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1.
Biomedical Engineering Advances ; : 100092, 2023.
Article in English | ScienceDirect | ID: covidwho-2325186

ABSTRACT

Digital polymerase chain reaction (dPCR) is an emerging technique for the absolute quantification of target nucleic acids. dPCR got attention as a precise quantification tool in preclinical research, particularly when used to detect genetic mutations and result in highly precise measurements. In dPCR, the statistic of Poisson distribution was followed for the random distribution of molecules in different partitions, which is essential for dPCR quantification. Amplified target sequences in different partitions are identified by fluorescence and each partition functions as a separate PCR microreactor. Without the need for calibration, the percentage of PCR-positive partitions is sufficient to estimate the concentration of the target sequence. The present revolution in digital quantification was made possible by advancements in microfluidics, which provided effective partitioning techniques. In this paper, the contrast of the underlying ideas of quantitative real-time PCR with dPCR for the measurement of nucleic acids quantity Polymerase chain reaction (q-PCR). This review study briefly introduced the background of dPCR and compared different types of PCR, particularly the quantity of real-time qPCR and digital PCR. The fundamental concept of dPCR is also explained and also briefly compares the advantages of dPCR over qPCR and analyzes the applications of dPCR as a diagnostic tool for cancer and different types of viral species.

2.
Biosensors (Basel) ; 13(4)2023 Apr 06.
Article in English | MEDLINE | ID: covidwho-2298134

ABSTRACT

Detection and quantification of DNA biomarkers relies heavily on the yield and quality of DNA obtained by extraction from different matrices. Although a large number of studies have compared the yields of different extraction methods, the repeatability and intermediate precision of these methods have been largely overlooked. In the present study, five extraction methods were evaluated, using digital PCR, to determine their efficiency in extracting DNA from three different Gram-negative bacteria in sputum samples. The performance of two automated methods (GXT NA and QuickPick genomic DNA extraction kit, using Arrow and KingFisher Duo automated systems, respectively), two manual kit-based methods (QIAamp DNA mini kit; DNeasy UltraClean microbial kit), and one manual non-kit method (CTAB), was assessed. While GXT NA extraction kit and the CTAB method have the highest DNA yield, they did not meet the strict criteria for repeatability, intermediate precision, and measurement uncertainty for all three studied bacteria. However, due to limited clinical samples, a compromise is necessary, and the GXT NA extraction kit was found to be the method of choice. The study also showed that dPCR allowed for accurate determination of extraction method repeatability, which can help standardize molecular diagnostic approaches. Additionally, the determination of absolute copy numbers facilitated the calculation of measurement uncertainty, which was found to be influenced by the DNA extraction method used.


Subject(s)
Acinetobacter baumannii , Klebsiella pneumoniae , Pseudomonas aeruginosa , Cetrimonium , DNA
3.
Genes Genomics ; 44(5): 617-628, 2022 05.
Article in English | MEDLINE | ID: covidwho-1838428

ABSTRACT

BACKGROUND: Since COVID-19 was declared the pandemic by the WHO, it has continued to spread. There is a need for rapid, efficient, and accurate diagnostic kits and techniques to control its spread. OBJECTIVE: The diagnostic capability of the qRT-PCR-based Real-Q 2019-nCoV Detection Kit and dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit was compared and evaluated. METHODS: Diagnostic tests for COVID-19 were performed using two different COVID-19 kits and 301 individual specimens with confirmed COVID-19 positive/negative at the government-accredited medical institution. Assessment of diagnostic capability was measured through diagnostic sensitivity, specificity, Cohen's Kappa coefficient, and dilutional linearity tests. RESULTS: The COVID-19 diagnostic test results using two kits and 301 individual specimens perfectly matched the pre-diagnosis results of the medical institution. In addition, the measurement results of diagnostic sensitivity and specificity were "1", indicating high diagnostic capability. Cohen's Kappa coefficient value is "1", which means that the diagnosis concordance between the two kits is "Almost Perfect". As a result of dilutional linearity tests to evaluate their detection capability, both kits were measured with very high detection reliability. CONCLUSION: Here, we propose that the dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit has the advantages of the dPCR method reported in the previous study and is suitable for point-of-care testing (POCT) by overcoming the limitations of space, test time, cross-over contamination, and biosafety due to omitting RNA extraction process.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , Point-of-Care Systems , Polymerase Chain Reaction , RNA, Viral/analysis , RNA, Viral/genetics , Reproducibility of Results , SARS-CoV-2/genetics
4.
International Journal of Conservation Science ; 13(3):973-980, 2022.
Article in English | Web of Science | ID: covidwho-2112272

ABSTRACT

Coronavirus disease 2019 is a contagious disease that occurs in humans caused by infection with the SARS-CoV-2 virus. Originally emerged in Wuhan, from Hubei Province, China, SARS-CoV-2 has spread rapidly around the world. In order to effectively combat this pandemic, a methodology must be found to be able to predict, early detect and monitor the extent of infections, which is vital for reducing the risk of transmission. Monitoring of SARSCoV-2 in wastewater to detect and quantify the virus, to estimate the number of infected subjects in a population in a given area has proven to be very promising. Wastewater monitoring has already been implemented in several European countries, as well as in Australia, China and the United States. Although the fact that SARS-CoV-2 may be present in wastewater has been reported in several studies and is being given special attention, a standard procedure for monitoring SARS-CoV-2 in wastewater is still missing. Our goal is to design and propose, based on information reported already in the literature, an efficient methodology for detecting and quantifying SARS-CoV-2 RNA in wastewater. In addition, we also performed a comparison based on performance characteristics of the two methods used to detect and quantify SARS-CoV-2 RNA in wastewater, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and digital PCR (dPCR).

5.
Sensors (Basel) ; 22(19)2022 Sep 23.
Article in English | MEDLINE | ID: covidwho-2066346

ABSTRACT

Thermal inkjet printing can generate more than 300,000 droplets of picoliter scale within one second stably, and the image analysis workflow is used to quantify the positive and negative values of the droplets. In this paper, the SimpleBlobDetector detection algorithm is used to identify and localize droplets with a volume of 24 pL in bright field images and suppress bright spots and scratches when performing droplet location identification. The polynomial surface fitting of the pixel grayscale value of the fluorescence channel image can effectively compensate and correct the image vignetting caused by the optical path, and the compensated fluorescence image can accurately classify positive and negative droplets by the k-means clustering algorithm. 20 µL of the sample solution in the result reading chip can produce more than 100,000 effective droplets. The effective droplet identification correct rate of 20 images of random statistical samples can reach more than 99% and the classification accuracy of positive and negative droplets can reach more than 98% on average. This paper overcomes the problem of effectively classifying positive and negative droplets caused by the poor image quality of photographed picolitre ddPCR droplets caused by optical hardware limitations.


Subject(s)
Algorithms , Image Processing, Computer-Assisted , Cluster Analysis , Polymerase Chain Reaction , Technology
6.
Front Bioeng Biotechnol ; 10: 947895, 2022.
Article in English | MEDLINE | ID: covidwho-2022646

ABSTRACT

Digital PCR is the most advanced PCR technology. However, due to the high price of the digital PCR analysis instrument, this powerful nucleic acid detection technology is still difficult to be popularized in the general biochemistry laboratory. Moreover, one of the biggest disadvantages of commercial digital PCR systems is the poor versatility of reagents: each instrument can only be used for a few customized kits. Herein, we built a low-cost digital PCR system. The system only relies on low-cost traditional flat-panel PCR equipment to provide temperature conditions for commercial dPCR chips, and the self-made fluorescence detection system is designed and optically optimized to meet a wide range of reagent requirements. More importantly, our system not only has a low cost (<8000 US dollars) but also has a much higher universality for nucleic acid detection reagents than the traditional commercial digital PCR system. In this study, several samples were tested. The genes used in the experiment were plasmids containing UPE-1a fragment, TP53 reference DNA, hepatitis B virus DNA, leukemia sample, SARS-COV-2 DNA, and SARS-COV-2 RNA. Under the condition that DNA can be amplified normally, the function of the dPCR system can be realized with simpler and low-price equipment. Some DNA cannot be detected by using the commercial dPCR system because of the special formula when it is configured as the reaction solution, but these DNA fluorescence signals can be clearly detected by our system, and the concentration can be calculated. Our system is more applicable than the commercial dPCR system to form a new dPCR system that is smaller and more widely applicable than commercially available machinery.

7.
Methods ; 201: 26-33, 2022 05.
Article in English | MEDLINE | ID: covidwho-1915093

ABSTRACT

In recent years, the usage of digital polymerase chain reaction (dPCR) for various clinical applications has increased exponentially. In this study, a dPCR assay optimized on the Clarity Plus™ dPCR system was evaluated for the absolute quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the global coronavirus disease 2019 (COVID-19) outbreak. The assay demonstrated good inter- and intra- assay precision, accuracy, as well as excellent linearity across a range of over 6 orders of magnitude for target gene quantification. In addition, a comparison of the assay on both dPCR and qPCR platforms revealed that dPCR exhibited a slightly higher sensitivity compared to its qPCR counterpart when quantifying SARS-CoV-2 at a lower concentration. Overall, the results showed that the dPCR assay is a reliable and effective approach for the absolute quantification of SARS-CoV-2 and can be a valuable molecular tool in clinical applications such as detecting low viral loads in patients as well as in wastewater surveillance of COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , RNA, Viral/analysis , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , Wastewater/analysis , Wastewater-Based Epidemiological Monitoring
8.
Clin Microbiol Rev ; 35(3): e0016821, 2022 09 21.
Article in English | MEDLINE | ID: covidwho-1731254

ABSTRACT

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing , Humans , Pandemics , Real-Time Polymerase Chain Reaction/methods , Reproducibility of Results , SARS-CoV-2/genetics , Sensitivity and Specificity
9.
Anal Bioanal Chem ; 413(29): 7195-7204, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1482198

ABSTRACT

The pandemic of the novel coronavirus disease 2019 (COVID-19) has caused severe harm to the health of people all around the world. Molecular detection of the pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), played a crucial role in the control of the disease. Reverse transcription digital PCR (RT-dPCR) has been developed and used in the detection of SARS-CoV-2 RNA as an absolute quantification method. Here, an interlaboratory assessment of quantification of SARS-CoV-2 RNA was organized by the National Institute of Metrology, China (NIMC), using in vitro transcribed RNA samples, among ten laboratories on six different dPCR platforms. Copy number concentrations of three genes of SARS-CoV-2 were measured by all participants. Consistent results were obtained with dispersion within 2.2-fold and CV% below 23% among different dPCR platforms and laboratories, and Z' scores of all the reported results being satisfactory. Possible reasons for the dispersion included PCR assays, partition volume, and reverse transcription conditions. This study demonstrated the comparability and applicability of RT-dPCR method for quantification of SARS-CoV-2 RNA and showed the capability of the participating laboratories at SARS-CoV-2 test by RT-dPCR platform.


Subject(s)
Laboratories/organization & administration , RNA, Viral/analysis , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , COVID-19/virology , Humans , Limit of Detection
10.
Genomics Inform ; 19(3): e34, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1463988

ABSTRACT

Digital PCR (dPCR) is the third-generation PCR that enables real-time absolute quantification without reference materials. Recently, global diagnosis companies have developed new dPCR equipment. In line with the development, the Lab On An Array (LOAA) dPCR analyzer (Optolane) was launched last year. The LOAA dPCR is a semiconductor chip-based separation PCR type equipment. The LOAA dPCR includes Micro Electro Mechanical System that can be injected by partitioning the target gene into 56 to 20,000 wells. The amount of target gene per wells is digitized to 0 or 1 as the number of well gradually increases to 20,000 wells because its principle follows Poisson distribution, which allows the LOAA dPCR to perform precise absolute quantification. LOAA determined region of interest first prior to dPCR operation. To exclude invalid wells for the quantification, the LOAA dPCR has applied various filtering methods using brightness, slope, baseline, and noise filters. As the coronavirus disease 2019 has now spread around the world, needs for diagnostic equipment of point of care testing (POCT) are increasing. The LOAA dPCR is expected to be suitable for POCT diagnosis due to its compact size and high accuracy. Here, we describe the quantitative principle of the LOAA dPCR and suggest that it can be applied to various fields.

11.
Methods ; 201: 5-14, 2022 05.
Article in English | MEDLINE | ID: covidwho-1373305

ABSTRACT

Coronavirus disease 2019 (COVID-19) is an infectious, acute respiratory disease caused mainly by person-to-person transmission of the coronavirus SARS-CoV-2. Its emergence has caused a world-wide acute health crisis, intensified by the challenge of reliably identifying individuals likely to transmit the disease. Diagnosis is hampered by the many unknowns surrounding this disease, including those relating to infectious viral burden. This uncertainty is exacerbated by disagreement surrounding the clinical relevance of molecular testing using reverse transcription quantitative PCR (RT-qPCR) for the presence of viral RNA, most often based on the reporting of quantification cycles (Cq), which is also termed the cycle threshold (Ct) or crossing point (Cp). Despite it being common knowledge that Cqs are relative values varying according to a wide range of different parameters, there have been efforts to use them as though they were absolute units, with Cqs below an arbitrarily determined value, deemed to signify a positive result and those above, a negative one. Our results investigated the effects of a range of common variables on Cq values. These data include a detailed analysis of the effect of different carrier molecules on RNA extraction. The impact of sample matrix of buccal swabs and saliva on RNA extraction efficiency was demonstrated in RT-qPCR and the impact of potentially inhibiting compounds in urine along with bile salts were investigated in RT-digital PCR (RT-dPCR). The latter studies were performed such that the impact on the RT step could be separated from the PCR step. In this way, the RT was shown to be more susceptible to inhibitors than the PCR. Together, these studies demonstrate that the consequent variability of test results makes subjective Cq cut-off values unsuitable for the identification of infectious individuals. We also discuss the importance of using reliable control materials for accurate quantification and highlight the substantial role played by dPCR as a method for their development.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , RNA, Viral/analysis , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcription , SARS-CoV-2/genetics , Sensitivity and Specificity
12.
Viruses ; 13(6)2021 05 28.
Article in English | MEDLINE | ID: covidwho-1256666

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in Wuhan, China, in late 2019 and is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) represents the gold standard for diagnostic assays even if it cannot precisely quantify viral RNA copies. Thus, we decided to compare qRT-PCR with digital polymerase chain reaction (dPCR), which is able to give an accurate number of RNA copies that can be found in a specimen. However, the aforementioned methods are not capable to discriminate if the detected RNA is infectious or not. For this purpose, it is necessary to perform an endpoint titration on cell cultures, which is largely used in the research field and provides a tissue culture infecting dose per mL (TCID50/mL) value. Both research and diagnostics call for a model that allows the comparison between the results obtained employing different analytical methods. The aim of this study is to define a comparison among two qRT-PCR protocols (one with preliminary RNA extraction and purification and an extraction-free qRT-PCR), a dPCR and a titration on cell cultures. The resulting correlations yield a faithful estimation of the total number of RNA copies and of the infectious viral burden from a Ct value obtained with diagnostic routine tests. All these estimations take into consideration methodological errors linked to the qRT-PCR, dPCR and titration assays.


Subject(s)
COVID-19/therapy , COVID-19/virology , Polymerase Chain Reaction/methods , RNA, Viral/analysis , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/isolation & purification , Viral Load/methods , Animals , Cells, Cultured , Chlorocebus aethiops , Digital Technology/methods , Humans , SARS-CoV-2/genetics , Vero Cells , Virus Cultivation
13.
Sci Total Environ ; 789: 147976, 2021 Oct 01.
Article in English | MEDLINE | ID: covidwho-1246178

ABSTRACT

Coronavirus disease 2019 (COVID-19) is caused by the SARS-CoV-2 virus and has been affecting the world since the end of 2019. The disease led to significant mortality and morbidity in Turkey, since the first case was reported on March 11th, 2020. Studies suggest a positive association between air pollution and SARS-CoV-2 infection. The aim of the present study was to investigate the role of ambient particulate matters (PM), as potential carriers for SARS-CoV-2. Ambient PM samples in various size ranges were collected from 13 sites including urban and urban-background locations and hospital gardens in 10 cities across Turkey between 13th of May and 14th of June 2020 to investigate the possible presence of SARS-CoV-2 RNA on ambient PM. A total of 203 daily samples (TSP, n = 80; PM2.5, n = 33; PM2.5-10, n = 23; PM10µm, n = 19; and 6 size segregated PM, n = 48) were collected using various samplers. The N1 gene and RdRP gene expressions were analyzed for the presence of SARS-CoV-2, as suggested by the Centers for Disease Control and Prevention (CDC). According to real time (RT)-PCR and three-dimensional (3D) digital (d) PCR analysis, dual RdRP and N1 gene positivity were detected in 20 (9.8%) samples. Ambient PM-bound SARS-CoV-2 was analyzed quantitatively and the air concentrations of the virus ranged from 0.1 copies/m3 to 23 copies/m3. The highest percentages of virus detection on PM samples were from hospital gardens in Tekirdag, Zonguldak, and Istanbul, especially in PM2.5 mode. Findings of this study have suggested that SARS-CoV-2 may be transported by ambient particles, especially at sites close to the infection hot-spots. However, whether this has an impact on the spread of the virus infection remains to be determined.


Subject(s)
Air Pollutants , COVID-19 , Air Pollutants/analysis , Cities , Humans , Particulate Matter/analysis , RNA, Viral , SARS-CoV-2 , Turkey/epidemiology
14.
J Virol Methods ; 295: 114185, 2021 09.
Article in English | MEDLINE | ID: covidwho-1243068

ABSTRACT

OBJECTIVE: Viral nucleic acid detection by real-time reverse transcription polymerase chain reaction (qPCR) is the current standard method for diagnosis of SARS-CoV-2 infection. However, due to low viral load in some COVID-19 patients, false negative results from this method have been repeatedly reported. METHOD: In this study, we compared the sensitivity and specificity of digital PCR (dPCR) in simulated samples and clinical samples with qPCR assay through a series of vigorous tests. RESULTS: The results showed that dPCR was more sensitive than qPCR especially for samples with low viral load (≤3 copies). In addition, dPCR had similar specificity as qPCR and could effectively distinguish other human coronaviruses and influenza virus from SARS-CoV-2. More importantly, dPCR was more sensitive than qPCR in detecting the virus in the "negative" samples from recurrent COVID-19 patients. CONCLUSIONS: In summary, dPCR could serve as a powerful complement to the current qPCR method for SARS-CoV-2 detection, especially for the samples with extremely low viral load, such as recurrent COVID-19 patients.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/isolation & purification , Viral Load , COVID-19/virology , Humans , RNA, Viral/genetics , Recurrence , SARS-CoV-2/genetics , Sensitivity and Specificity
15.
Microchem J ; 167: 106305, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1198979

ABSTRACT

Since December 2019, we have been in the battlefield with a new threat to the humanity known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this review, we describe the four main methods used for diagnosis, screening and/or surveillance of SARS-CoV-2: Real-time reverse transcription polymerase chain reaction (RT-PCR); chest computed tomography (CT); and different complementary alternatives developed in order to obtain rapid results, antigen and antibody detection. All of them compare the highlighting advantages and disadvantages from an analytical point of view. The gold standard method in terms of sensitivity and specificity is the RT-PCR. The different modifications propose to make it more rapid and applicable at point of care (POC) are also presented and discussed. CT images are limited to central hospitals. However, being combined with RT-PCR is the most robust and accurate way to confirm COVID-19 infection. Antibody tests, although unable to provide reliable results on the status of the infection, are suitable for carrying out maximum screening of the population in order to know the immune capacity. More recently, antigen tests, less sensitive than RT-PCR, have been authorized to determine in a quicker way whether the patient is infected at the time of analysis and without the need of specific instruments.

16.
Talanta ; 228: 122227, 2021 Jun 01.
Article in English | MEDLINE | ID: covidwho-1100758

ABSTRACT

Nucleic acid detection and quantification have been known to be important at various fields, from genetically modified organisms and gene expression to virus detection. For DNA molecules, digital PCR has been developed as an absolute quantification method which is not dependent on external calibrators. While when it comes to RNA molecules, reverse transcription (RT) step must be taken before PCR amplification to obtain cDNA. With different kinds of reverse transcriptase (RTase) and RT reaction conditions being used in laboratory assays, the efficiency of RT process differs a lot which led variety in quantification results of RNA molecules. In this study, we developed HPLC method combined with enzymatic digestion of RNA to nucleotides for quantification of RNA without RT process. This method was metrologically traceable to four nuceloside monophosphate (NMP) Certification Reference Materials of National Institute of Metrology, China (NIMC) for insurance of accuracy. The established method was used to evaluate the reverse transcription digital polymerase chain reaction (RT-dPCR) of three target genes of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) RNA, including open reading frame 1ab (ORF1ab), nucleocapsid protein (N) and envelope protein (E) gene. Three available RT kits had been evaluated and disparities were observed for the RT efficiency varied from 9% to 182%. It is thus demonstrated that HPLC combined with enzymatic digestion could be a useful method to quantify RNA molecules and evaluate RT efficiency. It is suggested that RT process should be optimized and identified in RNA quantification assays.


Subject(s)
Chromatography, High Pressure Liquid/methods , Phosphodiesterase I/chemistry , Proteolysis , RNA/analysis , Reverse Transcriptase Polymerase Chain Reaction/methods , Animals , Chromatography, High Pressure Liquid/standards , Coronavirus Nucleocapsid Proteins/genetics , Crotalinae , Middle East Respiratory Syndrome Coronavirus/chemistry , Middle East Respiratory Syndrome Coronavirus/genetics , Purine Nucleotides/standards , Pyrimidine Nucleotides/standards , RNA/chemistry , Reference Standards
17.
Chem Eng J ; 405: 126893, 2021 Feb 01.
Article in English | MEDLINE | ID: covidwho-952653

ABSTRACT

The unprecedented global spread of the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2 is depicting the distressing pandemic consequence on human health, economy as well as ecosystem services. So far novel coronavirus (CoV) outbreaks were associated with SARS-CoV-2 (2019), middle east respiratory syndrome coronavirus (MERS-CoV, 2012), and SARS-CoV-1 (2003) events. CoV relates to the enveloped family of Betacoronavirus (ßCoV) with positive-sense single-stranded RNA (+ssRNA). Knowing well the persistence, transmission, and spread of SARS-CoV-2 through proximity, the faecal-oral route is now emerging as a major environmental concern to community transmission. The replication and persistence of CoV in the gastrointestinal (GI) tract and shedding through stools is indicating a potential transmission route to the environment settings. Despite of the evidence, based on fewer reports on SARS-CoV-2 occurrence and persistence in wastewater/sewage/water, the transmission of the infective virus to the community is yet to be established. In this realm, this communication attempted to review the possible influx route of the enteric enveloped viral transmission in the environmental settings with reference to its occurrence, persistence, detection, and inactivation based on the published literature so far. The possibilities of airborne transmission through enteric virus-laden aerosols, environmental factors that may influence the viral transmission, and disinfection methods (conventional and emerging) as well as the inactivation mechanism with reference to the enveloped virus were reviewed. The need for wastewater epidemiology (WBE) studies for surveillance as well as for early warning signal was elaborated. This communication will provide a basis to understand the SARS-CoV-2 as well as other viruses in the context of the environmental engineering perspective to design effective strategies to counter the enteric virus transmission and also serves as a working paper for researchers, policy makers and regulators.

18.
Biotechniques ; 70(1): 7-20, 2021 01.
Article in English | MEDLINE | ID: covidwho-940124

ABSTRACT

A real-time dPCR system was developed to improve the sensitivity, specificity and quantification accuracy of end point dPCR. We compared three technologies - real-time qPCR, end point dPCR and real-time dPCR - in the context of SARS-CoV-2. Some improvement in limit of detection was obtained with end point dPCR compared with real-time qPCR, and the limit of detection was further improved with the newly developed real-time dPCR technology through removal of false-positive signals. Real-time dPCR showed increased linear dynamic range compared with end point dPCR based on quantitation from amplification curves. Real-time dPCR can improve the performance of TaqMan assays beyond real-time qPCR and end point dPCR with better sensitivity and specificity, absolute quantification and a wider linear range of detection.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , Real-Time Polymerase Chain Reaction , SARS-CoV-2/isolation & purification , COVID-19/diagnosis , COVID-19 Nucleic Acid Testing/statistics & numerical data , Endpoint Determination , Humans
19.
Talanta ; 224: 121726, 2021 Mar 01.
Article in English | MEDLINE | ID: covidwho-894232

ABSTRACT

The outbreak of COVID-19 caused by a novel Coronavirus (termed SARS-CoV-2) has spread to over 210 countries around the world. Currently, reverse transcription quantitative qPCR (RT-qPCR) is used as the gold standard for diagnosis of SARS-CoV-2. However, the sensitivity of RT-qPCR assays of pharyngeal swab samples are reported to vary from 30% to 60%. More accurate and sensitive methods are urgently needed to support the quality assurance of the RT-qPCR or as an alternative diagnostic approach. A reverse transcription digital PCR (RT-dPCR) method was established and evaluated. To explore the feasibility of RT-dPCR in diagnostic of SARS-CoV-2, a total of 196 clinical pharyngeal swab samples from 103 suspected patients, 77 close contacts and 16 supposed convalescents were analyzed by RT-qPCR and then measured by the proposed RT-dPCR. For the 103 fever suspected patients, 19 (19/25) negative and 42 (42/49) equivocal tested by RT-qPCR were positive according to RT-dPCR. The sensitivity of SARS-CoV-2 detection was significantly improved from 28.2% by RT-qPCR to 87.4% by RT-dPCR. For 29 close contacts (confirmed by additional sample and clinical follow up), 16 (16/17) equivocal and 1 negative tested by RT-qPCR were positive according to RT-dPCR, which is implying that the RT-qPCR is missing a lot of asymptomatic patients. The overall sensitivity, specificity and diagnostic accuracy of RT-dPCR were 91%, 100% and 93%, respectively. RT-dPCR is highly accurate method and suitable for detection of pharyngeal swab samples from COVID-19 suspected patients and patients under isolation and observation who may not be exhibiting clinical symptoms.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , RNA, Viral/analysis , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Coronavirus Envelope Proteins/genetics , Coronavirus Nucleocapsid Proteins/genetics , Humans , Pharynx/virology , Phosphoproteins/genetics , Polyproteins/genetics , Viral Proteins/genetics
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