SARS-CoV-2 detection and testing

SARS-CoV-2 sequencing artifacts associated with targeted PCR enrichment and read mapping

This study identifies sequencing artifacts in SARS-CoV-2 genome sequencing caused by PCR primers and reference genome choices, showing how they lead to ambiguous base calls and missed mutations.

Reducing Supply Chain Dependencies for Viral Genomic Surveillance: Get by with a Little HELP from Commercial Enzymes already in your Lab Freezer

The paper develops ARTIC HELP, an open-source alternative to ARTIC nanopore sequencing protocols using commercial enzymes, achieving comparable genome coverage for SARS-CoV-2 and Norovirus GII with reduced supply chain dependencies.

Benchmarking concentration and direct extraction methods for wastewater-based surveillance of eight human respiratory viruses: implications for rapid application to novel pathogens

This study benchmarks four concentration and extraction methods for detecting eight respiratory viruses in wastewater using dPCR, showing method-specific sensitivity and recovery efficiency.

A Benchmark of methods for SARS-CoV-2 whole genome sequencing and development of a more sensitive method

The paper benchmarks SARS-CoV-2 whole genome sequencing methods and introduces an improved ARTIC-Amp protocol for better coverage in low RNA samples.

Nanoparticle-Supported, Rapid, and Electronic Detection of SARS-CoV-2 Antibodies and Antigens at Sub-Femtomolar Level

This paper introduces NasRED, a rapid, sensitive, and cost-effective electronic detection platform for SARS-CoV-2 antibodies and antigens with sub-femtomolar sensitivity.

Digital Immunoassay for Rapid Detection of SARS-CoV-2 Infection in a Broad Spectrum of Animals

This paper develops a digital immunoassay for rapid detection of SARS-CoV-2 antibodies in multiple animal species with high sensitivity and specificity.

Inter-laboratory harmonization of microsphere immunoassays for SARS-CoV-2 antibody detection in dried blood spots and oral fluids

This study evaluates the interchangeability of dried blood spots and oral fluids for SARS-CoV-2 antibody detection across laboratories using microsphere immunoassays.

A COVID-19 Rapid Antigen Test Employing Upconversion Nanoparticles

This paper develops a rapid antigen test using upconversion nanoparticles for COVID-19, achieving high sensitivity and specificity in clinical trials.

A Label-free Nanowell-based Impedance Sensor for Ten-minute SARS-CoV-2 Detection

This paper develops a label-free nanowell-based impedance sensor for rapid SARS-CoV-2 detection within ten minutes using small sample volumes.

Nanoparticle-Supported, Rapid, Digital Quantification of Neutralizing Antibodies Against SARS-CoV-2 Variants

This paper introduces a rapid, portable assay to measure neutralizing antibodies against SARS-CoV-2 variants using gold nanoparticles and optical extinction detection.

Urban wastewater contains a functional human antibody repertoire of mucosal origin

The paper identifies and characterizes a human antibody repertoire from wastewater, showing it can track immune correlates and aid in vaccine efficacy assessment.

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

The paper evaluates nine computational tools for identifying SARS-CoV-2 lineages in wastewater sequencing data using simulated samples, finding most tools reliably detect lineages above 5% frequency.

VLP-Based Model for Study of Airborne Viral Pathogens

This paper develops a VLP-based model system to study airborne viral pathogens, demonstrating aerosolization and detection of VLP RNA using RT-LAMP assays.

Genomic Surveillance of SARS-CoV-2 Using Long-Range PCR Primers

This study introduces long-range PCR primers for SARS-CoV-2 sequencing to reduce amplicon dropout and coverage bias, improving genome quality and lineage accuracy.

In silico thermodynamic evaluation of the effectiveness of RT-LAMP primers to SARS-CoV-2 variants detection

The paper evaluates the effectiveness of RT-LAMP primers for detecting SARS-CoV-2 variants by analyzing the impact of mismatches on hybridization temperatures.

Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data

The paper evaluates how reference design affects SARS-CoV-2 lineage abundance estimation from wastewater sequencing data using synthetic and real-world datasets.

Targeted Amplification and Genetic Sequencing of the Severe Acute Respiratory Syndrome Coronavirus 2 Surface Glycoprotein

The paper develops SpikeSeq, a targeted sequencing method for the SARS-CoV-2 S-gene, showing high conservation and accuracy across variants.

A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing

This paper introduces a low-cost, high-throughput method for SARS-CoV-2 detection using whole genome sequencing, achieving high sensitivity and accuracy comparable to clinical tests.

Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance

This study investigates discordant sequence data in SARS-CoV-2 whole genome sequencing to improve bioinformatic quality standards and surveillance practices.

STRENGTH OF ASSOCIATION BETWEEN GENERALIZED/NONSPECIFIC COVID-19 SIGNS & SYMPTOMS WITH SARS-COV 2 SPECIFIC ORF, N, E GENES IDENTIFIED THROUGH REAL TIME PCR.

This study examines the association between SARS-CoV-2 gene presence (ORF, N, E) and generalized COVID-19 symptoms using RT-PCR data from 3375 patients.

Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR

This study evaluates the performance of four viral transport media for preserving SARS-CoV-2 RNA during storage at different temperatures and time points.

Effective Matrix Designs for COVID-19 Group Testing

The paper proposes a new group testing method for COVID-19 that improves pooling designs and decoding efficiency.

SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes

The paper introduces genotyping probes on a DNA chip to improve SARS-CoV-2 variant identification, enhancing sequencing coverage and accuracy.

Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings

This paper tests cleaning solutions for sentinel cards to improve temporal resolution of SARS-CoV-2 monitoring in schools by distinguishing new infections from persistent viral traces.

Rational Selection of PCR Primer/Probe Design Sites for SARS-CoV-2

The paper identifies conserved and mutated regions in SARS-CoV-2 genes to guide optimal qPCR primer/probe design.

Detection of antibodies neutralizing historical and emerging SARS-CoV-2 strains using a thermodynamically coupled de novo biosensor system

The paper introduces a thermodynamically coupled biosensor to rapidly detect neutralizing antibodies against SARS-CoV-2 strains in serum samples.

A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing

This paper presents an improved RT-LAMP assay for SARS-CoV-2 detection that is rapid, sensitive, and suitable for both laboratory and home testing.

Improving RT-LAMP Detection of SARS-CoV-2 RNA through Primer Set Selection and Combination

The paper evaluates 18 SARS-CoV-2 LAMP primer sets, identifies highly sensitive ones, and shows that combining primer sets improves sensitivity across multiple targets.

Profiling RT-LAMP tolerance of sequence variation for SARS-CoV-2 RNA detection

The paper evaluates how SARS-CoV-2 sequence variations affect RT-LAMP amplification, finding minimal impact on speed and no effect on sensitivity, highlighting RT-LAMP's robustness for viral RNA detection.

Dimerization of SARS-CoV-2 nucleocapsid protein affects sensitivity of ELISA based diagnostics of COVID-19