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Luciani L, Combe P, Touret F, Gazin C, Klitting R, Pezzi L, Thirion L, Charrel R, Grard G, de Lamballerie X, Nougairède A. Broad-spectrum dengue virus detection using the commercial RealStar dengue RT-PCR kit 3.0 (Altona) and an in-house combined real-time RT-PCR assay. Heliyon 2024; 10:e31252. [PMID: 38803933 PMCID: PMC11128986 DOI: 10.1016/j.heliyon.2024.e31252] [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: 11/07/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
In endemic areas, the genetic diversity among co-circulating dengue virus (DENV) strains is considerable and new, highly divergent strains are identified on a regular basis. It is thus critical to ensure that molecular diagnostic tools effectively detect virus genomes even in case of important genetic variation. Here, we tested both the pan-DENV detection capacity and the limit of detection of two real-time RT-PCR assays: (i) the commercial RealStar Altona 3.0 system and (ii) a laboratory developed test (LDT) combining two RT-PCR systems in a single reaction tube (DenAllDUO). We used a panel of DENV strains representative of the genetic diversity within DENV species, combined with three in vitro transcribed RNAs as surrogates for unavailable strains corresponding to recently discovered strains with substantial genetic divergence: DENV serotype 1 (DENV-1) Brun2014, DENV-2 QML22 and DENV-4 DKE121. Both systems (i) targeted the genome 3' untranslated region, (ii) displayed a broad detection spectrum, encompassing most of DENV species diversity, and (iii) detected the three aforementioned divergent strains. DenAllDUO detected all the strains tested, whereas the RealStar system failed to detect strains from DENV-4 genotype III. Altogether, our findings support the value of these two RT-PCR systems as part of the Dengue diagnostic arsenal.
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Affiliation(s)
- Léa Luciani
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Pierre Combe
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Céline Gazin
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Raphaëlle Klitting
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Laura Pezzi
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Rémi Charrel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Gilda Grard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- National Reference Center for Arboviruses, National Institute of Health and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
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Yaugel-Novoa M, Noailly B, Jospin F, Berger AE, Waeckel L, Botelho-Nevers E, Longet S, Bourlet T, Paul S. Prior COVID-19 Immunization Does Not Cause IgA- or IgG-Dependent Enhancement of SARS-CoV-2 Infection. Vaccines (Basel) 2023; 11:vaccines11040773. [PMID: 37112685 PMCID: PMC10141984 DOI: 10.3390/vaccines11040773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Antibody-dependent enhancement (ADE) can increase the rates and severity of infection with various viruses, including coronaviruses, such as MERS. Some in vitro studies on COVID-19 have suggested that prior immunization enhances SARS-CoV-2 infection, but preclinical and clinical studies have demonstrated the contrary. We studied a cohort of COVID-19 patients and a cohort of vaccinated individuals with a heterologous (Moderna/Pfizer) or homologous (Pfizer/Pfizer) vaccination scheme. The dependence on IgG or IgA of ADE of infection was evaluated on the serum samples from these subjects (twenty-six vaccinated individuals and twenty-one PCR-positive SARS-CoV-2-infected patients) using an in vitro model with CD16- or CD89-expressing cells and the Delta (B.1.617.2 lineage) and Omicron (B.1.1.529 lineage) variants of SARS-CoV-2. Sera from COVID-19 patients did not show ADE of infection with any of the tested viral variants. Some serum samples from vaccinated individuals displayed a mild IgA-ADE effect with Omicron after the second dose of the vaccine, but this effect was abolished after the completion of the full vaccination scheme. In this study, FcγRIIIa- and FcαRI-dependent ADE of SARS-CoV-2 infection after prior immunization, which might increase the risk of severe disease in a second natural infection, was not observed.
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Affiliation(s)
- Melyssa Yaugel-Novoa
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
| | - Blandine Noailly
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
| | - Fabienne Jospin
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
| | - Anne-Emmanuelle Berger
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
- Immunology Department, University Hospital of Saint-Etienne, F42055 Saint-Etienne, France
| | - Louis Waeckel
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
- Immunology Department, University Hospital of Saint-Etienne, F42055 Saint-Etienne, France
| | - Elisabeth Botelho-Nevers
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
- Infectious Diseases Department, University Hospital of Saint-Etienne, F42055 Saint-Etienne, France
| | - Stéphanie Longet
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
| | - Thomas Bourlet
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
- Infectious Agents and Hygiene Department, University Hospital of Saint-Etienne, F42055 Saint-Etienne, France
| | - Stéphane Paul
- CIRI—Centre International de Recherche en Infectiologie, Team GIMAP, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, F42023 Saint-Etienne, France
- Immunology Department, University Hospital of Saint-Etienne, F42055 Saint-Etienne, France
- CIC 1408 Inserm Vaccinology, University Hospital of Saint-Etienne, F42055 Saint-Etienne, France
- Correspondence:
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Preclinical study of a DNA vaccine targeting SARS-CoV-2. Curr Res Transl Med 2022; 70:103348. [PMID: 35489099 PMCID: PMC9020527 DOI: 10.1016/j.retram.2022.103348] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/09/2022] [Accepted: 04/16/2022] [Indexed: 01/31/2023]
Abstract
To fight against the worldwide COVID-19 pandemic, the development of an effective and safe vaccine against SARS-CoV-2 is required. As potential pandemic vaccines, DNA/RNA vaccines, viral vector vaccines and protein-based vaccines have been rapidly developed to prevent pandemic spread worldwide. In this study, we designed plasmid DNA vaccine targeting the SARS-CoV-2 Spike glycoprotein (S protein) as pandemic vaccine, and the humoral, cellular, and functional immune responses were characterized to support proceeding to initial human clinical trials. After intramuscular injection of DNA vaccine encoding S protein with alum adjuvant (three times at 2-week intervals), the humoral immunoreaction, as assessed by anti-S protein or anti-receptor-binding domain (RBD) antibody titers, and the cellular immunoreaction, as assessed by antigen-induced IFNγ expression, were up-regulated. In IgG subclass analysis, IgG2b was induced as the main subclass. Based on these analyses, DNA vaccine with alum adjuvant preferentially induced Th1-type T cell polarization. We confirmed the neutralizing action of DNA vaccine-induced antibodies by a binding assay of RBD recombinant protein with angiotensin-converting enzyme 2 (ACE2), a receptor of SARS-CoV-2, and neutralization assays using pseudo-virus, and live SARS-CoV-2. Further B cell epitope mapping analysis using a peptide array showed that most vaccine-induced antibodies recognized the S2 and RBD subunits. Finally, DNA vaccine protected hamsters from SARS-CoV-2 infection. In conclusion, DNA vaccine targeting the spike glycoprotein of SARS-CoV-2 might be an effective and safe approach to combat the COVID-19 pandemic.
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SARS-CoV-2-Antigenschnelltests. PRÄVENTION UND GESUNDHEITSFÖRDERUNG 2022. [PMCID: PMC9363140 DOI: 10.1007/s11553-022-00970-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Hintergrund Zur Detektion SARS-CoV-2-Infizierter („severe acute respiratory syndrome coronavirus 2“) ist die quantitative Real-Time-PCR (qRT-PCR) Goldstandard. Antigenschnelltests haben gegenüber der PCR-Diagnostik den Vorteil, dass sie schnell Ergebnisse liefern und vor Ort durchführbar sind. Nachteil der Schnelltests ist ihre schlechtere Sensitivität und Spezifität. Mittlerweile sind mehrere hundert Schnelltests auf der BfArm-Liste zu finden, die aber noch nicht alle herstellerunabhängig evaluiert wurden. Ziel der Arbeit Untersuchung der diagnostischen Performance von SARS-CoV-2-Antigenschnelltests unterschiedlicher Hersteller. Material und Methoden Es wurden naso- und oropharyngeale Abstrichtupfer verwendet, welche zuvor mittels qRT-PCR positiv auf SARS-CoV‑2 getestet wurden. Diese Tupfer wurden anschließend in verschiedenen Antigenschnelltests eingesetzt. Zum Ausschluss eines möglichen Verdünnungseffekts aufgrund erneuten Einsatzes der Tupfer erfolgte zuvor eine erneute PCR-Messung, in der sich die ursprünglich gemessenen Ct-Werte der Proben wiederfinden ließen. Ergebnisse Die von uns untersuchten Schnelltests erwiesen sich als sehr unterschiedlich in ihrer Fähigkeit, zwischen positiven und negativen Proben zu diskriminieren. Generell erwies sich jedoch der Einsatz von Schnelltests im Bereich niedriger Viruskonzentrationen (Ct-Wert > 30) als nicht zuverlässig. Für den sicheren Nachweis einer SARS-CoV-2-Infektion sind sie daher nicht geeignet. Diskussion Schnelltests mit hoher Sensitivität ermöglichen einen Einsatz vor Ort, der zügig hochinfektiöse Patienten identifizieren kann. Es gibt allerdings deutliche Unterschiede zwischen verschiedenen Herstellern. Hier ist, im Sinne einer validen Patientenversorgung, eine unabhängige, transparente Evaluation von Schnelltests zu fordern.
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Li X, Kulandaivelu J, Guo Y, Zhang S, Shi J, O'Brien J, Arora S, Kumar M, Sherchan SP, Honda R, Jackson G, Luby SP, Jiang G. SARS-CoV-2 shedding sources in wastewater and implications for wastewater-based epidemiology. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128667. [PMID: 35339834 PMCID: PMC8908579 DOI: 10.1016/j.jhazmat.2022.128667] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 05/21/2023]
Abstract
Wastewater-based epidemiology (WBE) approach for COVID-19 surveillance is largely based on the assumption of SARS-CoV-2 RNA shedding into sewers by infected individuals. Recent studies found that SARS-CoV-2 RNA concentration in wastewater (CRNA) could not be accounted by the fecal shedding alone. This study aimed to determine potential major shedding sources based on literature data of CRNA, along with the COVID-19 prevalence in the catchment area through a systematic literature review. Theoretical CRNA under a certain prevalence was estimated using Monte Carlo simulations, with eight scenarios accommodating feces alone, and both feces and sputum as shedding sources. With feces alone, none of the WBE data was in the confidence interval of theoretical CRNA estimated with the mean feces shedding magnitude and probability, and 63% of CRNA in WBE reports were higher than the maximum theoretical concentration. With both sputum and feces, 91% of the WBE data were below the simulated maximum CRNA in wastewater. The inclusion of sputum as a major shedding source led to more comparable theoretical CRNA to the literature WBE data. Sputum discharging behavior of patients also resulted in great fluctuations of CRNA under a certain prevalence. Thus, sputum is a potential critical shedding source for COVID-19 WBE surveillance.
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Affiliation(s)
- Xuan Li
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | | | - Ying Guo
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Shuxin Zhang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Jiahua Shi
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
| | - Jake O'Brien
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Woollongabba, Queensland 4072, Australia
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, 6E, Malviya Industrial Area, Malviya Nagar, Jaipur 302017, India
| | - Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India
| | - Samendra P Sherchan
- Department of Environmental health sciences, Tulane University, New Orleans, LA 70112, USA; Bioenvironmental Science Program, Morgan Staate University, Baltimore, MD 21251, USA
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Greg Jackson
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Woollongabba, Queensland 4072, Australia
| | - Stephen P Luby
- Stanford Center for Innovation in Global Health, and Stanford Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia.
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Gdoura M, Abouda I, Mrad M, Ben Dhifallah I, Belaiba Z, Fares W, Chouikha A, Khedhiri M, Layouni K, Touzi H, Sadraoui A, Hammemi W, Meddeb Z, Hogga N, Ben Fadhel S, Haddad-Boubaker S, Triki H. SARS-CoV2 RT-PCR assays: In vitro comparison of 4 WHO approved protocols on clinical specimens and its implications for real laboratory practice through variant emergence. Virol J 2022; 19:54. [PMID: 35346227 PMCID: PMC8959265 DOI: 10.1186/s12985-022-01784-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
Introduction RT-PCR testing on nasopharyngeal swabs is a key component in the COVID-19 fighting, provided to use sensitive and specific SARS-CoV2 genome targets. In this study, we aimed to evaluate and to compare 4 widely used WHO approved RT-PCR protocols on real clinical specimens, to decrypt the reasons of the diverging results and to propose recommendations for the choice of the genome targets. Methods 260 nasopharyngeal samples were randomly selected among the samples tested between Week-16, 2020 and week-16 2021, in the Institut Pasteur de Tunis, Tunisia, one of the referent laboratories of COVID-19 in Tunisia. All samples were tested by Charité, Berlin protocol (singleplex envelop (E) and singleplex RNA-dependent RNA polymerase (RdRp)), Hong Kong Universiy, China protocol (singleplex nucleoprotein (N) and singleplex Open reading frame Orf1b), commercial test DAAN Gene® (using the CDC China protocol), (triplex N, Orf1ab with internal control) and Institut Pasteur Paris protocol (IPP) (triplex IP2(nsp9) and IP4 (nsp12) with internal control). For IPP, a selection from samples positive by IP2 but negative with IP4 was re-tested by exactly the same protocol but this time in singleplex. New results were described and analyzed. Results In vitro analysis showed discordant results in 29.2% of cases (76 out of 260). The most discordant protocol is DAAN Gene® due to the false positive late signals with N target. Discordant results between the two protocol’s targets are more frequent when viral load are low (high Ct values). Our results demonstrated that the multiplexing has worsened the sensitivity of the IP4 target. Conclusion We provide concise recommendations for the choice of the genome targets, the interpretation of the results and the alarm signals which makes suspect a gene mutation.
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Affiliation(s)
- Mariem Gdoura
- Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia. .,Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia. .,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Imen Abouda
- Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia.,Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Mehdi Mrad
- Laboratory of Biochemistry and Hormonology, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Imen Ben Dhifallah
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Zeineb Belaiba
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Wasfi Fares
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Maroua Khedhiri
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Kaouther Layouni
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Walid Hammemi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Zina Meddeb
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Nahed Hogga
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Sihem Ben Fadhel
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Research Laboratory « Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health» LR20IPT02, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
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Lopez E, Barthélémy M, Baronti C, Masse S, Falchi A, Durbesson F, Vincentelli R, de Lamballerie X, Charrel R, Coutard B. Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants. iScience 2021; 24:103329. [PMID: 34697603 PMCID: PMC8529542 DOI: 10.1016/j.isci.2021.103329] [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: 08/23/2021] [Revised: 08/23/2021] [Accepted: 10/19/2021] [Indexed: 12/02/2022] Open
Abstract
Since the beginning of the COVID-19 pandemics, variants have emerged. Some of them display increased transmissibility and/or resistance to immune response. Most of the mutations involved in the functional adaptation are found in the receptor-binding motif (RBM), close to the interface with the receptor ACE2. We thus developed a fast molecular assay to detect mutations in the RBM coding sequence. After amplification, the amplicon is heat-denatured and hybridized with an amplicon of reference. The presence of a mutation can be detected using a mismatch-specific endonuclease and the cleavage pattern is analyzed by capillary electrophoresis. The method was validated on RNA of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants produced in vitro before being implemented for clinical samples. The assay showed 97.8% sensitivity and 97.8% specificity. The procedure can be set up for high-throughput identification of the presence of mutations and serve as a first-line screening to select the samples for full genome sequencing.
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Affiliation(s)
- Eva Lopez
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Margot Barthélémy
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Cécile Baronti
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Shirley Masse
- UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France
| | - Alessandra Falchi
- UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France
| | - Fabien Durbesson
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Rémi Charrel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- Comité de Lutte contre les Infections Nosocomiales, Hôpitaux Universitaires de Marseille, AP-HM, Marseille, France
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
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Van Poelvoorde LAE, Gand M, Fraiture MA, De Keersmaecker SCJ, Verhaegen B, Van Hoorde K, Cay AB, Balmelle N, Herman P, Roosens N. Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution. Curr Issues Mol Biol 2021; 43:1937-1949. [PMID: 34889894 PMCID: PMC8928932 DOI: 10.3390/cimb43030134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
The worldwide emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since 2019 has highlighted the importance of rapid and reliable diagnostic testing to prevent and control the viral transmission. However, inaccurate results may occur due to false negatives (FN) caused by polymorphisms or point mutations related to the virus evolution and compromise the accuracy of the diagnostic tests. Therefore, PCR-based SARS-CoV-2 diagnostics should be evaluated and evolve together with the rapidly increasing number of new variants appearing around the world. However, even by using a large collection of samples, laboratories are not able to test a representative collection of samples that deals with the same level of diversity that is continuously evolving worldwide. In the present study, we proposed a methodology based on an in silico and in vitro analysis. First, we used all information offered by available whole-genome sequencing data for SARS-CoV-2 for the selection of the two PCR assays targeting two different regions in the genome, and to monitor the possible impact of virus evolution on the specificity of the primers and probes of the PCR assays during and after the development of the assays. Besides this first essential in silico evaluation, a minimal set of testing was proposed to generate experimental evidence on the method performance, such as specificity, sensitivity and applicability. Therefore, a duplex reverse-transcription droplet digital PCR (RT-ddPCR) method was evaluated in silico by using 154 489 whole-genome sequences of SARS-CoV-2 strains that were representative for the circulating strains around the world. The RT-ddPCR platform was selected as it presented several advantages to detect and quantify SARS-CoV-2 RNA in clinical samples and wastewater. Next, the assays were successfully experimentally evaluated for their sensitivity and specificity. A preliminary evaluation of the applicability of the developed method was performed using both clinical and wastewater samples.
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Affiliation(s)
- Laura A. E. Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Marie-Alice Fraiture
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Sigrid C. J. De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Bavo Verhaegen
- Food Pathogens, Sciensano, 1050 Brussels, Belgium; (B.V.); (K.V.H.)
| | | | - Ann Brigitte Cay
- Enzootic, Vector-Borne and Bee Diseases, Sciensano, 1180 Brussels, Belgium; (A.B.C.); (N.B.)
| | - Nadège Balmelle
- Enzootic, Vector-Borne and Bee Diseases, Sciensano, 1180 Brussels, Belgium; (A.B.C.); (N.B.)
| | - Philippe Herman
- Expertise and Service Provision, Sciensano, 1050 Brussels, Belgium;
| | - Nancy Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
- Correspondence:
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Are Posterior Oropharyngeal Saliva Specimens an Acceptable Alternative to Nasopharyngeal Sampling for the Monitoring of SARS-CoV-2 in Primary-Care Settings? Viruses 2021; 13:v13050761. [PMID: 33926069 PMCID: PMC8145717 DOI: 10.3390/v13050761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 11/30/2022] Open
Abstract
Background: The present study was set up to evaluate the efficacy of virological surveillance using posterior oropharyngeal saliva samples to monitor the COVID-19 pandemic in general practice. Methods: Posterior oropharyngeal saliva samples were collected without restriction on timing or alimentation by general practitioners from patients with acute respiratory infection (ARI) seen in consultation. Saliva samples were tested by real-time reverse transcription polymerase chain reaction for SARS-CoV-2 and 21 other respiratory pathogens. Results for SARS-CoV-2 in saliva samples were compared to results obtained using a nasopharyngeal swab (NPS) collected in a certified medical laboratory before or after the ARI consultation. Results: Overall, 143 ARI patients were enrolled between 6 June 2020, and 19 January 2021. SARS-CoV-2 RNA was detected in 37.0% (n = 53) of saliva samples and in 39.0% (n = 56) of NPS. Both saliva and NPS were positive in 51 patients. Positive and negative results were concordant between saliva samples and NPS in 51 (96.2%) and in 85 (94.4%) patients, respectively, with a Cohen’s Kappa coefficient of 0.89 (95% CI 0.82–0.97, p < 0.001). Other respiratory viruses were detected in 28.0% (n = 40) of the 143 saliva samples. Conclusions: Findings suggest that saliva samples could represent an attractive alternative to NPS for surveillance of SARS-CoV-2 in patients consulting for an ARI in primary care.
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Bustin S, Mueller R, Shipley G, Nolan T. COVID-19 and Diagnostic Testing for SARS-CoV-2 by RT-qPCR-Facts and Fallacies. Int J Mol Sci 2021; 22:2459. [PMID: 33671091 PMCID: PMC7957603 DOI: 10.3390/ijms22052459] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/19/2022] Open
Abstract
Although molecular testing, and RT-qPCR in particular, has been an indispensable component in the scientific armoury targeting SARS-CoV-2, there are numerous falsehoods, misconceptions, assumptions and exaggerated expectations with regards to capability, performance and usefulness of the technology. It is essential that the true strengths and limitations, although publicised for at least twenty years, are restated in the context of the current COVID-19 epidemic. The main objective of this commentary is to address and help stop the unfounded and debilitating speculation surrounding its use.
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Affiliation(s)
- Stephen Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford CM1 1SQ, UK;
| | | | | | - Tania Nolan
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford CM1 1SQ, UK;
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Thirion L, Pezzi L, Pedrosa-Corral I, Sanbonmatsu-Gamez S, Lamballerie XD, Falchi A, Perez-Ruiz M, Charrel RN. Evaluation of a Trio Toscana Virus Real-Time RT-PCR Assay Targeting Three Genomic Regions within Nucleoprotein Gene. Pathogens 2021; 10:pathogens10030254. [PMID: 33668339 PMCID: PMC7996202 DOI: 10.3390/pathogens10030254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/01/2021] [Accepted: 02/16/2021] [Indexed: 12/30/2022] Open
Abstract
Toscana virus (TOSV) can cause central nervous system infections in both residents of and travelers to Mediterranean countries. Data mining identified three real-time RT-qPCR assays for detecting TOSV RNA targeting non-overlapping regions in the nucleoprotein gene. Here, they were combined to create a multi-region assay named Trio TOSV RT-qPCR consisting of six primers and three probes. In this study, (i) we evaluated in silico the three RT-qPCR assays available in the literature for TOSV detection, (ii) we combined the three systems to create the Trio TOSV RT-qPCR, (iii) we assessed the specificity and sensitivity of the three monoplex assays versus the Trio TOSV RT-qPCR assay, and (iv) we compared the performance of the Trio TOSV RT-qPCR assay with one of the reference monoplex assays on clinical samples. In conclusion, the Trio TOSV RT-qPCR assay performs equally or better than the three monoplex assays; therefore, it provides a robust assay that can be used for both research and diagnostic purposes.
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Affiliation(s)
- Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.T.); (L.P.); (X.D.L.)
| | - Laura Pezzi
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.T.); (L.P.); (X.D.L.)
- UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France;
| | - Irene Pedrosa-Corral
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs.Granada, 18014 Granada, Spain; (I.P.-C.); (S.S.-G.); (M.P.-R.)
| | - Sara Sanbonmatsu-Gamez
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs.Granada, 18014 Granada, Spain; (I.P.-C.); (S.S.-G.); (M.P.-R.)
| | - Xavier De Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.T.); (L.P.); (X.D.L.)
| | - Alessandra Falchi
- UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France;
| | - Mercedes Perez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs.Granada, 18014 Granada, Spain; (I.P.-C.); (S.S.-G.); (M.P.-R.)
| | - Remi N. Charrel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), 13005 Marseille, France; (L.T.); (L.P.); (X.D.L.)
- Correspondence:
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