Microelectrothermofluidic packaging for single chip integrated viral RNA extraction and RT-PCR microdevices

Author(s):  
Tae Goo Kang ◽  
Hong Miao Ji ◽  
Siow Pin Melvin Tan ◽  
Guang Kai Ignatius Tay ◽  
Ming Yi Daniel Ang ◽  
...  
Keyword(s):  
2016 ◽  
Vol 19 (3) ◽  
pp. 655-657 ◽  
Author(s):  
J. Kęsik-Maliszewska ◽  
M. Larska

Abstract The detection of Schmallenberg virus (SBV) in the breeding bull semen raised the question of the possibility of venereal transmission of SBV which could result in cost-intensive restrictions in the trade of bovine semen. In order to evaluate the presence of SBV RNA in bovine semen, 131 bull semen samples from four locations in Poland collected between 2013 and 2015 were analysed by RT-PCR for viral RNA. SBV RNA was detected in 5.3% of the samples. The study has revealed that application of an appropriate RNA extraction method is crucial to detect virus excretion via semen.


2004 ◽  
Vol 52 (2) ◽  
pp. 163-166 ◽  
Author(s):  
M. R. Seyfi Abad Shapouri ◽  
M. Mayahi ◽  
K. Assasi ◽  
S. Charkhkar

To evaluate the prevalence of infectious bronchitis virus (IBV) type 4/91 in Iran, tracheal swabs from 77 broiler flocks in 16 provinces were collected at the slaughterhouse. Swabs were subjected to RNA extraction and tested by RT-PCR, followed by a type-specific nested PCR. The viral RNA was detected in 33 samples (42.8%) from different provinces. The results indicate a relatively high prevalence of IBV type 4/91 in Iran and necessitate revising the vaccination programme against this disease.


Plant Disease ◽  
1997 ◽  
Vol 81 (2) ◽  
pp. 222-226 ◽  
Author(s):  
Donald J. MacKenzie ◽  
Morven A. McLean ◽  
Srima Mukerji ◽  
Margaret Green

An efficient procedure for the extraction of high-quality RNA from woody plants without the use of phenol, organic solvents, or alcohol precipitation is described. The method employs commercially available spin-column matrices and mitigates the inhibitory effects of plant polysaccharides and polyphenolic compounds commonly observed on subsequent polymerase chain reaction amplification when conventional extraction methods are applied to woody plant species. The method described has been successfully used in the development of highly sensitive reverse transcription-polymerase chain reaction (RT-PCR) techniques for the detection of a number of viruses in their woody hosts. The viruses detected included apple stem grooving capillovirus (ASGV), apple stem pitting virus, Prunus necrotic ringspot ilarvirus (PNRSV), grapevine fanleaf and Arabis mosaic nepoviruses, and grapevine leafroll-associated closterovirus type 3. The method described was equally effective for the extraction of viral RNA from either budwood, leaves, or flower blossoms as determined by the equivalent RT-PCR detection of ASGV and PNRSV from these tissues. Detection of viral RNA in samples of total plant RNA prepared using this method was found to be as sensitive as was previously described for the immunocapture RT-PCR technique.


Author(s):  
Olumuyiwa B. Salu ◽  
Ayorinde B. James ◽  
Bamidele O. Oke ◽  
Mercy R. Orenolu ◽  
Roosevelt A. Anyanwu ◽  
...  

Introduction: Global travel is an efficient route of transmission for highly infectious pathogens and increases the chances of such pathogens moving from high disease-endemic areas to new regions. We describe the rapid and safe identification of the first imported case of Ebola virus disease in a traveler to Lagos, Nigeria, using conventional reverse transcription polymerase chain reaction (RT-PCR) in a biosafety level (BSL)-2 facility.Case presentation: On 20 July 2014, a traveler arrived from Liberia at Lagos International Airport and was admitted to a private hospital in Lagos, with clinical suspicion of Ebola virus disease.Methodology and Outcome: Blood and urine specimens were collected, transported to the Virology Unit Laboratory at the College of Medicine, University of Lagos, and processed under stringent biosafety conditions for viral RNA extraction. RT-PCR was set-up to query the Ebola, Lassa and Dengue fever viruses. Amplicons for pan-filoviruses were detected as 300 bp bands on a 1.5% agarose gel image; there were no detectable bands for Lassa and Dengue viral RNA. Nucleotide BLAST and phylogenetic analysis of sequence data of the RNA-dependent RNA polymerase (L) gene confirmed the sequence to be Zaire ebolavirus (EBOV/Hsap/ NGA/2014/LIB-NIG 01072014; Genbank: KM251803.1).Conclusion: Our BSL-2 facility in Lagos, Nigeria, was able to safely detect Ebola virus disease using molecular techniques, supporting the reliability of molecular detection of highly infectious viral pathogens under stringent safety guidelines in BSL-2 laboratories. This is a significant lesson for the many under-facilitated laboratories in resource-limited settings, as is predominantly found in sub-Saharan Africa.


Author(s):  
Zhen Zhao ◽  
Haodong Cui ◽  
Wenxing Song ◽  
Xiaoling Ru ◽  
Wenhua Zhou ◽  
...  

1AbstractThe ongoing outbreak of the novel coronavirus disease 2019 (COVID-19) originating from Wuhan, China, draws worldwide concerns due to its long incubation period and strong infectivity. Although RT-PCR-based molecular diagnosis techniques are being widely applied for clinical diagnosis currently, timely and accurate diagnosis are still limited due to labour intensive and time-consuming operations of these techniques. To address the issue, herein we report the synthesis of poly (amino ester) with carboxyl groups (PC)-coated magnetic nanoparticles (pcMNPs), and the development of pcMNPs-based viral RNA extraction method for the sensitive detection of COVID-19 causing virus, the SARS-CoV-2. This method combines the lysis and binding steps into one step, and the pcMNPs-RNA complexes can be directly introduced into subsequent RT-PCR reactions. The simplified process can purify viral RNA from multiple samples within 20 min using a simple manual method or an automated high-throughput approach. By identifying two different regions (ORFlab and N gene) of viral RNA, a 10-copy sensitivity and a strong linear correlation between 10 and 105 copies of SARS-CoV-2 pseudovirus particles are achieved. Benefitting from the simplicity and excellent performances, this new extraction method can dramatically reduce the turn-around time and operational requirements in current molecular diagnosis of COVID-19, in particular for the early clinical diagnosis.


2020 ◽  
Author(s):  
Laura Dioni ◽  
Benedetta Albetti ◽  
Federica Rota ◽  
Valentina Bollati

Abstract In this protocol, we describe a method to investigate the presence of SARS-CoV-2 RNA in nasal swabs, using a commercially available high-throughput Real-Time Polymerase Chain Reaction (RT-PCR) assay (TaqPath™ Covid-19 kit, ThermoFisher Scientific) in a 384-Well Plate. After Viral RNA extraction with QIAamp Viral RNA Mini kit, reverse transcription and cDNA amplification, all samples are assessed for the presence of three specific SARS-CoV-2 viral genomic regions and an internal positive control (IPC), in one Multiplex RT-PCR reaction.


2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
C Fossard ◽  
E Farfour ◽  
A Benammar ◽  
M Filali ◽  
J Vandame ◽  
...  

Abstract Study question Is it possible to find viral Sars-Cov–2 RNA in FF of women undergoing treatment during Covid–19 pandemic that may compromise gamete and embryo safety? Summary answer No viral RNA was detected in tested FF of women undergoing IVF in compliance with recommendations. This was reassuring and supported good medical practice. What is known already Risks due to SARS-CoV–2 during IVF remain difficult to assess despite the screening recommended by French health authorities based on a symptom questionnaire of the couple (systematic testing by RT-PCR for the virus before egg retrieval (ER) is not mandatory). In this context, this is a real challenge for IVF laboratory to guarantee procedure, patients, gametes and embryos safety. Most studies have reported the absence of virus in sperm. No data are available for FF and only one study looked for the presence of the virus in oocytes of Covid-affected patients (Barragan M et al, 2020). Study design, size, duration Between June 17 and September 24, 2020, FF of consenting women were prospectively collected and symptom questionnaire recorded. During this period, women undergoing IVF in our center did not benefit from systematic PCR testing for the virus within 72 hours prior to ER through our health authorities’ recommendations. All collected FF were retrospectively tested to research viral RNA by RT-PCR and patients were recalled to answer an epidemiological follow-up questionnaire. Participants/materials, setting, methods For all couples, symptom questionnaires were prospectively recorded and verified at each step of IVF procedure. For all consenting women, a sample of 1 ml of FF was collected the day of ER and stored at –80 °C. After thawing, a Sars-Cov2 multiplex RT-PCR using CFX96 (Biorad*) was performed, after RNA extraction using Nimbus (Seegene*). A comprehensive epidemiological evaluation was made afterwards by phone interview and data were recorded and analyzed. Main results and the role of chance A total of 183 women was included out of the 214 treated during this period (85.5%). Retrospective epidemiological evaluation showed that 8 patients contracted Covid more than 2 months before the ER, 6 more than 2 months after and only one patient 1 month after ER (diagnosis based on pathognomonic signs as agueusia and anosmia or/and positive PCR ). We observed a prevalence of symptomatic Covid forms in our IVF population of 8.2% during a 6-month period surrounding their IVF cycle. Moreover, until the introduction of systematic testing by RT-PCR for the virus before ER since the end of September 2020, 3 patients have been cancelled out of the 403 planned for positive PCR despite a negative questionnaire, which represents a prevalence of asymptomatic forms on the day of the ER at 0.7%. All the 183 FF tested did not reveal any viral RNA detection, which was reassuring concerning our medical practice and patient compliance and transparency. The absence of detected viral RNA may be due to several reasons: 1) women were not infected the day of ER 2) women had an asymptomatic form of the disease with low viral load 3) FF is not a virus reservoir. Limitations, reasons for caution Not all patients were included (85.5%). Post-diagnosis stays uncertain because PCR tests at the beginning of the epidemic were not mandatory and hardly available. Wider implications of the findings: The absence of viral RNA in FF of women only screened through a symptom questionnaire is reassuring concerning the safety of IVF during Covid pandemic. Trial registration number Not applicable


2020 ◽  
Author(s):  
Masateru Taniguchi ◽  
Shohei Minami ◽  
Chikako Ono ◽  
Rina Hamajima ◽  
Ayumi Morimura ◽  
...  

Abstract High-throughput, high-accuracy detection of emerging viruses allows for pandemic prevention and control. Currently, reverse transcription-polymerase chain reaction (RT-PCR) is used to diagnose the presence of SARS-CoV-2. The principle of the test is to detect RNA in the virus using a pair of primers that specifically binds to the base sequence of the viral RNA. However, RT-PCR is a sophisticated technique requiring a time-consuming pretreatment procedure for extracting viral RNA from clinical specimens and to obtain high sensitivity. Here, we report a method for detecting novel coronaviruses with high sensitivity using artificial intelligent nanopores utilizing a simple procedure that does not require RNA extraction. Artificial intelligent nanopore platform consists of machine learning software on the servers, portable high-speed and high-precision current measuring instrument, and scalable, cost-effective semiconducting nanopore modules. Here we show that the artificial intelligent nanopores are successful in accurate identification of four types of coronaviruses, HCoV-229E, SARS-CoV, MERS-CoV, and SARS-CoV-2, which are usually extremely difficult to detect. The positive/negative diagnostics of the new coronavirus is achieved with a sensitivity of 95 % and specificity of 92 % with a 5-minute diagnosis. The platform enables high throughput diagnostics with low false negatives for the novel coronavirus.


2012 ◽  
Vol 78 (17) ◽  
pp. 6271-6279 ◽  
Author(s):  
Malak A. Esseili ◽  
Qiuhong Wang ◽  
Zhenwen Zhang ◽  
Linda J. Saif

ABSTRACTNoroviruses are the leading cause of food-borne outbreaks, including those that involve lettuce. The culturable porcine sapovirus (SaV) was used as a norovirus surrogate to study the persistence and the potential transfer of the virus from roots to leaves and from outer to inner leaves of lettuce plants. Treatment of lettuce with SaV was done through the roots of young plants, the soil, or the outer leaves of mature plants. Sampling of roots, xylem sap, and inner and outer leaves followed by RNA extraction and SaV-specific real-time reverse transcription (RT)-PCR was performed at 2 h and on postinoculation days (PID) 2, 5, 7, 14, and/or 28. When SaV was inoculated through the roots, viral RNA persisted on the roots and in the leaves until PID 28. When the virus was inoculated through the soil, viral RNA was detected on the roots and in the xylem sap until PID 14; viral RNA was detected in the leaves only until PID 2. No infectious virus was detected inside the leaves for either treatment. When SaV was inoculated through the outer leaves, viral RNA persisted on the leaves until PID 14; however, the virus did not transfer to inner leaves. Infectious viral particles on leaves were detected only at 2 h postinoculation. The milky sap (latex) of leaves, but not the roots' xylem sap, significantly decreased virus infectivity when testedin vitro. Collectively, our results showed the transfer of SaV from roots to leaves through the xylem system and the capacity of the sap of lettuce leaves to decrease virus infectivity in leaves.


Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 693
Author(s):  
Shiori Sano ◽  
Shuetsu Fukushi ◽  
Souichi Yamada ◽  
Shizuko Harada ◽  
Hitomi Kinoshita ◽  
...  

Detection of severe fever with thrombocytopenia syndrome (SFTS) virus (SFTSV) during the early phase of the disease is important for appropriate treatment, infection control, and prevention of further transmission. The reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a nucleic acid amplification method that amplifies the target sequence under isothermal conditions. Here, we developed an RT-LAMP with a novel primer/probe set targeting a conserved region of the SFTSV L segment after extraction of viral RNA (standard RT-LAMP). Both the Chinese and Japanese SFTSV strains, including various genotypes, were detected by the standard RT-LAMP. We also performed RT-LAMP using the same primer/probe set but without the viral RNA extraction step (called simplified RT-LAMP) and evaluated the diagnostic efficacy. The sensitivity and specificity of the simplified RT-LAMP were 84.9% (45/53) and 89.5% (2/19), respectively. The simplified RT-LAMP can detect SFTSV in human sera containing >103.5 copies/mL viral RNA. The two RT-LAMP positive but quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) negative samples were positive in the conventional RT-PCR, suggesting that there was no false positive reaction in the RT-LAMP. Both the standard and simplified RT-LAMP are useful for detecting the SFTSV genome in patients during the early phase of the disease.


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