Clinical COVID-19 diagnostic methods: Comparison of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and quantitative RT-PCR (qRT-PCR)

Kitajima, Heita; Tamura, Yoshitaka; Yoshida, Hiroko; Kinoshita, Hitomi; Katsuta, Hiroki; Matsui, Chika; Matsushita, Akane; Arai, T.; Hirano, Shoji; Iuchi, Atsuhiko; Hirashima, Tomonori; Morishita, Hiroshi; Matsuoka, Hiroto; Tanaka, Toshio; Nagai, Takayuki

doi:10.1016/j.jcv.2021.104813

Cited by 44 publications

(32 citation statements)

References 13 publications

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“…To effectively diagnose COVID-19, there exist two types of methods: (i) polymerase chain reaction (PCR), particularly real-time reverse-transcriptase PCR (rRT-PCR) with nasopharyngeal swab samples to test the existence of RNA fragments ( 1 ); and (ii) chest imaging (CI) examines the evidence of COVID-19 in the lung.…”

Section: Introductionmentioning

confidence: 99%

RETRACTED: Deep Fractional Max Pooling Neural Network for COVID-19 Recognition

Wang

Satapathy

Anderson

et al. 2021

Front. Public Health

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Aim: Coronavirus disease 2019 (COVID-19) is a form of disease triggered by a new strain of coronavirus. This paper proposes a novel model termed “deep fractional max pooling neural network (DFMPNN)” to diagnose COVID-19 more efficiently.Methods: This 12-layer DFMPNN replaces max pooling (MP) and average pooling (AP) in ordinary neural networks with the help of a novel pooling method called “fractional max-pooling” (FMP). In addition, multiple-way data augmentation (DA) is employed to reduce overfitting. Model averaging (MA) is used to reduce randomness.Results: We ran our algorithm on a four-category dataset that contained COVID-19, community-acquired pneumonia, secondary pulmonary tuberculosis (SPT), and healthy control (HC). The 10 runs on the test set show that the micro-averaged F1 (MAF) score of our DFMPNN is 95.88%.Discussions: This proposed DFMPNN is superior to 10 state-of-the-art models. Besides, FMP outperforms traditional MP, AP, and L2-norm pooling (L2P).

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Section: Introductionmentioning

confidence: 99%

RETRACTED: Deep Fractional Max Pooling Neural Network for COVID-19 Recognition

Wang

Satapathy

Anderson

et al. 2021

Front. Public Health

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“…25 RT-LAMP is a nucleic acid amplification assay like RT-PCR, which is a simple, low cost and fast method. 26 28 As the study consisted of random patients with routine positive results, the high confidence interval of the results makes it ideal for this method in which the LAMP system is applied. Unlike the studies in the literature, in the study, various kits and devices used in RT-PCR studies were com- or over new samples can solve this problem.…”

Section: Discussionmentioning

confidence: 99%

“…25 RT‐LAMP is a nucleic acid amplification assay like RT‐PCR, which is a simple, low cost and fast method. 26 Catarina Amaral et al created a one‐tube test based on RT‐LAMP which allows visual detection of less than 100 viral genome copies of SARS‐CoV‐2 within 30 min. In that study, 177 nasopharyngeal RNA samples for COVID‐19 were compared with RT‐PCR.…”

Section: Discussionmentioning

confidence: 99%

Comparison of COVID‐19 laboratory diagnosis by commercial kits: Effectivity of RT‐PCR to the RT‐LAMP

Artik

Coşğun²,

Cesur

et al. 2022

Journal of Medical Virology

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Coronavirus disease 2019 or COVID-19 caused by novel coronavirus/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV) is an ongoing pandemic that has emerging global effects and requires rapid and reliable diagnostic testing. Quantitative reverse transcription-polymerase chain reaction (q-RT-PCR) is the gold standard method for SARS-CoV-2 detections. On the other hand, new approaches remedy the diagnosis difficulties gradually. Reverse transcription loopmediated isothermal amplification (RT-LAMP) as one of these novel approaches may also contribute to faster and cheaper field-based testing. The present study was designed to evaluate this rapid screening diagnostic test that can give results in 30-45 min and to compare the effectiveness of LAMP to the q-RT-PCR. The 30 randomly chosen patient samples were generated by nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. The sample of quantification cycle (Cq) values was tested using RT-LAMP as well as by conventional q-RT-PCR. The patient samples were tested with four different kits (SENSObiz COVID-19 [SARS-CoV-2] LAMP Assay, the QIAseq DIRECT SARS-CoV-2 kit, Biospeedy SARS-CoV-2 Variant Plus kit, and CoVirion-CV19-2 SARS-CoV-2 OneStep RT-PCR kit) and two different PCR devices (GDS Rotor-Gene Q Thermocycler and Inovia TechnologiesGenX series). Based on 30 patient samples, the positive/negative ratio (P/N) was 30/0 as Biospeedy and Covirion (positivity 100%), 28/2 as Qiagen kit (positivity 93.3%) for the samples studied on the Inovia device while the same samples on the Rotor-Gene device were 30/0 as Biospeedy and Covirion (positivity 100%), 29/1 as Qiagen kit at the first day (96.7%). On the fifth day, the samples were studied in the Inovia device and the respective results were obtained: 27/3 as Biospeedy (positivity 90%), 16/14 as Qiagen (positivity 53.3%), 28/2 as Covirion kit (positivity 93.3%). When these samples were studied in the Rotor-Gene device, it was 29/1 in Biospeedy and Covirion (positivity 96.7%), 19/11 in the Qiagen kit (positivity 63.3%).When these samples were compared with the LAMP method it was found to be 19/11 (positivity 63.3%) on the first day and 18/12 (positivity 60%) on the fifth day. SARS-CoV-2 test studies will contribute to a proactive approach to the development of rapid diagnosis systems. The LAMP approach presents promising results to monitor exposed individuals and also improves screening efforts in potential ports of entry.

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“…The current standard method which is used to detect SARS-CoV-2 is RT-PCR [3, 4]. Regardless of its high sensitivity and specificity, this method has some drawbacks as it requires complex and expensive equipment, extensive training for users, and multiple hours to obtain the result.…”

Section: Introductionmentioning

confidence: 99%

Clinical validation and the evaluation of a colorimetric SARS-CoV-2 RT-LAMP assay identify its robustness against RT-PCR

Erdem

Andac-Ozketen²,

Ozketen

et al. 2022

Preprint

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The novel coronavirus has infected millions of people all around the world and has posed a great risk to global health. Rapid and accurate tests are needed to take early precautions and control the disease. The most routinely used method is real time polymerase chain reaction (RT-PCR) which stands as the gold standard in the detection of SARS-COV-2 viral RNA. However, robust assays as accurate as RT-PCR have been developed for rapid diagnosis and efficient control of the spread of the disease. Reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) is one of the time-saving, accurate and cost-effective alternative methods to RT-PCR. In this study, we study the improved RT-LAMP colorimetric assay (N-Fact) to detect SARS-COV-2 viral RNA within 30 minutes using a primer sets special to N gene. Moreover, RT-LAMP colorimetric assay is subjected to authorized clinical studies to test its ability to detect COVID-19 in its early phases. The results reveal RT-LAMP colorimetric assay is an efficient, robust, and rapid assay to be used as in vitro diagnostic tool display competitiveness compared to RT-PCR.

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Clinical COVID-19 diagnostic methods: Comparison of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and quantitative RT-PCR (qRT-PCR)

Cited by 44 publications

References 13 publications

RETRACTED: Deep Fractional Max Pooling Neural Network for COVID-19 Recognition

RETRACTED: Deep Fractional Max Pooling Neural Network for COVID-19 Recognition

Comparison of COVID‐19 laboratory diagnosis by commercial kits: Effectivity of RT‐PCR to the RT‐LAMP

Clinical validation and the evaluation of a colorimetric SARS-CoV-2 RT-LAMP assay identify its robustness against RT-PCR

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