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Erster O, Bar-Or I, Azar R, Assraf H, Kabat A, Mannasse B, Moshayoff V, Fleishon S, Preis SA, Yishai R, Teijman-Yarden N, Aguvaev I, Matar R, Aydenzon A, Mandelboim M, Zuckerman NS, Sofer D, Lustig Y. Incursion of SARS-CoV-2 BA.2.86.1 variant into Israel: National-scale wastewater surveillance using a novel quantitative real-time PCR assay. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173164. [PMID: 38735317 DOI: 10.1016/j.scitotenv.2024.173164] [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: 01/14/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
The emergence of the SARS-CoV-2 variant BA.2.86.1 raised a considerable concern, due to the large number of potentially virulent mutations. In this study, we developed a novel assay that specifically detects variant BA.2.86.1, and used it to screen environmental samples from wastewater treatment sites across Israel. By using a multiplex assay that included a general SARS-CoV-2 reaction, together with the BA.2.86.1-specific reaction and a control reaction, we quantified the absolute number of viral copies in each sample and its relative abundance, compared with the total copy number of circulating SARS-CoV-2. Evaluation of the new reactions showed that they are both sensitive and specific, detecting down to four copies per reaction, and maintain specificity in the presence of Omicron variants BA.1, 2 and 4 RNA. Examination of 279 samples from 30 wastewater collection sites during August-September 2023 showed that 35 samples (12.5 %) were positive, from 18 sites. Quantitative analysis of the samples showed that the relative abundance of variant BA.2.86.1 with respect to the total viral load of SARS-CoV-2 was very low and consisted between 0.01 % and 0.6 % of the total SARS-CoV-2 circulation. This study demonstrates the importance of combining wastewater surveillance with the development of specialized diagnostic assays, when clinical testing is insufficient. This approach may be useful for timely response by public health authorities in future outbreaks.
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Affiliation(s)
- Oran Erster
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel.
| | - Itay Bar-Or
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Roberto Azar
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Hadar Assraf
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Areej Kabat
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Batya Mannasse
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Vardit Moshayoff
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Shay Fleishon
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Ruth Yishai
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Irina Aguvaev
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Roaa Matar
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Alex Aydenzon
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Danit Sofer
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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2
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Hilti D, Wehrli F, Berchtold S, Bigler S, Bodmer T, Seth-Smith HMB, Roloff T, Kohler P, Kahlert CR, Kaiser L, Egli A, Risch L, Risch M, Wohlwend N. S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5. Microorganisms 2024; 12:321. [PMID: 38399725 PMCID: PMC10892681 DOI: 10.3390/microorganisms12020321] [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: 12/31/2023] [Revised: 01/24/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
During the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex TaqPathTM COVID-19 CE-IVD RT-PCR Kit for large-scale routine diagnostic testing in Switzerland and the principality of Liechtenstein. The TaqPath Kit is a widely used multiplex assay targeting three genes (i.e., ORF1AB, N, S). With emergence of the B.1.1.7 (Alpha) variant, a diagnostic flaw became apparent as the amplification of the S-gene target was absent in these samples due to a deletion (ΔH69/V70) in the Alpha variant genome. This S-gene target failure (SGTF) was the earliest indication of a new variant emerging and was also observed in subsequent variants such as Omicron BA.1 and BA4/BA.5. The Delta variant and Omicron BA.2 did not present with SGTF. From September 2020 to November 2022, we investigated the applicability of the SGTF as a surrogate marker for emerging variants such as B.1.1.7, B.1.617.2 (Delta), and Omicron BA.1, BA.2, and BA.4/BA.5 in samples with cycle threshold (Ct) values < 30. Next to true SGTF-positive and SGTF-negative samples, there were also samples presenting with delayed-type S-gene amplification (higher Ct value for S-gene than ORF1ab gene). Among these, a difference of 3.8 Ct values between the S- and ORF1ab genes was found to best distinguish between "true" SGTF and the cycle threshold variability of the assay. Samples above the cutoff were subsequently termed partial SGTF (pSGTF). Variant confirmation was performed by whole-genome sequencing (Oxford Nanopore Technology, Oxford, UK) or mutation-specific PCR (TIB MOLBIOL). In total, 17,724 (7.4%) samples among 240,896 positives were variant-confirmed, resulting in an overall sensitivity and specificity of 93.2% [92.7%, 93.7%] and 99.3% [99.2%, 99.5%], respectively. Sensitivity was increased to 98.2% [97.9% to 98.4%] and specificity lowered to 98.9% [98.6% to 99.1%] when samples with pSGTF were included. Furthermore, weekly logistic growth rates (α) and sigmoid's midpoint (t0) were calculated based on SGTF data and did not significantly differ from calculations based on comprehensive data from GISAID. The SGTF therefore allowed for a valid real-time estimate for the introduction of all dominant variants in Switzerland and Liechtenstein.
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Affiliation(s)
- Dominique Hilti
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
- Institute of Laboratory Medicine, Private University in the Principality of Liechtenstein (UFL), 9495 Triesen, Liechtenstein
| | - Faina Wehrli
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
| | | | - Susanna Bigler
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
| | - Thomas Bodmer
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
| | | | - Tim Roloff
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Philipp Kohler
- Zentrallabor, Kantonsspital Graubünden, 7000 Chur, Switzerland
| | - Christian R. Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, 9007 St. Gallen, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Lorenz Risch
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
- Institute of Laboratory Medicine, Private University in the Principality of Liechtenstein (UFL), 9495 Triesen, Liechtenstein
| | - Martin Risch
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, 9007 St. Gallen, Switzerland
| | - Nadia Wohlwend
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
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3
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Perez-Romero CA, Mendoza-Maldonado L, Tonda A, Coz E, Tabeling P, Vanhomwegen J, MacSharry J, Szafran J, Bobadilla-Morales L, Corona-Rivera A, Claassen E, Garssen J, Kraneveld AD, Lopez-Rincon A. An Innovative AI-based primer design tool for precise and accurate detection of SARS-CoV-2 variants of concern. Sci Rep 2023; 13:15782. [PMID: 37737287 PMCID: PMC10516913 DOI: 10.1038/s41598-023-42348-y] [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: 12/19/2022] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
As the COVID-19 pandemic winds down, it leaves behind the serious concern that future, even more disruptive pandemics may eventually surface. One of the crucial steps in handling the SARS-CoV-2 pandemic was being able to detect the presence of the virus in an accurate and timely manner, to then develop policies counteracting the spread. Nevertheless, as the pandemic evolved, new variants with potentially dangerous mutations appeared. Faced by these developments, it becomes clear that there is a need for fast and reliable techniques to create highly specific molecular tests, able to uniquely identify VOCs. Using an automated pipeline built around evolutionary algorithms, we designed primer sets for SARS-CoV-2 (main lineage) and for VOC, B.1.1.7 (Alpha) and B.1.1.529 (Omicron). Starting from sequences openly available in the GISAID repository, our pipeline was able to deliver the primer sets for the main lineage and each variant in a matter of hours. Preliminary in-silico validation showed that the sequences in the primer sets featured high accuracy. A pilot test in a laboratory setting confirmed the results: the developed primers were favorably compared against existing commercial versions for the main lineage, and the specific versions for the VOCs B.1.1.7 and B.1.1.529 were clinically tested successfully.
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Affiliation(s)
- Carmina Angelica Perez-Romero
- Departamento de Investigación, Universidad Central de Queretaro (UNICEQ), Av. 5 de Febrero 1602, San Pablo, Santiago de Querétaro, 76130, Qro., Mexico
| | - Lucero Mendoza-Maldonado
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", Salvador Quevedo y Zubieta 750, Independencia Oriente, C.P. 44340, Guadalajara, Jalisco, México
| | - Alberto Tonda
- UMR 518 MIA Paris-Saclay, INRAE, AgroParisTech, Université Paris-Saclay, 91120, Palaiseau, France
| | - Etienne Coz
- CBI, ESPCI Paris, Université PSL, CNRS, 75005, Paris, France
| | | | | | - John MacSharry
- School of Microbiology and School of Medicine, University College Cork, College Rd, University College, Cork, Ireland
| | - Joanna Szafran
- School of Microbiology and School of Medicine, University College Cork, College Rd, University College, Cork, Ireland
| | - Lucina Bobadilla-Morales
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", Salvador Quevedo y Zubieta 750, Independencia Oriente, C.P. 44340, Guadalajara, Jalisco, México
| | - Alfredo Corona-Rivera
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", Salvador Quevedo y Zubieta 750, Independencia Oriente, C.P. 44340, Guadalajara, Jalisco, México
| | - Eric Claassen
- Athena Institute, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
- Department Immunology, Danone Nutricia research, Uppsalalaan 12, 3584 CT, Utrecht, The Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Alejandro Lopez-Rincon
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands.
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
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4
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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5
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Eptaminitaki GC, Parakatselaki ME, Petroulaki C, Marinopoulou D, Pitsikaki A, Tseliou M, Zafiropoulos A, Sourvinos G. Rapid identification of SARS-CoV-2 variants: Validation of the Simplexa SARS-CoV-2 Variant Direct assay. J Virol Methods 2023:114759. [PMID: 37257757 PMCID: PMC10226276 DOI: 10.1016/j.jviromet.2023.114759] [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: 03/07/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/02/2023]
Abstract
The circulation of certain SARS-CoV-2 variants may have a great impact on the epidemiological status of a geographical area; therefore, it is important that their presence is monitored. Currently, the gold standard method used to identify newly emerged variants is sequencing of either genes or whole genomes. However, since this method is relatively expensive and has a long turnaround time, other rapid strategies should also be employed. The current study aimed to evaluate the performance of the Simplexa® SARS-CoV-2 Variants Direct assay, which is a RT-PCR that determines the variant present in a nasopharyngeal swab sample in approximately two hours. Totally, 527 positive samples for SARS-CoV-2 were analyzed from January until December 2022 and next-generation sequencing (NGS) was used as the reference method. The assay showed high sensitivity, ranging from 94.12% to 100%, depending on the variant. The assay also showed high specificity, reaching 100% for Delta and BA.1 variants, and 99.74% and 98.67% for BA.2 and BA.4/BA.5 variants, respectively. Moreover, the assay was able to identify the correct variant category in the presence of any subvariant in the sample. We conclude that the assay can be used to facilitate faster monitoring of circulating SARS-CoV-2 variants, however sequencing cannot be completely replaced, since new variants always emerge, and constant updates are needed, so that the user is able to interpret the melting curve patterns.
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Affiliation(s)
- Giasemi C Eptaminitaki
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Maria-Eleni Parakatselaki
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Chara Petroulaki
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Dimitra Marinopoulou
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Anthi Pitsikaki
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Melpomeni Tseliou
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Alexandros Zafiropoulos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - George Sourvinos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
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6
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Malaga JL, Pajuelo MJ, Okamoto M, Tsinda EK, Otani K, Tsukayama P, Mascaro L, Cuicapuza D, Katsumi M, Kawamura K, Nishimura H, Sakagami A, Ueki Y, Omiya S, Okamoto S, Nakayama A, Fujimaki SI, Yu C, Azam S, Kodama E, Dapat C, Oshitani H, Saito M. Rapid Detection of SARS-CoV-2 RNA Using Reverse Transcription Recombinase Polymerase Amplification (RT-RPA) with Lateral Flow for N-Protein Gene and Variant-Specific Deletion-Insertion Mutation in S-Protein Gene. Viruses 2023; 15:1254. [PMID: 37376555 DOI: 10.3390/v15061254] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Rapid molecular testing for severe acute respiratory coronavirus 2 (SARS-CoV-2) variants may contribute to the development of public health measures, particularly in resource-limited areas. Reverse transcription recombinase polymerase amplification using a lateral flow assay (RT-RPA-LF) allows rapid RNA detection without thermal cyclers. In this study, we developed two assays to detect SARS-CoV-2 nucleocapsid (N) gene and Omicron BA.1 spike (S) gene-specific deletion-insertion mutations (del211/ins214). Both tests had a detection limit of 10 copies/µL in vitro and the detection time was approximately 35 min from incubation to detection. The sensitivities of SARS-CoV-2 (N) RT-RPA-LF by viral load categories were 100% for clinical samples with high (>9015.7 copies/µL, cycle quantification (Cq): < 25) and moderate (385.5-9015.7 copies/µL, Cq: 25-29.9) viral load, 83.3% for low (16.5-385.5 copies/µL, Cq: 30-34.9), and 14.3% for very low (<16.5 copies/µL, Cq: 35-40). The sensitivities of the Omicron BA.1 (S) RT-RPA-LF were 94.9%, 78%, 23.8%, and 0%, respectively, and the specificity against non-BA.1 SARS-CoV-2-positive samples was 96%. The assays seemed more sensitive than rapid antigen detection in moderate viral load samples. Although implementation in resource-limited settings requires additional improvements, deletion-insertion mutations were successfully detected by the RT-RPA-LF technique.
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Affiliation(s)
- Jose L Malaga
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Monica J Pajuelo
- Laboratorio Microbiología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Emmanuel Kagning Tsinda
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
- Center for Biomedical Innovation, Sinskey Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kanako Otani
- National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Pablo Tsukayama
- Laboratorio de Genómica Microbiana, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Lucero Mascaro
- Laboratorio Microbiología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Diego Cuicapuza
- Laboratorio de Genómica Microbiana, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Masamichi Katsumi
- Sendai City Institute of Health, Sendai 984-0002, Japan
- Sendai Shirayuri Women's College, Sendai 981-3107, Japan
| | | | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan
| | - Akie Sakagami
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Sendai 983-0836, Japan
| | - Yo Ueki
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Sendai 983-0836, Japan
| | - Suguru Omiya
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan
| | - Satoshi Okamoto
- Department of Clinical Laboratory, Tohoku Kosai Hospital, Sendai 980-0803, Japan
| | - Asami Nakayama
- Department of Laboratory Medicine, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Shin-Ichi Fujimaki
- Department of Laboratory Medicine, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Chuyao Yu
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Sikandar Azam
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Eiichi Kodama
- International Research Institute of Disaster Science, Tohoku University, Sendai 980-8572, Japan
| | - Clyde Dapat
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
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7
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Specchiarello E, Matusali G, Carletti F, Gruber CEM, Fabeni L, Minosse C, Giombini E, Rueca M, Maggi F, Amendola A, Garbuglia AR. Detection of SARS-CoV-2 Variants via Different Diagnostics Assays Based on Single-Nucleotide Polymorphism Analysis. Diagnostics (Basel) 2023; 13:1573. [PMID: 37174964 PMCID: PMC10177602 DOI: 10.3390/diagnostics13091573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by fast evolution with the appearance of several variants. Next-Generation Sequencing (NGS) technology is considered the gold standard for monitoring known and new SARS-CoV-2 variants. However, the complexity of this technology renders this approach impracticable in laboratories located in areas with limited resources. We analyzed the capability of the ThermoFisher TaqPath COVID-19 RT-PCR (TaqPath) and the Seegene Novaplex SARS-CoV-2 Variant assay (Novaplex) to detect Omicron variants; the Allplex VariantII (Allplex) was also evaluated for Delta variants. Sanger sequencing (SaS) was the reference method. The results obtained with n = 355 nasopharyngeal samples were: negative with TaqPath, although positive with other qualitative molecular assays (n = 35); undetermined (n = 40) with both the assays; negative for the ∆69/70 mutation and confirmed as the Delta variant via SaS (n = 100); positive for ∆69/70 and confirmed as Omicron BA.1 via SaS (n = 80); negative for ∆69/70 and typed as Omicron BA.2 via SaS (n = 80). Novaplex typed 27.5% of samples as undetermined with TaqPath, 11.4% of samples as negative with TaqPath, and confirmed 100% of samples were Omicron subtypes. In total, 99/100 samples were confirmed as the Delta variant with Allplex with a positive per cent agreement (PPA) of 98% compared to SaS. As undermined samples with Novaplex showed RdRp median Ct values (Ct = 35.4) statistically higher than those of typed samples (median Ct value = 22.0; p < 0.0001, Mann-Whitney test), the inability to establish SARS-CoV-2 variants was probably linked to the low viral load. No amplification was obtained with SaS among all 35 negative TaqPath samples. Overall, 20% of samples which were typed as negative or undetermined with TaqPath, and among them, twelve were not typed even by SaS, but they were instead correctly identified with Novaplex. Although full-genome sequencing remains the elected method to characterize new strains, our data show the high ability of a SNP-based assay to identify VOCs, also resolving samples typed as undetermined with TaqPath.
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Affiliation(s)
- Eliana Specchiarello
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Giulia Matusali
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Fabrizio Carletti
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Claudia Minosse
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Alessandra Amendola
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
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8
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Chrysostomou AC, Aristokleous A, Rodosthenous JH, Christodoulou C, Stathi G, Kostrikis LG. Detection of Circulating SARS-CoV-2 Variants of Concern (VOCs) Using a Multiallelic Spectral Genotyping Assay. Life (Basel) 2023; 13:life13020304. [PMID: 36836661 PMCID: PMC9960118 DOI: 10.3390/life13020304] [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: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved, resulting in new variants, some of which possess increased infectivity, immune evasion, and virulence. Such variants have been denoted by the World Health Organization as variants of concern (VOC) because they have resulted in an increased number of cases, posing a strong risk to public health. Thus far, five VOCs have been designated, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), including their sublineages. Next-generation sequencing (NGS) can produce a significant amount of information facilitating the study of variants; however, NGS is time-consuming and costly and not efficient during outbreaks, when rapid identification of VOCs is urgently needed. In such periods, there is a need for fast and accurate methods, such as real-time reverse transcription PCR in combination with probes, which can be used for monitoring and screening of the population for these variants. Thus, we developed a molecular beacon-based real-time RT-PCR assay according to the principles of spectral genotyping. This assay employs five molecular beacons that target ORF1a:ΔS3675/G3676/F3677, S:ΔH69/V70, S:ΔE156/F157, S:ΔΝ211, S:ins214EPE, and S:ΔL242/A243/L244, deletions and an insertion found in SARS-CoV-2 VOCs. This assay targets deletions/insertions because they inherently provide higher discrimination capacity. Here, the design process of the molecular beacon-based real-time RT-PCR assay for detection and discrimination of SARS-CoV-2 is presented, and experimental testing using SARS-CoV-2 VOC samples from reference strains (cultured virus) and clinical patient samples (nasopharyngeal samples), which have been previously classified using NGS, were evaluated. Based on the results, it was shown that all molecular beacons can be used under the same real-time RT-PCR conditions, consequently improving the time and cost efficiency of the assay. Furthermore, this assay was able to confirm the genotype of each of the tested samples from various VOCs, thereby constituting an accurate and reliable method for VOC detection and discrimination. Overall, this assay is a valuable tool that can be used for screening and monitoring the population for VOCs or other emerging variants, contributing to limiting their spread and protecting public health.
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Affiliation(s)
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | | | | | - Georgia Stathi
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
- Correspondence: ; Tel.: +35-72-289-2885
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9
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Migueres M, Chapuy‐Regaud S, Miédougé M, Jamme T, Lougarre C, Da Silva I, Pucelle M, Staes L, Porcheron M, Diméglio C, Izopet J. Current immunoassays and detection of antibodies elicited by Omicron SARS-CoV-2 infection. J Med Virol 2023; 95:e28200. [PMID: 36207814 PMCID: PMC9874650 DOI: 10.1002/jmv.28200] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/12/2022] [Accepted: 10/03/2022] [Indexed: 01/27/2023]
Abstract
The present study aimed to determine whether current commercial immunoassays are adequate for detecting anti-Omicron antibodies. We analyzed the anti-SARS-CoV-2 antibody response of 23 unvaccinated individuals 1-2 months after an Omicron infection. All blood samples were tested with a live virus neutralization assay using a clinical Omicron BA.1 strain and four commercial SARS-CoV-2 immunoassays. We assessed three anti-Spike immunoassays (SARS-CoV-2 IgG II Quant [Abbott S], Wantaï anti-SARS-CoV-2 antibody ELISA [Wantaï], Elecsys Anti-SARS-CoV-2 S assay [Roche]) and one anti-Nucleocapsid immunoassay (Abbott SARS-CoV-2 IgG assay [Abbott N]). Omicron neutralizing antibodies were detected in all samples with the live virus neutralization assay. The detection rate of the Abbott S, Wantai, Roche, and Abbott N immunoassays were 65.2%, 69.6%, 86.9%, and 91.3%, respectively. The sensitivities of Abbott S and Wantai immunoassays were significantly lower than that of the live virus neutralization assay (p = 0.004, p = 0.009; Fisher's exact test). Antibody concentrations obtained with anti-S immunoassays were correlated with Omicron neutralizing antibody concentrations. These data provide clinical evidence of the loss of performance of some commercial immunoassays to detect antibodies elicited by Omicron infections. It highlights the need to optimize these assays by adapting antigens to the circulating SARS-CoV-2 strains.
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Affiliation(s)
- Marion Migueres
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
| | - Sabine Chapuy‐Regaud
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
| | - Marcel Miédougé
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Thibaut Jamme
- Laboratoire de Biochimie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | | | - Isabelle Da Silva
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Mélanie Pucelle
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Laetitia Staes
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Marion Porcheron
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance
| | - Chloé Diméglio
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
| | - Jacques Izopet
- Laboratoire de Virologie, CHU Toulouse, Hôpital PurpanInstitut Fédératif de BiologieToulouseFrance,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM UMR1291 ‐ CNRS UMR5051ToulouseFrance,Université Toulouse III Paul‐SabatierToulouseFrance
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10
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Migueres M, Mansuy JM, Vasseur S, Claverie N, Lougarre C, Soulier F, Trémeaux P, Izopet J. Omicron Wave SARS-CoV-2 Diagnosis: Evaluation of Saliva, Anterior Nasal, and Nasopharyngeal Swab Samples. Microbiol Spectr 2022; 10:e0252122. [PMID: 36318040 PMCID: PMC9769796 DOI: 10.1128/spectrum.02521-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
The Omicron variant differs from earlier strains of SARS-CoV-2 in the way it enters host cells and grows in vitro. We therefore reevaluated its diagnosis using saliva, nasopharyngeal swab (NPs), and anterior nasal swab (ANs) specimens from 202 individuals (64.9% symptomatic) tested at the Toulouse University Hospital SARS-CoV-2 drive-through testing center. All tests were done with the Thermo Fisher TaqPath COVID-19 reverse transcription-PCR (RT-PCR) kit. Overall, 92 subjects (45.5%) had one or more positive specimens. Global sensitivities of saliva, NPs, and ANs were 94.6%, 90.2%, and 82.6%, respectively. Saliva provided significantly greater sensitivity among symptomatic patients tested within 5 days of symptom onset (100%) than did ANs (83.1%) or NPs (89.8%). We obtained follow-up samples for 7/20 individuals with discordant results. Among them, 5 symptomatic patients were diagnosed positive on saliva sample only, soon after symptom onset; NPs and ANs became positive only later. Thus, saliva samples are effective tools for the detection of the Omicron variant. In addition to its many advantages, such as improved patient acceptance and reduced cost, saliva sampling could help limit viral spread through earlier viral detection. IMPORTANCE Diagnostic testing for SARS-CoV-2 is an essential component of the global strategy for the prevention and control of COVID-19. Since the beginning of the pandemic, numerous studies have evaluated the diagnostic sensitivity of different respiratory and oral specimens for SARS-CoV-2 detection. The pandemic has been since dominated by the emergence of new variants, the latest being the Omicron variant characterized by numerous mutations and changes in host tropism in vitro that might affect the diagnostic performance of tests depending on the sampling location. In this prospective study, we evaluated the clinical performance of NPs, ANs, and saliva for SARS-CoV-2 diagnosis during the Omicron wave. Our results highlight the effectiveness of saliva-based RT-PCR for the early detection of the Omicron variant. These findings may help to refine guidelines and support the use of a highly sensitive diagnostic method that allows earlier diagnosis, when transmission is the most critical.
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Affiliation(s)
- Marion Migueres
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jean-Michel Mansuy
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
| | - Sandrine Vasseur
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Nicolas Claverie
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Catherine Lougarre
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Françoise Soulier
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Pauline Trémeaux
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
| | - Jacques Izopet
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
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11
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Liotti FM, De Maio F, Ippoliti C, Santarelli G, Monzo FR, Sali M, Santangelo R, Ceccherini-Silberstein F, Sanguinetti M, Posteraro B. Two-Period Study Results from a Large Italian Hospital Laboratory Attesting SARS-CoV-2 Variant PCR Assay Evolution. Microbiol Spectr 2022; 10:e0292222. [PMID: 36409091 PMCID: PMC9769628 DOI: 10.1128/spectrum.02922-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/24/2022] [Indexed: 11/23/2022] Open
Abstract
In keeping with the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 causative agent, PCR assays have been developed to rapidly detect SARS-CoV-2 variants, which have emerged since the first (Alpha) variant was identified. Based on specific assortment of SARS-CoV-2 spike-protein mutations (ΔH69/V70, E484K, N501Y, W152C, L452R, K417N, and K417T) among the major variants known to date, Seegene Allplex SARS-CoV-2 Variants I and Variants II assays have been available since a few months before the last (Omicron) variant became predominant. Using S gene next-generation sequencing (NGS) as the SARS-CoV-2 variant identification reference method, we assessed the results of SARS-CoV-2-positive nasopharyngeal swab samples from two testing periods, before (n = 288, using only Variants I) and after (n = 77, using both Variants I and Variants II) the appearance of Omicron. The Variants I assay allowed correct identification for Alpha (37/37), Beta/Gamma (28/30), or Delta (220/221) variant-positive samples. The combination of the Variants I and Variants II assays allowed correct identification for 61/77 Omicron variant-positive samples. While 16 samples had the K417N mutation undetected with the Variants II assay, 74/77 samples had both ΔH69/V70 and N501Y mutations detected with the Variants I assay. If considering only the results by the Variants I assay, 6 (2 Beta variant positive, 1 Delta variant positive, and 3 Omicron variant positive) of 365 samples tested in total provided incorrect identification. We showed that the Variants I assay alone might be more suitable than both the Variants I and Variants II assays to identify currently circulating SARS-CoV-2 variants. Inclusion of additional variant-specific mutations should be expected in the development of future assays. IMPORTANCE Omicron variants of SARS-CoV-2 pose more important public health concerns than the previously circulating Alpha or Delta variants, particularly regarding the efficacy of anti-SARS-CoV-2 vaccines and therapeutics. Precise identification of these variants highly requires performant PCR-based assays that allow us to reduce the reliance on NGS-based assays, which remain the reference method in this topic. While the current epidemiological SARS-CoV-2 pandemic context suggests that PCR assays such as the Seegene Variants II may be dispensable, we took advantage of NGS data obtained in this study to show that the array of SARS-CoV-2 spike protein mutations in the Seegene Variants II assay may be suboptimal. This reinforces the concept that initially developed PCR assays for SARS-CoV-2 variant detection could be no longer helpful if the SARS-CoV-2 pandemic evolves to newly emerging variants.
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Affiliation(s)
- Flora Marzia Liotti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Flavio De Maio
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Chiara Ippoliti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulia Santarelli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesca Romana Monzo
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Michela Sali
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rosaria Santangelo
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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12
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Stanhope BJ, Peterson B, Knight B, Decadiz RN, Pan R, Davis P, Fraser A, Nuth M, vanWestrienen J, Wendlandt E, Goodwin B, Myers C, Stone J, Sozhamannan S. Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform. Front Public Health 2022; 10:1042647. [PMID: 36590003 PMCID: PMC9798920 DOI: 10.3389/fpubh.2022.1042647] [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: 09/12/2022] [Accepted: 11/11/2022] [Indexed: 12/16/2022] Open
Abstract
Many SARS-CoV-2 variants have emerged during the course of the COVID-19 pandemic. These variants have acquired mutations conferring phenotypes such as increased transmissibility or virulence, or causing diagnostic, therapeutic, or immune escape. Detection of Alpha and the majority of Omicron sublineages by PCR relied on the so-called S gene target failure due to the deletion of six nucleotides coding for amino acids 69-70 in the spike (S) protein. Detection of hallmark mutations in other variants present in samples relied on whole genome sequencing. However, whole genome sequencing as a diagnostic tool is still in its infancy due to geographic inequities in sequencing capabilities, higher cost compared to other molecular assays, longer turnaround time from sample to result, and technical challenges associated with producing complete genome sequences from samples that have low viral load and/or high background. Hence, there is a need for rapid genotyping assays. In order to rapidly generate information on the presence of a variant in a given sample, we have created a panel of four triplex RT-qPCR assays targeting 12 mutations to detect and differentiate all five variants of concern: Alpha, Beta, Gamma, Delta, and Omicron. We also developed an expanded pentaplex assay that can reliably distinguish among the major sublineages (BA.1-BA.5) of Omicron. In silico, analytical and clinical testing of the variant panel indicate that the assays exhibit high sensitivity and specificity. This panel can help fulfill the need for rapid identification of variants in samples, leading to quick decision making with respect to public health measures, as well as treatment options for individuals. Compared to sequencing, these genotyping PCR assays allow much faster turn-around time from sample to results-just a couple hours instead of days or weeks.
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Affiliation(s)
| | | | | | | | - Roger Pan
- Naval Health Research Center (NHRC), San Diego, CA, United States
| | | | - Anne Fraser
- Naval Health Research Center (NHRC), San Diego, CA, United States
| | | | | | - Erik Wendlandt
- Integrated DNA Technologies, Coralville, IA, United States
| | - Bruce Goodwin
- Defense Biological Product Assurance Office (DBPAO), Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Enabling Biotechnologies, Frederick, MD, United States
| | | | - Jennifer Stone
- MRIGlobal, Kansas City, MO, United States,*Correspondence: Jennifer Stone
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office (DBPAO), Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Enabling Biotechnologies, Frederick, MD, United States,Logistics Management Institute, Tysons, VA, United States,Shanmuga Sozhamannan
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13
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Wang PS, Ma H, Yan S, Lu X, Tang H, Xi XH, Peng XH, Huang Y, Bao YF, Cao MF, Wang H, Huang J, Liu G, Wang X, Ren B. Correlation coefficient-directed label-free characterization of native proteins by surface-enhanced Raman spectroscopy. Chem Sci 2022; 13:13829-13835. [PMID: 36544733 PMCID: PMC9710310 DOI: 10.1039/d2sc04775f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/30/2022] [Indexed: 12/24/2022] Open
Abstract
Investigation of proteins in their native state is the core of proteomics towards better understanding of their structures and functions. Surface-enhanced Raman spectroscopy (SERS) has shown its unique advantages in protein characterization with fingerprint information and high sensitivity, which makes it a promising tool for proteomics. It is still challenging to obtain SERS spectra of proteins in the native state and evaluate the native degree. Here, we constructed 3D physiological hotspots for a label-free dynamic SERS characterization of a native protein with iodide-modified 140 nm Au nanoparticles. We further introduced the correlation coefficient to quantitatively evaluate the variation of the native degree, whose quantitative nature allows us to explicitly investigate the Hofmeister effect on the protein structure. We realized the classification of a protein of SARS-CoV-2 variants in 15 min, which has not been achieved before. This study offers an effective tool for tracking the dynamic structure of proteins and biomedical research.
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Affiliation(s)
- Ping-Shi Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Hao Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Sen Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Xinyu Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Hui Tang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Xiao-Han Xi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Xiao-Hui Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Yajun Huang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Yi-Fan Bao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Mao-Feng Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Huimeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Jinglin Huang
- Laser Fusion Research Center, China Academy of Engineering PhysicsMianyang 621900China
| | - Guokun Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen UniversityXiamen 361005China
| | - Xiang Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamen 361005China
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14
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 35753493 DOI: 10.1101/2022.01.28.21268186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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15
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:156932. [PMID: 35753493 PMCID: PMC9225927 DOI: 10.1016/j.scitotenv.2022.156932] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 05/21/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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16
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Clark C, Schrecker J, Hardison M, Taitel MS. Validation of reduced S-gene target performance and failure for rapid surveillance of SARS-CoV-2 variants. PLoS One 2022; 17:e0275150. [PMID: 36190984 PMCID: PMC9529109 DOI: 10.1371/journal.pone.0275150] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
Abstract
SARS-CoV-2, the virus that causes COVID-19, has many variants capable of rapid transmission causing serious illness. Timely surveillance of new variants is essential for an effective public health response. Ensuring availability and access to diagnostic and molecular testing is key to this type of surveillance. This study utilized reverse transcription polymerase chain reaction (RT-PCR) and whole genome sequencing results from COVID-19-positive patient samples obtained through a collaboration between Aegis Sciences Corporation and Walgreens Pharmacy that has conducted more than 8.5 million COVID-19 tests at ~5,200 locations across the United States and Puerto Rico. Viral evolution of SARS-CoV-2 can lead to mutations in the S-gene that cause reduced or failed S-gene amplification in diagnostic PCR tests. These anomalies, labeled reduced S-gene target performance (rSGTP) and S-gene target failure (SGTF), are characteristic of variants carrying the del69-70 mutation, such as Alpha and Omicron (B.1.1.529, BA.1, and BA.1.1) lineages. This observation has been validated by whole genome sequencing and can provide presumptive lineage data following completion of diagnostic PCR testing in 24-48 hours from collection. Active surveillance of trends in PCR and sequencing results is key to the identification of changes in viral transmission and emerging variants. This study shows that rSGTP and SGTF can be utilized for near real-time tracking and surveillance of SARS-CoV-2 variants, and is superior to the use of SGTF alone due to the significant proportion of Alpha and Omicron (B.1.1.529, BA.1, and BA.1.1) lineages known to carry the del69-70 mutation and observed to have S-gene amplification. Adopting new tools and techniques to both diagnose acute infections and expedite identification of emerging variants is critical to supporting public health.
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Affiliation(s)
- Cyndi Clark
- Aegis Sciences Corporation, Nashville, TN, United States of America
| | - Joshua Schrecker
- Aegis Sciences Corporation, Nashville, TN, United States of America
| | - Matthew Hardison
- Aegis Sciences Corporation, Nashville, TN, United States of America
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17
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Dimeglio C, Migueres M, Bouzid N, Chapuy-Regaud S, Gernigon C, Da-Silva I, Porcheron M, Martin-Blondel G, Herin F, Izopet J. Antibody Titers and Protection against Omicron (BA.1 and BA.2) SARS-CoV-2 Infection. Vaccines (Basel) 2022; 10:1548. [PMID: 36146626 PMCID: PMC9506424 DOI: 10.3390/vaccines10091548] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/21/2022] Open
Abstract
The emergence of the SARS-CoV-2 variants of concern has greatly influenced the immune correlates of protection, and there are little data about the antibody threshold concentrations to protect against infection with SARS-CoV-2 Omicron BA.1 or BA.2. We analyzed the antibody responses of 259 vaccinated healthcare workers, some of whom had been previously infected by SARS-CoV-2. The median follow-up was 179 days (IQR: 171-182) after blood collection. We detected 88 SARS-CoV-2 Omicron infections during the follow-up period, 55 (62.5%) with SARS-CoV-2 BA.1, and 33 (37.5%) with SARS-CoV-2 BA.2. A neutralizing antibody titer below 8 provided no protection against a BA.1 infection, a titer of 16 or 32 gave 73.2% protection, and a titer of 64 or 128 provided 78.4% protection. Conversely, the BA.2 infection rate did not vary as a function of anti-BA.2 neutralizing antibody titers. Binding antibody concentrations below 6000 BAU/mL provided no protection against Omicron BA.1 infection, 6000-20,000 BAU/mL provided 55.6% protection, and 20,000 or more provided 87.7% protection. There was no difference in BA.2 infection depending on the binding antibody concentration. Further studies are needed to investigate the relationship between antibody concentrations and infection with the Omicron BA.4/5 variants that are becoming predominant worldwide.
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Affiliation(s)
- Chloé Dimeglio
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300 Toulouse, France
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France
| | - Marion Migueres
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300 Toulouse, France
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France
| | - Naémie Bouzid
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300 Toulouse, France
| | - Sabine Chapuy-Regaud
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300 Toulouse, France
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France
| | - Caroline Gernigon
- Occupational Diseases Department, Toulouse University Hospital, 31000 Toulouse, France
- UMR1295, Unité Mixte INSERM—Université Toulouse III Paul Sabatier, Centre for Epidemiology and Research in Population Health Unit (CERPOP), 31000 Toulouse, France
| | - Isabelle Da-Silva
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300 Toulouse, France
| | - Marion Porcheron
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300 Toulouse, France
| | - Guillaume Martin-Blondel
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France
- Infectious and Tropical Diseases Department, Toulouse University Hospital, 31300 Toulouse, France
| | - Fabrice Herin
- Occupational Diseases Department, Toulouse University Hospital, 31000 Toulouse, France
- UMR1295, Unité Mixte INSERM—Université Toulouse III Paul Sabatier, Centre for Epidemiology and Research in Population Health Unit (CERPOP), 31000 Toulouse, France
| | - Jacques Izopet
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300 Toulouse, France
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France
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18
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Sberna G, Fabeni L, Berno G, Carletti F, Specchiarello E, Colavita F, Meschi S, Matusali G, Garbuglia AR, Bordi L, Lalle E. Rapid and qualitative identification of SARS-CoV-2 mutations associated with variants of concern using a multiplex RT-PCR assay coupled with melting analysis. Int J Infect Dis 2022; 122:401-404. [PMID: 35760381 PMCID: PMC9233866 DOI: 10.1016/j.ijid.2022.06.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/20/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES Considering the spread of new genetic variants and their impact on public health, it is important to have assays that are able to rapidly detect SARS-CoV-2 variants. METHODS We retrospectively examined 118 positive nasopharyngeal swabs, first characterized by the Sanger sequencing, using the Simplexa® SARS-CoV-2 Variants Direct assay, with the aim of evaluating the performance of the assay to detect N501Y, G496S, Q498R, Y505H, E484K, E484Q, E484A, and L452R mutations. RESULTS A total of 111/118 nasopharyngeal swabs were in complete agreement with the Sanger sequencing, whereas the remaining seven samples were not amplified due to the low viral load. The evaluation of the ability of the assay to detect the E484Q mutation was performed using a viral isolate of the SARS-CoV-2 Kappa variant, showing concordance in 15/15 samples. Simplexa® SARS-CoV-2 Variant Direct assay was able to detect mutation pattern of Alpha, Beta, Gamma, Delta, and Omicron variants with 100% specificity and 94% sensitivity, whereas 100% sensitivity and specificity for the Kappa variant was observed. CONCLUSION The assay can be useful to obtain faster results, contributing to a prompt surveillance of SARS-CoV-2 variants; however, it requires to be confirmed by the Sanger method, especially in the case of pattern of mutations that are different from those expected and also requires updates as new variants emerge.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Licia Bordi
- Corresponding author: Licia Bordi, Laboratory of Virology, National Institute of Infectious Diseases “L. Spallanzani” – IRCCS, Via Portuense 292, 00149 Rome, Italy
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19
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Kotov I, Saenko V, Borisova N, Kolesnikov A, Kondrasheva L, Tivanova E, Khafizov K, Akimkin V. Effective Approaches to Study the Genetic Variability of SARS-CoV-2. Viruses 2022; 14:v14091855. [PMID: 36146662 PMCID: PMC9504788 DOI: 10.3390/v14091855] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Significant efforts are being made in many countries around the world to respond to the COVID-19 pandemic by developing diagnostic reagent kits, identifying infected people, determining treatment methods, and finally producing effective vaccines. However, novel coronavirus variants may potentially reduce the effectiveness of all these efforts, demonstrating increased transmissibility and abated response to therapy or vaccines, as well as the possibility of false negative results in diagnostic procedures based on nucleic acid amplification methods. Since the end of 2020, several variants of concern have been discovered around the world. When information about a new, potentially more dangerous strain of pathogen appears, it is crucial to determine the moment of its emergence in a region. Eventually, that permits taking timely measures and minimizing new risks associated with the spreading of the virus. Therefore, numerous nations have made tremendous efforts to identify and trace these virus variants, which necessitates serious technological processes to sequence a large number of viral genomes. Here, we report on our experience as one of the primary laboratories involved in monitoring SARS-CoV-2 variants in Russia. We discuss the various approaches used, describe effective protocols, and outline a potential technique combining several methods to increase the ability to trace genetic variants while minimizing financial and labor costs.
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Affiliation(s)
- Ivan Kotov
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 115184 Dolgoprudny, Russia
| | - Valeriia Saenko
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
| | - Nadezhda Borisova
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
| | - Anton Kolesnikov
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
| | - Larisa Kondrasheva
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
| | - Elena Tivanova
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
| | - Kamil Khafizov
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
- Correspondence:
| | - Vasily Akimkin
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
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20
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Umunnakwe CN, Makatini ZN, Maphanga M, Mdunyelwa A, Mlambo KM, Manyaka P, Nijhuis M, Wensing A, Tempelman HA. Evaluation of a commercial SARS-CoV-2 multiplex PCR genotyping assay for variant identification in resource-scarce settings. PLoS One 2022; 17:e0269071. [PMID: 35749403 PMCID: PMC9231807 DOI: 10.1371/journal.pone.0269071] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
The rapid emergence and spread of numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants across the globe underscores the crucial need for continuous SARS-CoV-2 surveillance to ensure that potentially more pathogenic variants are detected early and contained. Whole genome sequencing (WGS) is currently the gold standard for COVID-19 surveillance; however, it remains cost-prohibitive and requires specialized technical skills. To increase surveillance capacity, especially in resource-scarce settings, supplementary methods that are cost- and time-effective are needed. Real-time multiplex PCR genotyping assays offer an economical and fast solution for screening circulating and emerging variants while simultaneously complementing existing WGS approaches. In this study we evaluated the AllplexTM SARS-CoV-2 Variants II multiplex real-time PCR genotyping assay, Seegene (South Korea), and implemented it in retrospectively characterizing circulating SARS-CoV-2 variants in a rural South African setting between April and October 2021, prior to the emergence of the Omicron variant in South Africa. The AllplexTM SARS-CoV-2 Variants II real-time PCR assay demonstrated perfect concordance with whole-genome sequencing in detecting Beta and Delta variants and exhibited high specificity, sensitivity and reproducibility. Implementation of the assay in characterization of SARS-CoV-2 variants between April and October 2021 in a rural South African setting revealed a rapid shift from the Beta to the Delta variant between April and June. All specimens successfully genotyped in April were Beta variants and the Delta variant was not detected until May. By June, 78% of samples genotyped were Delta variants and in July >95% of all genotyped samples were Delta variants. The Delta variant continued to predominate through to the end of our analysis in October 2021. Taken together, a commercial SARS-CoV-2 variant genotyping assay detected the rapid rate at which the Delta variant displaced the Beta variant in Limpopo, an under-monitored province in South Africa. Such assays provide a quick and cost-effective method of monitoring circulating variants and should be used to complement genomic sequencing for COVID-19 surveillance especially in resource-scarce settings.
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Affiliation(s)
- Chijioke N. Umunnakwe
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
- Ndlovu Research Consortium, Dennilton, Limpopo Province, South Africa
- * E-mail:
| | - Zinhle N. Makatini
- Ndlovu Research Consortium, Dennilton, Limpopo Province, South Africa
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mathapelo Maphanga
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
| | - Anele Mdunyelwa
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
| | - Khamusi M. Mlambo
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
| | - Puseletso Manyaka
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
| | - Monique Nijhuis
- Ndlovu Research Consortium, Dennilton, Limpopo Province, South Africa
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Annemarie Wensing
- Ndlovu Research Consortium, Dennilton, Limpopo Province, South Africa
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Wits Reproductive Health and HIV Institute (Wits RHI), University of the Witwatersrand, Johannesburg, South Africa
| | - Hugo A. Tempelman
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
- Ndlovu Research Consortium, Dennilton, Limpopo Province, South Africa
- Wits Reproductive Health and HIV Institute (Wits RHI), University of the Witwatersrand, Johannesburg, South Africa
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21
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Aoki A, Mori Y, Okamoto Y, Jinno H. PCR-Based Screening Tests for SARS-CoV-2 Mutations: What Is the Best Way to Identify Variants? Clin Chem 2022; 68:1000-1001. [PMID: 35670710 PMCID: PMC9384179 DOI: 10.1093/clinchem/hvac087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 11/14/2022]
Affiliation(s)
- Akira Aoki
- Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya, Japan
| | - Yoko Mori
- Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya, Japan
| | | | - Hideto Jinno
- Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya, Japan
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22
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Borillo GA, Kagan RM, Marlowe EM. Rapid and Accurate Identification of SARS-CoV-2 Variants Using Real Time PCR Assays. Front Cell Infect Microbiol 2022; 12:894613. [PMID: 35619652 PMCID: PMC9127862 DOI: 10.3389/fcimb.2022.894613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/07/2022] [Indexed: 12/16/2022] Open
Abstract
Background Genomic surveillance efforts for SARS-CoV-2 are needed to understand the epidemiology of the COVID-19 pandemic. Viral variants may impact routine diagnostic testing, increase viral transmissibility, cause differences in disease severity, have decreased susceptibility to therapeutics, and/or confer the ability to evade host immunity. While viral whole-genome sequencing (WGS) has played a leading role in surveillance programs, many laboratories lack the expertise and resources for performing WGS. This study describes the performance of multiplexed real-time reverse transcription-PCR (RT-PCR) assays for identification of SARS-CoV-2 variants. Methods SARS-CoV-2 specimens were tested for spike-gene variants using a combination of allele-specific primer and allele-specific detection technology (PlexPrime® and PlexZyme®). Targeted detection of spike gene mutations by RT-PCR was compared to variant detection in positive specimens by WGS, including the recently emerged SARS-CoV-2 Omicron variant. Results A total of 398 SAR-CoV-2 RT-PCR positive and 39 negative specimens previously tested by WGS were re-tested by RT-PCR genotyping. PCR detection of spike gene mutations N501Y, E484K, and S982A correlated 100% with WGS for the 29 lineages represented, including Alpha (B.1.1.7), Beta (B.1.351), and Gamma (P.1). Incorporating the P681R spike gene mutation also allowed screening for the SARS-CoV-2 Delta variant (B.1.617.2 and AY sublineages). Further sampling of 664 specimens that were screened by WGS between June and August 2021 and then re-tested by RT-PCR showed strong agreement for Delta variant positivity: 34.5% for WGS vs 32.9% for RT-PCR in June; 100% vs 97.8% in August. In a blinded panel of 16 Omicron and 16 Delta specimens, results of RT-PCR were 100% concordant with WGS results. Conclusions These data demonstrate that multiplexed real-time RT-PCR genotyping has strong agreement with WGS and may provide additional SARS-CoV-2 variant screening capabilities when WGS is unavailable or cost-prohibitive. RT-PCR genotyping assays may also supplement existing sequencing efforts while providing rapid results at or near the time of diagnosis to help guide patient management.
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Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. Microbiol Spectr 2022; 10:e0217621. [PMID: 35285705 PMCID: PMC9045307 DOI: 10.1128/spectrum.02176-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In this report, we describe the development of a reverse transcription-quantitative PCR (RT-qPCR) assay, termed Alpha-Delta assay, which can detect all severe acute respiratory syndrome coronavirus 2 (SC-2) variants and distinguish between the Alpha (B.1.1.7) and Delta (B.1.617.2) variants. The Alpha- and Delta-specific reactions in the assay target mutations that are strongly linked to the target variant. The Alpha reaction targets the D3L substitution in the N gene, and the Delta reaction targets the spike gene 156 to 158 mutations. Additionally, we describe a second Delta-specific assay that we use as a confirmatory test for the Alpha-Delta assay that targets the 119 to 120 deletion in the Orf8 gene. Both reactions have similar sensitivities of 15 to 25 copies per reaction, similar to the sensitivity of commercial SC-2 detection tests. The Alpha-Delta assay and the Orf8119del assay were successfully used to classify clinical samples that were subsequently analyzed by whole-genome sequencing. Lastly, the capability of the Alpha-Delta assay and Orf8119del assay to identify correctly the presence of Delta RNA in wastewater samples was demonstrated. This study provides a rapid, sensitive, and cost-effective tool for detecting and classifying two worldwide dominant SC-2 variants. It also highlights the importance of a timely diagnostic response to the emergence of new SC-2 variants with significant consequences on global health. IMPORTANCE The new assays described herein enable rapid, straightforward, and cost-effective detection of severe acute respiratory syndrome coronavirus 2 (SC-2) with immediate classification of the examined sample as Alpha, Delta, non-Alpha, or non-Delta variant. This is highly important for two main reasons: (i) it provides the scientific and medical community with a novel diagnostic tool to rapidly detect and classify any SC-2 sample of interest as Alpha, Delta, or none and can be applied to both clinical and environmental samples, and (ii) it demonstrates how to respond to the emergence of new variants of concern by developing a variant-specific assay. Such assays should improve our preparedness and adjust the diagnostic capacity to serve clinical, epidemiological, and research needs.
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Rao Us V, Arakeri G, Rao U, Chandru V, Amaral Mendes R. We need to optimise genome surveillance and tracing of SARS-CoV-2 variants. BMJ 2022; 376:o601. [PMID: 35277422 DOI: 10.1136/bmj.o601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Vishal Rao Us
- Centre for Academic Research, Health Care Global Cancer Hospital, Bengaluru, Karnataka, India
| | - Gururaj Arakeri
- Centre for Academic Research, Health Care Global Cancer Hospital, Bengaluru, Karnataka, India
| | - Ujjwal Rao
- Department of Medical Services, Rector Healthcare, Pune, India
| | | | - Rui Amaral Mendes
- Department of Oral and Maxillofacial Medicine and Diagnostic Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- CINTESIS-Center for Health Technology and Services Research, Porto, Portugal
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Brito-Mutunayagam S, Maloney D, McAllister G, Dewar R, McHugh M, Templeton K. Rapid detection of SARS-CoV-2 variants using allele-specific PCR. J Virol Methods 2022; 303:114497. [PMID: 35182711 PMCID: PMC8848537 DOI: 10.1016/j.jviromet.2022.114497] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 02/03/2023]
Abstract
Tracking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants through whole genome sequencing (WGS) is vital for effective infection control and prevention (IPC) measures, but can be time-consuming and resource-heavy. We describe an in-house validation of an allele-specific polymerase chain reaction (ASP) variant assay to detect variants of concern (VOC). ASP sensitivity for detecting Delta, Alpha and Beta was 99.45 %, 100 %, and 66.67 %, respectively, compared with WGS. Specificity was 100 % in detecting all three VOC. ASP generated results 1.3 days faster compared with WGS. These findings suggest using variant assays such as ASP may enhance epidemiological surveillance and IPC measures.
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Affiliation(s)
- Sanjita Brito-Mutunayagam
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom.
| | - Daniel Maloney
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom.
| | - Gina McAllister
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom.
| | - Rebecca Dewar
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom.
| | - Martin McHugh
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom.
| | - Kate Templeton
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom.
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Influence of the Delta Variant and Vaccination on the SARS-CoV-2 Viral Load. Viruses 2022; 14:v14020323. [PMID: 35215916 PMCID: PMC8879069 DOI: 10.3390/v14020323] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/27/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Studies comparing SARS-CoV-2 nasopharyngeal (NP) viral load (VL) according to virus variant and host vaccination status have yielded inconsistent results. We conducted a single center prospective study between July and September 2021 at the drive-through testing center of the Toulouse University Hospital. We compared the NP VL of 3775 patients infected by the Delta (n = 3637) and Alpha (n = 138) variants, respectively. Patient’s symptoms and vaccination status (2619 unvaccinated, 636 one dose and 520 two doses) were recorded. SARS-CoV-2 RNA testing and variant screening were assessed by using Thermo Fisher® TaqPath™ COVID-19 and ID solutions® ID™ SARS-CoV-2/VOC evolution Pentaplex assays. Delta SARS-CoV-2 infections were associated with higher VL than Alpha (coef = 0.68; p ≤ 0.01) independently of patient’s vaccination status, symptoms, age and sex. This difference was higher for patients diagnosed late after symptom onset (coef = 0.88; p = 0.01) than for those diagnosed early (coef = 0.43; p = 0.03). Infections in vaccinated patients were associated with lower VL (coef = −0.18; p ≤ 0.01) independently of virus variant, symptom, age and sex. Our results suggest that Delta infections could lead to higher VL and for a longer period compared to Alpha infections. By effectively reducing the NP VL, vaccination could allow for limiting viral spread, even with the Delta variant.
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De Pace V, Bruzzone B, Orsi A, Ricucci V, Domnich A, Guarona G, Randazzo N, Stefanelli F, Battolla E, Dusi PA, Lillo F, Icardi G. Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. Microorganisms 2022; 10:microorganisms10020306. [PMID: 35208761 PMCID: PMC8876857 DOI: 10.3390/microorganisms10020306] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/18/2022] [Accepted: 01/26/2022] [Indexed: 11/16/2022] Open
Abstract
The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant panel (n = 72) of SARS-CoV-2-positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild-type strains circulating in Liguria (Italy) from January to August 2021. First, NGS libraries of study samples were prepared and mapped to the reference genome. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. The overall accuracy of these assays ranged from 96.9% to 100%. Specificity and sensitivity were 100% and 96–100%, respectively. We highly recommend the use of these assays as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics, as they are accurate, user friendly, low cost, may identify specific mutations in about 2–3 h and, therefore, optimize the surveillance of SARS-CoV-2 variants.
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Affiliation(s)
- Vanessa De Pace
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
- Correspondence: ; Tel.: +39-3341145967
| | - Bianca Bruzzone
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Andrea Orsi
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (A.O.); (G.G.); (G.I.)
| | - Valentina Ricucci
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Alexander Domnich
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Giulia Guarona
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (A.O.); (G.G.); (G.I.)
| | - Nadia Randazzo
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Federica Stefanelli
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Enrico Battolla
- Division of Clinical Pathology, Azienda Sanitaria Locale n°5, 19121 La Spezia, Italy;
| | - Pier Andrea Dusi
- Microbiology Department, Sanremo Hospital, 18038 Imperia, Italy;
| | - Flavia Lillo
- Laboratory of Clinical Pathology, ASL2 Savonese, 17100 Savona, Italy;
| | - Giancarlo Icardi
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (A.O.); (G.G.); (G.I.)
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