A semi-automated, isolation-free, high-throughput SARS-CoV-2 reverse transcriptase (RT) loop-mediated isothermal amplification (LAMP) test

Point-of-care isothermal nucleic acid amplification tests: progress and bottlenecks for extraction-free sample collection and preparation

INTRODUCTION

Suitable sample collection and preparation methods are essential to enable nucleic acid amplification testing at the point of care (POC). Strategies that allow direct isothermal nucleic acid amplification testing (iNAAT) of crude sample lysate without the need for nucleic acid extraction minimize time to result as well as the need for operator expertise and costly infrastructure.

AREAS COVERED

The authors review research to understand how sample matrix and preparation affect the design and performance of POC iNAATs. They focus on approaches where samples are directly combined with liquid reagents for preparation and amplification via iNAAT strategies. They review factors related to the type and method of sample collection, storage buffers, and lysis strategies. Finally, they discuss RNA targets and relevant regulatory considerations.

EXPERT OPINION

Limitations in sample preparation methods are a significant technical barrier preventing implementation of nucleic acid testing at the POC. The authors propose a framework for co-designing sample preparation and amplification steps for optimal performance with an extraction-free paradigm by considering a sample matrix and lytic strategy prior to an amplification assay and readout. In the next 5 years, the authors anticipate increasing priority on the co-design of sample preparation and iNAATs.

When False-Positives Arise: Troubleshooting a SARS-Coronavirus-2 (SARS-CoV-2) Detection Assay on a Semi-Automated Platform

BACKGROUND

During the COVID-19 pandemic, many molecular diagnostic laboratories performed high-throughput SARS-CoV-2 testing often with implementation of automated workflows. In parallel, vaccination campaigns resulted increasingly in specimens from fully vaccinated patients, with resultant clinical inquiries regarding positive results in this patient population. This prompted a quality improvement initiative to investigate the semi-automated testing workflow for false-positive results. The troubleshooting workflow is described and procedural improvements are outlined that serve as a resource for other molecular diagnostic laboratories that need to overcome testing anomalies in a semi-automated environment.

METHODS

This workflow utilized the MagMax-96 Viral RNA kit and the CDC 2019-nCoV RT-qPCR Panel on the Agilent Bravo Liquid-Handler (Bravo). Screening of the environment, personnel, and the mechanical performance of instrumentation using low Ct checkerboard challenges was executed to identify sources of cross-contamination. Evaluation of the assay and reporting design was conducted.

RESULTS

Specimen contamination was observed during the viral extraction process on the Bravo. Changes to the program reduced plate contamination by 50% and importantly revealed consistent hallmarks of contaminated samples. We adjusted the reporting algorithm using these indicators of false positives. False positives that were identified made up 0.11% of the 45 000+ tests conducted over the following 8 months.

CONCLUSIONS

These adjustments provided confident and quality results while maintaining turnaround time for patients and pandemic-related public health initiatives. This corrected false-positive rate is concordant with previously published studies from diagnostic laboratories utilizing automated systems and may be considered a laboratory performance standard for this type of testing.

Development of an optimized RT-LAMP test for the detection of SARS-CoV-2

SARS-COV-2 is the causative agent of an acute respiratory syndrome called Coronavirus disease 2019 (COVID-19) with a varying mortality rate from 2019 to 2022. There are several measures for control and prevention of Covid-19 including using mask, vaccine injections, as well as screening the potential cases. We aimed to design and develop a molecular method (RT-LAMP) for detecting coronavirus in biological samples that is cheaper, faster and easier than conventional molecular methods. In this study, various reaction components were explored to make the optimal combination of an RT-LAMP master mix composition. The results revealed the ability of this RT-LAMP test in specifically identifying 100 copies of mixture of N and E genes in just 30-45 min. This study demonstrated the reliable performance of the RT-LAMP method for the detection of SARS-COV-2 in biological samples. Given the significant advantages of this method compared to the gold standard qRT-PCR, it can be employed as a promising tool for the diagnosis of coronavirus as well as other pathogenic viruses.

A comprehensive overview on the transmission, pathogenesis, diagnosis, treatment, and prevention of SARS-CoV-2

Severe acute respiratory syndrome coronavirus (SARS-CoV) is a single positive-strand RNA virus that is responsible for the current pandemic that the world has been facing since 2019. The primary route of transmission of SARS-CoV-2 is through respiratory tract transmission. However, other transmission routes such as fecal-oral, vertical transmission, and aerosol-eye also exist. In addition, it has been found that the pathogenesis of this virus involves the binding of the virus's S protein to its host cell surface receptor angiotensin-converting enzyme 2, which results in the subsequent membrane fusion that is required for SARS-CoV-2 to replicate and complete its entire life. The clinical symptoms of patients infected with SARS-CoV-2 can range from asymptomatic to severe. The most common symptoms seen include fever, dry cough, and fatigue. Once these symptoms are observed, a nucleic acid test is done using reverse transcription-polymerase chain reaction. This currently serves as the main confirmatory tool for COVID-19. Despite the fact that no cure has been found for SARS-CoV-2, prevention methods such as vaccines, specific facial mask, and social distancing have proven to be quite effective. It is imperative to have a complete understanding of the transmission and pathogenesis of this virus. To effectively develop new drugs as well as diagnostic tools, more knowledge about this virus would be needed.

A Systematic Review and Meta-Analysis Comparing the Diagnostic Accuracy Tests of COVID-19

In this paper, we present a systematic review and meta-analysis that aims to evaluate the reliability of coronavirus disease diagnostic tests in 2019 (COVID-19). This article seeks to describe the scientific discoveries made because of diagnostic tests conducted in recent years during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Between 2020 and 2021, searches for published papers on the COVID-19 diagnostic were made in the PubMed database. Ninety-nine scientific articles that satisfied the requirements were analyzed and included in the meta-analysis, and the specificity and sensitivity of the diagnostic accuracy were assessed. When compared to serological tests such as the enzyme-linked immunosorbent assay (ELISA), chemiluminescence immunoassay (CLIA), lateral flow immunoassay (LFIA), and chemiluminescent microparticle immunoassay (CMIA), molecular tests such as reverse transcription polymerase chain reaction (RT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR) performed better in terms of sensitivity and specificity. Additionally, the area under the curve restricted to the false-positive rates (AUC_FPR) of 0.984 obtained by the antiviral neutralization bioassay (ANB) diagnostic test revealed significant potential for the identification of COVID-19. It has been established that the various diagnostic tests have been effectively adapted for the detection of SARS-CoV-2; nevertheless, their performance still must be enhanced to contain potential COVID-19 outbreaks, which will also help contain potential infectious agent outbreaks in the future.

Self-Sampled Gargle Water Direct RT-LAMP as a Screening Method for the Detection of SARS-CoV-2 Infections

We assessed the viability of self-sampled gargle water direct RT-LAMP (LAMP) for detecting SARS-CoV-2 infections by estimating its sensitivity with respect to the gold standard indirect RT-PCR of paired oro-nasopharyngeal swab samples. We also assessed the impact of symptom onset to test time (STT)—i.e., symptom days at sampling, on LAMP. In addition, we appraised the viability of gargle water self-sampling versus oro-nasopharyngeal swab sampling, by comparing paired indirect RT-PCR results. 202 oro-nasopharyngeal swab and paired self-sampled gargle water samples were collected from hospital patients with COVID-19 associated symptoms. LAMP, indirect and direct RT-PCR were performed on all gargle water samples, and indirect RT-PCR was performed on all oro-nasopharyngeal samples. LAMP presented a sensitivity of 80.8% (95% CI: 70.8–90.8%) for sample pairs with sub-25 Ct oro-nasopharyngeal indirect RT-PCR results, and 77.6% (66.2–89.1%) sensitivity for sub-30 Ct samples with STT ≤ 7 days. STT, independently of Ct value, correlated negatively with LAMP performance. 80.7% agreement was observed between gargle water and oro-nasopharyngeal indirect RT-PCR results. In conclusion, LAMP presents an acceptable sensitivity for low Ct and low STT samples. Gargle water may be considered as a viable sampling method, and LAMP as a screening method, especially for symptomatic persons with low STT values.

Inhibition of Non-specific Amplification in Loop-Mediated Isothermal Amplification via Tetramethylammonium Chloride

Loop-mediated isothermal amplification (LAMP) may be used in molecular and point-of-care diagnostics for pathogen detection. The amplification occurs under isothermal conditions using up to six primers. However, non-specific amplification is frequently observed in LAMP. Non-specific amplification has the potential to be triggered by forward and reverse internal primers. And the relatively low reaction temperature (55-65 °C) induces the secondary structure via primer-primer interactions. Primer redesign and probe design have been recommended to solve this problem. LAMP primers have strict conditions, such as Tm, GC contents, primer dimer, and distance between primers compared to conventional PCR primers. Probe design requires specialized knowledge to have high specificity for a target. In polymerase chain reaction (PCR), some chemicals or proteins are used for improving specificity and efficiency. Therefore, we hypothesized that additives can suppress the non-specific amplification. In this study, tetramethylammonium chloride (TMAC), formamide, dimethyl sulfoxide, Tween 20, and bovine serum albumin have been used as LAMP additives. In our study, TMAC was presented as a promising additive for suppressing non-specific amplification in LAMP.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13206-022-00070-3.