Detection of multiple viral sequences in the respiratory tract samples of suspected Middle East respiratory syndrome coronavirus patients in Jakarta, Indonesia 2015–2016

Setianingsih, Tri Yuli; Wiyatno, Ageng; Hartono, Teguh Sarry; Hindawati, Evi; Rosamarlina,; Dewantari, Aghnianditya Kresno; Myint, Khin Saw Aye; Lisdawati, Vivi; Safari, Dodi

doi:10.1016/j.ijid.2019.06.022

Cited by 30 publications

(27 citation statements)

References 40 publications

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“…Afterwards, the PCR is performed and followed by the detection of PCR product through specific detection methods or instruments. Among these, gel visualization and sequencing after PCR are the conventional methods for the detection of coronaviruses [8,9]. However, due to its time-consuming process and high cost, these methods are not commonly used in clinical samples.…”

Section: Pcr-based Methodsmentioning

confidence: 99%

Recent advances and perspectives of nucleic acid detection for coronavirus

Shen

Zhou

et al. 2020

Journal of Pharmaceutical Analysis

476

423

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Keywords:Coronavirus Nucleic acid detection PCR-Based methods Isothermal nucleic acid amplification-based methods Microarray-based methods a b s t r a c tThe recent pneumonia outbreak caused by a novel coronavirus (SARS-CoV-2) in Chinais posing a great threat to global public health. Therefore, rapid and a accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. It is important to establish a quick standard diagnostic test for the detection of the infectious disease (COVID-19) to prevent subsequent secondary spread. Polymerase chain reaction (PCR) is regarded as a gold standard test for the molecular diagnosis of viral and bacterial infections with high sensitivity and specificity. Isothermal nucleic acid amplification is considered to be a highly promising candidate method due to its fundamental advantage in quick procedure time at constant temperature without thermocycler operation. A variety of improved or new approaches also have been developed. This review summarizes the currently available detection methods for coronavirus nucleic acid. It is anticipated that this will assist researchers and clinicians in developing better techniques for timely and effective detection of coronavirus infection.

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Section: Pcr-based Methodsmentioning

confidence: 99%

Recent advances and perspectives of nucleic acid detection for coronavirus

Shen

Zhou

et al. 2020

Journal of Pharmaceutical Analysis

476

423

View full text Add to dashboard Cite

show abstract

“…Owing to its simplicity, high sensitivity, and high sequence specificity, PCR-based methods are routinely and reliably capable of detecting coronavirus infection in patients [3,11,12]. In principle, such assays are employed following conversion of coronavirus RNA into complementary DNA by reverse transcription, following which PCR is performed and resultant amplification of DNA subject to specific detection or analytical methods such as electrophoresis or sequencing [3,13,14].…”

Section: Pcr Based Methods Of Viral Detectionmentioning

confidence: 99%

Loop mediated isothermal amplification (LAMP) assays as a rapid diagnostic for COVID-19

2020

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Recently, a novel coronavirus (SARS-CoV-2; coronavirus disease 2019, COVID-19) has emerged, rapidly spreading and severely straining the capacity of the global health community. Many nations are employing combinations of containment and mitigation strategies, where early diagnosis of COVID-19 is vital in controlling illness progression and limiting viral spread within the population. Thus, rapid and accurate methods of early detection are vital to contain COVID-19 and prevent further spread and predicted subsequent infectious waves of viral recurrence in future. Immediately after its initial characterization, Chinese and American Centers for Disease Control and Prevention (CDCs) rapidly employed molecular assays for detection of COVID-19, mostly employing real-time polymerase chain reaction (RT-PCR) methods. However, such methods require specific expensive items of equipment and highly trained analysts, requiring upwards of 4-8 h to process. These requirements coupled with associated financial pressures may prevent effective deployment of such diagnostic tests. Loop mediated isothermal amplification (LAMP) is method of nucleic acid amplification which exhibits increased sensitivity and specificity are significantly rapid, and do not require expensive reagents or instruments, which aids in cost reduction for coronavirus detection. Studies have shown the successful application of LAMP assays in various forms to detect coronavirus RNA in patient samples, demonstrating that 1-10 copies of viral RNA template per reaction are sufficient for successful detection,~100-fold more sensitive than conventional RT-PCR methods. Importantly, studies have also now demonstrated the effectiveness of LAMP methodology in the detection of SARS-CoV-2 RNA at significantly low levels, particularly following numerous improvements to LAMP assay protocols. We hypothesise that recent advancements in enhanced LAMP protocols assay perhaps represent the best chance for a rapid and robust assay for field diagnosis of COVID-19, without the requirement of specialized equipment and highly trained professionals to interpret results. Herein, we present our arguments with a view to disseminate such findings, to assist the combat of this virus that is proving so devastating. We hope that this strategy could be applied rapidly, and confirmed for viability with clinical samples, before being rolled out for mass-diagnostic testing in these current times.

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“…In another study, real-time reverse-transcription PCR assays for detecting the different parts (ORF1b and N) of the viral genome were carried out. Accordingly, the probe and primer were designed in such a way that they could react to this new SARS-CoV-2 and other SARS-CoV viruses including SARS and MERS [71]. They used two different kits; for RNA extractions, they used the viral RNA purification kit (QIAamp Viral RNA Mini Kit, Qiagen), and for DNA extractions they used the DNA plasmid purification kit (QIAprep Spin Miniprep Kit, Qiagen).…”

Section: Pcr-based Methodsmentioning

confidence: 99%

Potential Diagnostic Systems for Coronavirus Detection: a Critical Review

et al. 2020

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Currently there are no effective anti-viral drugs for SARS-CoV-2, so the primary line of defense is to detect infected cases as soon as possible. The high rate of contagion for this virus and the highly nonspecific symptoms of the disease (Coronovirus disease 2019, (Covid-19)) that it causes, such as respiratory symptoms, cough, dyspnea, fever, and viral pneumonia, require the urgent establishment of precise and fast diagnostic tests to verify suspected cases, screen patients, and conduct virus surveillance. Nowadays, several virus detection methods are available for viral diseases, which act on specific properties of each virus or virus family, therefore, further investigations and trials are needed to find a highly efficient and accurate detection method to detect and prevent the outcomes of the disease. Hence, there is an urgent need for more and precise studies in this field. In this review, we discussed the properties of a new generation of coronaviruses (SARS-CoV-2) following routine virus detection methods and proposed new strategies and the use of potential samples for SARS-CoV-2 detection.

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Detection of multiple viral sequences in the respiratory tract samples of suspected Middle East respiratory syndrome coronavirus patients in Jakarta, Indonesia 2015–2016

Cited by 30 publications

References 40 publications

Recent advances and perspectives of nucleic acid detection for coronavirus

Recent advances and perspectives of nucleic acid detection for coronavirus

Loop mediated isothermal amplification (LAMP) assays as a rapid diagnostic for COVID-19

Potential Diagnostic Systems for Coronavirus Detection: a Critical Review

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