Rapid detection of novel coronavirus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by reverse transcription-loop-mediated isothermal amplification

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Abstract

Novel Corona virus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2 or 2019-nCoV), and the subsequent disease caused by the virus (coronavirus disease 2019 or COVID-19), is an emerging global health concern that requires a rapid diagnostic test. Quantitative reverse transcription PCR (qRT-PCR) is currently the standard for SARS-CoV-2 detection; however, Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) may allow for faster and cheaper field based testing at point-of-risk. The objective of this study was to develop a rapid screening diagnostic test that could be completed in 30–45 minutes. Simulated patient samples were generated by spiking serum, urine, saliva, oropharyngeal swabs, and nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. RNA isolated from nasopharyngeal swabs collected from actual COVID-19 patients was also tested. The samples were tested using RT-LAMP as well as by conventional qRT-PCR. Specificity of the RT-LAMP was evaluated by also testing against other related coronaviruses. RT-LAMP specifically detected SARS-CoV-2 in both simulated patient samples and clinical specimens. This test was performed in 30–45 minutes. This approach could be used for monitoring of exposed individuals or potentially aid with screening efforts in the field and potential ports of entry.

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Viral load of SARS-CoV-2 in clinical samples

Yang Pan, Daitao Zhang, Peng Yang … (2020)

An outbreak caused by a novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Wuhan in December 2019, 1 and has since spread within China and to other countries. Real-time RT-PCR assays are recommended for diagnosis of SARS-CoV-2 infection. 2 However, viral dynamics in infected patients are still yet to be fully determined. Here, we report our findings from different types of clinical specimens collected from 82 infected individuals. Serial samples (throat swabs, sputum, urine, and stool) from two patients in Beijing were collected daily after their hospitalisation (patient 1, days 3–12 post-onset; patient 2, days 4–15 post-onset). These samples were examined by an N-gene-specific quantitative RT-PCR assay, as described elsewhere. 3 The viral loads in throat swab and sputum samples peaked at around 5–6 days after symptom onset, ranging from around 104 to 107 copies per mL during this time (figure A, B ). This pattern of changes in viral load is distinct from the one observed in patients with SARS, which normally peaked at around 10 days after onset. 4 Sputum samples generally showed higher viral loads than throat swab samples. No viral RNA was detected in urine or stool samples from these two patients. Figure Viral dynamics of SARS-CoV-2 in infected patients Viral load (mean [SD]) from serial throat swab and sputum samples in patient 1 (A) and patient 2 (B). (C) Viral load (median [IQR]) in throat and sputum samples collected from 80 patients at different stages after disease onset. (D) Correlation between viral load in throat swab samples and viral load in sputum samples. We also studied respiratory samples (nasal [n=1] and throat swabs [n=67], and sputum [n=42]) collected from 80 individuals at different stages of infection. The viral loads ranged from 641 copies per mL to 1·34 × 1011 copies per mL, with a median of 7·99 × 104 in throat samples and 7·52 × 105 in sputum samples (figure C). The only nasal swab tested in this study (taken on day 3 post-onset) showed a viral load of 1·69 × 105 copies per mL. Overall, the viral load early after onset was high (>1 × 106 copies per mL). However, a sputum sample collected on day 8 post-onset from a patient who died had a very high viral load (1·34 × 1011 copies per mL). Notably, two individuals, who were under active surveillance because of a history of exposure to SARS-CoV-2-infected patients showed positive results on RT-PCR a day before onset, suggesting that infected individuals can be infectious before them become symptomatic. Among the 30 pairs of throat swab and sputum samples available, viral loads were significantly correlated between the two sample types for days 1–3 (R2=0·50, p=0·022), days 4–7 (R2=0·93, p<0·001), and days 7–14 (R2=0·95, p=0·028). From 17 confirmed cases of SARS-CoV-2 infection with available data (representing days 0–13 after onset), stool samples from nine (53%; days 0–11 after onset) were positive on RT-PCR analysis. Although the viral loads were less than those of respiratory samples (range 550 copies per mL to 1·21 × 105 copies per mL), precautionary measures should be considered when handling faecal samples.

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Loop-mediated isothermal amplification (LAMP) – review and classification of methods for sequence-specific detection

Lisa Becherer, Nadine Borst, Mohammed Ahmed Bakheit … (2020)

This comprehensive review provides a systematic classification and a comparative evaluation of current sequence-specific detection methods for LAMP. In the course of the last 20 years, isothermal nucleic acid amplification tests have emerged as an important diagnostic tool, not only for clinical applications, but also for food quality control and environmental monitoring. Loop-mediated isothermal amplification (LAMP) is well known for its robust and highly sensitive and specific amplification of target DNA, which is achieved by utilizing up to six primers. Moreover, LAMP excels through its isothermal and energy efficient amplification requirements, rendering it a prime candidate for low-cost diagnostics and analysis at the point of need. Recently, methods for sequence-specific detection have gained more importance because, unlike sequence-independent detection methods, they are highly specific towards the target DNA. In the last 13 years, a variety of sequence-specific methods have emerged, based on a very diverse range of sensing techniques, including optical, magnetic, piezoelectric, electrochemical and magnetoresistive sensing. To give structure to the diverse multitude of sequence-specific methods, we created a systematic classification and provide a critical comparative evaluation according to a catalogue of criteria (analytical performance, multiplexing, quantification and instrumental requirements). Fluorescence-based detection, making up half of the methods, can be processed on open platforms and satisfies all the criteria listed before. Instrumental requirements are discussed in terms of complexity, portability and fluidic cartridges. In addition, the technological readiness level and the kind of platform (open versus method-tailored) are evaluated, the latter playing an important role in the miniaturization and automation of operational process steps. We also observe an increase in the use of smartphone-integrated sensors to improve LAMP-based point-of-need testing. In summary, recent developments in methods for the sequence-specific detection of LAMP demonstrate high potential for many future applications.

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Development and evaluation of reverse transcription-loop-mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus.

M Parida, S Santhosh, P. Dash … (2006)

The standardization and validation of a one-step, single-tube accelerated quantitative reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay is reported for rapid and real-time detection of Japanese encephalitis virus (JEV). The RT-LAMP assay reported in this study is very simple and rapid; the amplification can be obtained in 30 min under isothermal conditions at 63 degrees C by employing a set of six primers targeting the E gene of JEV. The RT-LAMP assay demonstrated exceptionally higher sensitivity compared to that of RT-PCR, with a detection limit of 0.1 PFU. The specificities of the selected primer sets were established by cross-reactivity studies with other closely related members of the JEV serocomplex as well as by evaluation of healthy human volunteers. The comparative evaluation of the RT-LAMP assay for clinical diagnosis with a limited number of patient cerebrospinal fluid samples revealed 85% concordance with conventional RT-PCR, with a sensitivity and a specificity of 100% and 86%, respectively. The concentration of virus in most of the clinical samples was 10(2) to 10(5) PFU/ml, as determined from the standard curve based on the time of positivity in the samples. In addition, the monitoring of gene amplification can also be visualized with the naked eye by using SYBR green I fluorescent dye. Thus, due to easy operation without a requirement of sophisticated equipment and skilled personnel, the RT-LAMP assay reported here is a valuable tool for the rapid and real-time detection of JEV not only by well-equipped laboratories but also by peripheral diagnostic laboratories with limited financial resources in developing countries.