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Santos DJAD, Oliveira TRD, Araújo GMD, Pott-Junior H, Melendez ME, Sabino EC, Leite OD, Faria RC. An electrochemical genomagnetic assay for detection of SARS-CoV-2 and Influenza A viruses in saliva. Biosens Bioelectron 2024; 255:116210. [PMID: 38537427 DOI: 10.1016/j.bios.2024.116210] [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: 12/31/2023] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 04/15/2024]
Abstract
Viral respiratory infections represent a major threat to the population's health globally. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease and in some cases the symptoms can be confused with Influenza disease caused by the Influenza A viruses. A simple, fast, and selective assay capable of identifying the etiological agent and differentiating the diseases is essential to provide the correct clinical management to the patient. Herein, we described the development of a genomagnetic assay for the selective capture of viral RNA from SARS-CoV-2 and Influenza A viruses in saliva samples and employing a simple disposable electrochemical device for gene detection and quantification. The proposed method showed excellent performance detecting RNA of SARS-CoV-2 and Influenza A viruses, with a limit of detection (LoD) and limit of quantification (LoQ) of 5.0 fmol L-1 and 8.6 fmol L-1 for SARS-CoV-2, and 1.0 fmol L-1 and 108.9 fmol L-1 for Influenza, respectively. The genomagnetic assay was employed to evaluate the presence of the viruses in 36 saliva samples and the results presented similar responses to those obtained by the real-time reverse transcription-polymerase chain reaction (RT-PCR), demonstrating the reliability and capability of a method as an alternative for the diagnosis of COVID-19 and Influenza with point-of-care capabilities.
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Affiliation(s)
| | | | | | - Henrique Pott-Junior
- Department of Medicine, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | | | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Oldair Donizeti Leite
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil; Federal Technological University of Paraná, Campus Medianeira, Medianeira, PR, 85884-000, Brazil.
| | - Ronaldo Censi Faria
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil.
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2
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G/meskel W, Desta K, Diriba R, Belachew M, Evans M, Cantarelli V, Urrego M, Sisay A, Gebreegziabxier A, Abera A. SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction-based assays in Addis Ababa, Ethiopia. IJID REGIONS 2024; 11:100363. [PMID: 38634071 PMCID: PMC11021353 DOI: 10.1016/j.ijregi.2024.100363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024]
Abstract
Objectives This study aimed to determine the SARS-CoV-2 variants in the first four COVID-19 waves using polymerase chain reaction (PCR)-based variant detection in Addis Ababa, Ethiopia. Methods A cross-sectional study was conducted using repository nasopharyngeal samples stored at the Ethiopian Public Health Institute COVID-19 testing laboratory. Stored positive samples were randomly selected from the first four waves based on their sample collection date. A total of 641 nasopharyngeal samples were selected and re-tested for SARS-CoV-2. RNA was extracted using nucleic acid purification instrument. Then, SARS-CoV-2 detection was carried out using 10 μl RNA and 20 μl reverse transcription-PCR fluorescent mix. Cycle threshold values <38 were considered positive. Results A total of 374 samples qualified for B.1.617 Lineage and six spike gene mutation variant typing kits. The variant typing kits identified 267 (71.4%) from the total qualifying samples. Alpha, Beta, Delta, and Omicron were dominantly identified variants from waves I, II, III, and IV, respectively. From the total identified positive study samples, 243 of 267 (91%) of variants identified from samples had cycle threshold values <30. Conclusions The study data demonstrated that reverse transcription-PCR-based variant typing can provide additional screening opportunities where sequencing opportunity is inaccessible. The assays could be implemented in laboratories performing SARS-CoV-2 molecular testing.
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Affiliation(s)
- Wodneh G/meskel
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Kassu Desta
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Regasa Diriba
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Mahlet Belachew
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Martin Evans
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Vlademir Cantarelli
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Maritza Urrego
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | | | - Adugna Abera
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
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3
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Morecchiato F, Coppi M, Niccolai C, Antonelli A, Di Gloria L, Calà P, Mancuso F, Ramazzotti M, Lotti T, Lubello C, Rossolini GM. Evaluation of different molecular systems for detection and quantification of SARS-CoV-2 RNA from wastewater samples. J Virol Methods 2024:114956. [PMID: 38796134 DOI: 10.1016/j.jviromet.2024.114956] [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: 11/29/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
Wastewater-based epidemiology has proved to be a suitable approach for tracking the spread of epidemic agents including SARS-CoV-2 RNA. Different protocols have been developed for quantitative detection of SARS-CoV-2 RNA from wastewater samples, but little is known on their performance. In this study we compared three protocols based on Reverse Transcription Real Time-PCR (RT-PCR) and one based on Droplet Digital PCR (ddPCR) for SARS-CoV-2 RNA detection from 35 wastewater samples. Overall, SARS-CoV-2 RNA was detected by at least one method in 85.7% of samples, while 51.4%, 22.8% and 8.6% resulted positive with two, three or all four methods, respectively. Protocols based on commercial RT-PCR assays and on Droplet Digital PCR showed an overall higher sensitivity vs. an in-house assay. The use of more than one system, targeting different genes, could be helpful to increase detection sensitivity.
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Affiliation(s)
- Fabio Morecchiato
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3 - 50134 Firenze (FI), Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3 - 50134 Firenze (FI), Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3 - 50134 Firenze (FI), Italy
| | - Claudia Niccolai
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3 - 50134 Firenze (FI), Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3 - 50134 Firenze (FI), Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3 - 50134 Firenze (FI), Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3 - 50134 Firenze (FI), Italy
| | - Leandro Di Gloria
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50 - 50134 Firenze (FI), Italy
| | - Piergiuseppe Calà
- Tuscany Region, Department of Prevention Local Health Authority Tuscany Center, Via S. Salvi, 12 - 50135 Firenze (FI), Italy
| | - Fabrizio Mancuso
- Ingegnerie Toscane - Area R&D, Via Bellatalla, 1 - 56121 Pisa (PI), Italy
| | - Matteo Ramazzotti
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50 - 50134 Firenze (FI), Italy
| | - Tommaso Lotti
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3 - 50139 Firenze (FI), Italy
| | - Claudio Lubello
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3 - 50139 Firenze (FI), Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3 - 50134 Firenze (FI), Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3 - 50134 Firenze (FI), Italy.
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4
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Thakali O, Mercier É, Eid W, Wellman M, Brasset-Gorny J, Overton AK, Knapp JJ, Manuel D, Charles TC, Goodridge L, Arts EJ, Poon AFY, Brown RS, Graber TE, Delatolla R, DeGroot CT. Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation. Sci Rep 2024; 14:3728. [PMID: 38355869 PMCID: PMC10866965 DOI: 10.1038/s41598-024-54319-y] [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: 08/02/2023] [Accepted: 02/11/2024] [Indexed: 02/16/2024] Open
Abstract
Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity of RT-qPCR has been achieved, in part, by monitoring two or more genomic loci of SARS-CoV-2. In Ontario, Canada, the provincial Wastewater Surveillance Initiative reports the average copies of the CDC N1 and N2 loci normalized to the fecal biomarker pepper mild mottle virus. In November 2021, the emergence of the Omicron variant of concern, harboring a C28311T mutation within the CDC N1 probe region, challenged the accuracy of the consensus between the RT-qPCR measurements of the N1 and N2 loci of SARS-CoV-2. In this study, we developed and applied a novel real-time dual loci quality assurance and control framework based on the relative difference between the loci measurements to the City of Ottawa dataset to identify a loss of sensitivity of the N1 assay in the period from July 10, 2022 to January 31, 2023. Further analysis via sequencing and allele-specific RT-qPCR revealed a high proportion of mutations C28312T and A28330G during the study period, both in the City of Ottawa and across the province. It is hypothesized that nucleotide mutations in the probe region, especially A28330G, led to inefficient annealing, resulting in reduction in sensitivity and accuracy of the N1 assay. This study highlights the importance of implementing quality assurance and control criteria to continually evaluate, in near real-time, the accuracy of the signal produced in wastewater surveillance applications that rely on detection of pathogens whose genomes undergo high rates of mutation.
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Affiliation(s)
- Ocean Thakali
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Martin Wellman
- The Ottawa Hospital Research Institute, 1053 Carling Ave, Ottawa, ON, K1Y 4E9, Canada
| | - Julia Brasset-Gorny
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Alyssa K Overton
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Jennifer J Knapp
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Douglas Manuel
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
- Department of Family Medicine, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON, K1N 6N5, Canada
- School of Epidemiology and Public Health, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON, K1N 6N5, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Lawrence Goodridge
- Department of Food Science, Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Art F Y Poon
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - R Stephen Brown
- School of Environmental Studies and Department of Chemistry, Queen's University, Kingston, ON, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher T DeGroot
- Department of Mechanical and Materials Engineering, Western University, London, ON, N6A 5B9, Canada.
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5
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Chung PYJ, Dhillon SK, Simoens C, Cuypers L, Laenen L, Bonde J, Corbisier P, Buttinger G, Cocuzza CE, Van Gucht S, Van Ranst M, Arbyn M. Assessment of the clinical and analytical performance of three Seegene Allplex SARS-CoV-2 assays within the VALCOR framework. Microbiol Spectr 2024; 12:e0239723. [PMID: 38189291 PMCID: PMC10846132 DOI: 10.1128/spectrum.02397-23] [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: 06/09/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic demonstrated the need for accurate diagnostic testing for the early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although the pandemic has ended, accurate assays are still needed to monitor viral spread at national levels and beyond through population and wastewater surveillance. To enhance early detection, SARS-CoV-2 assays should have high diagnostic accuracy and should be validated to assure accurate results. Three distinct SARS-CoV-2 assays were evaluated with clinical samples using the VALCOR (VALidation of SARS-CORona Virus-2 assays) framework, with the TaqPath COVID-19 assay (ThermoFisher Scientific, USA) as a comparator. We evaluated clinical sensitivity, specificity, limit of detection (LOD), and overall concordance between comparator and three index Allplex SARS-CoV-2 assays (Seegene, South Korea): Allplex-SC2, Allplex-SC2Fast (Fast PCR), and Allplex-SC2FabR (SARS-CoV-2/FluA/FluB/respiratory syncytial virus). Analytical performance and LOD of index assays were assessed using a dilution series of three synthetic SARS-CoV-2 sequence reference materials (RMs). Ninety SARS-CoV-2 positives and 90 SARS-CoV-2 negatives were tested. All Allplex assays had 100.0% sensitivity (95%CI = 95.9%-100.0%). Allplex-SC2 and Allplex-SC2Fast assays had 97.8% specificity (95%CI = 92.3%-99.7%) and 98.9% overall concordance [κ = 0.978 (95%CI = 0.947-1.000)]. Allplex-SC2FabR assay showed 100.0% specificity (95%CI = 95.9%-100.0%) and 100.0% overall concordance [κ = 1.000 (95%CI = 1.000-1.000)]. LOD assessment of index assays revealed detection down to 2.61 × 102 copies/mL in clinical samples, while the analytical LOD was 9.00 × 102 copies/mL. In conclusion, the evaluation of the three Seegene Allplex SARS-CoV-2 assays showed high sensitivity and specificity and an overall good assay concordance with the comparator. The assays showed low analytical LOD using RM and even a slightly lower LOD in clinical samples. Non-overlapping target gene sequences between SARS-CoV-2 assays and RMs emphasize the need for aligning targeted sequences of diagnostic assays and RMs.IMPORTANCEThe coronavirus disease 2019 pandemic has a significant impact on global public health, economies, and societies. As shown through the first phases of the pandemic, accurate and timely diagnosis is crucial for disease control, prevention, and monitoring. Though the pandemic phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has concluded, diagnostic assays remain in demand to monitor SARS-CoV-2 at the individual patient level, regionally, and nationally, as well as to remain an infectious disease preparedness instrument to monitor any new SARS-CoV-2 dissemination across borders using population and wastewater surveillance. The anticipation by WHO and central health care policy entities such as the Center for Disease Control, EMA, and multiple national health authorities is that SARS-CoV-2 will reside as an endemic respiratory disease for years to come. The key strategic consideration is hence shifting from combating a pandemic situation with a high number of patients to instead allowing precise diagnostics of suspected patients with the intention of correct management in a low-prevalence setting.
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Affiliation(s)
- Pui Yan Jenny Chung
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
| | - Sharonjit K. Dhillon
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
| | - Cindy Simoens
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
| | - Lize Cuypers
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Lies Laenen
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Jesper Bonde
- Molecular Pathology Laboratory, Department of Pathology, AHH-Hvidovre Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Clementina E. Cocuzza
- Laboratory of Clinical Microbiology and Virology, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marc Arbyn
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
- Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, University of Ghent, Ghent, Belgium
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6
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Rai A, Ammi Z, Anes-Boulahbal DL, Assadi AA, Amrane A, Baaloudj O, Mouni L. Molecular Amplification and Cell Culturing Efficiency for Enteroviruses' Detection in Cerebrospinal Fluids of Algerian Patients Suffering from Meningitis. Viruses 2024; 16:170. [PMID: 38399946 PMCID: PMC10891896 DOI: 10.3390/v16020170] [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: 01/05/2024] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/25/2024] Open
Abstract
Enteroviruses (EVs) represent a major cause of viral meningitis, being responsible for nearly 1 billion infections each year worldwide. Several techniques were developed to obtain better diagnostic results of EV infections. Herein, we evaluated the efficiency of EV detection through isolation on both Rhabdomyosarcoma (RD) and Vero cell line cultures, conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR. Thus, 50 cerebrospinal fluid (CSF) samples belonging to patients suspected to have viral meningitis in northern Algeria were collected, anonymously numbered from 1 to 50 and subjected to the above-mentioned techniques for EV detection. Using real-time RT-PCR, 34 CSF samples were revealed to be positive for viral origin of meningitis (68%). Thirteen of them were positive when the conventional RT-PCR was used (26%), and only three samples gave positive results when the cell culture technique was used (6%). Surprisingly, two cell culture-positive CSF samples, namely, 31 and 39, were negative using RT-PCR directly on the original samples. However, they turned to be positive when amplification was carried out on their corresponding cell culture supernatant. The cell-cultured viral isolates were then identified by sequencing their viral genome's VP1 regions. All of them were revealed to belong to the echovirus 27 strain. This investigation demonstrates that RT-PCR techniques are often more sensitive, accurate and much faster, providing reliable results within a clinically acceptable timeframe. However, viral isolation on cell cultures remains crucial to obtain enough viral load for serological tests or even to avoid the rare, but existing, false negative PCR.
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Affiliation(s)
- Abdelwahab Rai
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité, Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
| | - Zohra Ammi
- Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
| | - Dahbia Leila Anes-Boulahbal
- Laboratoire des Entérovirus, Département de Virologie, Institut Pasteur d’Alger, Annexe de Sidi-Fredj, Alger 16000, Algeria;
| | - Aymen Amin Assadi
- College of Engineering, Imam Mohammad Ibn Saud Islamic University, IMSIU, Riyadh 11432, Saudi Arabia;
- Ecole Nationale Supérieure de Chimie de Rennes, University Rennes, CNRS, ISCR-UMR 6226, 35000 Rennes, France;
| | - Abdeltif Amrane
- Ecole Nationale Supérieure de Chimie de Rennes, University Rennes, CNRS, ISCR-UMR 6226, 35000 Rennes, France;
| | - Oussama Baaloudj
- Laboratory of Reaction Engineering, Faculty of Mechanical Engineering and Process Engineering, Université des Sciences et de la Technologie Houari Boumediene, BP 32, Algiers 16111, Algeria;
| | - Lotfi Mouni
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité, Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
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Saldivar-Espinoza B, Garcia-Segura P, Novau-Ferré N, Macip G, Martínez R, Puigbò P, Cereto-Massagué A, Pujadas G, Garcia-Vallve S. The Mutational Landscape of SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24109072. [PMID: 37240420 DOI: 10.3390/ijms24109072] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mutation research is crucial for detecting and treating SARS-CoV-2 and developing vaccines. Using over 5,300,000 sequences from SARS-CoV-2 genomes and custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in the SARS-CoV-2 genome has mutated at some time, the substantial differences in the frequency and regularity of mutations warrant further examination. C>U mutations are the most common. They are found in the largest number of variants, pangolin lineages, and countries, which indicates that they are a driving force behind the evolution of SARS-CoV-2. Not all SARS-CoV-2 genes have mutated in the same way. Fewer non-synonymous single nucleotide variations are found in genes that encode proteins with a critical role in virus replication than in genes with ancillary roles. Some genes, such as spike (S) and nucleocapsid (N), show more non-synonymous mutations than others. Although the prevalence of mutations in the target regions of COVID-19 diagnostic RT-qPCR tests is generally low, in some cases, such as for some primers that bind to the N gene, it is significant. Therefore, ongoing monitoring of SARS-CoV-2 mutations is crucial. The SARS-CoV-2 Mutation Portal provides access to a database of SARS-CoV-2 mutations.
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Affiliation(s)
- Bryan Saldivar-Espinoza
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Pol Garcia-Segura
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Nil Novau-Ferré
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Guillem Macip
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | | | - Pere Puigbò
- Department of Biology, University of Turku, 20500 Turku, Finland
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, 43007 Tarragona, Spain
- Eurecat, Technology Centre of Catalonia, Unit of Nutrition and Health, 43204 Reus, Spain
| | - Adrià Cereto-Massagué
- EURECAT Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Santiago Garcia-Vallve
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
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8
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Liu X, Wang X, Zhang H, Yan Z, Gaňová M, Lednický T, Řezníček T, Xu Y, Zeng W, Korabečná M, Neužil P. Smartphone integrated handheld (SPEED) digital polymerase chain reaction device. Biosens Bioelectron 2023; 232:115319. [PMID: 37087984 DOI: 10.1016/j.bios.2023.115319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023]
Abstract
We demonstrate a smartphone integrated handheld (SPEED) digital polymerase chain reaction (dPCR) device for point-of-care application. The device has dimensions of ≈100 × 200 × 35 mm3 and a weight of ≈400 g. It can perform 45 PCR cycles in ≈49 min. The device also features integrated, miniaturized modules for thermal cycling, image taking, and wireless data communication. These functions are controlled by self-developed Android-based applications. The only consumable is the developed silicon-based dPCR chip, which has the potential to be recycled. The device's precision and accuracy are comparable with commercial dPCR machines. We have verified the SPEED dPCR prototype's utility in the testing of severe acute respiratory syndrome coronavirus 2, the detection of cancer-associated gene sequences, and the confirmations of Down syndrome diagnoses. Due to its low upfront capital investment, as well as its nominal running cost, we envision that the SPEED dPCR device will help to perform cancer screenings and non-invasive prenatal tests for the general population. It will also aid in the timely identification and monitoring of infectious disease testing, thereby expediting alerts with respect to potential emerging pandemics.
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Affiliation(s)
- Xiaocheng Liu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Xinlu Wang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Haoqing Zhang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Ministry of Education Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, PR China
| | - Zhiqiang Yan
- School of Marine Science and Technology, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, PR China
| | - Martina Gaňová
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300, Brno, Czech Republic; Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600, Brno, Czech Republic
| | - Tomáš Lednický
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300, Brno, Czech Republic
| | - Tomáš Řezníček
- ITD Tech s.r.o, Osvoboditelu 1005, 735 81, Bohumín, Czech Republic
| | - Ying Xu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Wen Zeng
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital of Prague, Albertov 4, 12800, Prague, Czech Republic
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600, Brno, Czech Republic.
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