SARS-CoV-2 detection and testing

Systematic evaluation of 24 extraction and library preparation combinations for metagenomic sequencing of SARS-CoV-2 in saliva

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.

Investigating the use of human COVID-19 rapid assays to detect antibody and antigen in domesticated dogs (Canis lupus familiaris) and cats (Felis catus)

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.

Suppressing Primer-Driven Nonspecific Amplification in LAMP Using TrueLAMP

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.

Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates

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

Viral adsorption to Moore swabs in passive wastewater sampling

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.

Decay and Solid-Liquid Partitioning of Mpox and Vaccinia Viruses in Primary Influent and Settled Solids to Guide Wastewater-Based Epidemiology Practices

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

Extraction-free colorimetric RT-LAMP for SARS-CoV-2 RNA detection from saliva

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.

Rapid Detection of Active Coronavirus Infection by Lateral Flow Test Strips: A New Approach to Distinguish Replicating Viruses from Non-Replicating Viruses

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.

Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater

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.

Bridging genomic gaps: A versatile SARS-CoV-2 benchmark dataset for adaptive laboratory workflows

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.

Virus-like DNA tracers for characterizing wastewater-based pathogen monitoring systems

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.

Reference materials for SARS-CoV-2 molecular diagnostic quality control: validation of encapsulated synthetic RNAs for room temperature storage and shipping

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.

A laboratory framework for ongoing optimisation of amplification based genomic surveillance programs

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

SWAMPy: Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python

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

wastewaterSPAdes: SARS-CoV-2 strain deconvolution using SPAdes toolkit

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.

Efficient SARS-CoV-2 detection utilizing chitin-immobilized nanobodies synthesized in Ustilago maydis

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

Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance

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

Surface detection of SARS-CoV-2 by lateral flow LAMP

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.

Confirming Multiplex Q-PCR Use in COVID-19 with Next Generation Sequencing: Strategies for Epidemiological Advantage

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.

SARS-CoV-2 Omicron Variant AI-based Primers

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

Evaluation of an optimized protocol and Illumina ARTIC V4 primer pool for sequencing of SARS-CoV-2 using COVIDSeq™ and DRAGEN™ COVID Lineage App workflow

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 Omicron variant mutation at position 28,311 in the SARS-CoV-2 N gene does not perturb CDC N1 target detection

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.

Inexpensive and colorimetric RNA detection by E. coli cell-free protein synthesis platform at room temperature

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: Detecting SARS-CoV-2 Variants of Concern in Metagenomic Wastewater Samples

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

DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing

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.

Design of Specific Primer Sets for the Detection of SARS-CoV-2 Variants of Concern B.1.1.7, B.1.351, P.1, B.1.617.2 using Artificial Intelligence

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

Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays

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

A Viral Fragmentation Signature for SARS-CoV-2 in Clinical Samples Correlating with Contagiousness

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: a web application to monitor mutations in COVID-19 diagnostic assays.

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

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

V3 primer pools with 22 extra alternates improve coverage; revised library preps raise double-barcode demultiplexing from 42.15% to 74.5%, cut misassignment 35x and bring reagent cost near £10 per sample.