SARS-CoV-2 detection and testing

This paper describes a low-cost, colorimetric method for detecting SARS-CoV-2 RNA using E. coli cell-free protein synthesis at room temperature.

The paper evaluates how mutations in primer binding sites affect RT-qPCR detection of SARS-CoV-2 using synthetic transcripts and identifies mismatches in commercial assays.

The paper optimizes a magnetic bead-based nucleic acid extraction protocol for SARS-CoV-2 testing to reduce cross-well contamination while maintaining sensitivity.

This study evaluates the impact of freezing cobas PCR Media on SARS-CoV-2 RNA integrity and whole genome sequencing results, finding no significant negative effects.

EUAdb is a database that standardizes information about FDA-authorized SARS-CoV-2 diagnostic tests to improve comparability and reproducibility.

The paper compares five SARS-CoV-2 sequence capture panels using ddPCR and NGS to identify the most sensitive and specific method for full-length genome recovery.

This paper predicts how SARS-CoV-2 RNA secondary structure affects qRT-PCR primer efficiency and identifies mutations that may reduce test sensitivity.

This study benchmarks seven SARS-CoV-2 whole-genome sequencing protocols using patient samples, finding performance differences based on viral input and sequencing parameters.

SwabExpress is a simplified COVID-19 testing protocol that eliminates the need for transport media and nucleic acid extraction, achieving high sensitivity and specificity.

MMMVI identifies SARS-CoV-2 variants of concern in metagenomic wastewater samples by detecting reads with multiple signature mutations.

This paper evaluates RT-ddPCR primer/probe sets for SARS-CoV-2 RNA quantification, identifies optimal sets, and establishes a method to convert Ct values to RNA copy numbers.

The paper analyzes how SARS-CoV-2 mutations affect RT-PCR primer specificity and finds a 2% monthly increase in mismatches and geographic-specific virus detection.

FELUDA uses FnCas9 for rapid, accurate nucleobase detection and is implemented in a point-of-care diagnostic tool for SARS-CoV-2.

The paper introduces DNA spike-ins to detect contamination in SARS-CoV-2 amplicon-based sequencing and demonstrates their utility in a real-world outbreak investigation.

This paper describes a method for rapid whole genome sequencing of SARS-CoV-2 using one-step RT-PCR on a microfluidic platform followed by MiSeq amplicon sequencing.

The paper evaluates sample pooling strategies for SARS-CoV-2 screening, finding that pools of up to 7 samples can be effectively tested, but recommends a 4-in-1 pooling ratio to maintain accuracy and improve efficiency.

The paper evaluates how DNA mismatches in PCR primers and probes affect hybridization temperatures for SARS-CoV-2 detection and finds that mismatches can improve alignment to SARS-CoV-2 but also increase cross-reactivity with other coronaviruses.

This study evaluates the COVIDSeq protocol for SARS-CoV-2 detection and genetic epidemiology, showing high concordance with RT-PCR and identifying novel variants and lineages.

This paper introduces chimeric RNA standards for SARS-CoV-2 testing to simultaneously validate positive and negative controls in diagnostic assays.

This paper presents a scalable, easy-to-deploy protocol for detecting SARS-CoV-2 genetic material using Cas13-based technology paired with PCR and low-cost instrumentation.

The paper designs specific primer sets for SARS-CoV-2 variants using AI, showing high accuracy and potential for multiplexed testing.

This study evaluates how SARS-CoV-2 mutations affect RT-PCR assay sensitivity by analyzing sequence variability in primer/probe binding regions.

The paper designs a specific primer set for detecting the B.1.1.7 SARS-CoV-2 variant using deep learning, achieving >99% accuracy with in-silico validation.

This paper introduces a viral fragmentation score based on NGS to assess SARS-CoV-2 RNA integrity, showing it correlates with infectiousness and time since disease onset.

The paper develops a RT-qPCR assay using a thermostable reverse transcriptase/DNA polymerase (RTX) and provides protocols for reagent production, aiming to improve testing scalability and reliability in resource-limited settings.

The paper identifies genome gap frequencies in SARS-CoV-2 sequences and proposes an alternative primer set and sequencing scheme to improve genome coverage and quality.

This study evaluates how viral transport media and freeze-thaw cycles affect qRT-PCR sensitivity for SARS-CoV-2 detection using synthetic RNA and DNA simulants.

The paper compares four SARS-CoV-2 nucleic acid amplification tests, finding that Bioperfectus had lower sensitivity and higher limit of detection compared to the others.

assayM monitors mutations in SARS-CoV-2 diagnostic assays by analyzing global genome datasets against WHO and custom primer sequences.

PEARL is a fast, low-cost method for isolating RNA, DNA, and proteins to detect SARS-CoV-2 without commercial kits.