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Jeon JH, Harano T, Rodman JCS, Sheth M, Wightman SC, Atay SM, Kim AW. Early outcomes of lung transplantation with lung allografts from coronavirus disease 2019 (COVID-19)-positive donors. J Thorac Cardiovasc Surg 2024; 167:1955-1964.e3. [PMID: 37625616 DOI: 10.1016/j.jtcvs.2023.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/24/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023]
Abstract
OBJECTIVE Coronavirus disease 2019 (COVID-19) can be detected for extended periods of time with nucleic acid amplification test even after transmissibility becomes negligible. Lung allografts from COVID-19-positive donors have been used for transplantation in highly selected cases. This study aimed to clarify the early outcomes of lung transplantation with COVID-19-positive donors. METHODS The Organ Procurement and Transplantation Network/United Network for Organ Sharing database between April 2020 and June 2022 was retrospectively analyzed. RESULTS In the study period, 1297 COVID-19-positive donors were identified and the lungs were transplanted from 47 donors (3.6%). Of 47 donors, 44 donors were positive for COVID-19 NAT with nasopharyngeal swabs and the other 3 were positive with bronchoalveolar lavage. The COVID-19-positive lung donors were younger than the COVID-19-negative donors (28.4 ± 11.6 years vs 35.4 ± 13.6 years, P < .001). Recipients of the COVID-19-positive lungs (n = 47) were more likely have a greater lung allocation score (57.1 ± 22.9 vs 50.5 ± 19.7, P = .057) than recipients of COVID-19-negative lungs (n = 5501). The posttransplant length of hospital stay (39.8 ± 43.6 days vs 30.6 ± 34.5 days, P = .181), need for extracorporeal membrane oxygenation support at 72 hours after transplantation (2.6% [1/38] vs 10.4% [541/5184], P = .18), and 1-year overall survival rate (85.6% vs 87.1%, P = .63) were comparable between the 2 groups. CONCLUSIONS Carefully selected lung allografts from COVID-19-positive donors had comparable early posttransplant outcomes to lung allografts from COVID-19-negative donors.
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Affiliation(s)
- Jae Hyun Jeon
- Division of Thoracic Surgery, Department of Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, Calif; Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Takashi Harano
- Division of Thoracic Surgery, Department of Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, Calif.
| | - John C S Rodman
- Biostatistics, Epidemiology, and Research Design, Southern California Clinical and Translational Science Institute, University of Southern California, Los Angeles, Calif
| | - Megha Sheth
- Keck School of Medicine of the University of Southern California, Los Angeles, Calif
| | - Sean C Wightman
- Division of Thoracic Surgery, Department of Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, Calif
| | - Scott M Atay
- Division of Thoracic Surgery, Department of Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, Calif
| | - Anthony W Kim
- Division of Thoracic Surgery, Department of Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, Calif
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2
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Song K, Xue W, Li X, Chang Y, Liu M. Self-Assembly of Single-Virus SERS Hotspots for Highly Sensitive In Situ Detection of SARS-CoV-2 on Solid Surfaces. Anal Chem 2024; 96:8830-8836. [PMID: 38693713 DOI: 10.1021/acs.analchem.4c01607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Microbial surface transmission has aroused great attention since the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Developing a simple in situ detection method for viruses on solid surfaces is of great significance for timely public health surveillance. Taking advantage of the natural structure of SARS-CoV-2, we reported the assembly of Au@AgNPs on the surface of a single virus by the specific aptamer-spike protein interaction. Multiple hotspots can be created between the neighboring Au@AgNPs for the highly sensitive surface-enhanced Raman scattering (SERS) detection of SARS-CoV-2. Using two different aptamers labeled with Cy3 and Au@AgNPs, in situ SERS detection of pseudotyped SARS-CoV-2 (PSV) on packaging surfaces was achieved within 20 min, with a detection limit of 5.26 TCID50/mL. For the blind testing of 20 PSV-contaminated packaging samples, this SERS aptasensor had a sensitivity of 100% and an accuracy of 100%. This assay has been successfully applied to in situ detection of PSV on the surfaces of different packaging materials, suggesting its potential applicability.
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Affiliation(s)
- Kaiyun Song
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT laboratory, Dalian University of Technology, Dalian 116024, China
| | - Wei Xue
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT laboratory, Dalian University of Technology, Dalian 116024, China
| | - Xiaona Li
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT laboratory, Dalian University of Technology, Dalian 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT laboratory, Dalian University of Technology, Dalian 116024, China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT laboratory, Dalian University of Technology, Dalian 116024, China
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3
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Mo L, Yuan R, Hong Y, Yang C, Lin W. Accelerated diagnosis: a crosslinking catalytic hairpin assembly system for rapid and sensitive SARS-CoV-2 RNA detection. Mikrochim Acta 2024; 191:333. [PMID: 38753167 DOI: 10.1007/s00604-024-06396-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024]
Abstract
The COVID-19 pandemic has underscored the urgent need for rapid and reliable strategies for early detection of SARS-CoV-2. In this study, we propose a DNA nanosphere-based crosslinking catalytic hairpin assembly (CCHA) system for the rapid and sensitive SARS-CoV-2 RNA detection. The CCHA system employs two DNA nanospheres functionalized with catalytic hairpin assembly (CHA) hairpins. The presence of target SARS-CoV-2 RNA initiated the crosslinking of DNA nanospheres via CHA process, leading to the amplification of fluorescence signals. As a result, the speed of SARS-CoV-2 diagnosis was enhanced by significantly increasing the local concentration of the reagents in a crosslinked DNA product, leading to a detection limit of 363 fM within 5 min. The robustness of this system has been validated in complex environments, such as fetal bovine serum and saliva. Hence, the proposed CCHA system offers an efficient and simple approach for rapid detection of SARS-CoV-2 RNA, holding substantial promise for enhancing COVID-19 diagnosis.
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Affiliation(s)
- Liuting Mo
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China
| | - Rongzheng Yuan
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China
| | - Yan Hong
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China
| | - Chan Yang
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China
| | - Weiying Lin
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China.
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4
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Lu Y, Zhang L, Wang J, Bian L, Ding Z, Yang C. Hyperspectral upgrade solution for biomicroscope combined with Transformer network to classify infectious bacteria. JOURNAL OF BIOPHOTONICS 2024; 17:e202300484. [PMID: 38297446 DOI: 10.1002/jbio.202300484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
Infectious diseases caused by bacterial pathogens pose a significant public health threat, emphasizing the need for swift and accurate bacterial species detection methods. Hyperspectral microscopic imaging (HMI) offers nondestructive, rapid, and data-rich advantages, making it a promising tool for microbial detection. In this research, we present a highly compatible and cost-effective approach to extend a standard biomicroscope system into a hyperspectral biomicroscope using a prism-grating-prism configuration. Using this prototype, we generate 600 hyperspectral data cubes for Listeria, Bacillus typhi, Bacillus pestis, and Bacillus anthracis. Additionally, we propose a Transformer-based classification network that achieves a 99.44% accuracy in classifying these infectious pathogens, outperforming traditional methods. Our results suggest that the successful combination of HMI and the optimized Transformer-based classification network highlights the potential for rapid and precise detection of infectious disease pathogens .
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Affiliation(s)
- You Lu
- Engineering Research Center of Semiconductor Power Device Reliability Ministry of Education, Guizhou University, Guiyang, China
| | - Lan Zhang
- Engineering Research Center of Semiconductor Power Device Reliability Ministry of Education, Guizhou University, Guiyang, China
| | - Jihong Wang
- Engineering Research Center of Semiconductor Power Device Reliability Ministry of Education, Guizhou University, Guiyang, China
| | - Lifeng Bian
- Frontier Institute of Chip and System, Fudan University, Shanghai, China
| | - Zhao Ding
- Engineering Research Center of Semiconductor Power Device Reliability Ministry of Education, Guizhou University, Guiyang, China
| | - Chen Yang
- Engineering Research Center of Semiconductor Power Device Reliability Ministry of Education, Guizhou University, Guiyang, China
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5
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Jung J, Sung JS, Bong JH, Kim TH, Kwon S, Bae HE, Kang MJ, Jose J, Lee M, Shin HJ, Pyun JC. One-step immunoassay of SARS-CoV-2 using screened Fv-antibodies and switching peptides. Biosens Bioelectron 2024; 245:115834. [PMID: 37995624 DOI: 10.1016/j.bios.2023.115834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/21/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
The Fv-antibodies were correponded to VH region of immunoglobulin G, which were composed of three complementarity determining regions (CDRs) for the specific binding of antigens. In this work, the Fv-antibodies against SARS-CoV-2 spike protein (SP) were screened from an autodisplayed Fv-antibody library which was expressed on E. coli outer membrane, and the receptor binding domain (RBD) of SP was used as a screening probe. The screened target clones were analyzed to have quantitative binding properties to the RBD, and the Fv-antibodies from the screened target clones were expressed as soluble proteins. The binding affinity (KD) of expressed Fv-antibodies to the RBD was estimated to be 70-85 nM using SPR biosensor. The specific binding properties of Fv-antibodies were analyzed for pseudo-virus particles with SARS-CoV-2 SP on the Lenti-virus envelope, such as wild type (Wuhan-1) and variants (Delta, Omicron BA.2, Omicron BA.4/5) using a SPR biosensor. The detection of real SARS-CoV-2 (Wild type, Wuhan-1) based on a SPR biosensor was also presented using the Fv-antibodies with the binding constant (KD) of cycle threshold value (Ct) = 33.8-32.9 (2.19-4.08 copies/μL) and LOD of 0.67-0.83 copies/μL (Ct = 35.5-35.2). Finally, one-step immunoassay based on switching peptide was demonstrated for the detection of the real SARS-CoV-2 (Wuhan-1) without any washing step. The binding constant (KD) was estimated to be Ct = 35.2-33.9 (0.83-2.04 copies/μL), and LOD was estimated to be 0.14-0.47 copies/μL (Ct = 37.8-36.0). Considering the LOD of the conventional RT-PCR (Ct = 35), the LOD of the one-step immunoassay based on the switching peptide was determined to be feasible for the medical diagnosis of COVID-19.
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Affiliation(s)
- Jaeyong Jung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Jeong Soo Sung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Ji-Hong Bong
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Tae-Hun Kim
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Soonil Kwon
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Hyung Eun Bae
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Min-Jung Kang
- Korea Institute of Science and Technology (KIST), Seoul, 02456, South Korea
| | - Joachim Jose
- Institute of Pharmaceutical and Medical Chemistry, Westphalian Wilhelms-University Münster, Münster 48149, Germany
| | - Misu Lee
- Institute for New Drug Development, College of Life Science and Bioengineering, Incheon National University, Incheon, 22012, South Korea
| | - Hyun-Jin Shin
- College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, South Korea
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.
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6
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Dolan AM, FitzGerald S. When the answer is a maybe: a retrospective review of indeterminate SARS-CoV-2 results and their associations. J Hosp Infect 2024; 143:115-122. [PMID: 37451406 DOI: 10.1016/j.jhin.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/26/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using reverse transcriptase polymerase chain reaction (RT-PCR) may generate indeterminate results (with a cycle threshold ≥30), requiring further investigation to determine the clinical significance. Patient variables which could predict a definitive result ('Detected'/'Not detected') post indeterminate result would aid in optimization of bed management and utilization of limited resources. A retrospective observational study of indeterminate SARS-CoV-2 results in an Irish tertiary hospital from March 2020 to March 2022 was performed to determine whether demographics, comorbidities and immunosuppression were associated with a definitive result upon subsequent investigation. Data was obtained from patient and laboratory records. Analysis of association was explored using Fisher's exact test, and predictability was tested using logistic regression. Of 411 patients with an initial indeterminate test, investigation showed that 299 (72.2%) patients had a subsequent definitive result; 29 were Detected and 270 were Not detected. In the Detected group, a prior diagnosis of COVID-19 was associated with a reduced risk of becoming Detected (crude odds ratio (COR) = 0.10, 95% CI 0.03-0.35). In the Not detected group, vaccinated patients were less likely to have a Not detected result on subsequent testing (adjusted odds ratio (AOR) = 0.57, 95% CI 0.34-0.94). Patients with previous COVID-19 infection were less likely to have a Detected result and vaccinated patients were less likely to have a Not detected result upon investigation of an indeterminate result. This study emphasizes the need for a good clinical and medical history in the management of SARS-CoV-2.
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Affiliation(s)
- A M Dolan
- Department of Microbiology, St Vincent's University Hospital, Dublin, Republic of Ireland.
| | - S FitzGerald
- Department of Microbiology, St Vincent's University Hospital, Dublin, Republic of Ireland
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7
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Salazar-Ardiles C, Asserella-Rebollo L, Cornejo C, Arias D, Vasquez-Muñoz M, Toledo C, Andrade DC. Molecular diagnostic approaches for SARS-CoV-2 detection and pathophysiological consequences. Mol Biol Rep 2023; 50:10367-10382. [PMID: 37817022 DOI: 10.1007/s11033-023-08844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023]
Abstract
SARS-CoV-2, a novel coronavirus within the Coronaviridae family, is the causative agent behind the respiratory ailment referred to as COVID-19. Operating on a global scale, COVID-19 has led to a substantial number of fatalities, exerting profound effects on both public health and the global economy. The most frequently reported symptoms encompass fever, cough, muscle or body aches, loss of taste or smell, headaches, and fatigue. Furthermore, a subset of individuals may manifest more severe symptoms, including those consistent with viral pneumonitis, which can be so profound as to result in fatalities. Consequently, this situation has spurred the rapid advancement of disease diagnostic technologies worldwide. Predominantly employed in diagnosing COVID-19, the real-time quantitative reverse transcription PCR has been the foremost diagnostic method, effectively detecting SARS-CoV-2 viral RNA. As the pandemic has evolved, antigen and serological tests have emerged as valuable diagnostic tools. Antigen tests pinpoint specific viral proteins of SARS-CoV-2, offering swift results, while serological tests identify the presence of antibodies in blood samples. Additionally, there have been notable strides in sample collection methods, notably with the introduction of saliva-based tests, presenting a non-invasive substitute to nasopharyngeal swabs. Given the ongoing mutations in SARS-CoV-2, there has been a continuous need for genomic surveillance, encompassing full genome sequencing and the identification of new variants through Illumina technology and, more recently, nanopore metagenomic sequencing (SMTN). Consequently, while diagnostic testing methods for COVID-19 have experienced remarkable progress, no test is flawless, and there exist limitations with each technique, including sensitivity, specificity, sample collection, and the minimum viral load necessary for accurate detection. These aspects are comprehensively addressed within this current review.
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Affiliation(s)
- Camila Salazar-Ardiles
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | | | - Carlos Cornejo
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | - Dayana Arias
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | - Manuel Vasquez-Muñoz
- Dirección de Docencia de Especialidades Médicas, Dirección de Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
| | - Camilo Toledo
- Laboratory of Cardiorespiratory and Sleep Physiology, Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - David C Andrade
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile.
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Wertenauer C, Pfeifer C, Roskos M, März W. Rapid antigen tests for SARS-CoV-2-a synopsis of the medical evidence. Diagn Microbiol Infect Dis 2023; 107:116027. [PMID: 37516068 DOI: 10.1016/j.diagmicrobio.2023.116027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 07/31/2023]
Abstract
SARS-CoV-2, the causative agent of the COVID-19 pandemic, continues to influence health, economy, and stability worldwide. Diagnostic testing for SARS-CoV-2 is important to contain the COVID-19 pandemic. With the commercial availability of certified antigen (Ag) rapid diagnostic tests (RDTs), which can be used to identify an infection with SARS-CoV-2 an easy-to-use tool was introduced. Self-tests can offer advantages to complement professionally administered rapid antigen detection or nucleic acid amplification testing (NAAT). Compared to real-time polymerase chain reaction (RT-PCR), Ag-RDTs are cost inexpensive, do not need specialized laboratory equipment, facilitating high-throughput testing. However, Ag-RDT sensitivities are strongly dependent on the viral load within the specimen, which has limited their application in clinical settings so far. The methodical limitations of Ag-RDTs may produce false negative test results, particularly when specimens with low viral loads are examined. This may facilitate viral transmissions if protective measurements are lifted mistakenly.
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Affiliation(s)
- Christoph Wertenauer
- Medical Clinic V, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.
| | | | | | - Winfried März
- Medical Clinic V, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
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9
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Jung J, Bong JH, Sung JS, Park JH, Kim TH, Kwon S, Kang MJ, Jose J, Pyun JC. Immunoaffinity biosensors for the detection of SARS-CoV-1 using screened Fv-antibodies from an autodisplayed Fv-antibody library. Biosens Bioelectron 2023; 237:115439. [PMID: 37301177 PMCID: PMC10223632 DOI: 10.1016/j.bios.2023.115439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
The detection of severe acute respiratory syndrome coronavirus (SARS-CoV-1) was demonstrated using screened Fv-antibodies for SPR biosensor and impedance spectrometry. The Fv-antibody library was first prepared on the outer membrane of E. coli using autodisplay technology and the Fv-variants (clones) with a specific affinity toward the SARS-CoV-1 spike protein (SP) were screened using magnetic beads immobilized with the SP. Upon screening the Fv-antibody library, two target Fv-variants (clones) with a specific binding affinity toward the SARS-CoV-1 SP were determined and the Fv-antibodies on two clones were named "Anti-SP1" (with CDR3 amino acid sequence: 1GRTTG5NDRPD11Y) and "Anti-SP2" (with CDR3 amino acid sequence: 1CLRQA5GTADD11V). The binding affinities of the two screened Fv-variants (clones) were analyzed using flow cytometry and the binding constants (KD) were estimated to be 80.5 ± 3.6 nM for Anti-SP1 and 45.6 ± 8.9 nM for Anti-SP2 (n = 3). In addition, the Fv-antibody including three CDR regions (CDR1, CDR2, and CDR3) and frame regions (FRs) between the CDR regions was expressed as a fusion protein (Mw. 40.6 kDa) with a green fluorescent protein (GFP) and the KD values of the expressed Fv-antibodies toward the SP estimated to be 15.3 ± 1.5 nM for Anti-SP1 (n = 3) and 16.3 ± 1.7 nM for Anti-SP2 (n = 3). Finally, the expressed Fv-antibodies screened against SARS-CoV-1 SP (Anti-SP1 and Anti-SP2) were applied for the detection of SARS-CoV-1. Consequently, the detection of SARS-CoV-1 was demonstrated to be feasible using the SPR biosensor and impedance spectrometry utilizing the immobilized Fv-antibodies against the SARS-CoV-1 SP.
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Affiliation(s)
- Jaeyong Jung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Ji-Hong Bong
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Jeong Soo Sung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Jun-Hee Park
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Tae-Hun Kim
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Soonil Kwon
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Min-Jung Kang
- Korea Institute of Science and Technology (KIST), Seoul, South Korea
| | - Joachim Jose
- Institute of Pharmaceutical and Medical Chemistry, Westphalian Wilhelms-University Münster, Münster, 48149, Germany
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.
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10
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Heudobler M, Baurecht H, Schmied H, Heudobler D, Jochem C, Sedlmeier AM, Weber A, Bauernfeind S, Leitzmann M, Salzberger B, Lampl BMJ. Association of epidemiological and clinical features with PCR cycle threshold values of SARS-CoV-2 infection: a cross-sectional study. Pathog Glob Health 2023; 117:476-484. [PMID: 36519354 PMCID: PMC10262808 DOI: 10.1080/20477724.2022.2158003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The cycle threshold (Ct) in quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR) is inversely correlated to the amount of viral nucleic acid or viral load and can be regarded as an indicator of infectivity. We examined the association of socio-demographic and clinical characteristics of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) polymerase chain reaction (PCR) positive cases with PCR cycle threshold (Ct) values at the time of diagnosis. SARS-CoV-2 cases reported between 12 October 2020 and 24 January 2021 in Regensburg were analyzed employing bivariate and multivariable methods. We included 3,029 SARS-CoV-2 cases (31% asymptomatic at diagnosis) and analyzed the association of case characteristics with Ct values in 2,606 cases. Among symptomatic patients, cough (38.0%), rhinitis (32.4%), headache (32.0), and fever/chills (29.9%) were the most frequent complaints. Ct values ≤20 were more frequent in symptomatic cases (20.9% vs. 11.3%), whereas Ct values >30 were more common in asymptomatic cases (32.6% vs. 18.0%). Ct values >20 and ≤30 were most common in symptomatic and asymptomatic cases (48.0% vs 40.7%). We observed lower median Ct values of E and N gene in symptomatic cases. In a random forest model, the total number of symptoms, respiratory symptoms, and age were most strongly associated with low Ct values. In conclusion, certain symptoms and age were associated with lower Ct values. Ct values can be used as a pragmatic approach in estimating infectivity at the first notification of a case and, thus, in guiding containment measures.
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Affiliation(s)
- Marlies Heudobler
- Regensburg Department of Public Health, Altmühlstraße 3, Regensburg, Germany
| | - Hansjörg Baurecht
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Helen Schmied
- Regensburg Department of Public Health, Altmühlstraße 3, Regensburg, Germany
| | - Daniel Heudobler
- Department of Internal Medicine 3, University Hospital Regensburg, Regensburg, Germany
| | - Carmen Jochem
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Anja M Sedlmeier
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Andrea Weber
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Stilla Bauernfeind
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - Michael Leitzmann
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Bernd Salzberger
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - Benedikt M J Lampl
- Regensburg Department of Public Health, Altmühlstraße 3, Regensburg, Germany
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
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11
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Salvati A, Ferravante C, Lamberti J, Rocco T, Alexandrova E, D'Agostino Y, Sorokin M, Efimov V, Buzdin A, Strianese O, Nassa G, Tarallo R, Weisz A, Rizzo F, Giurato G. Host nasopharyngeal transcriptome dataset of a SARS-CoV-2 positive Italian cohort. Sci Data 2023; 10:379. [PMID: 37316506 PMCID: PMC10264883 DOI: 10.1038/s41597-023-02289-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people worldwide and has significant implications for public health. Host transcriptomics profiling provides comprehensive understanding of how the virus interacts with host cells and how the host responds to the virus. COVID-19 disease alters the host transcriptome, affecting cellular pathways and key molecular functions. To contribute to the global effort to understand the virus's effect on host cell transcriptome, we have generated a dataset from nasopharyngeal swabs of 35 individuals infected with SARS-CoV-2 from the Campania region in Italy during the three outbreaks, with different clinical conditions. This dataset will help to elucidate the complex interactions among genes and can be useful in the development of effective therapeutic pathways.
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Affiliation(s)
- Annamaria Salvati
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Carlo Ferravante
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Jessica Lamberti
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Teresa Rocco
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Ylenia D'Agostino
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
| | - Maksim Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- OmicsWay Corp, Walnut, USA
- Oncobox Ltd., Moscow, Russia
| | - Victor Efimov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Oncobox Ltd., Moscow, Russia
- World-Class Research Center 'Digital biodesign and personalized healthcare', Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anton Buzdin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- World-Class Research Center 'Digital biodesign and personalized healthcare', Sechenov First Moscow State Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Oriana Strianese
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy
| | - Giovanni Nassa
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy
| | - Roberta Tarallo
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy
| | - Alessandro Weisz
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy
| | - Francesca Rizzo
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy.
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy.
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy.
| | - Giorgio Giurato
- Molecular Pathology and Medical Genomics Program, Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi 14 d'Aragona', Università di Salerno, Salerno, 84131, Italy.
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi (Sa), 84081, Italy.
- Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi (Sa), 84081, Italy.
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12
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Fan G, Jin Y, Wang Q, Yue Y. Assessing the comparability of cycle threshold values derived from five external quality assessment rounds for omicron nucleic acid testing. Virol J 2023; 20:119. [PMID: 37291570 PMCID: PMC10249569 DOI: 10.1186/s12985-023-02032-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 04/07/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND A variety of open-system real-time reverse transcriptase polymerase chain reaction (RT-PCR) assays for several acute respiratory syndrome coronavirus 2 are currently in use. This study aimed to ensure the quality of omicron nucleic acid testing and to assess the comparability of cycle threshold (Ct) values derived from RT-PCR. METHODS Five external quality assessment (EQA) rounds using the omicron virus-like particles were organized between February 2022 and June 2022. RESULTS A total of 1401 qualitative EQA reports have been collected. The overall positive percentage agreement was 99.72%, the negative percentage agreement was 99.75%, and the percent agreement was 99.73%. This study observed a significant variance in Ct values derived from different test systems. There was a wide heterogeneity in PCR efficiency among different RT-PCR kits and inter-laboratories. CONCLUSION There was strong concordance among laboratories performing qualitative omicron nucleic acid testing. Ct values from qualitative RT-PCR tests should not be used for clinical or epidemiological decision-making to avoid the potential for misinterpretation of the results.
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Affiliation(s)
- Gaowei Fan
- Department of Clinical Laboratory, Beijing Chao-Yang Hospital, Capital Medical University, 8 Gongren Tiyuchang Nanlu, Chaoyang District, Beijing, China
- Beijing Medical Laboratory Quality Control and Improvement Center, Beijing, China
| | - Yali Jin
- Beijing Center for Clinical Laboratory, Beijing, China
| | - Qingtao Wang
- Department of Clinical Laboratory, Beijing Chao-Yang Hospital, Capital Medical University, 8 Gongren Tiyuchang Nanlu, Chaoyang District, Beijing, China.
- Beijing Center for Clinical Laboratory, Beijing, China.
- Beijing Medical Laboratory Quality Control and Improvement Center, Beijing, China.
| | - Yuhong Yue
- Department of Clinical Laboratory, Beijing Chao-Yang Hospital, Capital Medical University, 8 Gongren Tiyuchang Nanlu, Chaoyang District, Beijing, China.
- Beijing Center for Clinical Laboratory, Beijing, China.
- Beijing Medical Laboratory Quality Control and Improvement Center, Beijing, China.
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13
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Conrad S, Gant Kanegusuku A, Conklin SE. Taking a step back from testing: Preanalytical considerations in molecular infectious disease diagnostics. Clin Biochem 2023; 115:22-32. [PMID: 36495954 PMCID: PMC9729171 DOI: 10.1016/j.clinbiochem.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Recent studies evaluating the preanalytical factors that impact the outcome of nucleic-acid based methods for the confirmation of SARS-CoV-2 have illuminated the importance of identifying variables that promoted accurate testing, while using scarce resources efficiently. The majority of laboratory errors occur in the preanalytical phase. While there are many resources identifying and describing mechanisms for main laboratory testing on automated platforms, there are fewer comprehensive resources for understanding important preanalytical and environmental factors that affect accurate molecular diagnostic testing of infectious diseases. This review identifies evidence-based factors that have been documented to impact the outcome of nucleic acid-based molecular techniques for the diagnosis of infectious diseases.
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Affiliation(s)
- Stephanie Conrad
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | | | - Steven E Conklin
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA; Department of Anatomic & Clinical Pathology, Tufts University School of Medicine, Boston, MA, USA.
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14
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Kim JJ, Park HM, Kyoung AY, Lim SK, Cha SH, Lee JE, Park BC. Com probe implemented STexS II greatly enhances specificity in SARS-CoV-2 variant detection. Sci Rep 2023; 13:1036. [PMID: 36658190 PMCID: PMC9850334 DOI: 10.1038/s41598-022-24530-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/16/2022] [Indexed: 01/20/2023] Open
Abstract
The initial introduction of utilizing double helix structural oligonucleotides known as SNP typing with excellent specificity (STexS) in a standard PCR greatly improved the detection of single nucleotide polymorphisms (SNP) by enhancing amplification rates of primer-matching strands and interrupting mismatched strands by constant instability of kinetics regarding alignment attaching and detaching. The model was beneficial overall in detecting SNP variants consisting of large amounts of wildtype strands such as EGFR mutation genotyping for early detection of non-small cell lung cancer. While the STexS PCR is advantageous in detecting SNPs and biomarkers, limitations were yet observed. Despite the ability to detect variants 10 times more effective than a typical amplification-refractory mutation system PCR, it could only perform optimally in DNA concentrations around 101 ~ 105. To further enhance STexS specificity to perform detecting viral-RNA variants such as the infamous SARS-CoV-2, a novel improvement of the regular TaqMan Probe using Com-probes to inhibit high copy wild targets and amplify low copy mutant targets. By introducing the novel STexS II, omicron variants of SARS-CoV-2 were able to be successfully detected in high concentrations of normal genes.
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Affiliation(s)
- Jae Jong Kim
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Hyoung-Min Park
- Biometrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - A Young Kyoung
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Si-Kyu Lim
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
| | - Sun Ho Cha
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - J Eugene Lee
- Biometrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Byoung Chul Park
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34145, Republic of Korea.
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15
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Intestinal Shedding of SARS-CoV-2 in Children: No Evidence for Infectious Potential. Microorganisms 2022; 11:microorganisms11010033. [PMID: 36677323 PMCID: PMC9864026 DOI: 10.3390/microorganisms11010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The clinical courses of COVID-19 in children are often mild and may remain undiagnosed, but prolonged intestinal virus shedding has been documented, thus potentially enabling fecal-oral transmission. However, the infectious potential of SARS-CoV-2 viruses excreted with feces has remained unclear. Here, we investigated 247 stool specimens from 213 pediatric patients to assess the prevalence of intestinal SARS-CoV-2 shedding in hospitalized children without or with COVID-19 and determined the infectious capacity of stool-borne viruses. Upon RT-qPCR screening, the infectivity of virus-positive samples was tested in cell culture using the Vero-E6 permissive cell line. SARS-CoV-2 RNA was detected by RT-qPCR in 32 (13%) stool specimens, but the analysis of virus-positive samples in cell culture revealed no cytopathic effects attributable to SARS-CoV-2-related cell damage. Our findings do not support the notion of potential fecal-oral SARS-CoV-2 spreading, thus questioning the role of hygienic measures designed to prevent this mode of viral transmission.
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16
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Rapid Evaluation of the Xpert ® Xpress CoV-2 plus and Xpert ® Xpress CoV-2/Flu/RSV plus Tests. Diagnostics (Basel) 2022; 13:diagnostics13010034. [PMID: 36611325 PMCID: PMC9818900 DOI: 10.3390/diagnostics13010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/25/2022] Open
Abstract
The Xpert® Xpress SARS-CoV-2 and Xpert® Xpress SARS-CoV-2/Flu/RSV tests were rapidly developed and widely used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. In response to emerging genetic variability, a new SARS-CoV-2 target (RNA-dependent RNA-polymerase) has been added to both tests: Xpert® Xpress CoV-2 plus and Xpert® Xpress CoV-2/Flu/RSV plus test. A rapid evaluation of both tests was performed in South Africa, using residual respiratory specimens. Residual respiratory specimens (n = 125) were used to evaluate the Xpert® Xpress CoV-2 plus test and included 50 genotyped specimens. The Xpert® Xpress CoV-2/Flu/RSV plus test was assessed using 45 genotyped SARS-CoV-2 specimens, 10 influenza A, 10 influenza B and 20 respiratory syncytial virus specimens. Results were compared to in-country standard-of-care tests. Genotyped specimens tested the performance of the test under pressure from circulating SARS-CoV-2 variants of concern. Reference material was included to assess the test limits and linearity. The Xpert® Xpress CoV-2 plus test performance compared to reference results across residual respiratory specimens was good (positive percentage agreement (PPA) = 95.2%, negative percentage agreement (NPA) = 95.0%) The Xpert® Xpress CoV-2/Flu/RSV plus test showed good performance across all residual respiratory specimens (PPA = 100%, NPA = 98.3%). All genotyped variants of concern were detected by both tests. The Xpert® Xpress CoV-2 plus and Xpert® Xpress CoV-2/Flu/RSV plus tests can be used to diagnose SARS-CoV-2, and to diagnose and differentiate SARS-CoV-2, influenza A, influenza B and respiratory syncytial virus, respectively. The NPA was lower than the recommended 99%, but was influenced by the low number of negative specimens tested. The variants of concern assessed did not affect test performance. It is recommended that sites perform their own assessments compared to in-country standard-of-care tests.
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17
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Sakhabutdinova AR, Gazizov RR, Chemeris AV, Garafutdinov RR. Reverse transcriptase-free detection of viral RNA using Hemo Klentaq DNA polymerase. Anal Biochem 2022; 659:114960. [PMID: 36306819 PMCID: PMC9597527 DOI: 10.1016/j.ab.2022.114960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2022]
Abstract
COVID-19 pandemic highlighted the demand for the fast and reliable detection of viral RNA. Although various methods for RNA amplification and detection have been proposed, some limitations, including those caused by reverse transcription (RT), need to be overcome. Here, we report on the direct detection of specific RNA by conventional polymerase chain reaction (PCR) requiring no prior RT step. It was found that Hemo KlenTaq (HKTaq), which is posed as DNA-dependent DNA polymerase, possesses reverse transcriptase activity and provides reproducible amplification of RNA targets with an efficiency comparable to common RT-PCR. Using nasopharyngeal swab extracts from COVID-19-positive patients, the high reliability of SARS-CoV-2 detection based on HKTaq was demonstrated. The most accurate detection of specific targets are provided by nearby primers, which allow to determine RNA in solutions affected to multiple freeze-thaw cycles. HKTaq can be used for elaboration of simplified amplification techniques intended for the analysis of any specific RNA and requiring only one DNA polymerase.
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18
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Iqbal R, Khan S, Ali HM, Khan M, Wahab S, Khan T. Application of nanomaterials against SARS-CoV-2: An emphasis on their usefulness against emerging variants of concern. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.1060756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Researchers are now looking to nanomaterials to fight serious infectious diseases that cause outbreaks and even pandemics. SARS-CoV-2 brought chaos to almost every walk of life in the past 2 years and has challenged every available treatment method. Although vaccines were developed in no time against it, the most pressing issue was the emergence of variants of concern arising because of the rapidly evolving viral strains. The higher pathogenicity and, in turn, the higher mortality rate of infections caused by these variants renders the existing vaccines less effective and the effort to produce further vaccines a costly endeavor. While several techniques, such as immunotherapy and repurposed pharmaceutical research, are being studied to minimize viral infection, the fundamentals of nanotechnology must also be considered to enhance the anti-SARS-CoV-2 efforts. For instance, silver nanoparticles (AgNPs) have been applied against SARS-CoV-2 effectively. Similarly, nanomaterials have been tested in masks, gloves, and disinfectants to aid in controlling SARS-CoV-2. Nanotechnology has also contributed to diagnoses such as rapid and accurate detection and treatment such as the delivery of mRNA vaccines and other antiviral agents into the body. The development of polymeric nanoparticles has been dubbed a strategy of choice over traditional drugs because of their tunable release kinetics, specificity, and multimodal drug composition. Our article explores the potential of nanomaterials in managing the variants of concern. This will be achieved by highlighting the inherent ability of nanomaterials to act against the virus on fronts such as inhibition of SARS-CoV-2 entry, inhibition of RNA replication in SARS-CoV-2, and finally, inhibition of their release. In this review, a detailed discussion on the potential of nanomaterials in these areas will be tallied with their potential against the current and emerging future variants of concern.
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19
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Gholami M, Sakhaee F, Sotoodehnejadnematalahi F, Zamani MS, Ahmadi I, Anvari E, Fateh A. Increased risk of COVID-19 mortality rate in IFITM3 rs6598045 G allele carriers infected by SARS-CoV-2 delta variant. Hum Genomics 2022; 16:60. [PMID: 36403064 PMCID: PMC9675951 DOI: 10.1186/s40246-022-00434-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/12/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The interferon-induced transmembrane-protein 3 (IFITM3) is a vital component of the immune system's defense against viral infection. Variants in the IFITM3 gene have been linked to changes in expression and the risk of severe Coronavirus disease 2019 (COVID-19). This study aimed to investigate whether IFITM3 rs6598045, quantitative polymerase chain reaction (qPCR) cycle threshold (Ct) values, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are associated with an increased mortality rate of COVID-19. METHODS The genotyping of IFITM3 rs6598045 polymorphism was analyzed using the amplification refractory mutation system-polymerase chain reaction in 1342 recovered and 1149 deceased patients positive for SARS-CoV-2. RESULTS In this study, IFITM3 rs6598045 G allele as minor allele frequency was significantly more common in the deceased patients than in the recovered ones. Furthermore, the highest mortality rates were observed in Delta variant and lowest qPCR Ct values. COVID-19 mortality was associated with IFITM3 rs6598045 GG and AG in Delta variant and IFITM3 rs6598045 AG in Alpha variant. A statistically significant difference was observed in the qPCR Ct values between individuals with GG and AG genotypes and those with an AA genotype. CONCLUSION A possible correlation was observed between the mortality rate of COVID-19, the G allele of IFITM3 rs6598045, and SARS-CoV-2 variants. However, large-scale research is still required to validate our results.
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Affiliation(s)
- Melika Gholami
- grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran ,grid.420169.80000 0000 9562 2611Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Sakhaee
- grid.420169.80000 0000 9562 2611Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fattah Sotoodehnejadnematalahi
- grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Saber Zamani
- grid.412501.30000 0000 8877 1424Immunoregulation Research Center, Shahed University, Tehran, Iran
| | - Iraj Ahmadi
- grid.449129.30000 0004 0611 9408Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- grid.449129.30000 0004 0611 9408Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Abolfazl Fateh
- grid.420169.80000 0000 9562 2611Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran ,grid.420169.80000 0000 9562 2611Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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20
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Al-Naabi MJ, Maddali MM, Al Aliyani KR, Al-Balushi A. Anaesthetic Management of Pulmonary Metastasectomy in a Patient Infected with Novel Corona Virus SARS-CoV-2. Sultan Qaboos Univ Med J 2022; 22:578-582. [PMID: 36407706 PMCID: PMC9645507 DOI: 10.18295/squmj.9.2021.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/04/2021] [Accepted: 08/15/2021] [Indexed: 11/16/2022] Open
Abstract
Prioritisation of individual patients for thoracic surgeries gained importance during the current COVID-19 pandemic to ensure optimal utilisation of resources. We report a 76-year-old-male patient who presented to a tertiary care hospital in Muscat, Oman, 2020, with bilateral pulmonary metastasis. The patient underwent an urgent pulmonary metastasectomy with successful anaesthesia management in an elderly patient despite him testing positive for COVID-19 twice via real-time reverse transcription-polymerase chain reaction. At the 3-month follow-up some pulmonary abnormalities persisted but the patient was recovering well. This report discusses the rationale to perform surgery in this case and highlights the precautions taken for reducing aerosol generation during the various stages of anaesthesia.
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Affiliation(s)
- Mohammed J. Al-Naabi
- Department of Cardiac Anesthesia, National Heart Center, Royal Hospital, Muscat, Oman
| | - Madan M. Maddali
- Department of Cardiac Anesthesia, National Heart Center, Royal Hospital, Muscat, Oman
| | | | - Ahmed Al-Balushi
- Department of Cardiothoracic Surgery, National Heart Center, Royal Hospital, Muscat, Oman
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21
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Baldanti F, Ganguly NK, Wang G, Möckel M, O’Neill LA, Renz H, dos Santos Ferreira CE, Tateda K, Van Der Pol B. Choice of SARS-CoV-2 diagnostic test: challenges and key considerations for the future. Crit Rev Clin Lab Sci 2022; 59:445-459. [PMID: 35289222 PMCID: PMC8935452 DOI: 10.1080/10408363.2022.2045250] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/15/2021] [Accepted: 02/18/2022] [Indexed: 01/27/2023]
Abstract
A plethora of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests are available, each with different performance specifications, detection methods, and targets. This narrative review aims to summarize the diagnostic technologies available and how they are best selected to tackle SARS-CoV-2 infection as the pandemic evolves. Seven key settings have been identified where diagnostic tests are being deployed: symptomatic individuals presenting for diagnostic testing and/or treatment of COVID-19 symptoms; asymptomatic individuals accessing healthcare for planned non-COVID-19-related reasons; patients needing to access emergency care (symptom status unknown); patients being discharged from healthcare following hospitalization for COVID-19; healthy individuals in both single event settings (e.g. airports, restaurants, hotels, concerts, and sporting events) and repeat access settings (e.g. workplaces, schools, and universities); and vaccinated individuals. While molecular diagnostics remain central to SARS-CoV-2 testing strategies, we have offered some discussion on the considerations for when other tools and technologies may be useful, when centralized/point-of-care testing is appropriate, and how the various additional diagnostics can be deployed in differently resourced settings. As the pandemic evolves, molecular testing remains important for definitive diagnosis, but increasingly widespread point-of-care testing is essential to the re-opening of society.
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Affiliation(s)
- Fausto Baldanti
- Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | | | - Guiqiang Wang
- The Center for Liver Diseases, Peking University First Hospital, Beijing, China
| | | | - Luke A. O’Neill
- Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Harald Renz
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps University Marburg, University Hospital Giessen and Marburg GmbH, Giessen, Germany
- Department of Clinical Immunology and Allergology, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Barbara Van Der Pol
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
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22
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El-Moghazy AY, Amaly N, Sun G, Nitin N. Development and clinical evaluation of commercial glucose meter coupled with nanofiber based immuno-platform for self-diagnosis of SARS-CoV-2 in saliva. Talanta 2022. [DOI: 10.1016/j.talanta.2022.124117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Yin T, Ye Y, Dong W, Jie G. Electrochemiluminescence resonance energy transfer biosensing platform between g-C 3N 4 nanosheet and Ru-SiO 2@FA for dual-wavelength ratiometric detection of SARS-CoV-2 RdRp gene. Biosens Bioelectron 2022; 215:114580. [PMID: 35917609 PMCID: PMC9299981 DOI: 10.1016/j.bios.2022.114580] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/15/2022] [Accepted: 07/17/2022] [Indexed: 01/31/2023]
Abstract
Rational detection of syndrome coronavirus 2 (SARS-CoV-2) is crucial to prevention, control, and treatment of disease. Herein, a dual-wavelength ratiometric electrochemiluminescence (ECL) biosensor based on resonance energy transfer (RET) between g-C3N4 nanosheets and Ru-SiO2@folic acid (FA) nanomaterials was designed to realize ultrasensitive detection of SARS-CoV-2 virus (RdRp gene). Firstly, the unique g-C3N4 nanosheets displayed very intense and stable ECL at 460 nm, then the triple helix DNA was stably and vertically bound to g-C3N4 on electrode by high binding affinity between ssDNA and g-C3N4. Meanwhile, trace amounts of target genes were converted to a large number of output by three-dimensional (3D) DNA walker multiple amplification, and the output bridged a multifunctional probe Ru-SiO2@FA to electrode. Ru-SiO2@FA not only showed high ECL at 620 nm, but also effectively quenched g-C3N4 ECL. As a result, ECL decreased at 460 nm and increased at 620 nm, which was used to design a rational ECL biosensor for detection of SARS gene. The results show that the biosensor has excellent detection sensitivity for RdRp gene with a dynamic detection range of 1 fM to 10 nM and a limit of detection (LOD) of 0.18 fM. The dual-wavelength ratio ECL biosensor has inestimable value and application prospects in the fields of biosensing and clinical diagnosis.
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24
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Comparison and Harmonization of Different Semi-Automated and Automated qRT-PCR Assays in the Assessment of SARS-CoV-2. Viruses 2022; 14:v14102239. [PMID: 36298793 PMCID: PMC9610219 DOI: 10.3390/v14102239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/25/2022] [Accepted: 10/07/2022] [Indexed: 11/22/2022] Open
Abstract
In SARS-CoV-2 diagnostics, cycle threshold (Ct) values from qRT-PCRs semi-quantitatively estimate a patient’s viral load. However, relevant analytical differences between qRT-PCR assays are often neglected. This study was designed (i) to identify such differences between five commonly used assays and (ii) to demonstrate a straightforward strategy to harmonize them. QRT-PCRs for SARS-CoV-2 were carried out in 85 oropharyngeal swab samples using three fully automated (Alinity m, cobas®6800 and GeneXpert) and two semi-automated (genesig® and RIDA®GENE) assays. Qualitative results (positive/negative) showed excellent comparability between the fully automated assays, but not between the Alinity m and semi-automated methods. Ct values significantly varied between all the methods, with the median values ranging from 22.76 (Alinity m) to 30.89 (RIDA®GENE) and 31.50 (genesig®), indicating the lowest sensitivity for semi-automated methods. Passing–Bablok analysis further revealed systemic biases. Assay-specific viral load concentration calculations—based on generated individual standard curves—resulted in much better comparability between the assays. Applying these calculations, significant differences were no longer detectable. This study highlights relevant analytical differences between SARS-CoV-2 qRT-PCR assays, leading to divergent decisions about the mandatory isolation of infected individuals. Secondly, we propose a strategy to harmonize qRT-PCR assays to achieve better comparability. Our findings are of particular interest for laboratories utilizing different assays.
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25
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Shirvaliloo M, Sheervalilou R, Ahmadpour E, Safiri S, Bannazadeh Baghi H. Diagnostic accuracy of clinically applied nanoparticle-based biosensors at detecting SARS-CoV-2 RNA and surface proteins in pharyngeal swabs compared to RT-PCR as a reference test. Expert Rev Mol Diagn 2022; 22:881-894. [PMID: 36224104 DOI: 10.1080/14737159.2022.2135434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Nanoparticle-based biosensors (NPBs) are point-of-care diagnostic platforms that can be used for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high accuracy. AREAS COVERED EBSCOhost Web, Embase, ProQuest, PubMed/MEDLINE, Scopus, Web of Science, and WHO Global Literature on Coronavirus Disease 2019 (COVID-19) were searched for relevant records published from 1 November 2019 to 30 April 2022. Records reporting original data on the accuracy of clinically applied nanoparticle-based biosensors at detecting SARS-CoV-2 RNA and surface proteins from pharyngeal swab specimens were considered. Findings were reported based on the PRISMA 2020 statement. The QUADAS-2 tool was used for assessment of quality and risk of bias among the included studies. EXPERT OPINION A total of 50 relevant records were identified, of which 13 were included. The included studies explored the diagnostic performance of 13 clinically applied distinct nanoparticle-based biosensors in a total of 789 pharyngeal swabs collected from 376 COVID-19 patients and 413 otherwise healthy individuals. The mean sensitivity, specificity, and accuracy were 97.07%, 94.43%, and 96.91%, respectively, in comparison to RT-qPCR as the reference test. Considering their ease-of-operation, portability, low-cost manufacturing, NPBs could be considered suitable candidate diagnostic platforms for substituting RT-qPCR.
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Affiliation(s)
- Milad Shirvaliloo
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Future Science Group, Unitec House, 2 Albert Place, London, N3 1QB, UK
| | | | - Ehsan Ahmadpour
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeid Safiri
- Neurosciences Research Center, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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26
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Szunerits S, Saada H, Pagneux Q, Boukherroub R. Plasmonic Approaches for the Detection of SARS-CoV-2 Viral Particles. BIOSENSORS 2022; 12:548. [PMID: 35884352 PMCID: PMC9313406 DOI: 10.3390/bios12070548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022]
Abstract
The ongoing highly contagious Coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlines the fundamental position of diagnostic testing in outbreak control by allowing a distinction of the infected from the non-infected people. Diagnosis of COVID-19 remains largely based on reverse transcription PCR (RT-PCR), identifying the genetic material of the virus. Molecular testing approaches have been largely proposed in addition to infectivity testing of patients via sensing the presence of viral particles of SARS-CoV-2 specific structural proteins, such as the spike glycoproteins (S1, S2) and the nucleocapsid (N) protein. While the S1 protein remains the main target for neutralizing antibody treatment upon infection and the focus of vaccine and therapeutic design, it has also become a major target for the development of point-of care testing (POCT) devices. This review will focus on the possibility of surface plasmon resonance (SPR)-based sensing platforms to convert the receptor-binding event of SARS-CoV-2 viral particles into measurable signals. The state-of-the-art SPR-based SARS-CoV-2 sensing devices will be provided, and highlights about the applicability of plasmonic sensors as POCT for virus particle as well as viral protein sensing will be discussed.
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Affiliation(s)
- Sabine Szunerits
- University of Lille, CNRS, Centrale Lille, University Polytechnique Hauts-de-France, UMR 8520-IEMN, F-59000 Lille, France; (H.S.); (Q.P.); (R.B.)
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27
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Tao C, Du J, Tang Y, Wang J, Dong K, Yang M, Hu B, Zhang Z. A Deep-Learning Based System for Rapid Genus Identification of Pathogens under Hyperspectral Microscopic Images. Cells 2022; 11:cells11142237. [PMID: 35883680 PMCID: PMC9315805 DOI: 10.3390/cells11142237] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/06/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022] Open
Abstract
Infectious diseases have always been a major threat to the survival of humanity. Additionally, they bring an enormous economic burden to society. The conventional methods for bacteria identification are expensive, time-consuming and laborious. Therefore, it is of great importance to automatically rapidly identify pathogenic bacteria in a short time. Here, we constructed an AI-assisted system for automating rapid bacteria genus identification, combining the hyperspectral microscopic technology and a deep-learning-based algorithm Buffer Net. After being trained and validated in the self-built dataset, which consists of 11 genera with over 130,000 hyperspectral images, the accuracy of the algorithm could achieve 94.9%, which outperformed 1D-CNN, 2D-CNN and 3D-ResNet. The AI-assisted system we developed has great potential in assisting clinicians in identifying pathogenic bacteria at the single-cell level with high accuracy in a cheap, rapid and automatic way. Since the AI-assisted system can identify the pathogenic genus rapidly (about 30 s per hyperspectral microscopic image) at the single-cell level, it can shorten the time or even eliminate the demand for cultivating. Additionally, the system is user-friendly for novices.
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Affiliation(s)
- Chenglong Tao
- Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (C.T.); (J.D.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Biomedical Spectroscopy of Xi’an, Xi’an 710119, China
| | - Jian Du
- Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (C.T.); (J.D.); (J.W.)
- Key Laboratory of Biomedical Spectroscopy of Xi’an, Xi’an 710119, China
| | | | - Junjie Wang
- Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (C.T.); (J.D.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Dong
- The Second Affiliated Hospital of Air Force Military Medical University, Xi’an 710119, China; (K.D.); (M.Y.)
| | - Ming Yang
- The Second Affiliated Hospital of Air Force Military Medical University, Xi’an 710119, China; (K.D.); (M.Y.)
| | - Bingliang Hu
- Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (C.T.); (J.D.); (J.W.)
- Key Laboratory of Biomedical Spectroscopy of Xi’an, Xi’an 710119, China
- Correspondence: (B.H.); (Z.Z.)
| | - Zhoufeng Zhang
- Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (C.T.); (J.D.); (J.W.)
- Key Laboratory of Biomedical Spectroscopy of Xi’an, Xi’an 710119, China
- Correspondence: (B.H.); (Z.Z.)
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28
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Dutta D, Naiyer S, Mansuri S, Soni N, Singh V, Bhat KH, Singh N, Arora G, Mansuri MS. COVID-19 Diagnosis: A Comprehensive Review of the RT-qPCR Method for Detection of SARS-CoV-2. Diagnostics (Basel) 2022; 12:diagnostics12061503. [PMID: 35741313 PMCID: PMC9221722 DOI: 10.3390/diagnostics12061503] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 12/15/2022] Open
Abstract
The world is grappling with the coronavirus disease 2019 (COVID-19) pandemic, the causative agent of which is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 symptoms are similar to the common cold, including fever, sore throat, cough, muscle and chest pain, brain fog, dyspnoea, anosmia, ageusia, and headache. The manifestation of the disease can vary from being asymptomatic to severe life-threatening conditions warranting hospitalization and ventilation support. Furthermore, the emergence of mutecated variants of concern (VOCs) is paramount to the devastating effect of the pandemic. This highly contagious virus and its emergent variants challenge the available advanced viral diagnostic methods for high-accuracy testing with faster result yields. This review is to shed light on the natural history, pathology, molecular biology, and efficient diagnostic methods of COVID-19, detecting SARS-CoV-2 in collected samples. We reviewed the gold standard RT-qPCR method for COVID-19 diagnosis to confer a better understanding and application to combat the COVID-19 pandemic. This comprehensive review may further develop awareness about the management of the COVID-19 pandemic.
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Affiliation(s)
- Debashis Dutta
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence: (D.D.); (M.S.M.)
| | - Sarah Naiyer
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60616, USA;
| | | | - Neeraj Soni
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Vandana Singh
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Khalid Hussain Bhat
- SKUAST Kashmir, Division of Basic Science and Humanities, Faculty of Agriculture, Wadura Sopore 193201, JK, India;
| | - Nishant Singh
- Cell and Gene Therapy Absorption System, Exton, PA 19335, USA;
| | - Gunjan Arora
- Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - M. Shahid Mansuri
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Correspondence: (D.D.); (M.S.M.)
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Morris S, Anjan S, Pallikkuth S, Frattaroli P, Courel S, Fernandez A, Natori A, Abbo L, Pahwa S, Guerra G, Natori Y. Reinfection with SARS-CoV-2 in solid-organ transplant recipients: Incidence density and convalescent immunity prior to reinfection. Transpl Infect Dis 2022; 24:e13827. [PMID: 35338554 PMCID: PMC9115288 DOI: 10.1111/tid.13827] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Long-term protective immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains poorly characterized, particularly in solid organ transplant (SOT) patients. METHOD We determined the incidence density of SARS-CoV-2 reinfection in a cohort of adult SOT recipients initially infected between March 1st, 2020 and March 30th, 2021 and included those with initial infection before or after transplantation. Incidence density was the total cases divided by total days after initial diagnosis with active graft. RESULTS Of 210 infected recipients, five (2.4%) developed reinfection, including two who had received full mRNA vaccination, but none developed hypoxia. The incidence density for reinfection was 9.4 (95% confidence interval [CI] 3.9-22.6) and for primary infection the density was 9.1 (95% CI 7.9-10.5) cases/100,000 patient days. Two recipients had immunity evaluated in the weeks prior to reinfection, by measuring immunoglobulin-G (IgG) antibody titer to the SARS-CoV-2 receptor binding domain and virus-specific CD4+ and CD8+ T-cell reactivity following stimulation with SARS-CoV-2 peptide pools. Both mounted virus specific CD4 T-cell responses prior to reinfection (1.19% and 0.28% of total CD4 T cells) and both had reactive IgG testing (1.30 and 4.99 signal/cut off ratio). CONCLUSIONS This suggests that SOT recipients infected with SARS-CoV-2 remain at high risk for reinfection even after generating cellular and humoral immune responses.
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Affiliation(s)
- Stephen Morris
- Division of Infectious Disease, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Shweta Anjan
- Division of Infectious Disease, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA.,Miami Transplant Institute, Jackson Health System, Miami, Florida, USA
| | - Suresh Pallikkuth
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Paola Frattaroli
- Department of Medicine, Jackson Health System, Miami, Florida, USA
| | - Steve Courel
- Department of Human Genetics and John P. Hussman Institute for Human genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | | | - Akina Natori
- Division of Oncology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Lilian Abbo
- Division of Infectious Disease, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA.,Miami Transplant Institute, Jackson Health System, Miami, Florida, USA
| | - Savita Pahwa
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Giselle Guerra
- Miami Transplant Institute, Jackson Health System, Miami, Florida, USA.,Division of Nephrology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Yoichiro Natori
- Division of Infectious Disease, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA.,Miami Transplant Institute, Jackson Health System, Miami, Florida, USA
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30
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Skarzynski M, McAuley EM, Maier EJ, Fries AC, Voss JD, Chapleau RR. SARS-CoV-2 Genome-Based Severity Predictions Correspond to Lower qPCR Values and Higher Viral Load. Glob Health Epidemiol Genom 2022; 2022:6499217. [PMID: 35707747 PMCID: PMC9173902 DOI: 10.1155/2022/6499217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/13/2022] [Indexed: 11/18/2022] Open
Abstract
The 2019 coronavirus disease (COVID-19) pandemic has demonstrated the importance of predicting, identifying, and tracking mutations throughout a pandemic event. As the COVID-19 global pandemic surpassed one year, several variants had emerged resulting in increased severity and transmissibility. Here, we used PCR as a surrogate for viral load and consequent severity to evaluate the real-world capabilities of a genome-based clinical severity predictive algorithm. Using a previously published algorithm, we compared the viral genome-based severity predictions to clinically derived PCR-based viral load of 716 viral genomes. For those samples predicted to be "severe" (probability of severe illness >0.5), we observed an average cycle threshold (Ct) of 18.3, whereas those in in the "mild" category (severity probability <0.5) had an average Ct of 20.4 (P=0.0017). We also found a nontrivial correlation between predicted severity probability and cycle threshold (r = -0.199). Finally, when divided into severity probability quartiles, the group most likely to experience severe illness (≥75% probability) had a Ct of 16.6 (n = 10), whereas the group least likely to experience severe illness (<25% probability) had a Ct of 21.4 (n = 350) (P=0.0045). Taken together, our results suggest that the severity predicted by a genome-based algorithm can be related to clinical diagnostic tests and that relative severity may be inferred from diagnostic values.
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Affiliation(s)
| | | | | | - Anthony C. Fries
- US Air Force School of Aerospace Medicine, Wright Patterson AFB, OH 45433, USA
| | - Jameson D. Voss
- US Air Force Medical Readiness Agency, Falls Church, VA 22042, USA
| | - Richard R. Chapleau
- US Air Force School of Aerospace Medicine, Wright Patterson AFB, OH 45433, USA
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31
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Huang SC, Pak TK, Graber CP, Searby CC, Liu G, Marcy J, Yaszemski AK, Bedell K, Bui E, Perlman S, Zhang Q, Wang K, Sheffield VC, Carter CS. An open source and convenient method for the wide-spread testing of COVID-19 using deep throat sputum samples. PeerJ 2022; 10:e13277. [PMID: 35573180 PMCID: PMC9104087 DOI: 10.7717/peerj.13277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/24/2022] [Indexed: 01/13/2023] Open
Abstract
Importance The rise of novel, more infectious SARS-CoV-2 variants has made clear the need to rapidly deploy large-scale testing for COVID-19 to protect public health. However, testing remains limited due to shortages of personal protective equipment (PPE), naso- and oropharyngeal swabs, and healthcare workers. Simple test methods are needed to enhance COVID-19 screening. Here, we describe a simple, and inexpensive spit-test for COVID-19 screening called Patient Self-Collection of Sample-CoV2 (PSCS-CoV2). Objective To evaluate an affordable and convenient test for COVID-19. Methods The collection method relies on deep throat sputum (DTS) self-collected by the subject without the use of swabs, and was hence termed the Self-Collection of Sample for SARS-CoV-2 (abbreviated PSCS-CoV2). We used a phenol-chloroform extraction method for the viral RNA. We then tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction with primers against at least two coding regions of the viral nucleocapsid protein (N1 and N2 or E) of SARS-CoV-2. We evaluted the sensitivity and specificity of our protocol. In addition we assess the limit of detection, and efficacy of our Viral Inactivating Solution. We also evaluated our protocol, and pooling strategy from volunteers on a local college campus. Results We show that the PSCS-CoV2 method accurately identified 42 confirmed COVID-19 positives, which were confirmed through the nasopharyngeal swabbing method of an FDA approved testing facility. For samples negative for COVID-19, we show that the cycle threshold for N1, N2, and RP are similar between the PSCS-CoV2 and nasopharynx swab collection method (n = 30). We found a sensitivity of 100% (95% Confidence Interval [CI], 92-100) and specifity of 100% (95% CI, 89-100) for our PSCS-CoV2 method. We determined our protocol has a limit of detection of 1/10,000 for DTS from a COVID-19 patient. In addition, we show field data of the PSCS-CoV2 method on a college campus. Ten of the twelve volunteers (N1 < 30) that we tested as positive were subsequently tested positive by an independent laboratory. Finally, we show proof of concept of a pooling strategy to test for COVID-19, and recommend pool sizes of four if the positivity rate is less than 15%. Conclusion and Relevance We developed a DTS-based protocol for COVID-19 testing with high sensitivity and specificity. This protocol can be used by non-debilitated adults without the assistance of another adult, or by non-debilitated children with the assistance of a parent or guardian. We also discuss pooling strategies based on estimated positivity rates to help conserve resources, time, and increase throughput. The PSCS-CoV2 method can be a key component of community-wide efforts to slow the spread of COVID-19.
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Affiliation(s)
- Sunny C. Huang
- Medical Scientist Training Program / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America,Stead Family Department of Pediatrics/ Division of Medical Genetics and Genomic / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Thomas K. Pak
- Medical Scientist Training Program / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America,Stead Family Department of Pediatrics/ Division of Medical Genetics and Genomic / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Cameron P. Graber
- Stead Family Department of Pediatrics/ Division of Medical Genetics and Genomic / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Charles C. Searby
- Stead Family Department of Pediatrics/ Division of Medical Genetics and Genomic / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Guanghao Liu
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, IA, United States of America
| | - Jennifer Marcy
- Stead Family Department of Pediatrics/ Division of Medical Genetics and Genomic / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Alexandra K. Yaszemski
- Department of Neurology / Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, United States of America
| | - Kurt Bedell
- Department of Microbiology and Immunology / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Emily Bui
- Stead Family Department of Pediatrics/ Division of Medical Genetics and Genomic / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Stanley Perlman
- Stead Family Department of Pediatrics/ Division of Medical Genetics and Genomic / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America,Department of Microbiology and Immunology / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Qihong Zhang
- Stead Family Department of Pediatrics/ Division of Medical Genetics and Genomic / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Kai Wang
- Department of Biostatistics / University of Iowa College of Public Health, University of Iowa, Iowa City, IA, United States of America
| | - Val C. Sheffield
- Stead Family Department of Pediatrics/ Division of Medical Genetics and Genomic / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America,Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, IA, United States of America
| | - Calvin S. Carter
- Stead Family Department of Pediatrics/ Division of Medical Genetics and Genomic / Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
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Militello KT, Nedelkovska H. An undergraduate laboratory to detect viruses in human DNA samples using qPCR. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 50:319-325. [PMID: 35412013 DOI: 10.1002/bmb.21620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
The COVID-19 pandemic has necessitated the need to reliably detect the presence of viral genomes in human clinical samples. The most accurate viral tests involve the use of qPCR. Thus, it is important for students to understand the mechanism to detect viral genomes by qPCR including critical qPCR controls and how to properly interpret qPCR data. Herein, we describe a 2-week undergraduate laboratory to detect a viral genome in a human DNA sample. The strategy follows a SARS-CoV-2 qPCR test in numerous ways. Students are provided isolated DNA representing a mock human patient sample, and determine if a viral genome (bacteriophage lambda) is present using qPCR. A battery of control samples and patient pooling strategies are utilized. The laboratory exercise is successful based on high rates of student success in detecting viral genomes, pre-quiz and post-quiz assessments focusing on viral qPCR testing, and positive student comments.
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Affiliation(s)
- Kevin T Militello
- Biology Department, State University of New York at Geneseo, Geneseo, New York, USA
| | - Hristina Nedelkovska
- Biology Department, State University of New York at Geneseo, Geneseo, New York, USA
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Qaqish B, Sallam M, Al-Khateeb M, Reisdorf E, Mahafzah A. Assessment of COVID-19 Molecular Testing Capacity in Jordan: A Cross-Sectional Study at the Country Level. Diagnostics (Basel) 2022; 12:909. [PMID: 35453957 PMCID: PMC9024853 DOI: 10.3390/diagnostics12040909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic control measures rely on the accurate and timely diagnosis of infected individuals. Real-time polymerase chain reaction (qPCR) remains the gold-standard method for laboratory diagnosis of the disease. Delayed diagnosis due to challenges that face laboratories performing COVID-19 testing can hinder public health control measures. Such challenges may be related to shortages in staff, equipment or materials, improper inventory management, flawed workflow, or long turnaround time (TAT). The aim of the current study was to assess the overall COVID-19 molecular testing capacity in Jordan as of April 2021. In addition, the study’s objectives included the identification of potential defects that could comprise the utility of the COVID-19 molecular testing capacity in the country. All laboratories certified by the Ministry of Health (MoH) in Jordan to conduct molecular testing for SARS-CoV-2 were invited to participate in this study. Data were obtained from the participating laboratories (those which agreed to participate) by either telephone interviews or a self-reported written questionnaire with items assessing the key aspects of COVID-19 molecular testing. The full molecular testing capacity in each laboratory was self-reported considering 24 working hours. The total number of participating laboratories was 51 out of 77 (66.2%), with the majority being affiliated with MoH (n = 17) and private laboratories (n = 20). The total molecular COVID-19 testing capacity among the participating laboratories was estimated at 574,441 tests per week, while the actual highest number of tests performed over a single week was 310,047 (54.0%, reported in March 2021). Laboratories affiliated with the MoH were operating at a level closer to their maximum capacity (87.2% of their estimated full capacity for COVID-19 testing) compared to private hospital laboratories (41.3%, p = 0.004), private laboratories (20.8%, p < 0.001), and academic/research laboratories (14.7%, p < 0.001, ANOVA). The national average daily COVID-19 molecular testing was 349.2 tests per 100,000 people in April 2021. The average TAT over the first week of April 2021 for COVID-19 testing was 932 min among the participating laboratories, with the longest TAT among MoH laboratories (mean: 1959 min) compared to private laboratories (mean: 333 min, p < 0.001). Molecular COVID-19 testing potential in Jordan has not been fully utilized, particularly for private laboratories and those belonging to academic/research centers. Supply-chain challenges and shortages in staff were identified as potential obstacles hindering the exploitation of full molecular testing capacity for COVID-19 in the country.
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Affiliation(s)
- Bara’a Qaqish
- Abt Associates, United States Agency for International Development (USAID) Funded Local Health System Sustainability Project (LHSS), Amman 11822, Jordan;
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22184 Malmo, Sweden
| | | | - Erik Reisdorf
- Infectious Disease Detection and Surveillance (IDDS), Rockville, MD 20894, USA;
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
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Antoine D, Mohammadi M, Vitt M, Dickie JM, Jyoti SS, Tilbury MA, Johnson PA, Wawrousek KE, Wall JG. Rapid, Point-of-Care scFv-SERS Assay for Femtogram Level Detection of SARS-CoV-2. ACS Sens 2022; 7:866-873. [PMID: 35271769 PMCID: PMC8961876 DOI: 10.1021/acssensors.1c02664] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/02/2022] [Indexed: 12/19/2022]
Abstract
Rapid, sensitive, on-site identification of SARS-CoV-2 infections is an important tool in the control and management of COVID-19. We have developed a surface-enhanced Raman scattering (SERS) immunoassay for highly sensitive detection of SARS-CoV-2. Single-chain Fv (scFv) recombinant antibody fragments that bind the SARS-CoV-2 spike protein were isolated by biopanning a human scFv library. ScFvs were conjugated to magnetic nanoparticles and SERS nanotags, followed by immunocomplex formation and detection of the SARS-CoV-2 spike protein with a limit of detection of 257 fg/mL in 30 min in viral transport medium. The assay also detected B.1.1.7 ("alpha"), B.1.351 ("beta"), and B.1.617.2 ("delta") spike proteins, while no cross-reactivity was observed with the common human coronavirus HKU1 spike protein. Inactivated whole SARS-CoV-2 virus was detected at 4.1 × 104 genomes/mL, which was 10-100-fold lower than virus loads typical of infectious individuals. The assay exhibited higher sensitivity for SARS-CoV-2 than commercial lateral flow assays, was compatible with viral transport media and saliva, enabled rapid pivoting to detect new virus variants, and facilitated highly sensitive, point-of-care diagnosis of COVID-19 in clinical and public health settings.
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Affiliation(s)
- Delphine Antoine
- Microbiology,
College of Science and Engineering, and SFI Centre for Medical Devices
(CÚRAM), National University of Ireland,
Galway (NUI Galway), Galway H91 TK33, Ireland
| | - Moein Mohammadi
- Chemical
Engineering, University of Wyoming, Laramie, Wyoming 82072, United States
| | - Madison Vitt
- Chemical
Engineering, University of Wyoming, Laramie, Wyoming 82072, United States
| | - Julia Marie Dickie
- Chemical
Engineering, University of Wyoming, Laramie, Wyoming 82072, United States
| | | | - Maura A. Tilbury
- Microbiology,
College of Science and Engineering, and SFI Centre for Medical Devices
(CÚRAM), National University of Ireland,
Galway (NUI Galway), Galway H91 TK33, Ireland
| | - Patrick A. Johnson
- Chemical
Engineering, University of Wyoming, Laramie, Wyoming 82072, United States
| | - Karen E. Wawrousek
- Chemical
Engineering, University of Wyoming, Laramie, Wyoming 82072, United States
| | - J. Gerard Wall
- Microbiology,
College of Science and Engineering, and SFI Centre for Medical Devices
(CÚRAM), National University of Ireland,
Galway (NUI Galway), Galway H91 TK33, Ireland
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35
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Twigg C, Wenk J. Review and Meta‐Analysis: SARS‐CoV‐2 and Enveloped Virus Detection in Feces and Wastewater. CHEMBIOENG REVIEWS 2022. [PMCID: PMC9083821 DOI: 10.1002/cben.202100039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Detection and quantification of viruses supplies key information on their spread and allows risk assessment for public health. In wastewater, existing detection methods have been focusing on non‐enveloped enteric viruses due to enveloped virus transmission, such as coronaviruses, by the fecal‐oral route being less likely. Since the beginning of the SARS‐CoV‐2 pandemic, interest and importance of enveloped virus detection in wastewater has increased. Here, quantitative studies on SARS‐CoV‐2 occurrence in feces and raw wastewater and other enveloped viruses via quantitative real‐time reverse transcription polymerase chain reaction (RT‐qPCR) during the early stage of the pandemic until April 2021 are reviewed, including statistical evaluation of the positive detection rate and efficiency throughout the detection process involving concentration, extraction, and amplification stages. Optimized and aligned sampling protocols and concentration methods for enveloped viruses, along with SARS‐CoV‐2 surrogates, in wastewater environments may improve low and variable recovery rates providing increased detection efficiency and comparable data on viral load measured across different studies.
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Affiliation(s)
- Charlotte Twigg
- University of Bath Department of Chemical Engineering and Water Innovation and Research Centre (WIRC@Bath) Claverton Down BA2 7AY Bath Somerset United Kingdom
| | - Jannis Wenk
- University of Bath Department of Chemical Engineering and Water Innovation and Research Centre (WIRC@Bath) Claverton Down BA2 7AY Bath Somerset United Kingdom
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36
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Kundrod KA, Natoli ME, Chang MM, Smith CA, Paul S, Ogoe D, Goh C, Santhanaraj A, Price A, Eldin KW, Patel KP, Baker E, Schmeler KM, Richards-Kortum R. Sample-to-answer, extraction-free, real-time RT-LAMP test for SARS-CoV-2 in nasopharyngeal, nasal, and saliva samples: Implications and use for surveillance testing. PLoS One 2022; 17:e0264130. [PMID: 35213596 PMCID: PMC8880874 DOI: 10.1371/journal.pone.0264130] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 02/03/2022] [Indexed: 12/19/2022] Open
Abstract
The global COVID-19 pandemic has highlighted the need for rapid, accurate and accessible nucleic acid tests to enable timely identification of infected individuals. We optimized a sample-to-answer nucleic acid test for SARS-CoV-2 that provides results in <1 hour using inexpensive and readily available reagents. The test workflow includes a simple lysis and viral inactivation protocol followed by direct isothermal amplification of viral RNA using RT-LAMP. The assay was validated using two different instruments, a portable isothermal fluorimeter and a standard thermocycler. Results of the RT-LAMP assay were compared to traditional RT-qPCR for nasopharyngeal swabs, nasal swabs, and saliva collected from a cohort of patients hospitalized due to COVID-19. For all three sample types, positive agreement with RT-LAMP performed using the isothermal fluorimeter was 100% for samples with Ct <30 and 69-91% for samples with Ct <40. Following validation, the test was successfully scaled to test the saliva of up to 400 asymptomatic individuals per day as part of the campus surveillance program at Rice University. Successful development, validation, and scaling of this sample-to-answer, extraction-free real-time RT-LAMP test for SARS-CoV-2 adds a highly adaptable tool to efforts to control the COVID-19 pandemic, and can inform test development strategies for future infectious disease threats.
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Affiliation(s)
- Kathryn A. Kundrod
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Mary E. Natoli
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Megan M. Chang
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Chelsey A. Smith
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Sai Paul
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Dereq Ogoe
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Christopher Goh
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Akshaya Santhanaraj
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Anthony Price
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Karen W. Eldin
- McGovern Medical School, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ellen Baker
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Kathleen M. Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
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Santarelli IM, Sierra M, Vaulet MLG, Fermepin MR, Fernández SI. Clinical Course of COVID-19 and Cycle Threshold in Patients with Haematological Neoplasms. Prague Med Rep 2022; 123:250-257. [DOI: 10.14712/23362936.2022.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The SARS-CoV-2 viral load in a respiratory sample can be inversely quantified using the cycle threshold (Ct), defined as the number of amplification cycles required to detect the viral genome in a quantitative PCR assay using reverse transcriptase (RT-qPCR). It may be classified as high (Ct < 25), intermediate (25–30) and low (Ct > 30). We describe the clinical course of 3 patients with haematological neoplasms who contracted COVID-19. None of them had been vaccinated. Firstly, a 22-year-old male with a refractory acute lymphoblastic leukaemia experienced an oligosymptomatic COVID-19 and had a Ct of 23 with an ascending curve. Another male, aged 23, had recently begun treatment for a promyelocytic leukaemia. He had a subacute course with high oxygen requirements. His Ct dropped from 28, when he only experienced fever, to 14.8, during the most critical period and on the edge of ventilatory support. Viral clearance was documented 126 days after the beginning of the symptoms. Finally, a 60-year-old male had received rituximab as maintenance therapy for a follicular lymphoma 3 months before contracting COVID-19. He had a fulminant course and required mechanical ventilation a few days later. We highlight the association between the course of CoViD-19 and the Ct. Viral shedding was longer than in immunocompetent hosts.
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38
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Zhang K, Fan Z, Huang Y, Ding Y, Xie M. A strategy combining 3D-DNA Walker and CRISPR-Cas12a trans-cleavage activity applied to MXene based electrochemiluminescent sensor for SARS-CoV-2 RdRp gene detection. Talanta 2022; 236:122868. [PMID: 34635250 PMCID: PMC8429000 DOI: 10.1016/j.talanta.2021.122868] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 12/22/2022]
Abstract
Early diagnosis and timely management of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are the keys to preventing the spread of the epidemic and controlling new infection clues. Therefore, strengthening the surveillance of the epidemic and timely screening and confirming SARS-CoV-2 infection is the primary task. In this work, we first proposed the idea of activating CRISPR-Cas12a activity using double-stranded DNA amplified by a three-dimensional (3D) DNA walker. We applied it to the design of an electrochemiluminescent (ECL) biosensor to detect the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) gene. We first activated the cleavage activity of CRISPR-Cas12a by amplifying the target DNA into a segment of double-stranded DNA through the amplification effect of a 3D DNA walker. At the same time, we designed an MXene based ECL material: PEI-Ru@Ti3C2@AuNPs, and constructed an ECL biosensor to detect the RdRp gene based on this ECL material as a framework. Activated CRISPR-Cas12a cleaves the single-stranded DNA on the surface of this sensor and causes the ferrocene modified at one end of the DNA to move away from the electrode surface, increasing the ECL signal. The extent of the change in electrochemiluminescence reflects the concentration of the gene to be measured. Using this system, we detected the SARS-CoV-2 RdRp gene with a detection limit of 12.8 aM. This strategy contributes to the rapid and convenient detection of SARS-CoV-2-associated nucleic acids and promotes the clinical application of ECL biosensors based on CRISPR-Cas12a and novel composite materials.
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Affiliation(s)
- Kai Zhang
- NHC Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China.
| | - Zhenqiang Fan
- NHC Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Yue Huang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Yuedi Ding
- NHC Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Minhao Xie
- NHC Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China.
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39
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Konka A, Lejawa M, Gaździcka J, Bochenek A, Fronczek M, Strzelczyk JK. RT-PCR Detection of SARS-CoV-2 among Individuals from the Upper Silesian Region-Analysis of 108,516 Tests. Diagnostics (Basel) 2021; 12:diagnostics12010007. [PMID: 35054172 PMCID: PMC8774892 DOI: 10.3390/diagnostics12010007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 02/06/2023] Open
Abstract
Background: The COVID-19 pandemic triggered by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has left a huge mark on everyday lives, introducing restrictions and plunging the global economy. This study aimed to analyze the available epidemiological data from the register of one of the largest laboratories testing for SARS-CoV-2 in the Silesian voivodship of Poland. Methods: This analysis is based upon the epidemiological records collected between 30 March 2020, and 30 April 2021, by the Silesian Park of Medical Technology Kardio-Med Silesia (Zabrze, Poland). In addition, we performed SARS-CoV-2 variant detection in samples from patients reinfected with SARS-CoV-2. Results: Our results confirm that SARS-CoV-2 infections are more common in urban areas. Laboratory-confirmed COVID-19 cases represent 13.21% of all RT-PCR test results during the 13 months of our laboratory diagnostics for SARS-CoV-2 infections. Detection of SARS-CoV-2 variants in samples of potentially reinfected patients showed discrepancies in the results. Conclusions: Due to the higher risk of SARS-CoV-2 infection among the Upper Silesian population, the region is at greater risk of deteriorating economic situation and healthcare as compared to other areas of Poland. RT-PCR methods are inexpensive and suitable for large-scale screening, but they can be untrustworthy so detection of SARS-CoV-2 variants in samples should be confirmed by sequencing.
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Affiliation(s)
- Adam Konka
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.L.); (A.B.); (M.F.)
- Correspondence: ; Tel.: +48-32-705-03-05
| | - Mateusz Lejawa
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.L.); (A.B.); (M.F.)
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Jordana 38 Str., 41-808 Zabrze, Poland
| | - Jadwiga Gaździcka
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19 Str., 41-808 Zabrze, Poland; (J.G.); (J.K.S.)
| | - Aneta Bochenek
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.L.); (A.B.); (M.F.)
| | - Martyna Fronczek
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.L.); (A.B.); (M.F.)
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Jordana 38 Str., 41-808 Zabrze, Poland
| | - Joanna Katarzyna Strzelczyk
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19 Str., 41-808 Zabrze, Poland; (J.G.); (J.K.S.)
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40
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Agaoglu NB, Yildiz J, Akgun Dogan O, Kose B, Alkurt G, Kendir Demirkol Y, Irvem A, Doganay L, Dinler Doganay G. COVID-19 PCR test performance on samples stored at ambient temperature. J Virol Methods 2021; 301:114404. [PMID: 34921841 PMCID: PMC8673954 DOI: 10.1016/j.jviromet.2021.114404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 11/20/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022]
Abstract
The WHO-named Coronavirus Disease 2019 (COVID-19) infection had become a pandemic within a short time period since it was detected in Wuhan. The outbreak required the screening of millions of samples daily and overwhelmed diagnostic laboratories worldwide. During this pandemic, the handling of patient specimens according to the universal guidelines was extremely difficult as the WHO, CDC and ECDC required cold chain compliance during transport and storage of the swab samples. The aim of this study was to compare the effects of two different storage conditions on the COVID-19 real-time PCR assay on 30 positive nasopharyngeal and/or oropharyngeal samples stored at both ambient temperature (22 ± 2 °C) and +4 °C. The results revealed that all the samples stored at ambient temperature remain PCR positive for at least six days without any false-negative result. In conclusion, transporting and storing these types of swab samples at ambient temperature for six days under resource-limited conditions during the COVID-19 pandemics are acceptable.
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Affiliation(s)
- Nihat Bugra Agaoglu
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Medical Genetics, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Jale Yildiz
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Ozlem Akgun Dogan
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Pediatric Genetics, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Betsi Kose
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Gizem Alkurt
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Yasemin Kendir Demirkol
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Medical Genetics, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Arzu Irvem
- Department of Microbiology, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Levent Doganay
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Gastroenterology, Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Gizem Dinler Doganay
- Genomic Laboratory (GLAB), Umraniye Teaching and Research Hospital, University of Health Sciences, Istanbul, Turkey; Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.
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41
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Taylor SC. A practical approach to SARS-CoV-2 testing in a pre and post-vaccination era. JOURNAL OF CLINICAL VIROLOGY PLUS 2021; 1:100044. [PMID: 35262025 PMCID: PMC8500693 DOI: 10.1016/j.jcvp.2021.100044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/23/2021] [Accepted: 10/02/2021] [Indexed: 11/26/2022] Open
Abstract
As countries globally are in the process of planning, introducing or implementing mass vaccination strategies while continuing to deal with the ongoing SARS-CoV-2 pandemic, an evolution in testing strategies may be required to minimize spread in mixed vaccinated and non-vaccinated populations. This mini-review explores the key public health questions associated with the widely varying efficacy of commercially available vaccines and their persistence of protection in the context of a growing number of variant virus strains. A new strategy for SARS-CoV-2 testing that accommodates the current and evolving pandemic paradigm is proposed.
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Affiliation(s)
- Sean C Taylor
- GENSCRIPT USA INC. 860 Centennial Ave., Piscataway 08854, NJ, United States
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42
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Adedoyin O, Brijmohan S, Lavine R, Lisung FG. Undetectable SARS-CoV-2 active adaptive immunity-post-vaccination or post-COVID-19 severe disease-after immunosuppressants use. BMJ Case Rep 2021; 14:14/11/e246308. [PMID: 34844968 PMCID: PMC8634224 DOI: 10.1136/bcr-2021-246308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Since the beginning of COVID-19 vaccination in New Jersey in December 2020, we have observed multiple cases of undetectable adaptive immunity, post-vaccination or post-COVID-19 infection, in patients using immunosuppressants. Here, we present three cases of patients using immunosuppressants: mycophenolate and tacrolimus for renal transplant; ocrelizumab for multiple sclerosis and rituximab for peripheral ulcerative keratitis. All three patients were admitted for acute respiratory distress syndrome (ARDS) from COVID-19 pneumonia; two patients reported having received full COVID-19 vaccination prior to admission and one unvaccinated patient required readmission. Our findings showed that these patients tested negative for SARS-CoV-2 IgM spike and CoV-2 IgG nucleocapsid antibodies. All three patients were treated with standard-of-care remdesivir, dexamethasone and convalescent plasma; two recovered successfully and one patient died from respiratory failure secondary to worsening ARDS from COVID-19 pneumonia. We highlight the challenges of treating immunosuppressed patients with COVID-19 pneumonia, in an era where dissemination of such information is paramount to helping doctors standardise and improve the quality of care for these patients.
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Affiliation(s)
- Oluwafeyi Adedoyin
- Internal Medicine Residency Program, Englewood Hospital and Medical Center, Englewood, New Jersey, USA
| | - Sharmela Brijmohan
- Internal Medicine Residency Program, Englewood Hospital and Medical Center, Englewood, New Jersey, USA
| | - Ross Lavine
- Internal Medicine Residency Program, Englewood Hospital and Medical Center, Englewood, New Jersey, USA
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43
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Asai S, Seki A, Akai Y, Tazawa H, Kakizoe H, Ravzanaaadii MA, Miyachi H. Nationwide external quality assessment of SARS-CoV-2 nucleic acid amplification tests in Japan. Int J Infect Dis 2021; 115:86-92. [PMID: 34800690 PMCID: PMC8595969 DOI: 10.1016/j.ijid.2021.11.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/27/2022] Open
Abstract
Objectives We conducted a nationwide external quality assessment (EQA) study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid amplification testing in Japan. Methods A total of 563 public health and private sector laboratories participated. The EQA samples comprised 6 RNA and full-process controls. Results The overall agreements were 99.3% and 97.9% for the RNA and full-process controls, respectively. A total of 530/563 (94.1%) laboratories reported correct results; public health laboratories had the highest accuracy. Thirty-three laboratories reported at least one incorrect result (26 laboratories of medical facilities, 5 commercial laboratories, 1 public health laboratory, and 1 other). Sixteen laboratories of medical facilities that used a fully automated assay system failed to detect the presence of the full-process control, due to inherent insufficiency in the limit of detection (LOD). Other causes of incorrect results included failure to ensure the LOD (n = 13), error in result judging or reporting (n = 3), and error in sample handling (n = 1). Conclusions Performance was mostly dependent on the laboratory category and assay evaluation, particularly the LOD. Guidance should be developed based on these results, particularly in the phase of new entry into laboratory services for SARS-CoV-2.
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Affiliation(s)
- Satomi Asai
- Department of Laboratory Medicine, Tokai University School of Medicine, Isehara Kanagawa, Japan.
| | - Akira Seki
- Department of Laboratory Medicine, Tokai University School of Medicine, Isehara Kanagawa, Japan.
| | - Yasumasa Akai
- Scientific Research, Scientific Affairs, Sysmex corporation, Kobe, Japan.
| | - Hiromitsu Tazawa
- Clinical Bioresource Center, Kyoto University Hospital, Kyoto, Japan.
| | - Hidehumi Kakizoe
- Department of Laboratory Medicine, Tokai University School of Medicine, Isehara Kanagawa, Japan.
| | - Mend-Amar Ravzanaaadii
- Department of Laboratory Medicine, Tokai University School of Medicine, Isehara Kanagawa, Japan.
| | - Hayato Miyachi
- Department of Laboratory Medicine, Tokai University School of Medicine, Isehara Kanagawa, Japan.
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Hober A, Tran-Minh KH, Foley D, McDonald T, Vissers JPC, Pattison R, Ferries S, Hermansson S, Betner I, Uhlén M, Razavi M, Yip R, Pope ME, Pearson TW, Andersson LN, Bartlett A, Calton L, Alm JJ, Engstrand L, Edfors F. Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis. eLife 2021; 10:e70843. [PMID: 34747696 PMCID: PMC8626084 DOI: 10.7554/elife.70843] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/04/2021] [Indexed: 12/11/2022] Open
Abstract
Reliable, robust, large-scale molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for monitoring the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a scalable analytical approach to detect viral proteins based on peptide immuno-affinity enrichment combined with liquid chromatography-mass spectrometry (LC-MS). This is a multiplexed strategy, based on targeted proteomics analysis and read-out by LC-MS, capable of precisely quantifying and confirming the presence of SARS-CoV-2 in phosphate-buffered saline (PBS) swab media from combined throat/nasopharynx/saliva samples. The results reveal that the levels of SARS-CoV-2 measured by LC-MS correlate well with their correspondingreal-time polymerase chain reaction (RT-PCR) read-out (r = 0.79). The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with a quantitative read-out of viral proteins corresponding to cycle thresholds (Ct) equivalents ranging from 21 to 34. Using RT-PCR as a reference, we demonstrate that the LC-MS-based method has 100% negative percent agreement (estimated specificity) and 95% positive percent agreement (estimated sensitivity) when analyzing clinical samples collected from asymptomatic individuals with a Ct within the limit of detection of the mass spectrometer (Ct ≤ 30). These results suggest that a scalable analytical method based on LC-MS has a place in future pandemic preparedness centers to complement current virus detection technologies.
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Affiliation(s)
| | - Khue Hua Tran-Minh
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
| | | | | | | | | | | | | | | | - Mathias Uhlén
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
| | | | - Richard Yip
- SISCAPA Assay Technologies, IncVictoriaCanada
| | | | | | | | | | | | - Jessica J Alm
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology & National Pandemic Center, Karolinska InstitutetSolnaSweden
| | - Lars Engstrand
- Microbiology, Tumour and Cell Biology, Karolinska InstitutetStockholmSweden
| | - Fredrik Edfors
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
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A semi-automated, isolation-free, high-throughput SARS-CoV-2 reverse transcriptase (RT) loop-mediated isothermal amplification (LAMP) test. Sci Rep 2021; 11:21385. [PMID: 34725400 PMCID: PMC8560768 DOI: 10.1038/s41598-021-00827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Shortages of reverse transcriptase (RT)-polymerase chain reaction (PCR) reagents and related equipment during the COVID-19 pandemic have demonstrated the need for alternative, high-throughput methods for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-mass screening in clinical diagnostic laboratories. A robust, SARS-CoV-2 RT-loop-mediated isothermal amplification (RT-LAMP) assay with high-throughput and short turnaround times in a clinical laboratory setting was established and compared to two conventional RT-PCR protocols using 323 samples of individuals with suspected SARS-CoV-2 infection. Limit of detection (LoD) and reproducibility of the isolation-free SARS-CoV-2 RT-LAMP test were determined. An almost perfect agreement (Cohen's kappa > 0.8) between the novel test and two classical RT-PCR protocols with no systematic difference (McNemar's test, P > 0.05) was observed. Sensitivity and specificity were in the range of 89.5 to 100% and 96.2 to 100% dependent on the reaction condition and the RT-PCR method used as reference. The isolation-free RT-LAMP assay showed high reproducibility (Tt intra-run coefficient of variation [CV] = 0.4%, Tt inter-run CV = 2.1%) with a LoD of 95 SARS-CoV-2 genome copies per reaction. The established SARS-CoV-2 RT-LAMP assay is a flexible and efficient alternative to conventional RT-PCR protocols, suitable for SARS-CoV-2 mass screening using existing laboratory infrastructure in clinical diagnostic laboratories.
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46
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Maltezou HC, Tseroni M, Daflos C, Anastassopoulou C, Vasilogiannakopoulos A, Daligarou O, Panagiotou M, Botsa E, Spanakis N, Lourida A, Tsakris A. Environmental testing for SARS-CoV-2 in three tertiary-care hospitals during the peak of the third COVID-19 wave. Am J Infect Control 2021; 49:1435-1437. [PMID: 34455029 PMCID: PMC8388137 DOI: 10.1016/j.ajic.2021.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 11/21/2022]
Abstract
Contamination of surfaces has been implicated in transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We tested by real-time PCR for SARS-CoV-2 contamination environmental samples from three hospitals during the peak of the third pandemic wave. Overall, 19 of 463 (4.1%) samples tested positive: 12 of 173 (6.9%) samples from a COVID-19 hospital, 3 of 177 (1.7%) samples from a non-COVID-19 hospital, and 4 of 113 (3.5%) samples from a pediatric hospital with dedicated COVID-19 clinics. Most positive samples originated from emergency departments (EDs) (47.3%) and the intensive care units (ICUs) (26.3%) of the COVID-19 hospital. Positive samples belonged almost exclusively (18/19) to the highly transmissible B.1.1.7 cluster, that might explain environmental contamination at this stage of the pandemic. The frequency and efficiency of disinfection in high-risk patient areas, such as EDs and ICUs, should be reinforced, especially during this period where highly transmissible variants of concern are widespread.
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47
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Zhang R, Tan P, Feng L, Li R, Yang J, Zhang R, Li J. External quality assessment of molecular testing of 9 viral encephalitis-related viruses in China. Virus Res 2021; 306:198598. [PMID: 34653568 DOI: 10.1016/j.virusres.2021.198598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Eastern equine encephalitis virus (EEEV), Western equine encephalitis virus (WEEV), Venezuelan equine encephalitis virus (VEEV), Hendra virus (HeV), Nipah virus (NiV), Yellow fever virus (YFV), West Nile virus (WNV), Saint Louis encephalitis virus (SLEV) and Tick-borne encephalitis virus (TBEV) have been detected in travelers returning to China and potentially pose a serious threat to public health. Real-time reverse transcription polymerase chain reaction (rRT-PCR) plays an important role in the detection of these viruses. Although these viruses are not mainly prevalent in China, occasionally imported cases have been reported with the increase in population mobility and entry-exit activities. Therefore, it is necessary to monitor the ability of major domestic laboratories to detect and identify exotic arbovirus infections in travelers. METHODS An external quality assessment program for the molecular detection of EEEV, VEEV, WEEV, SLEV, WNV, YFV, TBEV, HeV and NiV was organized. The assessment panel included 26 negative and positive samples with different concentrations of virus-like particles and distributed to 31 laboratories to evaluate the accuracy of virus detection. RESULTS At the laboratory level, 87.5% (7/8, EEEV), 85.7% (12/14, WEEV), 100% (13/13, VEEV), 87.5% (7/8, HeV), 76.5% (13/17, NiV), 92.6% (25/27, YFV), 81.3% (13/16, WNV), 100% (5/5, SLEV) and 75.0% (6/8, TBEV) of the participants were considered "competent". Of all the results, the false-positive and false-negative rates were 0.3% and 0.7%, respectively. The sensitivity of most detection assays (15/17, 88.2%) was more than 90%. In addition, we observed significantly different cycle threshold values when using primer-probe sets in different target regions to detect EEEV and SLEV. CONCLUSIONS Most laboratories have reliable virus detection capabilities. However, laboratory testing capabilities need to be improved to avoid cross-contamination and to better manage undetected false-negative samples.
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Affiliation(s)
- Runling Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Ping Tan
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Lei Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Rui Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Jing Yang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
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Chauhan N, Soni S, Jain U. Optimizing testing regimes for the detection of COVID-19 in children and older adults. Expert Rev Mol Diagn 2021; 21:999-1016. [PMID: 34324823 PMCID: PMC8425447 DOI: 10.1080/14737159.2021.1962708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Introduction: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is a major pandemic and continuously emerging due to unclear prognosis and unavailability of reliable detection tools. Older adults are more susceptible to COVID-19 than children showing mature Angiotensin-Converting Enzyme 2 (ACE2), low concentration of immune targets, and comorbid conditions. Several detection platforms have been commercialized to date and more are in pipeline, however, the rate of false-positive results and rapid mutation of SARS-CoV-2 is increasing. Additionally, physiological, and geographical variations of affected individuals are also calling for diagnostic methods optimization.Areas Covered: Extensive information related to the optimization and usefulness of SARS-CoV-2 diagnostic methods based on sensitivity and specificity as definitive and feasible investigative tools is discussed. Moreover, an option of combining laboratory diagnostic methods to improve diagnostic strategies is also proposed and discussed in the comparative section of optimization studies.Expert Opinion: The review article explains the importance of optimization strategies for SARS-CoV-2 detection in children and older adults. There are advancements in COVID-19 detection including CRISPR-based, electrochemical, and optical-based sensing systems. However, the lack of sufficient studies on a comparative evaluation of standardized SARS-CoV-2 diagnostic methods among children and older adults, limit the authentication of commercialized kits.
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Affiliation(s)
- Nidhi Chauhan
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida, India
| | - Shringika Soni
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida, India
| | - Utkarsh Jain
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida, India
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Mallach G, Kasloff SB, Kovesi T, Kumar A, Kulka R, Krishnan J, Robert B, McGuinty M, den Otter-Moore S, Yazji B, Cutts T. Aerosol SARS-CoV-2 in hospitals and long-term care homes during the COVID-19 pandemic. PLoS One 2021; 16:e0258151. [PMID: 34591919 PMCID: PMC8483369 DOI: 10.1371/journal.pone.0258151] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/19/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Few studies have quantified aerosol concentrations of SARS-CoV-2 in hospitals and long-term care homes, and fewer still have examined samples for viability. This information is needed to clarify transmission risks beyond close contact. METHODS We deployed particulate air samplers in rooms with COVID-19 positive patients in hospital ward and ICU rooms, rooms in long-term care homes experiencing outbreaks, and a correctional facility experiencing an outbreak. Samplers were placed between 2 and 3 meters from the patient. Aerosol (small liquid particles suspended in air) samples were collected onto gelatin filters by Ultrasonic Personal Air Samplers (UPAS) fitted with <2.5μm (micrometer) and <10 μm size-selective inlets operated for 16 hours (total 1.92m3), and with a Coriolis Biosampler over 10 minutes (total 1.5m3). Samples were assayed for viable SARS-CoV-2 virus and for the viral genome by multiplex PCR using the E and N protein target sequences. We validated the sampling methods by inoculating gelatin filters with viable vesicular stomatitis virus (VSV), and with three concentrations of viable SARS-CoV-2, operating personal samplers for 16hrs, and quantifying viable virus recovery by TCID50 assay. RESULTS In total, 138 samples were collected from 99 rooms. RNA samples were positive in 9.1% (6/66) of samples obtained with the UPAS 2.5μm samplers, 13.5% (7/52) with the UPAS 10μm samplers, and 10.0% (2/20) samples obtained with the Coriolis samplers. Culturable virus was not recovered in any samples. Viral RNA was detected in 15.1% of the rooms sampled. There was no significant difference in viral RNA recovery between the different room locations or samplers. Method development experiments indicated minimal loss of SARS-CoV-2 viability via the personal air sampler operation.
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Affiliation(s)
- Gary Mallach
- Water and Air Quality Bureau, Health Canada, Ottawa, Canada
| | - Samantha B. Kasloff
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Tom Kovesi
- Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, Canada
| | - Anand Kumar
- Sections of Critical Care Medicine and Infectious Diseases, Departments of Medicine, Medical Microbiology and Pharmacology, University of Manitoba, Winnipeg, Canada
| | - Ryan Kulka
- Water and Air Quality Bureau, Health Canada, Ottawa, Canada
| | - Jay Krishnan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Benoit Robert
- Department of Family Medicine, University of Ottawa, Ottawa, Canada
| | - Michaeline McGuinty
- Department of Medicine, Ottawa Hospital, University of Ottawa, Ottawa, Canada
| | | | - Bashour Yazji
- Department of Medicine, Ottawa Hospital, University of Ottawa, Ottawa, Canada
| | - Todd Cutts
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
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Comparison of SARS-CoV-2 Detection by Rapid Antigen and by Three Commercial RT-qPCR Tests: A Study from Martin University Hospital in Slovakia. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18137037. [PMID: 34280974 PMCID: PMC8295881 DOI: 10.3390/ijerph18137037] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/10/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022]
Abstract
The global pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is having a tremendous impact on the global economy, health care systems and the lives of almost all people in the world. The Central European country of Slovakia reached one of the highest daily mortality rates per 100,000 inhabitants in the first 3 months of 2021, despite implementing strong prophylactic measures, lockdowns and repeated nationwide antigen testing. The present study reports a comparison of the performance of the Standard Q COVID-19 antigen test (SD Biosensor) with three commercial RT-qPCR kits (vDetect COVID-19-MultiplexDX, gb SARS-CoV-2 Multiplex-GENERI BIOTECH Ltd. and Genvinset COVID-19 [E]-BDR Diagnostics) in the detection of infected individuals among employees of the Martin University Hospital in Slovakia. Health care providers, such as doctors and nurses, are classified as “critical infrastructure”, and there is no doubt about the huge impact that incorrect results could have on patients. Out of 1231 samples, 14 were evaluated as positive for SARS-CoV-2 antigen presence, and all of them were confirmed by RT-qPCR kit 1 and kit 2. As another 26 samples had a signal in the E gene, these 40 samples were re-isolated and subsequently re-analysed using the three kits, which detected the virus in 22, 23 and 12 cases, respectively. The results point to a divergence not only between antigen and RT-qPCR tests, but also within the “gold standard” RT-qPCR testing. Performance analysis of the diagnostic antigen test showed the positive predictive value (PPV) to be 100% and negative predictive value (NPV) to be 98.10%, indicating that 1.90% of individuals with a negative result were, in fact, positive. If these data are extrapolated to the national level, where the mean daily number of antigen tests was 250,000 in April 2021, it points to over 4700 people per day being misinterpreted and posing a risk of virus shedding. While mean Ct values of the samples that were both antigen and RT-qPCR positive were about 20 (kit 1: 20.47 and 20.16 for Sarbeco E and RdRP, kit 2: 19.37 and 19.99 for Sarbeco E and RdRP and kit 3: 17.47 for ORF1b/RdRP), mean Ct values of the samples that were antigen-negative but RT-qPCR-positive were about 30 (kit 1: 30.67 and 30.00 for Sarbeco E and RdRP, kit 2: 29.86 and 31.01 for Sarbeco E and RdRP and kit 3: 27.47 for ORF1b/RdRP). It confirms the advantage of antigen test in detecting the most infectious individuals with a higher viral load. However, the reporting of Ct values is still a matter of ongoing debates and should not be conducted without normalisation to standardised controls of known concentration.
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