SARS-CoV-2 detection and testing

The paper evaluates 24 metagenomic sequencing workflows for SARS-CoV-2 detection in saliva, finding that RNA-Seq library preparation has a greater impact on viral read recovery than extraction methods.

This study evaluates the effectiveness of human COVID-19 rapid antigen and antibody tests in dogs and cats, finding moderate sensitivity and specificity compared to RT-PCR and PRNT.

TrueLAMP improves LAMP specificity by inhibiting nonspecific amplification, achieving 100% specificity in no-template controls and a 250 copies/reaction detection limit for SARS-CoV-2.

The paper quantifies post-sampling RNA degradation in wastewater samples and shows it leads to underestimation of viral concentrations, affecting public health surveillance.

This paper characterizes viral adsorption to Moore swabs using isotherm models, finding the Redlich-Peterson model best describes the relationship between viral concentration and swab uptake over time.

This study examines the decay and solid-liquid partitioning of mpox and vaccinia viruses in wastewater to improve wastewater-based epidemiology practices.

This study develops a colorimetric RT-LAMP assay for SARS-CoV-2 RNA detection in saliva without RNA extraction, achieving high sensitivity and comparable specificity to qRT-PCR.

This paper develops a CRISPR-based lateral flow assay to detect active coronavirus infection by targeting negative-sense RNA, distinguishing replicating from non-replicating viruses.

This paper compares three amplicon sequencing methods for SARS-CoV-2 variant detection in wastewater, finding ARTIC V4 most accurate for variant identification and abundance estimation.

This paper develops a benchmark dataset for SARS-CoV-2 amplicon sequencing to improve genomic surveillance in resource-constrained labs, finding that basecaller choice has minimal impact on consensus quality.

The paper evaluates the effectiveness of RT-qPCR primers and probes for detecting new and old SARS-CoV-2 variants by analyzing mutation frequencies in key genes.

The paper introduces virus-like DNA tracers to improve the accuracy and resolution of wastewater-based pathogen monitoring systems by assessing assay performance and signal decay.

This paper validates encapsulated synthetic RNAs for SARS-CoV-2 molecular diagnostics, showing they remain stable at room temperature for long-term storage and use.

This study develops a framework to optimize sequencing efficiency for genomic surveillance by adjusting primer pooling and sets based on evolving viral populations.

SWAMPy generates realistic SARS-CoV-2 wastewater amplicon metagenomes to test and improve analysis methods.

This paper introduces wastewaterSPAdes, an assembly-based method for SARS-CoV-2 strain deconvolution from wastewater samples without read alignment, showing accurate strain identification and abundance estimation.

This paper develops an inexpensive SARS-CoV-2 antigen detection method using chitin-immobilized nanobodies produced in Ustilago maydis.

The paper optimizes the Illumina COVIDSeq protocol to reduce costs while maintaining accuracy for decentralized SARS-CoV-2 genomic surveillance.

This paper develops a novel LAMP-based assay for detecting SARS-CoV-2 on surfaces using a lateral flow readout, demonstrating sensitivity down to 100 genomic copies and viability after a week of dry-down.

This study compares Q-PCR and NGS for detecting SARS-CoV-2 variants, showing Q-PCR's effectiveness for screening known mutations in a cost-effective manner.

This paper uses AI to develop a primer set for the SARS-CoV-2 Omicron variant, validated in silico and preliminarily in lab tests.

The paper compares two SARS-CoV-2 sequencing primer pools, finding that the ARTIC V4 pool performs better, especially in low viral load samples.

The paper evaluates the impact of the Omicron variant's N gene mutation on CDC N1 target detection and finds no significant reduction in assay performance.

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

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

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.

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.

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.

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