SARS-CoV-2 detection and testing

An enhanced isothermal amplification assay for viral detection

The paper develops a rapid, sensitive, and scalable isothermal amplification method for detecting SARS-CoV-2 from patient samples.

Sample pooling methods for efficient pathogen screening: Practical implications

This paper evaluates sample pooling methods for pathogen screening, finding that existing methods excel in some areas but not others, and introduces a new method that performs well across multiple criteria.

Analysis of the potential impact of genomic variants in SARS-CoV-2 genomes from India on molecular diagnostic assays

The paper analyzes genomic variants in SARS-CoV-2 isolates from India and their potential impact on molecular diagnostic assays.

Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results

The CDC SARS-CoV-2 extraction control can produce false-negative results due to patient DNA cross-reactivity, but a redesigned control can fix this issue.

A simple RNA preparation method for SARS-CoV-2 detection by RT-qPCR

This paper presents a simple RNA extraction method for SARS-CoV-2 detection by RT-qPCR using common reagents, which is faster and more accessible than commercial kits during shortages.

A Rapid COVID-19 RT-PCR Detection Assay for Low Resource Settings

This paper demonstrates a rapid RT-PCR assay for COVID-19 detection that can be performed in 12 minutes using simple equipment in low-resource settings.

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.

Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

The paper identifies a SARS-CoV-2 N gene polymorphism that reduces RT-PCR assay sensitivity and emphasizes the need for multi-target testing.

Rapid, large-scale, and effective detection of COVID-19 via non-adaptive testing

This paper introduces a non-adaptive pooling method for rapid and efficient COVID-19 detection using PCR, reducing testing time and resource use.

Rapid cost-effective viral genome sequencing by V-seq

The paper introduces V-seq, a cost-effective method for viral genome sequencing that uses multiplexed RT primers to improve coverage and reduce costs.

Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein

The paper develops a mass-spectrometry-based method to detect SARS-CoV-2 virus by identifying the nucleocapsid N protein in nasopharyngeal swabs, showing high sensitivity and simplicity.

Quickly and simply detection for coronaviruses including SARS-CoV-2 on the mobile Real-Time PCR without treating RNA in advance

The paper evaluates methods to detect coronaviruses, including SARS-CoV-2, using a mobile real-time PCR device, showing faster and simpler detection without prior RNA treatment.

SCV-2000bp: a primer panel for SARS-CoV-2 full-genome sequencing

The paper describes a primer panel for amplifying the full SARS-CoV-2 genome using 17 primer pairs and demonstrates its effectiveness with clinical samples.

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs

This paper develops a high-throughput method to generate host and pathogen genomic data from single nasopharyngeal swabs of COVID-19 patients.

SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission

This study compares whole genome sequencing methods for SARS-CoV-2, showing improved detection and cost-effectiveness with target enrichment.

In silico design and validation of commercial kit GPSTM CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012

The paper validates a commercial RT-qPCR test for SARS-CoV-2 using ISO standards and shows it has high specificity and sensitivity.

Evaluation of commercial qPCR kits for detection of SARS-CoV-2 in pooled samples

This study evaluates commercial qPCR kits for SARS-CoV-2 detection in pooled samples, finding that pooling up to 60 samples does not reduce kit efficiency and that RdRp is a better target than E protein.

A CRISPR-based SARS-CoV-2 diagnostic assay that is robust against viral evolution and RNA editing

The paper introduces a CRISPR-based diagnostic assay for SARS-CoV-2 that is robust against viral mutations and RNA editing, demonstrating high specificity and sensitivity.

Rapid, sensitive, full genome sequencing of Severe Acute Respiratory Syndrome Virus Coronavirus 2 (SARS-CoV-2)

The paper describes validated protocols for rapid, sensitive full-genome sequencing of SARS-CoV-2 using multiplex RT-PCR with MinION/MiSeq or singleplex nested RT-PCR with Sanger sequencing.

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

This study evaluates four NGS methods for SARS-CoV-2 whole-genome sequencing, finding that amplicon-based methods are most sensitive for low viral loads while mNGS and RVOP produce the most complete genomes for mid viral loads.

Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples

This paper compares amplicon, hybrid capture, and metatranscriptomic sequencing methods for directly sequencing SARS-CoV-2 genomes from clinical samples, finding differences in bias, sensitivity, and accuracy.

Resource optimization in COVID-19 diagnosis

This study optimizes RT-qPCR reaction volume and tests cotton swabs as an alternative sample collection method for COVID-19 diagnosis, finding that cotton swabs can be used without compromising assay sensitivity.

CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes

CoronaHiT is a method for high-throughput SARS-CoV-2 genome sequencing that improves coverage and throughput compared to existing protocols.

Comparing library preparation methods for SARS-CoV-2 multiplex amplicon sequencing on the Illumina MiSeq platform

This study compares three library preparation methods for SARS-CoV-2 amplicon sequencing, showing minimal impact on consensus base calling and phylogenetic analysis.

ROBOCOV: An affordable open-source robotic platform for COVID-19 testing by RT-qPCR

ROBOCOV provides an affordable open-source robotic platform for automated SARS-CoV-2 RT-qPCR testing using open-source robots and commercial reagents.

An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance

The paper develops an inexpensive RT-nPCR assay for SARS-CoV-2 that matches RT-qPCR performance and highlights low detection efficiency in real-world RT-qPCR testing.

Quantitative PCR for cannabis flower containing SARs-CoV-2

The paper develops a qPCR assay to detect SARs-CoV-2 in cannabis flower and assesses its stability after gamma irradiation.

HiDRA-seq: High-Throughput SARS-CoV-2 Detection by RNA Barcoding and Amplicon Sequencing

HiDRA-seq enables high-throughput, low-cost SARS-CoV-2 testing using barcoded cDNA and NGS, allowing thousands of samples to be sequenced per run.

Brief Communication: Magnetic Immuno-Detection of SARS-CoV-2 specific Antibodies

This paper describes a magnetic immuno-detection method for SARS-CoV-2 specific antibodies in human serum, showing higher sensitivity and faster results compared to ELISA.

INSIGHT: a population scale COVID-19 testing strategy combining point-of-care diagnosis with centralised high-throughput sequencing

The paper introduces a two-stage COVID-19 testing strategy combining point-of-care diagnosis with centralised high-throughput sequencing to enable population-scale testing.