scholarly journals A simple and fast spectroscopy-based technique for Covid-19 diagnosis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Driss Lahlou Kitane ◽  
Salma Loukman ◽  
Nabila Marchoudi ◽  
Alvaro Fernandez-Galiana ◽  
Fatima Zahra El Ansari ◽  
...  
Keyword(s):  
Developing Countries ◽  
Multivariate Analysis ◽  
Spectroscopic Method ◽  
Rna Extraction ◽  
Limited Resources ◽  
Clinical Samples ◽  
Testing Time ◽  
Rt Pcr ◽  
The World ◽  
Testing Techniques

AbstractThe coronavirus pandemic, which appeared in Wuhan, China, in December 2019, rapidly spread all over the world in only a few weeks. Faster testing techniques requiring less resources are key in managing the pandemic, either to enable larger scale testing or even just provide developing countries with limited resources, particularly in Africa, means to perform tests to manage the crisis. Here, we report an unprecedented, rapid, reagent-free and easy-to-use screening spectroscopic method for the detection of SARS-CoV-2 on RNA extracts. This method, validated on clinical samples collected from 280 patients with quantitative predictive scores on both positive and negative samples, is based on a multivariate analysis of FTIR spectra of RNA extracts. This technique, in agreement with RT-PCR, achieves 97.8% accuracy, 97% sensitivity and 98.3% specificity while reducing the testing time post RNA extraction from hours to minutes. Furthermore, this technique can be used in several laboratories with limited resources.

scholarly journals Rapid isothermal amplification and portable detection system for SARS-CoV-2

2020 ◽  
Vol 117 (37) ◽  
pp. 22727-22735 ◽  
Author(s):  
Anurup Ganguli ◽  
Ariana Mostafa ◽  
Jacob Berger ◽  
Mehmet Y. Aydin ◽  
Fu Sun ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Detection System ◽  
Alternative Pathway ◽  
Rna Extraction ◽  
Lamp Assay ◽  
Isothermal Amplification ◽  
Clinical Samples ◽  
Complete Agreement ◽  
Rt Pcr ◽  
Viral Transport Medium

The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay protocols and primer sequences become widely known, many laboratories perform diagnostic tests using methods such as RT-PCR or reverse transcription loop mediated isothermal amplification (RT-LAMP). Here, we report an RT-LAMP isothermal assay for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and demonstrate the assay on clinical samples using a simple and accessible point-of-care (POC) instrument. We characterized the assay by dipping swabs into synthetic nasal fluid spiked with the virus, moving the swab to viral transport medium (VTM), and sampling a volume of the VTM to perform the RT-LAMP assay without an RNA extraction kit. The assay has a limit of detection (LOD) of 50 RNA copies per μL in the VTM solution within 30 min. We further demonstrate our assay by detecting SARS-CoV-2 viruses from 20 clinical samples. Finally, we demonstrate a portable and real-time POC device to detect SARS-CoV-2 from VTM samples using an additively manufactured three-dimensional cartridge and a smartphone-based reader. The POC system was tested using 10 clinical samples, and was able to detect SARS-CoV-2 from these clinical samples by distinguishing positive samples from negative samples after 30 min. The POC tests are in complete agreement with RT-PCR controls. This work demonstrates an alternative pathway for SARS-CoV-2 diagnostics that does not require conventional laboratory infrastructure, in settings where diagnosis is required at the point of sample collection.

scholarly journals Improved Detection of Rhinoviruses in Clinical Samples by Using a Newly Developed Nested Reverse Transcription-PCR Assay

1999 ◽  
Vol 37 (3) ◽  
pp. 524-530 ◽  
Author(s):  
Arno C. Andeweg ◽  
Theo M. Bestebroer ◽  
Martijn Huybreghs ◽  
Tjeerd G. Kimman ◽  
Jan C. de Jong
Keyword(s):  
Reverse Transcription ◽  
Rna Extraction ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Noncoding Regions ◽  
Reverse Transcription Pcr ◽  
Highly Sensitive ◽  
Virus Culture ◽  
Culture Positive

This paper describes the development and evaluation of a new nested reverse transcription (RT)-PCR for the detection of rhinovirus in clinical samples. The nucleotide sequences of the 5′ noncoding regions of 39 rhinoviruses were determined in order to map the most conserved subregions. We designed a set of rhinovirus-specific primers and probes directed to these subregions and developed a new nested RT-PCR. The new assay includes an optimal RNA extraction method and amplicon identification with probe hybridization to discriminate between rhinoviruses and the closely related enteroviruses. It proved to be highly sensitive and specific. When tested on a dilution series of cultured viruses, the new PCR protocol scored positive at 10- to 100-fold-higher dilutions than a previously used nested RT-PCR. When tested on a collection of clinical samples obtained from 1,070 acute respiratory disease patients who had consulted their general practitioners, the new assay demonstrated a rhinovirus in 24% of the specimens, including all culture-positive samples, whereas the previously used PCR assay or virus culture detected a rhinovirus in only 3.5 to 6% of the samples. This new assay should help determine the disease burden associated with rhinovirus infections.

scholarly journals Sensitive quantitative detection of SARS-CoV-2 in clinical samples using digital warm-start CRISPR assay

2020 ◽  
Author(s):  
Xiong Ding ◽  
Kun Yin ◽  
Ziyue Li ◽  
Maroun M. Sfeir ◽  
Changchun Liu
Keyword(s):  
Room Temperature ◽  
Rna Extraction ◽  
Clinical Samples ◽  
Quantitative Detection ◽  
High Tolerance ◽  
Rt Pcr ◽  
One Pot ◽  
Nucleoprotein Gene ◽  
Warm Start ◽  
Heat Treated

AbstractQuantifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is crucial for assessing the infectivity of coronavirus disease 2019 and the efficacy of antiviral drugs. Here, we describe a digital warm-start CRISPR (WS-CRISPR) assay for sensitive quantitative detection of SARS-CoV-2 in clinical samples. The WS-CRISPR assay combines low-temperature reverse transcription dual-priming mediated isothermal amplification (RT-DAMP) and CRISPR-Cas12a-based detection in one-pot, attributed to the mediation role by pyrophosphatase and phosphorothioated primers. The WS-CRISPR assay is initiated at above 50 °C and overcomes undesired premature target amplification at room temperature, enabling accurate digital nucleic acid quantification. By targeting SARS-CoV-2’s nucleoprotein gene, digital WS-CRISPR assay is able to detect down to 5 copies/μl SARS-CoV-2 RNA in the chip within 90 minutes. It is clinically validated by quantitatively determining 32 clinical swab samples and three clinical saliva samples, showing 100% agreement with RT-PCR results. Moreover, the digital WS-CRISPR assay has been demonstrated to directly detect SARS-CoV-2 in heat-treated saliva samples without RNA extraction, showing high tolerance to inhibitors. Thus, the digital WS-CRISPR method, as a sensitive and reliable CRISPR assay, facilitates accurate SARS-CoV-2 detection toward digitized quantification.

Role of Plasma miRNA-501 Expression Profile as a Marker of Hepatocellular Carcinoma (HCC) Progression With Hepatitis C Virus Infection

2019 ◽  
Vol 152 (Supplement_1) ◽  
pp. S134-S134
Author(s):  
Mohamed Shedid ◽  
Mohamed Abdelmonem ◽  
Ayman Boraik ◽  
Alaa Elmetwalli ◽  
Ahmed Esmael
Keyword(s):  
Rna Extraction ◽  
Control Group ◽  
Hepatitis C Virus Infection ◽  
Rt Pcr ◽  
The World ◽  
Noninvasive Biomarker ◽  
Biological Aspects ◽  
Plasma Mirna

Abstract Introduction HCV is a health problem that confronts many countries in the world. Those patients will develop complications like cirrhosis and HCC, which is one of the most common cancers in the world, especially in Egypt, and considered the third leading cause of death worldwide. The prognosis of HCC is still dismal due to the late diagnosis. miRNAs are small, short noncoding RNAs, which have roles in the diagnosis of HCC. In our study, we focus on biological aspects of miRNAs. We report that miR-501 is strongly expressed and observed in the process of HCC development. miR-501 regulation is important as an oncofetal relevant to the diagnosis of HCC. Method This study was conducted on 100 adult patients; 25 patients were positive for anti-HCV and 25 patients were negative for HCV and enrolled as a control group. Patients were categorized into three groups: fibrosis (n = 25), CHC (n = 25), and HCC (n = 25) related to HCV evident by CT abdomen. All patients and controls were subjected to full clinical assessment and laboratory investigation. Blood (8 mL) was withdrawn from subjects, and 3 mL was collected in EDTA tubes for processing total RNA extraction and miRNA. The remaining 5 mL was left for determination of biochemical parameters. miRN-501 expression levels were determined by RT-PCR. Results The data revealed a significant increase in levels of AST, ALT, ALP, and CBC in both HCC and CHC groups compared to controls. The results of miRNA expression showed that miR-501 was higher in the HCC group than non-HCC group at P1.1. Conclusion miR-501 can be used as a noninvasive biomarker for early diagnosis of HCC among patients with HCV on account of its affectability for HCC.

The importance of timely diagnosis and replacement of medical equipment in healthcare institutions

2022 ◽  
pp. 6-14
Author(s):  
I.P. Abysheva ◽  
Keyword(s):  
Health Care ◽  
Developing Countries ◽  
Healthcare System ◽  
Medical Devices ◽  
Medical Equipment ◽  
Review Article ◽  
Limited Resources ◽  
High Quality ◽  
The World ◽  
Provision Of Services

The health care system around the world, both in developed and developing countries, is struggling with the problem of managing the provision of health care in conditions of limited resources. The availability and use of various medical equipment at all levels of the healthcare system were emphasized for the efficient and high-quality provision of services. The main purpose of this review article is to assess the availability and use of medical devices and identify the registered causes affecting the availability and use of medical devices in healthcare institutions.

scholarly journals Determinants Of Destination Image And Competitiveness In Sibu Heritage Trail: A PLS-SEM Approach

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Chin Ying Sin ◽  
Abang Azlan Mohamad ◽  
Lo May Chiun ◽  
Mohamad Kadim Suaidi ◽  
Ha Shiaw Tong
Keyword(s):  
Developing Countries ◽  
Destination Image ◽  
Limited Resources ◽  
Destination Competitiveness ◽  
The World ◽  
Destination Attractiveness ◽  
Tourism Destinations

Tourism is the largest sector in the world and contributes significantly to the economies of the most advanced and developing countries. A major concern on limited resources and acknowledgement of competitiveness all led to the expansion of the literature on the competitiveness of tourism destinations. While, there are limited studies that investigate destination image and destination competitiveness, no studies have been found to examine the determinants of destination image and destination competitiveness. Thus, the present study attempts to explore whether accessibility quality, accommodation quality, destination attractiveness & resources on destination image and competitiveness. Data were collected from 132 tourists who have visited Sibu Heritage Trail. The research employs PLS-SEM, and the result specified that there are total of four hypotheses were supported. The implications and limitations of the present study were further discussed.

scholarly journals Comparative analysis of the diagnostic performance of five commercial COVID-19 qRT PCR kits used in India

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
J. Singh ◽  
A. K. Yadav ◽  
A. Pakhare ◽  
P. Kulkarni ◽  
L. Lokhande ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
Diagnostic Performance ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Clinical Samples ◽  
Diagnostic Process ◽  
Control Group ◽  
Rt Pcr ◽  
Short Period ◽  
Commercial Kits

AbstractTo meet the unprecedented requirement of diagnostic testing for SARS-CoV-2, a large number of diagnostic kits were authorized by concerned authorities for diagnostic use within a short period of time during the initial phases of the ongoing pandemic. We undertook this study to evaluate the inter-test agreement and other key operational features of 5 such commercial kits that have been extensively used in India for routine diagnostic testing for COVID-19. The five commercial kits were evaluated, using a panel of positive and negative respiratory samples, considering the kit provided by National Institute of Virology, Indian Council of Medical Research (2019-nCoV Kit) as the reference. The positive panel comprised of individuals who fulfilled the 3 criteria of being clinically symptomatic, having history of contact with diagnosed cases and testing positive in the reference kit. The negative panel included both healthy and disease controls, the latter being drawn from individuals diagnosed with other respiratory viral infections. The same protocol of sample collection, same RNA extraction kit and same RT-PCR instrument were used for all the kits. Clinical samples were collected from a panel of 92 cases and 60 control patients, who fulfilled our inclusion criteria. The control group included equal number of healthy individuals and patients infected with other respiratory viruses (n = 30, in each group). We observed varying sensitivity and specificity among the evaluated kits, with LabGun COVID-19 RT-PCR kit showing the highest sensitivity and specificity (94% and 100% respectively), followed by TaqPath COVID-19 Combo and Allplex 2019-nCoV assays. The extent of inter-test agreement was not associated with viral loads of the samples. Poor correlation was observed between Ct values of the same genes amplified using different kits. Our findings reveal the presence of wide heterogeneity and sub-optimal inter-test agreement in the diagnostic performance of the evaluated kits and hint at the need of adopting stringent standards for fulfilling the quality assurance requirements of the COVID-19 diagnostic process.

scholarly journals Detection of SARS CoV-2 reinfections by rapid inexpensive techniques

2021 ◽  
Author(s):  
Sherko Subhan Niranji ◽  
Sirwan M.A. Al-Jaf
Keyword(s):  
Developing Countries ◽  
Dna Sequences ◽  
Rapid Detection ◽  
Phylogenetic Analyses ◽  
Immunocompetent Patient ◽  
Clinical Samples ◽  
Specific Primers ◽  
Persistent Infections ◽  
The World ◽  
The Uk

Abstract Reinfections of SARS CoV-2 are rare in the world and it is difficult to be confirmed whether it is a reinfection or persistent infection. The most prominent factors used for differentiating the reinfections from persistent infections are whole genome sequencings and phylogenetic analyses that require times and funds, which may not be feasible in most developing countries. We previously developed rapid economical methods to identify both D614G and N501Y mutations in clinical samples using rRT PCR probes and endpoint PCR specific primers. Current study has found an immunocompetent patient with a SARS CoV-2 N501Y reinfection without comorbidities. The results suggested that the initial infection was due to a variant contained only D614G mutation while the reinfection was potentially as result of the UK variant contained three mutations confirmed by DNA sequences, including D614G, N501Y and A570D mutations. Seven cases of reinfections were also confirmed by these methods suggested that these techniques will support rapid detection of SARS CoV-2 reinfections in developing countries where sequencing tools are unavailable.

scholarly journals Open-source RNA extraction and RT-qPCR methods for SARS-CoV-2 detection

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246647
Author(s):  
Thomas G. W. Graham ◽  
Claire Dugast-Darzacq ◽  
Gina M. Dailey ◽  
Xammy H. Nguyenla ◽  
Erik Van Dis ◽  
...  
Keyword(s):  
Open Source ◽  
Strong Correlation ◽  
Limit Of Detection ◽  
Effective Means ◽  
Rna Extraction ◽  
Clinical Samples ◽  
Testing Methods ◽  
Direct Addition ◽  
Extraction Step ◽  
The World

Re-opening of communities in the midst of the ongoing COVID-19 pandemic has ignited new waves of infections in many places around the world. Mitigating the risk of reopening will require widespread SARS-CoV-2 testing, which would be greatly facilitated by simple, rapid, and inexpensive testing methods. This study evaluates several protocols for RNA extraction and RT-qPCR that are simpler and less expensive than prevailing methods. First, isopropanol precipitation is shown to provide an effective means of RNA extraction from nasopharyngeal (NP) swab samples. Second, direct addition of NP swab samples to RT-qPCRs is evaluated without an RNA extraction step. A simple, inexpensive swab collection solution suitable for direct addition is validated using contrived swab samples. Third, an open-source master mix for RT-qPCR is described that permits detection of viral RNA in NP swab samples with a limit of detection of approximately 50 RNA copies per reaction. Quantification cycle (Cq) values for purified RNA from 30 known positive clinical samples showed a strong correlation (r2 = 0.98) between this homemade master mix and commercial TaqPath master mix. Lastly, end-point fluorescence imaging is found to provide an accurate diagnostic readout without requiring a qPCR thermocycler. Adoption of these simple, open-source methods has the potential to reduce the time and expense of COVID-19 testing.

scholarly journals Rapid and Visual Detection of SARS-CoV-2 Using Multiplex Reverse Transcription Loop-Mediated Isothermal Amplification Linked With Gold Nanoparticle-Based Lateral Flow Biosensor

2021 ◽  
Vol 11 ◽  
Author(s):  
Xu Chen ◽  
Qingxue Zhou ◽  
Shijun Li ◽  
Hao Yan ◽  
Bingcheng Chang ◽  
...  
Keyword(s):  
Reverse Transcription ◽  
Prevention And Control ◽  
Limit Of Detection ◽  
Rna Extraction ◽  
Lateral Flow ◽  
Isothermal Amplification ◽  
Clinical Samples ◽  
Loop Mediated Isothermal Amplification ◽  
The World ◽  
And Control

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that has caused the outbreak of coronavirus disease 2019 (COVID-19) all over the world. In the absence of appropriate antiviral drugs or vaccines, developing a simple, rapid, and reliable assay for SARS-CoV-2 is necessary for the prevention and control of the COVID-19 transmission.MethodsA novel molecular diagnosis technique, named multiplex reverse transcription loop-mediated isothermal amplification, that has been linked to a nanoparticle-based lateral flow biosensor (mRT-LAMP-LFB) was applied to detect SARS-CoV-2 based on the SARS-CoV-2 RdRp and N genes, and the mRT-LAMP products were analyzed using nanoparticle-based lateral flow biosensor. The mRT-LAMP-LFB amplification conditions, including the target RNA concentration, amplification temperature, and time were optimized. The sensitivity and specificity of the mRT-LAMP-LFB method were tested in the current study, and the mRT-LAMP-LFB assay was applied to detect the SARS-CoV-2 virus from clinical samples and artificial sputum samples.ResultsThe SARS-CoV-2 specific primers based on the RdRp and N genes were valid for the establishment of mRT-LAMP-LFB assay to detect the SARS-CoV-2 virus. The multiple-RT-LAMP amplification condition was optimized at 63°C for 30 min. The full process, including reaction preparation, viral RNA extraction, RT-LAMP, and product identification, could be achieved in 80 min. The limit of detection (LoD) of the mRT-LAMP-LFB technology was 20 copies per reaction. The specificity of mRT-LAMP-LFB detection was 100%, and no cross-reactions to other respiratory pathogens were observed.ConclusionThe mRT-LAMP-LFB technique developed in the current study is a simple, rapid, and reliable method with great specificity and sensitivity when it comes to identifying SARS-CoV-2 virus for prevention and control of the COVID-19 disease, especially in resource-constrained regions of the world.

Sign in / Sign up

Export Citation Format

Share Document