Evaluation of RT-LAMP and Dry Swab RNA Extraction Free Method for Detection of SARS-CoV-2 Infection
Background: A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in December 2019 in Wuhan, China. Due to high infectious rate of SARS-CoV-2, detection of positive patients is one of the key points to controlling the outbreak. The gold standard for diagnosis of SARS-CoV-2 remains RT-PCR. In the current pandemic, a more rapid and high throughput method is in growing concern.
Objectives: To evaluate the RT-LAMP and dry swab RNA extraction free method in diagnosing SARS-CoV-2 infection, using reverse transcription polymerase chain reaction (RT-PCR) as gold standard.
Methods: A laboratory based cross-sectional descriptive study was carried out from September 2022 to October 2022 at molecular laboratory of No (1) Defence Services General Hospital. Ninety-four nasopharyngeal swabs were collected and tested for the presence of SARS-CoV-2 infection by RT-PCR (gold standard), RT-LAMP and dry swab method.
Result: In this study, 68 (72.3%) out of 94 patients were positive for SARS CoV-2 infection by RT-PCR. The overall sensitivity, specificity, positive predictive value and negative predictive value of RT-LAMP was 76.5%, 100%, 100% and 62%. The overall sensitivity, specificity, positive predictive value and negative predictive value of dry swab method was 66%, 100%, 100% and 53%. Hundred percent sensitivity was occurred in RT-LAMP and Dry swab method with Ct<20. In Ct 20-30, sensitivity of RT-LAMP and Dry swab method was 94.8% and 89.7%.
Conclusions: RT-PCR method exist as a gold standard for diagnosis of SARS CoV-2, it required molecular laboratory; RT-PCR machine and reagents; they are expensive; trained technician; and it takes several hours to get the results. Although sensitivity and specificity of RT-LAMP and dry swab methods are inferior to RT-PCR, they can be performed easily in the short period of time (less than 2 hours). Therefore, faster, cheaper and easier alternative molecular diagnostic methods should be considered for diagnosis of SARs CoV-2 infection.
Keywords:SARS-CoV-2, RT-PCR, RT-LAMP
WJ Guan; W Liang; Y Zhao; H Liang; Z Chen; Y Li; X Liu; R Chen; C Tang; T Wang; et al. Comorbidity and Its impact on 1590 patients with Covid 19 in China; A Nationwide analysis, 2020
VM Corman, O Landt, M Kaiser, R Molenkamp, A Meijer, DK Chu, T Bleicker, S Brünink, J Schneider, ML Schmidt, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25:2000045
T Notomi, H Okayama, H Masubuchi, T Yonekawa, K Watanabe, N Amino, T Hase. Loop-mediated isothermal amplifcation of DNA. Nucleic Acids Res. 2000;28:E63
I Smyrlaki, M Ekman, A Lentini. (2020) Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR. Nature Communications 11, 4812.
U Kiran, CG Gokulan, SK Kuncha, D Vedagiri, BT Chander, AV Sekhar, S Dontamala, AL Reddy, KB Tallapaka, RK Mishra, KH Harshan. Easing diagnosis and pushing the detection limits of SARS-CoV-2. Biol Methods Protoc. 2020 Aug 20;5(1):bpaa017. doi: 10.1093/biomethods/bpaa017. PMID: 33072873; PMCID: PMC7454390.
L Mosi, AA Sylverken, K Oyebola, K Babu, N Dukhi, N Goonoo, PK Mante, J Zahouli, EF Amankwaa, MF Tolba, AF Fagbamigbe, DK de Souza, D Matoke-Muhia. Correlating WHO COVID 19 interim guideline 2020.5 and testing capacity, accuracy, and logistical challenges in Africa. Pan Afr Med J. 2021 May 31;39:89. Doi; 10.11604/pamj.2021.39.89.27522. PMID: 34466191; PMCID: PMC8379409
EA Bruce, ML Huang, GA Perchetti, S Tighe, P Laagu- iby, JJ Hoffman. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step. PLoS Biol 2020; 18(10): e3000896.
A Badawi, SG Ryoo. Prevalence of comorbidities in the Middle East respiratory syndrome coronavirus (MERS-CoV): a systematic review and meta-analysis. Int J Infect Dis 2016; 49: 129-133.
N Chen, M Zhou, X Dong, J Qu, F Gong, Y Han. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, Chi- na: a descriptive study. Lancet 2020; 395: 507-513.
MS Dhakad, S Gogoi, A Kumari, A K Singh, M B Jais, A Prakash, G Pangtey, R Kaur. Comperative evaluation of cost-effective extraction free molecular technique for detection of SARs CoV-2 with reference to standard VTM based RT-qPCR method.IJM 2021; Vol 13. 748-756
B Mishra, J Ranjan, P Purushotham, S Saha, P Payal, P Kar, S Das, V Deshmukh. High Proportion of low cycle threshold value as an early indicator of COVID 19 surge. J Med Virol. 2022 Jan; 94(1): 240-245
MN Esbin, ON Whitney, S Chong, A Maurer, X Dar- zacq, R Tjian. Overcoming the bottleneck to wide- spread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection. RNA 2020; 26: 771-783.
J Bullard, K Dust, D Funk. Predicting Infectious Severe Acute Respiratory Syndrome Coronavirus 2 From Diagnostic Samples, Clin. Infect. Dis, Volume 71, Issue 10, 15 November 2020, Pages 2663–2666. https://doi.org/10.1093/cid/ciaa638
Copyright (c) 2023 Kyaw Khine Win, Aung Yan Lin, Kyaw Wunna, Khine Khine Su
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Any non-commercial use, distribution, adaptation, and reproduction in any medium is permitted as long as the original work is properly cited. However, caution and responsibility are required when reusing as the articles on the preprint server are not peer-reviewed. Readers are advised to check for the availability of any updated or peer-reviewed version.