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1.
J Clin Microbiol ; 59(7): e0007521, 2021 06 18.
Article in English | MEDLINE | ID: covidwho-1276884

ABSTRACT

Diagnostic assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential for patient management, infection prevention, and the public health response for coronavirus disease 2019 (COVID-19). The efficacy and reliability of these assays are of paramount importance in both tracking and controlling the spread of the virus. Real-time reverse transcription-PCR (RT-PCR) assays rely on a fixed genetic sequence for primer and probe binding. Mutations can potentially alter the accuracy of these assays and lead to unpredictable analytical performance characteristics and false-negative results. Here, we identify a G-to-U transversion (nucleotide 26372) in the SARS-CoV-2 E gene in three specimens with reduced viral detection efficiency using a widely available commercial assay. Further analysis of the public GISAID repository led to the identification of 18 additional genomes with this mutation, which reflect five independent mutational events. This work supports the use of dual-target assays to reduce the number of false-negative PCR results.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction , Reverse Transcription , Sensitivity and Specificity
2.
Protein Expr Purif ; 186: 105908, 2021 10.
Article in English | MEDLINE | ID: covidwho-1243167

ABSTRACT

The current standard for the diagnosis of COVID-19 is the nucleic acid test of SARS-CoV-2 RNA, however, virus antibody detection has the advantages of convenient sample collection, high throughout, and low cost. When combining detection with nucleic acid detection, antibody detection can effectively compensate for nucleic acid detection. Virus infection always induce high antibody titer against SARS-CoV-2 nucleocapsid protein (N protein), which can be used to detect COVID-19 at both infected and convalescent patients. In this study we reported the expression and purification of N protein in E.coli from inclusion bodies by a combination of two cation exchange chromatography, and the yield of N protein was around 50 mg/L fermentation broth with more than 90% purity. A corresponding colloidal gold detection kit prepared with our purified N protein was used to verify the efficiency and accuracy our N protein in antibody detection method. Of the 58 COVID-19 PCR positive patients' inactivated serum samples, 40 samples were IgM positive (69.0%), and 42 samples were IgG positive (72.4%), and all 95 COVID-19 negative patients' inactivated serum samples were both IgM and IgG negative. Our results indicates that the refolded soluble N protein could be used for the preliminary detection of IgG and IgM antibodies against SARS-CoV- 2.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/methods , Coronavirus Nucleocapsid Proteins/genetics , Coronavirus Nucleocapsid Proteins/immunology , SARS-CoV-2/immunology , Coronavirus Nucleocapsid Proteins/biosynthesis , Coronavirus Nucleocapsid Proteins/isolation & purification , Escherichia coli/genetics , Humans , Immunoglobulin G/blood , Immunoglobulin M/blood , Inclusion Bodies , Phosphoproteins/biosynthesis , Phosphoproteins/genetics , Phosphoproteins/immunology , Phosphoproteins/isolation & purification , Recombinant Proteins/biosynthesis , Recombinant Proteins/immunology , Recombinant Proteins/isolation & purification , SARS-CoV-2/genetics , Sensitivity and Specificity
3.
J Clin Microbiol ; 59(7): e0007521, 2021 06 18.
Article in English | MEDLINE | ID: covidwho-1203933

ABSTRACT

Diagnostic assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential for patient management, infection prevention, and the public health response for coronavirus disease 2019 (COVID-19). The efficacy and reliability of these assays are of paramount importance in both tracking and controlling the spread of the virus. Real-time reverse transcription-PCR (RT-PCR) assays rely on a fixed genetic sequence for primer and probe binding. Mutations can potentially alter the accuracy of these assays and lead to unpredictable analytical performance characteristics and false-negative results. Here, we identify a G-to-U transversion (nucleotide 26372) in the SARS-CoV-2 E gene in three specimens with reduced viral detection efficiency using a widely available commercial assay. Further analysis of the public GISAID repository led to the identification of 18 additional genomes with this mutation, which reflect five independent mutational events. This work supports the use of dual-target assays to reduce the number of false-negative PCR results.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction , Reverse Transcription , Sensitivity and Specificity
4.
Sensors (Basel) ; 21(5)2021 Mar 05.
Article in English | MEDLINE | ID: covidwho-1128798

ABSTRACT

A method for the rapid detection of coronaviruses is presented on the example of the transmissible gastroenteritis virus (TGEV) directly in aqueous solutions with different conductivity. An acoustic sensor based on a slot wave in an acoustic delay line was used for the research. The addition of anti-TGEV antibodies (Abs) diluted in an aqueous solution led to a change in the depth and frequency of resonant peaks on the frequency dependence of the insertion loss of the sensor. The difference in the output parameters of the sensor before and after the biological interaction of the TGE virus in solutions with the specific antibodies allows drawing a conclusion about the presence/absence of the studied viruses in the analyzed solution. The possibility for virus detection in aqueous solutions with the conductivity of 1.9-900 µs/cm, as well as in the presence of the foreign viral particles, has been demonstrated. The analysis time did not exceed 10 min.


Subject(s)
Coronavirus , Transmissible gastroenteritis virus , Acoustics , Antibodies , Electric Conductivity
5.
Life Sci ; 273: 119117, 2021 May 15.
Article in English | MEDLINE | ID: covidwho-1065431

ABSTRACT

Biosensors are important devices in clinical diagnostics, food processing, and environmental monitoring for detecting various analytes, especially viruses. These biosensors provide rapid and effective instruments for qualitative and quantitative detection of infectious diseases in real-time. Here, we report the development of biosensors based on various techniques. Additionally, we will explain the mechanisms, advantages, and disadvantages of the most common biosensors that are currently used for viral detection, which could be optical (e.g., surface-enhanced Raman scattering (SERS), Surface plasmon resonance (SPR)) and electrochemical biosensors. Based on that, this review recommends methods for efficient, simple, low-cost, and rapid detection of SARS-CoV-2 (the causative agent of COVID-19) that employ the two types of biosensors depending on attaching hemoglobin ß-chain and binding of specific antibodies with SARS-CoV-2 antigens, respectively.


Subject(s)
Biosensing Techniques/methods , COVID-19 Testing/methods , COVID-19/diagnosis , Biosensing Techniques/instrumentation , COVID-19/virology , COVID-19 Testing/instrumentation , Clinical Laboratory Techniques/instrumentation , Clinical Laboratory Techniques/methods , Equipment Design , Humans , SARS-CoV-2/isolation & purification
6.
Biosens Bioelectron ; 178: 113004, 2021 Apr 15.
Article in English | MEDLINE | ID: covidwho-1032329

ABSTRACT

The outbreak of life-threatening pandemic like COVID-19 necessitated the development of novel, rapid and cost-effective techniques that facilitate detection of viruses like SARS-CoV-2. The presently popular approach of a collection of samples using the nasopharyngeal swab method and subsequent detection of RNA using the real-time polymerase chain reaction suffers from false-positive results and a longer diagnostic time scale. Alternatively, various optical techniques namely optical sensing, spectroscopy, and imaging shows a great promise in virus detection. Herein, a comprehensive review of the various photonics technologies employed for virus detection, particularly the SARS-CoV family, is discussed. The state-of-art research activities in utilizing the photonics tools such as near-infrared spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, fluorescence-based techniques, super-resolution microscopy, surface plasmon resonance-based detection, for virus detection accounted extensively with an emphasis on coronavirus detection. Further, an account of emerging photonics technologies of SARS-CoV-2 detection and future possibilities is also explained. The progress in the field of optical techniques for virus detection unambiguously show a great promise in the development of rapid photonics-based devices for COVID-19 detection.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/virology , SARS-CoV-2/isolation & purification , Biosensing Techniques/methods , COVID-19 Testing/trends , Humans , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , Optical Phenomena , Pandemics , SARS-CoV-2/genetics , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, Raman , Surface Plasmon Resonance
7.
Sensors (Basel) ; 20(23)2020 Dec 04.
Article in English | MEDLINE | ID: covidwho-965897

ABSTRACT

Biosensors are measurement devices that can sense several biomolecules, and are widely used for the detection of relevant clinical pathogens such as bacteria and viruses, showing outstanding results. Because of the latent existing risk of facing another pandemic like the one we are living through due to COVID-19, researchers are constantly looking forward to developing new technologies for diagnosis and treatment of infections caused by different bacteria and viruses. Regarding that, nanotechnology has improved biosensors' design and performance through the development of materials and nanoparticles that enhance their affinity, selectivity, and efficacy in detecting these pathogens, such as employing nanoparticles, graphene quantum dots, and electrospun nanofibers. Therefore, this work aims to present a comprehensive review that exposes how biosensors work in terms of bacterial and viral detection, and the nanotechnological features that are contributing to achieving a faster yet still efficient COVID-19 diagnosis at the point-of-care.


Subject(s)
Bacteria/genetics , Biosensing Techniques/methods , Viruses/genetics , Animals , COVID-19/diagnosis , COVID-19/virology , Humans , Nanotechnology/methods , Pandemics/prevention & control , SARS-CoV-2/genetics
8.
Chembiochem ; 22(7): 1176-1189, 2021 04 06.
Article in English | MEDLINE | ID: covidwho-967966

ABSTRACT

The recent pandemic of the novel coronavirus disease 2019 (COVID-19) has caused huge worldwide disruption due to the lack of available testing locations and equipment. The use of optical techniques for viral detection has flourished in the past 15 years, providing more reliable, inexpensive, and accurate detection methods. In the current minireview, optical phenomena including fluorescence, surface plasmons, surface-enhanced Raman scattering (SERS), and colorimetry are discussed in the context of detecting virus pathogens. The sensitivity of a viral detection method can be dramatically improved by using materials that exhibit surface plasmons or SERS, but often this requires advanced instrumentation for detection. Although fluorescence and colorimetry lack high sensitivity, they show promise as point-of-care diagnostics because of their relatively less complicated instrumentation, ease of use, lower costs, and the fact that they do not require nucleic acid amplification. The advantages and disadvantages of each optical detection method are presented, and prospects for applying optical biosensors in COVID-19 detection are discussed.


Subject(s)
Biosensing Techniques/methods , COVID-19/diagnosis , Chemistry Techniques, Analytical/methods , SARS-CoV-2/isolation & purification , Animals , Humans
9.
J Proteome Res ; 19(11): 4380-4388, 2020 11 06.
Article in English | MEDLINE | ID: covidwho-889125

ABSTRACT

One of the most widely used methods to detect an acute viral infection in clinical specimens is diagnostic real-time polymerase chain reaction. However, because of the COVID-19 pandemic, mass-spectrometry-based proteomics is currently being discussed as a potential diagnostic method for viral infections. Because proteomics is not yet applied in routine virus diagnostics, here we discuss its potential to detect viral infections. Apart from theoretical considerations, the current status and technical limitations are considered. Finally, the challenges that have to be overcome to establish proteomics in routine virus diagnostics are highlighted.


Subject(s)
Coronavirus Infections/diagnosis , Mass Spectrometry/methods , Pneumonia, Viral/diagnosis , Proteomics/methods , Virology/methods , Betacoronavirus/chemistry , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques , Coronavirus Infections/virology , Humans , Pandemics , Pneumonia, Viral/virology , Real-Time Polymerase Chain Reaction , SARS-CoV-2 , Virus Diseases/diagnosis , Virus Diseases/virology
10.
Vet Clin North Am Food Anim Pract ; 36(2): 321-332, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-825203

ABSTRACT

Advances in viral detection in bovine respiratory disease (BRD) have resulted from advances in viral sequencing of respiratory tract samples. New viruses detected include influenza D virus, bovine coronavirus, bovine rhinitis A, bovine rhinitis B virus, and others. Serosurveys demonstrate widespread presence of some of these viruses in North American cattle. These viruses sometimes cause disease after animal challenge, and some have been found in BRD cases more frequently than in healthy cattle. Continued work is needed to develop reagents for identification of new viruses, to confirm their pathogenicity, and to determine whether vaccines have a place in their control.


Subject(s)
Cattle Diseases/virology , Coronavirus, Bovine/genetics , Diarrhea Viruses, Bovine Viral/genetics , Genetic Testing/veterinary , Herpesvirus 1, Bovine/genetics , Respiratory Tract Diseases/veterinary , Animals , Cattle , Coronavirus, Bovine/isolation & purification , Diarrhea Viruses, Bovine Viral/isolation & purification , Genomics/methods , Herpesvirus 1, Bovine/isolation & purification , Respiratory Tract Diseases/virology
12.
Virus Res ; 288: 198129, 2020 10 15.
Article in English | MEDLINE | ID: covidwho-719033

ABSTRACT

The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.


Subject(s)
Betacoronavirus/genetics , CRISPR-Cas Systems , Clinical Laboratory Techniques/methods , Colorimetry/methods , Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Pneumonia, Viral/diagnosis , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques/instrumentation , Colorimetry/instrumentation , Coronavirus Infections/virology , Endodeoxyribonucleases/chemistry , Humans , Molecular Diagnostic Techniques/instrumentation , Nucleic Acid Amplification Techniques/instrumentation , Pandemics , Pneumonia, Viral/virology , Point-of-Care Systems , Rheology , SARS-CoV-2 , Sensitivity and Specificity
13.
ACS Sens ; 5(9): 2663-2678, 2020 09 25.
Article in English | MEDLINE | ID: covidwho-714278

ABSTRACT

The global sanitary crisis caused by the emergence of the respiratory virus SARS-CoV-2 and the COVID-19 outbreak has revealed the urgent need for rapid, accurate, and affordable diagnostic tests to broadly and massively monitor the population in order to properly manage and control the spread of the pandemic. Current diagnostic techniques essentially rely on polymerase chain reaction (PCR) tests, which provide the required sensitivity and specificity. However, its relatively long time-to-result, including sample transport to a specialized laboratory, delays massive detection. Rapid lateral flow tests (both antigen and serological tests) are a remarkable alternative for rapid point-of-care diagnostics, but they exhibit critical limitations as they do not always achieve the required sensitivity for reliable diagnostics and surveillance. Next-generation diagnostic tools capable of overcoming all the above limitations are in demand, and optical biosensors are an excellent option to surpass such critical issues. Label-free nanophotonic biosensors offer high sensitivity and operational robustness with an enormous potential for integration in compact autonomous devices to be delivered out-of-the-lab at the point-of-care (POC). Taking the current COVID-19 pandemic as a critical case scenario, we provide an overview of the diagnostic techniques for respiratory viruses and analyze how nanophotonic biosensors can contribute to improving such diagnostics. We review the ongoing published work using this biosensor technology for intact virus detection, nucleic acid detection or serological tests, and the key factors for bringing nanophotonic POC biosensors to accurate and effective COVID-19 diagnosis on the short term.


Subject(s)
Betacoronavirus , Coronavirus Infections/diagnosis , Nanostructures/chemistry , Pneumonia, Viral/diagnosis , Surface Plasmon Resonance/methods , Antigens, Viral/analysis , Betacoronavirus/chemistry , Betacoronavirus/isolation & purification , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques , Genome, Viral , Humans , Immunoassay/methods , Nanostructures/radiation effects , Pandemics , SARS-CoV-2 , Serologic Tests/methods
14.
PLoS One ; 15(4): e0230802, 2020.
Article in English | MEDLINE | ID: covidwho-46041

ABSTRACT

The recent emergence of bat-borne zoonotic viruses warrants vigilant surveillance in their natural hosts. Of particular concern is the family of coronaviruses, which includes the causative agents of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and most recently, Coronavirus Disease 2019 (COVID-19), an epidemic of acute respiratory illness originating from Wuhan, China in December 2019. Viral detection, discovery, and surveillance activities were undertaken in Myanmar to identify viruses in animals at high risk contact interfaces with people. Free-ranging bats were captured, and rectal and oral swabs and guano samples collected for coronaviral screening using broadly reactive consensus conventional polymerase chain reaction. Sequences from positives were compared to known coronaviruses. Three novel alphacoronaviruses, three novel betacoronaviruses, and one known alphacoronavirus previously identified in other southeast Asian countries were detected for the first time in bats in Myanmar. Ongoing land use change remains a prominent driver of zoonotic disease emergence in Myanmar, bringing humans into ever closer contact with wildlife, and justifying continued surveillance and vigilance at broad scales.


Subject(s)
Chiroptera/virology , Coronavirus/classification , Coronavirus/isolation & purification , Anal Canal/virology , Animals , Coronavirus/genetics , Feces/virology , Mouth/virology , Myanmar , Population Surveillance
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