RT-LAMP in SARS-CoV-2 detection: point to improve primer designing and decrease molecular diagnosis pitfalls

ABSTRACT

Background

Due to the high transmission rate of SARS-CoV-2, diagnostic tests have become tools for identifying patients. The key points were the virus genomes survey to design RT-LAMP primers; comparing the sensitivity and specificity of RT-LAMP and RT-qPCR; and determining the relationship among clinical symptoms, CT scan, RT-qPCR, and RT-LAMP results.

Methods

This cohort study included 444 symptomatic patients. The specificity and sensitivity of RT-LAMP were assayed. The five statistical models, simultaneously, by RapidMiner to find the best method for detecting the virus were done through the correlation between the clinical symptoms, RT-LAMP, RT-qPCR, and CT scan results. The chi-square test by SPSS 26.0 was used to calculate kappa agreement.

Results

The virus genome was detected in all the positive samples (198) by RT-qPCR and RT-LAMP. In addition, 246 samples were negative by RT-qPCR, while 88 were positive by RT-LAMP. Data mining analysis indicated that there were most associations between the RT-LAMP and CT scan data compared to RT-qPCR and CT scan data.

Conclusions

RT-LAMP could detect SARS-CoV-2 with great simplicity, speed, and cheapness. Therefore, it is logical to screen, a large number of patients by RT-LAMP, and then RT-qPCR can be used on the limited samples.

GRAPHICAL ABSTRACT

KEYWORDS:

• Data mining
• detection
• CT scan
• RT-LAMP
• RT-qPCR
• SARS-CoV-2

Declaration of interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Reviewers Disclosure

Peer reviewers on this manuscript have no relevant financial relationships or otherwise to disclose.

Ethical consideration

This project is based on the tenets of Helsinki and was approved by the Ethics Committee [IR.GOUMS.REC.1398.388]. The research was explained to all participants, and they were asked to sign an informed consent form. All participants had the right to exit the study at any time and their data would not be included in the study. Both patients and control groups were asked to fill a questionnaire containing demographic information, including age, gender, weight, history of any disease, and history of dairy consumption.

Additional information

Funding

This paper was not funded.