scholarly journals Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow

2020 ◽  
Author(s):  
Jingjing Li ◽  
Weipeng Quan ◽  
Shuge Yan ◽  
Shuangju Wu ◽  
Jianhu Qin ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Respiratory Viruses ◽  
Nucleic Acid Amplification ◽  
Lamp Method ◽  
Global Public Health ◽  
One Step ◽  
Rapid Amplification ◽  
Novel Coronavirus ◽  
Amplification Reaction

AbstractThe ongoing novel coronavirus (COVID-19) outbreak as a global public health emergency infected by SARC-CoV-2 has caused devastating loss around the world. Currently, a lot of diagnosis methods have been used to detect the infection. The nucleic acid (NA) testing is reported to be the clinical standard for COVID-19 infection. Evidence shows that a faster and more convenient method to detect in the early phase will control the spreading of SARS-CoV-2. Here, we propose a method to detect SARC-Cov-2 infection within two hours combined with Loop-mediated Isothermal Amplification (LAMP) reaction and nanopore Flongle workflow. In this approach, RNA reverse transcription and nucleic acid amplification reaction with one step in 30 minutes at 60-65°C constant temperature environment, nanopore Flongle rapidly adapter ligated within 10 minutes. Flongle flow cell sequencing and analysis in real-time. This method described here has the advantages of rapid amplification, convenient operation and real-time detection which is the most important for rapid and reliable clinical diagnosis of COVID-19. Moreover, this approach not only can be used for SARS-CoV-2 detection but also can be extended to other respiratory viruses and pathogens.

scholarly journals Rapid Detection of SARS-CoV-2 Using Reverse transcription RT-LAMP method

2020 ◽  
Author(s):  
Weihua Yang ◽  
Xiaofei Dang ◽  
Qingxi Wang ◽  
Mingjie Xu ◽  
Qianqian Zhao ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Reverse Transcription ◽  
Virus Disease ◽  
Lamp Assay ◽  
Nucleic Acid Amplification ◽  
N Gene ◽  
Nucleic Acid Detection ◽  
Lamp Method ◽  
Rt Pcr ◽  
Rapid Amplification

AbstractCorona Virus Disease 2019 (COVID-19) is a recently emerged life-threatening disease caused by SARS-CoV-2. Real-time fluorescent PCR (RT-PCR) is the clinical standard for SARS-CoV-2 nucleic acid detection. To detect SARS-CoV-2 early and control the disease spreading on time, a faster and more convenient method for SARS-CoV-2 nucleic acid detecting, RT-LAMP method (reverse transcription loop-mediated isothermal amplification) was developed. RNA reverse transcription and nucleic acid amplification were performed in one step at 63 °C isothermal conditions, and the results can be obtained within 30 minutes. ORF1ab gene, E gene and N gene were detected at the same time. ORF1ab gene was very specific and N gene was very sensitivity, so they can guarantee both sensitivity and specificity for SARS-CoV-2. The sensitivity of RT-LAMP assay is similar to RT-PCR, and specificity was 99% as detecting 208 clinical specimens. The RT-LAMP assay reported here has the advantages of rapid amplification, simple operation, and easy detection, which is useful for the rapid and reliable clinical diagnosis of SARS-CoV-2.

scholarly journals Rapid Diagnosis of Tick-Borne Illnesses by Use of One-Step Isothermal Nucleic Acid Amplification and Bio-Optical Sensor Detection

2018 ◽  
Vol 64 (3) ◽  
pp. 556-565 ◽  
Author(s):  
Ji Yeun Kim ◽  
Bonhan Koo ◽  
Choong Eun Jin ◽  
Min Chul Kim ◽  
Yong Pil Chong ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Real Time Pcr ◽  
Scrub Typhus ◽  
Nucleic Acid Amplification ◽  
Blood Samples ◽  
Clinical Sensitivity ◽  
Isothermal Nucleic Acid Amplification ◽  
One Step ◽  
Sensor Detection

Abstract BACKGROUND Scrub typhus and severe fever with thrombocytopenia syndrome (SFTS) are the most common tick-borne illnesses in South Korea. Early differentiation of SFTS from scrub typhus in emergency departments is essential but difficult because of their overlapping epidemiology, shared risk factors, and similar clinical manifestations. METHODS We compared the diagnostic performance of one-step isothermal nucleic acid amplification with bio-optical sensor detection (iNAD) under isothermal conditions, which is rapid (20–30 min), with that of real-time PCR, in patients with a confirmed tick-borne illness. Fifteen patients with confirmed SFTS who provided a total of 15 initial blood samples and 5 follow-up blood samples, and 21 patients with confirmed scrub typhus, were evaluated. RESULTS The clinical sensitivity of iNAD (100%; 95% CI, 83–100) for SFTS was significantly higher than that of real-time PCR (75%; 95% CI, 51–91; P = 0.047), while its clinical specificity (86%; 95% CI, 65–97) was similar to that of real-time PCR (95%; 95% CI, 77–99; P = 0.61). The clinical sensitivity of iNAD for scrub typhus (100%; 95% CI, 81–100) was significantly higher than that of real-time PCR for scrub typhus (67%; 95% CI, 43–85; P = 0.009), while its clinical specificity (90%; 95% CI, 67–98) was similar to that of real-time PCR (95%; 95% CI, 73–100; P > 0.99). CONCLUSIONS iNAD is a valuable, rapid method of detecting SFTS virus and Orientia tsutsugamushi with high clinical sensitivity and specificity.

scholarly journals Ultrastaging Using Ex Vivo Sentinel Lymph Node Mapping and One-Step Nucleic Acid Amplification (OSNA) in Gastric Cancer: Experiences of a European Center

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2683
Author(s):  
Bruno Märkl ◽  
Bianca Grosser ◽  
Kerstin Bauer ◽  
Dmytro Vlasenko ◽  
Gerhard Schenkirsch ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Detection Rate ◽  
Ex Vivo ◽  
Sentinel Lymph Node Mapping ◽  
Nucleic Acid Amplification ◽  
Lymph Node Mapping ◽  
Single Positive ◽  
Conventional Histology ◽  
One Step ◽  
Sensitivity Specificity

Background: In this study, the effectiveness of One-step nucleic acid amplification (OSNA) in combination with ex vivo SLN mapping is compared with conventional histology including immunohistochemistry. Methods: LNs were retrieved from gastrectomy specimens in an unfixed state. After ex vivo SLN mapping using methylene-blue, LNs were sliced to provide samples for histology and OSNA. Results: In total, 334 LNs were retrieved in the fresh state from 41 patients. SLN detection was intended in 40 cases but was successful in only 29, with a correct LN status prediction in 23 cases (79%). Excluding one case out of 41 with a failure likely caused by a processing error, OSNA showed a high effectiveness with sensitivity, specificity, and accuracy rates of 85.4%, 93.5%, and 92.4%, respectively. The LN status could be predicted in all but one case, in which the single positive LN was not eligible for OSNA testing. Moreover, OSNA evaluation led to upstaging from N0 to N+ in three cases (14%). Conclusion: The ex vivo SLN protocol used resulted in a relatively poor detection rate. However, the OSNA method was not hampered by this detection rate and proved its potential to increase the sensitivity of metastases detection.

Concordance study between one-step nucleic acid amplification and morphologic techniques to detect lymph node metastasis in papillary carcinoma of the thyroid

2016 ◽  
Vol 48 ◽  
pp. 132-141 ◽  
Author(s):  
Sofía del Carmen ◽  
Sonia Gatius ◽  
Guzmán Franch-Arcas ◽  
José Antonio Baena ◽  
Oscar Gonzalez ◽  
...  
Keyword(s):  
Lymph Node ◽  
Nucleic Acid ◽  
Lymph Node Metastasis ◽  
Papillary Carcinoma ◽  
Nucleic Acid Amplification ◽  
Node Metastasis ◽  
Detect Lymph Node Metastasis ◽  
One Step

One-step nucleic acid amplification vs ultrastaging in the detection of sentinel lymph node metastasis in endometrial cancer patients

2018 ◽  
Vol 119 (3) ◽  
pp. 361-369 ◽  
Author(s):  
Jan Kosťun ◽  
Martin Pešta ◽  
Jiří Sláma ◽  
Robert Slunéčko ◽  
Pavel Vlasák ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Lymph Node ◽  
Nucleic Acid ◽  
Sentinel Lymph Node ◽  
Lymph Node Metastasis ◽  
Cancer Patients ◽  
Nucleic Acid Amplification ◽  
Sentinel Lymph Node Metastasis ◽  
Node Metastasis ◽  
One Step
Sign in / Sign up

Export Citation Format

Share Document