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Comparative Study
. 2024 Jul 9;24(1):679.
doi: 10.1186/s12879-024-09574-9.

Evaluation and comparison of one-step real-time PCR and one-step RT-LAMP methods for detection of SARS-CoV-2

Hooman Hanifehpour  1 , Fatemeh Ashrafi  1 , Elham Siasi  1 , Shirzad Fallahi  2   3
Affiliations
Comparative Study

Evaluation and comparison of one-step real-time PCR and one-step RT-LAMP methods for detection of SARS-CoV-2

Hooman Hanifehpour et al. BMC Infect Dis. .

Abstract

Background: There is an increasing disease trend for SARS-COV-2, so need a quick and affordable diagnostic method. It should be highly accurate and save costs compared to other methods. The purpose of this research is to achieve these goals.

Methods: This study analyzed 342 samples using TaqMan One-Step RT-qPCR and fast One-Step RT-LAMP (Reverse Transcriptase Loop-Mediated Isothermal Amplification). The One-Step LAMP assay was conducted to assess the sensitivity and specificity.

Results: The research reported positive samples using two different methods. In the RT-LAMP method, saliva had 92 positive samples (26.9%) and 250 negative samples (73.09%) and nasopharynx had 94 positive samples (27.4%) and 248 negative samples (72.51%). In the RT-qPCR method, saliva had 86 positive samples (25.1%) and 256 negative samples (74.8%) and nasopharynx had 93 positive samples (27.1%) and 249 negative samples (72.8%). The agreement between the two tests in saliva and nasopharynx samples was 93% and 94% respectively, based on Cohen's kappa coefficient (κ) (P < 0.001). The rate of sensitivity in this technique was reported at a dilution of 1 × 101 and 100% specificity.

Conclusions: Based on the results of the study the One-Step LAMP assay has multiple advantages. These include simplicity, cost-effectiveness, high sensitivity, and specificity. The One-Step LAMP assay shows promise as a diagnostic tool. It can help manage disease outbreaks, ensure prompt treatment, and safeguard public health by providing rapid, easy-to-use testing.

Keywords: Detection; One-step LAMP; One-step RT-qPCR; Rapid; SARS-CoV-2; Sensitive.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Stages of Identification of SARS-CoV-2 utilizing the One-Step LAMP method. Positive control (P) Negative control (N)
Fig. 2
Fig. 2
Monitoring of LAMP amplification of the SARS-CoV-2 RNA. A Visual inspection of the RNA amplification by fluorescence of the reaction mixture under normal light. B Agarose gel analysis of LAMP amplified product. Positive control (P); Negative control (N) (100 bp molecular weight marker)
Fig. 3
Fig. 3
Analytical sensitivity of the One-step LAMP assay for the detection of SARS-CoV-2 RNA based on the N gene amplification. Tenfold serial dilutions of the RNA standard of SARS-CoV-2 from 1 × 107 to 1 × 10−2 copies per reaction
Fig. 4
Fig. 4
Diagnostic methods of SARS-CoV-2
See this image and copyright information in PMC

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