A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva

Article Medical Laboratory Technology

Rapid and Extraction-Free Detection of SARS-CoV-2 from Saliva by Colorimetric Reverse-Transcription Loop-Mediated Isothermal Amplification

Matthew A. Lalli et al.

Summary: The study developed a rapid colorimetric assay for SARS-CoV-2 detection using saliva samples without RNA extraction, achieving high accuracy and sensitivity.

CLINICAL CHEMISTRY (2021)

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Editorial Material Microbiology

When Should Asymptomatic Persons Be Tested for COVID-19?

Audrey N. Schuetz et al.

Summary: Initially, CDC suggested that asymptomatic individuals do not necessarily need to be tested for COVID-19, but later updated its guidance to support testing, especially for those who have had contact with confirmed SARS-CoV-2 cases. A commentary from the American Society for Microbiology urges CDC to consult primary stakeholders of COVID-19 testing when making impactful changes in testing guidance.

JOURNAL OF CLINICAL MICROBIOLOGY (2021)

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Article Microbiology

SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia

John Everett et al.

Summary: The first wave of COVID-19 in Philadelphia showed similarities with lineages from New York, suggesting primary transmission from that location, but also indicated local spread. Some patients had heterogeneous viral populations within them, with variations in genome sequences between time points and body sites. There was no clear link between different lineages and disease outcomes, underscoring the importance of individual-specific vulnerability.

MBIO (2021)

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Review Medicine, General & Internal

Comparison of Saliva and Nasopharyngeal Swab Nucleic Acid Amplification Testing for Detection of SARS-CoV-2 A Systematic Review and Meta-analysis

Guillaume Butler-Laporte et al.

Summary: This study evaluated the diagnostic accuracy of saliva NAAT for COVID-19 and found that its accuracy is similar to that of nasopharyngeal swab NAAT, especially in ambulatory settings. This suggests the potential for saliva NAAT as an alternative to nasopharyngeal swabs and supports further research in this area.

JAMA INTERNAL MEDICINE (2021)

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Article Biochemical Research Methods

Development of multiplexed reverse-transcription loop-mediated isothermal amplification for detection of SARS-CoV-2 and influenza viral RNA

Yinhua Zhang et al.

Summary: This study enhances loop-mediated isothermal amplification through multiplexed real-time and end point detection of SARS-CoV-2 combined with influenza and control targets. By enabling multiple target detection, loop-mediated isothermal amplification can be even more widely used for diagnostics in settings where multiple viral targets are potential infectious agents and where higher-throughput testing is advantageous.

BIOTECHNIQUES (2021)

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Article Pathology

Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping

Joel J. Credle et al.

Summary: The novel detection method cRASL-seq proposed in the study can efficiently and sensitively detect pathogens, the analysis of COVID-19 patient samples does not require nucleic acid purification or reverse transcription, with low cost and easy operation, it is a powerful new technology.

MODERN PATHOLOGY (2021)

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Article Multidisciplinary Sciences

Ultra-rapid detection of SARS-CoV-2 in public workspace environments

Ozlem Yaren et al.

Summary: Managing the pandemic requires new testing capabilities, with a focus on rapid, simple, and cost-effective tests. High sensitivity may not be necessary in all cases, and in lower-risk environments, speed and simplicity take precedence over sensitivity.

PLOS ONE (2021)

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Article Cell Biology

Early sample tagging and pooling enables simultaneous SARS-CoV-2 detection and variant sequencing

Alon Chappleboim et al.

Summary: This study introduces a novel NGS diagnostic method called ApharSeq, which significantly improves virus detection efficiency and accuracy, while reducing labor costs and reagent requirements.

SCIENCE TRANSLATIONAL MEDICINE (2021)

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Article Multidisciplinary Sciences

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

Daniel Butler et al.

Summary: By utilizing a fast colorimetric test (LAMP) for SARS-CoV-2 infection and large-scale shotgun metatranscriptomics for host, viral, and microbial profiling, the authors provide insights into the viral genetic features of the New York City outbreak and associate specific host responses and gene expression perturbations with SARS-CoV-2 infection.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

A multiplexed, next generation sequencing platform for high-throughput detection of SARS-CoV-2

Marie-Ming Aynaud et al.

Summary: The study introduces a platform called C19-SPAR-Seq, which can analyze tens of thousands of patient samples for SARS-CoV-2 in a single run, with high specificity and sensitivity demonstrated through experimental trials in clinical diagnostics.

NATURE COMMUNICATIONS (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 Microbiology

Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing

Leon Peto et al.

Summary: LamPORE is a novel diagnostic platform for detecting SARS-CoV-2 RNA with high sensitivity and specificity, making it suitable for high-throughput testing.

JOURNAL OF CLINICAL MICROBIOLOGY (2021)

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News Item Multidisciplinary Sciences

Five reasons why COVID herd immunity is probably impossible

Christie Aschwanden

Summary: Despite vaccination efforts in full force, the theoretical threshold for conquering COVID-19 appears to be unattainable.

NATURE (2021)

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Article Multidisciplinary Sciences

Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow

Fernanda de Mello Malta et al.

Summary: Since the first reported case of the new coronavirus infection in Wuhan, Chinese scientists rapidly identified the pathogen known as SARS-CoV-2 and developed the RT-PCR assays for COVID19 diagnosis. However, due to supply shortages, many countries are facing limitations in testing capacity. Therefore, researchers have proposed a cost-effective NGS-based molecular test with high scalability and accuracy compared to RT-qPCR.

SCIENTIFIC REPORTS (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 Multidisciplinary Sciences

EUAdb: A resource for COVID-19 test development and comparison

Alyssa Woronik et al.

Summary: A relational database containing standardized ontology and curated data about COVID-19 diagnostic tests with Emergency Use Authorizations by the FDA aims to improve global SARS-CoV-2 testing capability, provide comparisons between tests to avoid duplication, and establish a technological foundation for future emerging disease testing.

PLOS ONE (2021)

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Article Multidisciplinary Sciences

COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

Michele Simonetti et al.

Summary: Genomic surveillance of SARS-CoV-2 variants is crucial, and a new sequencing method, COVseq, allows cost-effective and scalable surveillance that can be easily adapted to other viruses.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq

Ramesh Yelagandula et al.

Summary: The SARSeq method presented in this study uses a dual indexing strategy in a multiplexed RT-PCR reaction to diagnose SARS-CoV-2 at scale with high sensitivity and robustness. It can also be used for simultaneous detection of other viruses and expanded to detect other pathogens.

NATURE COMMUNICATIONS (2021)

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Article Medicine, General & Internal

Accuracy of novel antigen rapid diagnostics for SARS-CoV-2: A living systematic review and meta-analysis

Lukas E. Brummer et al.

Summary: A systematic review and meta-analysis was conducted to evaluate the clinical accuracy of commercially available Ag-RDTs for SARS-CoV-2. The study found that Ag-RDTs can detect the vast majority of infected individuals in the early phase of the disease and those with high viral load, making them valuable diagnostic tools. However, concerns were raised regarding bias across datasets and the need for standardization in conducting and reporting clinical accuracy studies for improved comparability and data utilization.

PLOS MEDICINE (2021)

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Article Engineering, Biomedical

Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples

Joshua S. Bloom et al.

Summary: Frequent and widespread testing of asymptomatic individuals for SARS-CoV-2 is crucial for virus transmission mitigation. A new testing method called SwabSeq, utilizing molecular barcodes for pooled samples, allows for testing thousands of samples in a single run without the need for RNA extraction, with comparable sensitivity and specificity to traditional qPCR tests.

NATURE BIOMEDICAL ENGINEERING (2021)

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Review Infectious Diseases

Viral Load Difference between Symptomatic and Asymptomatic COVID-19 Patients: Systematic Review and Meta-Analysis

Marco Zuin et al.

Summary: The systematic review and meta-analysis found no significant difference in viral load between asymptomatic and symptomatic COVID-19 patients, based on real-time RT-PCR data for RdRp, E, and N genes' expression. Asymptomatic subjects may act as a reservoir for the infection and contribute significantly to the spread of the pandemic.

INFECTIOUS DISEASE REPORTS (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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Editorial Material Pathology