

Summary: The presented RKI/ZBS1 SARS-CoV-2 protocol offers a cost-effective alternative for detecting SARS-CoV-2 RNA, especially when facing shortages of commercially available ready-to-use kits. By running two duplex real-time RT-PCR assays simultaneously, the protocol enables testing specimens in duplicate and increases testing capacity while saving reagents.

VIROLOGY JOURNAL (2021)

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Article Engineering, Environmental

Rapid screening for SARS-CoV-2 variants of concern in clinical and environmental samples using nested RT-PCR assays targeting key mutations of the spike protein

G. La Rosa et al.

Summary: A nested RT-PCR assay was developed to detect key mutations of SARS-CoV-2 variants, showing potential for rapid screening of clinical samples and detection of variants in sewage. The study highlights the importance of wastewater surveillance in exploring SARS-CoV-2 diversity and distribution.

WATER RESEARCH (2021)

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Article Biotechnology & Applied Microbiology

Detection of SARS-CoV-2 RNA using RT-LAMP and molecular beacons

Scott Sherrill-Mix et al.

Summary: The rapid spread of SARS-CoV-2 has created a need for fast and affordable diagnostic assays. The RT-LAMP method, using molecular beacons for sequence-specific detection, provides an alternative to RT-PCR with potential cost savings. Implementation of LAMP-BEAC assay has allowed robust screening of thousands of saliva samples per week, showing good concordance with RT-qPCR on clinical samples.

GENOME BIOLOGY (2021)

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Article Biochemical Research Methods

A microfluidic-integrated lateral flow recombinase polymerase amplification (MI-IF-RPA) assay for rapid COVID-19 detection

Dan Liu et al.

Summary: The MI-IF-RPA assay developed in this study offers a rapid and sensitive detection of SARS-CoV-2, integrating RT-RPA and LF detection systems into a single microfluidic chip. The assay provides easily interpretable results with a short testing time of approximately 30 minutes, showing high sensitivity and specificity, making it a cost-effective screening tool for resource-limited areas in complement to RT-PCR.

LAB ON A CHIP (2021)

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Article Chemistry, Analytical

Rapid molecular diagnostics of COVID-19 by RT-LAMP in a centrifugal polystyrene-toner based microdevice with end-point visual detection

Kezia Gomes de Oliveira et al.

Summary: Infection by the new coronavirus is a serious global public health issue, with mass testing being a key strategy. Loop-mediated isothermal amplification (LAMP) simplifies infectious disease diagnostics, with easy visual result detection, but caution is required to avoid contamination and false positives. LAMP on microfluidic platforms minimizes false positives and offers potential for point-of-care applications.

ANALYST (2021)

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Article Biochemical Research Methods

Thin-film-transistor digital microfluidics for high value in vitro diagnostics at the point of need

Sally Anderson et al.

Summary: The latest development in TFT-DMF technology, aQdrop (TM), shows promising applications in molecular diagnostics, including COVID-19 testing. With 41,000 independently addressable electrodes, TFT-DMF can manipulate droplets of any size and shape to perform multiple parallel reactions, demonstrating its potential for complex assays and sample processing.

LAB ON A CHIP (2021)

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Article Medicine, Research & Experimental

Saliva Direct: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity

Chantal B. F. Vogels et al.

Summary: SalivaDirect simplifies saliva-based diagnostic testing for SARS-CoV-2, demonstrating high positive agreement with traditional swab testing. This innovative approach can make large scale testing more accessible and affordable, offering an alternative solution to supply chain issues.

MED (2021)

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Article Nanoscience & Nanotechnology

Aligner-Mediated Cleavage-Based Isothermal Amplification for SARS-CoV-2 RNA Detection

Chao Zhang et al.

Summary: The AMC-SDA method presented in this study allows for rapid and accurate detection of SARS-CoV-2 RNA with high sensitivity. The procedure is simple, time-efficient, and has shown 100% diagnostic accuracy in simulated samples, making it a potential universal platform for detecting emerging infectious diseases.

ACS APPLIED BIO MATERIALS (2021)

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Article Chemistry, Analytical

Colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a visual diagnostic platform for the detection of the emerging coronavirus SARS-CoV-2

Kawin Nawattanapaiboon et al.

Summary: This study developed a visual diagnostic platform for SARS-CoV-2 based on colorimetric RT-LAMP with sensitivity and specificity comparable to commercial qRT-PCR assays. The method showed high accuracy and reliability in clinical specimens, indicating its potential beneficial use as a diagnostic platform for COVID-19 screening.

ANALYST (2021)

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Article Chemistry, Analytical

Colorimetric loop-mediated isothermal amplification (LAMP) for cost-effective and quantitative detection of SARS-CoV-2: the change in color in LAMP-based assays quantitatively correlates with viral copy number

Everardo Gonzalez-Gonzalez et al.

Summary: The study demonstrated a loop-mediated isothermal amplification (LAMP) method using specially designed initiators to detect and amplify SARS-CoV-2 genetic sequences, showing a quantitative ability to detect nucleic acids in a range of 62 to 2 x 10(5) DNA copies. The colorimetric LAMP was found to have diagnostic performance comparable to RT-qPCR, with a sensitivity of 92.85% and specificity of 81.25% in analyzing a set of 44 RNA extracts from patients in a hospital setting.

ANALYTICAL METHODS (2021)

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Review Dentistry, Oral Surgery & Medicine

Exploring salivary diagnostics in COVID-19: a scoping review and research suggestions

Priyanka Kapoor et al.

Summary: Saliva as an alternate diagnostic sample for SARS-CoV-2 infection offers advantages such as simple sample collection method, point-of-care testing for initial screening in community or hospital settings, and reducing patient discomfort. However, there is heterogeneity and gaps in methodology in the current literature, highlighting the need for more robust study design to generate higher levels of evidence.

BDJ OPEN (2021)

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Article Infectious Diseases

Sensitive detection and quantification of SARS-CoV-2 by multiplex droplet digital RT-PCR

Remco de Kock et al.

Summary: The study developed a one-step droplet digital RT-PCR multiplex assay for reliable quantification of SARS-CoV-2 RNA, which could be used for screening and monitoring Covid-19 patients. By determining the fractional abundance of viral RNA with respect to a human housekeeping gene, viral loads from different samples can be compared.

EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES (2021)

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Article Biotechnology & Applied Microbiology

CRISPR/Cas9-Based Lateral Flow and Fluorescence Diagnostics

Mark J. Osborn et al.

Summary: This study demonstrates two different detection methods based on CRISPR/Cas, one for the specific detection of SARS-CoV-2 genes and the other for detecting and differentiating multiple respiratory viruses in a single reaction. These two methods are fast, simple, and efficient, suitable for on-site diagnosis and testing.

BIOENGINEERING-BASEL (2021)

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Article Chemistry, Analytical

Can a field molecular diagnosis be accurate? A performance evaluation of colorimetric RT-LAMP for the detection of SARS-CoV-2 in a hospital setting

Livia do Carmo Silva et al.

Summary: Research indicates that using colorimetric RT-LAMP for detecting SARS-CoV-2 in hospital settings shows high sensitivity and accuracy, with results consistent with tests conducted in reference laboratories. A perfect agreement of 100% was achieved when comparing RT-LAMP results with RT-qPCR results for samples with Ct values <30.

ANALYTICAL METHODS (2021)

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Article Infectious Diseases

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Victor M. Corman et al.

EUROSURVEILLANCE (2020)

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Article Medicine, General & Internal

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

Roujian Lu et al.

LANCET (2020)

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Letter Medicine, General & Internal

SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients

Lirong Zou et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Article Microbiology

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

Alexander E. Gorbalenya et al.

NATURE MICROBIOLOGY (2020)

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Article Chemistry, Multidisciplinary

Selective Naked-Eye Detection of SARS-CoV-2 Mediated by N Gene Targeted Antisense Oligonucleotide Capped Plasmonic Nanoparticles

Parikshit Moitra et al.

ACS NANO (2020)

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Article Chemistry, Analytical

Novel One-Step Single-Tube Nested Quantitative Real-Time PCR Assay for Highly Sensitive Detection of SARS-CoV-2

Ji Wang et al.

ANALYTICAL CHEMISTRY (2020)

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Article Biochemistry & Molecular Biology

The Architecture of SARS-CoV-2 Transcriptome

Dongwan Kim et al.

CELL (2020)

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Article Biochemistry & Molecular Biology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Alexandra C. Walls et al.

CELL (2020)

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Article Medical Laboratory Technology

Rapid Detection of SARS-CoV-2 by Low Volume Real-Time Single Tube Reverse Transcription Recombinase Polymerase Amplification Using an Exo Probe with an Internally Linked Quencher (Exo-IQ)

Ole Behrmann et al.

CLINICAL CHEMISTRY (2020)

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Article Immunology

Evaluation of COVID-19 RT-qPCR Test in Multi sample Pools

Idan Yelin et al.

CLINICAL INFECTIOUS DISEASES (2020)

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Article Infectious Diseases

An alternative workflow for molecular detection of SARS-CoV-2-escape from the NA extraction kit-shortage, Copenhagen, Denmark, March 2020

Anna S. Fomsgaard et al.

EUROSURVEILLANCE (2020)

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Article Medicine, General & Internal

SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate

Manuel Becerra-Flores et al.

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Article Biochemistry & Molecular Biology

A Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2

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INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

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Article Microbiology

Evaluation of Transport Media and Specimen Transport Conditions for the Detection of SARS-CoV-2 by Use of Real-Time Reverse Transcription-PCR

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Editorial Material Microbiology

Understanding, Verifying, and Implementing Emergency Use Authorization Molecular Diagnostics for the Detection of SARS-CoV-2 RNA

Stephanie L. Mitchell et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2020)

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Letter Microbiology

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Kyle G. Rodino et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2020)

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Letter Microbiology

Saliva as a Noninvasive Specimen for Detection of SARS-CoV-2

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Article Microbiology

Performance of Abbott ID Now COVID-19 Rapid Nucleic Acid Amplification Test Using Nasopharyngeal Swabs Transported in Viral Transport Media and Dry Nasal Swabs in a New York City Academic Institution

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Review Virology

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REVIEWS IN MEDICAL VIROLOGY (2020)

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Letter Virology

Pooling of nasopharyngeal swab specimens for SARS-CoV-2 detection by RT-PCR

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JOURNAL OF MEDICAL VIROLOGY (2020)

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Article Virology

SARS-CoV-2 can be detected in urine, blood, anal swabs, and oropharyngeal swabs specimens

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Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (BARS-CoV-2) Is Comparable in Clinical Samples Preserved in Saline or Viral Transport Medium

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Nucleic acid lateral flow assay with recombinase polymerase amplification: Solutions for highly sensitive detection of RNA virus

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TALANTA (2020)

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Article Immunology

ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens

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EMERGING MICROBES & INFECTIONS (2020)

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The influence of a swab type on the results of point-of-care tests

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AMB EXPRESS (2020)

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SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis

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MSYSTEMS (2020)

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Structure of replicating SARS-CoV-2 polymerase

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Massively multiplexed nucleic acid detection with Cas13

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Letter Biotechnology & Applied Microbiology

Diagnostics and the coronavirus: don't let the standards slip

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Letter Cell Biology

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CELL DISCOVERY (2020)

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SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission

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CLINICAL CHEMISTRY (2020)

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Variplex™ test system fails to reliably detect SARS-CoV-2 directly from respiratory samples without RNA extraction

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Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCR and real-time PCR

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EXPERIMENTAL AND MOLECULAR MEDICINE (2020)

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CELL (2020)

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The ORF3a protein of SARS-CoV-2 induces apoptosis in cells

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CELLULAR & MOLECULAR IMMUNOLOGY (2020)

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Rapid Direct Nucleic Acid Amplification Test without RNA Extraction for SARS-CoV-2 Using a Portable PCR Thermocycler

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GENES (2020)

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INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2020)

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Sensitivity assessment of droplet digital PCR for SARS-CoV-2 detection

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INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE (2020)

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Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs

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Comparative Analysis of Primer-Probe Sets for RT-qPCR of COVID-19 Causative Virus (SARS-CoV-2)

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ACS INFECTIOUS DISEASES (2020)

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Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome

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ROYAL SOCIETY OPEN SCIENCE (2020)

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Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets

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NATURE MICROBIOLOGY (2020)

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Performance Assessment of SARS-CoV-2 PCR Assays Developed by WHO Referral Laboratories

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Letter Microbiology

Comparison of Extraction Methods and Thermocyclers for SARS-CoV-2 Molecular Detection Using Clinical Specimens

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Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection

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A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay

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Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection

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Self-Collected Anterior Nasal and Saliva Specimens versus Health Care Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2

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Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting

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Rapid and sensitive detection of SARS-CoV-2 RNA using the Simplexa™ COVID-19 direct assay

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Evaluation of simple nucleic acid extraction methods for the detection of SARS-CoV-2 in nasopharyngeal and saliva specimens during global shortage of extraction kits

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Evaluation of the Aptima™ transcription-mediated amplification assay (Hologic®) for detecting SARS-CoV-2 in clinical specimens

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High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2

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Self-collection: An appropriate alternative during the SARS-CoV-2 pandemic

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JOURNAL OF CLINICAL VIROLOGY (2020)

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Ad hoc laboratory -based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples

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SARS-CoV-2 detection by direct rRT-PCR without RNA extraction

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A Novel Multiplex qRT-PCR Assay to Detect SARS-CoV-2 Infection: High Sensitivity and Increased Testing Capacity

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MICROORGANISMS (2020)

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BIOSENSORS-BASEL (2020)

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Suboptimal Biological Sampling as a Probable Cause of False-Negative COVID-19 Diagnostic Test Results

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Willingness to Use Home Collection Methods to Provide Specimens for SARS-CoV-2/COVID-19 Research: Survey Study

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JOURNAL OF MEDICAL INTERNET RESEARCH (2020)

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Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA

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Rapid Differential Diagnosis of Seven Human Respiratory Coronaviruses Based on Centrifugal Microfluidic Nucleic Acid Assay

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Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages

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ARCHIVES OF MEDICAL RESEARCH (2020)

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Homogeneous circle-to-circle amplification for real-time optomagnetic detection of SARS-CoV-2 RdRp coding sequence

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BIOSENSORS & BIOELECTRONICS (2020)

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Letter Medicine, General & Internal

Swabs Collected by Patients or Health Care Workers for SARS-CoV-2 Testing

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NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Pooled RNA sample reverse transcriptase real time PCR assay for SARS CoV-2 infection: A reliable, faster and economical method

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Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection

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Highly sensitive and specific diagnosis of COVID-19 by reverse transcription multiple cross-displacement amplification-labelled nanoparticles biosensor

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EUROPEAN RESPIRATORY JOURNAL (2020)

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Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses

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SMALL (2020)

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SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP

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VIRUSES-BASEL (2020)

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VIRUSES-BASEL (2020)

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Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein

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GENOME MEDICINE (2020)

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Analysis of Inactivation of SARS-CoV-2 by Specimen Transport Media, Nucleic Acid Extraction Reagents, Detergents, and Fixatives

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Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials

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Methods of Inactivation of SARS-CoV-2 for Downstream Biological Assays

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Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis

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MICROBES AND INFECTION (2020)

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Letter Medicine, General & Internal

Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2

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NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Letter Medicine, General & Internal

Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing

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NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients

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SARS-CoV-2 detection using isothermal amplification and a rapid, inexpensive protocol for sample inactivation and purification

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Rapid isothermal amplification and portable detection system for SARS-CoV-2

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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VIROLOGY JOURNAL (2020)

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Evaluation of Commercially Available Viral Transport Medium (VTM) for SARS-CoV-2 Inactivation and Use in Point-of-Care (POC) Testing

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Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection

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Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR

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PLOS BIOLOGY (2020)

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Positive Selection of ORF1ab, ORF3a, and ORF8 Genes Drives the Early Evolutionary Trends of SARS-CoV-2 During the 2020 COVID-19 Pandemic

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FRONTIERS IN MICROBIOLOGY (2020)

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FRONTIERS IN MEDICINE (2020)

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Self-Collected versus Healthcare Worker-Collected Swabs in the Diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2

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NATURE COMMUNICATIONS (2020)

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SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication

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MATTER (2020)

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VIRULENCE (2020)

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Review Medicine, General & Internal

Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection (Review)

Jacqueline Dinnes et al.

COCHRANE DATABASE OF SYSTEMATIC REVIEWS (2020)

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Article Virology

Amplification chemistries in clinical virology

Sherry Dunbar et al.

JOURNAL OF CLINICAL VIROLOGY (2019)

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Article Multidisciplinary Sciences

Comparison of the new fully automated extraction platform eMAG to the MagNA PURE 96 and the well-established easyMAG for detection of common human respiratory viruses

Musa Hindiyeh et al.

PLOS ONE (2019)

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Article Microbiology

GLAPD: Whole Genome Based LAMP Primer Design for a Set of Target Genomes

Ben Jia et al.

FRONTIERS IN MICROBIOLOGY (2019)

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Review Microbiology

CRISPR-Cas Biology and Its Application to Infectious Diseases

Jeffrey R. Strich et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2019)

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Article Chemistry, Analytical

An Affordable and Portable Thermocycler for Real-Time PCR Made of 3D-Printed Parts and Off-the-Shelf Electronics

Roberto A. Mendoza-Gallegos et al.

ANALYTICAL CHEMISTRY (2018)

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Review Chemistry, Multidisciplinary

Exponential Isothermal Amplification of Nucleic Acids and Assays for Proteins, Cells, Small Molecules, and Enzyme Activities: An EXPAR Example

Michael S. Reid et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

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Review Chemistry, Analytical

dPCR: A Technology Review

Phenix-Lan Quan et al.

SENSORS (2018)

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Article Biochemical Research Methods

Development of a universal internal positive control

Mark F. Kavlick

BIOTECHNIQUES (2018)

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Review Biochemical Research Methods

Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection

Susana Barreda-Garcia et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2018)

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Article Multidisciplinary Sciences

Ultrasensitive, rapid and inexpensive detection of DNA using paper based lateral flow assay

Miriam Jauset-Rubio et al.

SCIENTIFIC REPORTS (2016)

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Review Medical Laboratory Technology

Real-time PCR detection chemistry

E. Navarro et al.

CLINICA CHIMICA ACTA (2015)

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Article Multidisciplinary Sciences

Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification

Yi Wang et al.

SCIENTIFIC REPORTS (2015)

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Article Virology

A Case for the Ancient Origin of Coronaviruses

Joel O. Wertheim et al.

JOURNAL OF VIROLOGY (2013)

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Review Medical Laboratory Technology

Quality assurance and quality control in the routine molecular diagnostic laboratory for infectious diseases

Harald H. Kessler et al.

CLINICAL CHEMISTRY AND LABORATORY MEDICINE (2012)

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Article Biochemistry & Molecular Biology

DNA detection using recombination proteins

Olaf Piepenburg et al.

PLOS BIOLOGY (2006)

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