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Ortiz-Gómez T, Gomez AC, Chuima B, Zevallos A, Ocampo K, Torres D, Pinto JA. Frequency of SARS-CoV-2 variants identified by real-time PCR in the AUNA healthcare network, Peru. Front Public Health 2024; 11:1244662. [PMID: 38410127 PMCID: PMC10894931 DOI: 10.3389/fpubh.2023.1244662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/26/2023] [Indexed: 02/28/2024] Open
Abstract
Introduction In Peru, on 11 February 2023, the Ministry of Health registered 4 million patients infected with COVID-19 and around 219,260 deaths. In 2020, the SARS-CoV-2 virus was acquiring mutations that impacted the properties of transmissibility, infectivity, and immune evasion, leading to new lineages. In the present study, the frequency of COVID-19 variants was determined during 2021 and 2022 in patients treated in the AUNA healthcare network. Methods The methodology used to detect mutations and identify variants was the Allplex™ SARS-CoV-2 Variants Assay I, II, and VII kit RT-PCR. The frequency of variants was presented by epidemiological weeks. Results In total, 544 positive samples were evaluated, where the Delta, Omicron, and Gamma variants were identified. The Delta variant was found in 242 (44.5%) patients between epidemiological weeks 39 and 52 in 2021. In the case of Gamma, it was observed in 8 (1.5%) patients at weeks 39, 41, 43, 45, and 46 of 2021. The Omicron variant was the most frequent with 289 (53.1%) patients during weeks 49 to 52 of 2021 and 1 to 22 of 2022. During weeks 1 through 22 of 2022, it was possible to discriminate between BA. 1 (n = 32) and BA.2 (n = 82). Conclusion The rapid identification of COVID-19 variants through the RT-PCR methodology contributes to timely epidemiological surveillance, as well as appropriate patient management.
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Affiliation(s)
| | - Andrea C. Gomez
- Centro de Investigación Básica y Translacional, AUNA IDEAS, Lima, Peru
| | | | - Alejandra Zevallos
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - Karen Ocampo
- Laboratorios AUNA, Área de Biología Molecular, Lima, Peru
| | - Diana Torres
- Laboratorios AUNA, Área de Biología Molecular, Lima, Peru
- Escuela Profesional de Medicina Humana, Universidad Privada Norbert Wiener, Lima, Peru
| | - Joseph A. Pinto
- Centro de Investigación Básica y Translacional, AUNA IDEAS, Lima, Peru
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Liu Y, Yang Y, Wang G, Wang D, Shao PL, Tang J, He T, Zheng J, Hu R, Liu Y, Xu Z, Niu D, Lv J, Yang J, Xiao H, Wu S, He S, Tang Z, Liu Y, Tang M, Jiang X, Yuan J, Dai H, Zhang B. Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device. Nat Biomed Eng 2023; 7:1636-1648. [PMID: 37735541 DOI: 10.1038/s41551-023-01092-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Portable assays for the rapid identification of lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to aid large-scale efforts in monitoring the evolution of the virus. Here we report a multiplexed assay in a microarray format for the detection, via isothermal amplification and plasmonic-gold-enhanced near-infrared fluorescence, of variants of SARS-CoV-2. The assay, which has single-nucleotide specificity for variant discrimination, single-RNA-copy sensitivity and does not require RNA extraction, discriminated 12 lineages of SARS-CoV-2 (in three mutational hotspots of the Spike protein) and detected the virus in nasopharyngeal swabs from 1,034 individuals at 98.8% sensitivity and 100% specificity, with 97.6% concordance with genome sequencing in variant discrimination. We also report a compact, portable and fully automated device integrating the entire swab-to-result workflow and amenable to the point-of-care detection of SARS-CoV-2 variants. Portable, rapid, accurate and multiplexed assays for the detection of SARS-CoV-2 variants and lineages may facilitate variant-surveillance efforts.
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Affiliation(s)
- Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dou Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Pan-Lin Shao
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tingzhen He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jintao Zheng
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yiyi Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ziyi Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dan Niu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jingkai Yang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Hongjun Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Shuai Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Shuang He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Zhongrong Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yan Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | | | - Xingyu Jiang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
| | - Jing Yuan
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.
| | - Hongjie Dai
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
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Muñoz-Gallego I, Meléndez Carmona MÁ, Martín Higuera C, Viedma E, Delgado R, Folgueira MD. Rapid screening of SARS-CoV-2 variants, a key tool for pandemic surveillance. Sci Rep 2023; 13:11094. [PMID: 37422474 PMCID: PMC10329708 DOI: 10.1038/s41598-023-37866-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
The utility of reverse transcription-polymerase chain reaction (RT-PCR) in analysis SARS-COV-2 variants was evaluated. RT-PCR tests were used to analyse the majority of new SARS-CoV-2 cases (n = 9315) in a tertiary hospital (Madrid, Spain) throughout 2021. Subsequently, whole genome sequencing (WGS) was conducted on 10.8% of these samples (n = 1002). Notably, the Delta and Omicron variants emerged rapidly. There were no discrepancies between RT-PCR and WGS results. Continuous surveillance of SARS-CoV-2 variants is essential, and RT-PCR is a highly useful method, specially during periods of high COVID-19 incidence. This feasible technique can be implemented in all SARS-CoV-2 laboratories. However, WGS remains the gold standard method for comprehensive detection of all existing SARS-CoV-2 variants.
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Affiliation(s)
- Irene Muñoz-Gallego
- Laboratory of Virology, Microbiology Department, Hospital Universitario, 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain.
- Biomedical Research Institute imas12, Hospital Universitario 12 de Octubre, Madrid, Spain.
| | - María Ángeles Meléndez Carmona
- Laboratory of Virology, Microbiology Department, Hospital Universitario, 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
- Biomedical Research Institute imas12, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Carmen Martín Higuera
- Laboratory of Virology, Microbiology Department, Hospital Universitario, 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
- Biomedical Research Institute imas12, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Esther Viedma
- Laboratory of Virology, Microbiology Department, Hospital Universitario, 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
- Biomedical Research Institute imas12, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Rafael Delgado
- Laboratory of Virology, Microbiology Department, Hospital Universitario, 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
- Biomedical Research Institute imas12, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Medicine, School of Medicine, Universitario Complutense, Madrid, Spain
| | - María Dolores Folgueira
- Laboratory of Virology, Microbiology Department, Hospital Universitario, 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
- Biomedical Research Institute imas12, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Medicine, School of Medicine, Universitario Complutense, Madrid, Spain
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Mangwana N, Archer E, Muller CJF, Preiser W, Wolfaardt G, Kasprzyk-Hordern B, Carstens A, Brocker L, Webster C, McCarthy D, Street R, Mathee A, Louw J, Mdhluli M, Johnson R. Sewage surveillance of SARS-CoV-2 at student campus residences in the Western Cape, South Africa. Sci Total Environ 2022; 851:158028. [PMID: 35973539 PMCID: PMC9375247 DOI: 10.1016/j.scitotenv.2022.158028] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/15/2022] [Accepted: 08/10/2022] [Indexed: 05/28/2023]
Abstract
The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic capacity is limited in defined communities, posing a challenge in tracking and tracing new infections. Monitoring student residences, which are considered infection hotspots, with targeted wastewater surveillance is crucial. This study evaluated the efficacy of SARS-CoV-2 targeted wastewater surveillance for outbreak mitigation at Stellenbosch University's student residences in South Africa. Using torpedo-style passive sampling devices, wastewater samples were collected biweekly from manholes at twelve Stellenbosch University Tygerberg (SUT) campus and Stellenbosch University-Main (SUM) campus student residences. The surveillance led to an early warning detection of SARS-CoV-2 presence on campus, followed by an informed management strategy leading to restriction of student activities on campus and a delay in the onset of the third wave that was experienced throughout the country. Moreover, the study highlighted the extent of possible infections at defined locations even when a low number of confirmed coronavirus disease 2019 (COVID-19) cases were reported. The study also tracked the surge of the Delta and Omicron variants in the student residences using the Thermo Fisher TaqMan® RT-qPCR genotyping assay.
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Affiliation(s)
- Noluxabiso Mangwana
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town 7505, South Africa; Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Edward Archer
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Christo J F Muller
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town 7505, South Africa; Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardiometabolic Research in Africa, Stellenbosch University, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine & Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; National Health Laboratory Services, Tygerberg Hospital, Tygerberg, Cape Town 7505, South Africa
| | - Gideon Wolfaardt
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa; Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Barbara Kasprzyk-Hordern
- Department of Chemistry, Faculty of Science, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Alno Carstens
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Ludwig Brocker
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Candice Webster
- Environment and Health Research Unit, South African Medical Research Council (SAMRC), Johannesburg, South Africa
| | - David McCarthy
- Environmental and Public Health Microbiology Lab (EPHM LAB), Monash Infrastructure Institute, Department of Civil Engineering, Monash University, Clayton 3800, Australia
| | - Renee Street
- Environment and Health Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
| | - Angela Mathee
- Environment and Health Research Unit, South African Medical Research Council (SAMRC), Johannesburg, South Africa
| | - Johan Louw
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town 7505, South Africa
| | - Mongezi Mdhluli
- Chief Research Operations Office, South African Medical Research Council, Tygerberg 7050, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town 7505, South Africa; Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardiometabolic Research in Africa, Stellenbosch University, South Africa.
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6
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Juthi RT, Sazed SA, Zamil MF, Alam MS. Clinical Evaluation of Three Commercial RT-PCR Kits for Routine COVID-19 Diagnosis. Pathogens 2022; 11:1389. [DOI: 10.3390/pathogens11111389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
Amongst the multiple ways to diagnose coronavirus disease-2019 (COVID-19), reverse transcription polymerase chain reaction (RT-PCR) remains the reference gold standard, providing fast and accurate results. This study evaluated and compared the performance of three commercially available COVID-19 RT-PCR kits-Aridia® COVID-19 Real-Time PCR Test (CTK Biotech, Inc., Poway, CA, USA), Novel Coronavirus (2019-nCoV) Nucleic Acid Detection Kit (Sansure Biotech Inc., Changsha, China) and AllplexTM 2019-nCoV assay (Seegene Inc., Seoul, Republic of Korea) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A total of 326 clinically suspected patients were enrolled for the study, and among them, 209 were diagnosed as positive and 117 as negative when tested with the reference method, US CDC 2019-Novel Coronavirus (2019-nCoV) Real Time RT-PCR Diagnostic Panel. The Aridia® kit showed total agreement with the reference test, with a sensitivity of 100% (95% CI: 98.25% to 100.0%) and a specificity of 100% (96.90% to 100.00%). The AllplexTM kit also showed 100% specificity (95% CI: 96.90% to 100.00%), but a lower sensitivity (98.09%, 95% CI: 95.17% to 99.48%). Among the three kits, the Novel Coronavirus (2019-nCoV) Nucleic Acid Detection Kit showed the worst performance, with a sensitivity of 98.6% (95% CI: 95.9% to 99.7%) and a specificity of 95.73, 95% (CI: 90.31% to 98.60%). While all these kits conform to the requirement for routine molecular diagnosis with high performances, the Aridia® COVID-19 Real-Time PCR Test showed the best performance among the three kits.
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Wratil PR, Kotter K, Bischof ML, Hollerbach S, Apak E, Kalteis AL, Nayeli-Pflantz T, Kaderali L, Adorjan K, Keppler OT. Vaccine-hesitant individuals accumulate additional COVID-19 risk due to divergent perception and behaviors related to SARS-CoV-2 testing: a population-based, cross-sectional study. Infection 2022:10.1007/s15010-022-01947-z. [PMID: 36355269 PMCID: PMC9647754 DOI: 10.1007/s15010-022-01947-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022]
Abstract
Purpose To investigate the perception of SARS-CoV-2 detection methods, information sources, and opinions on appropriate behavior after receiving negative or positive test results. Methods In a questionnaire-based, cross-sectional study conducted between September 1 and November 17, 2021, epidemiological, behavioral, and COVID-19-related data were acquired from the public in Munich, Germany. Results Most of the 1388 participants obtained information from online media (82.8%) as well as state and federal authorities (80.3%). 93.4% believed in the accuracy of SARS-CoV-2 PCR testing and 41.2% in the accuracy of rapid antigen tests (RATs). However, RATs were preferred for testing (59.1%) over PCR (51.1%). 24.0% of all individuals were willing to ignore hygiene measures and 76.9% were less afraid of SARS-CoV-2 transmission after receiving a negative PCR test (5.9% and 48.8% in case of a negative RAT). 28.8% reported not to self-isolate after receiving a positive RAT. Multivariate analyses revealed that non-vaccinated individuals relied less on information from governmental authorities (p = 0.0004) and more on social media (p = 0.0216), disbelieved in the accuracy of the PCR test (p ≤ 0.0001) while displaying strong preference towards using RATs (p ≤ 0.0001), were more willing to abandon pandemic-related hygiene measures (p ≤ 0.0001), less afraid of transmitting SARS-CoV-2 after a negative RAT (p ≤ 0.0001), and less likely to isolate after a positive RAT (p ≤ 0.0001). Conclusion Insights into preferred information sources as well as perception, preferences, and behavior related to SARS-CoV-2 testing and hygiene measures are key to refining public health information and surveillance campaigns. Non-vaccinated individuals’ divergent believes and behaviors possibly increase their COVID-19 risk. Supplementary Information The online version contains supplementary material available at 10.1007/s15010-022-01947-z .
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Affiliation(s)
- Paul R Wratil
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
| | - Katharina Kotter
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marie L Bischof
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Sophie Hollerbach
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Elif Apak
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Anna-Lena Kalteis
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Tamara Nayeli-Pflantz
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Kristina Adorjan
- Department of Psychiatry and Psychotherapy, University Hospital, LMU München, Nußbaumstraße 7, 80336, Munich, Germany.
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
- Faculty of Medicine, Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.
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8
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Lowry K, Wang C, Bordin A, Buckley C, Badman S, Harris P, Mackay I, Whiley D. SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern. Diagnostics (Basel) 2022; 12:diagnostics12092056. [PMID: 36140458 PMCID: PMC9497716 DOI: 10.3390/diagnostics12092056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
The continuous transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has required that diagnostic capabilities be constantly monitored and updated as new variants emerge and prior variants disappear. Although whole genome sequencing provides full characterisation of SARS-CoV-2 directly from patient samples, this has limited throughput and requires sufficient resources. To enhance screening for circulating variants, we designed a rapid in-house RT-PCR assay to target a spike mutation (D950N) in Delta variants, which is not detected in the remaining variants of concern (VOCs). Assay sensitivity for detecting Delta variants was 93% and specificity was 100% using a sequenced sample bank of several lineages. As the D950N mutation is prevalent in >95% of the global Delta variant sequences deposited in GISAID, this assay has the potential to provide rapid results to determine if the samples are presumptively Delta variants and can support clinicians in timely clinical decision-making for effective treatments and surveillance.
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Affiliation(s)
- Kym Lowry
- The Queensland Paediatric Infectious Diseases (QPID) Research Group, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia
- Correspondence:
| | - Claire Wang
- The Queensland Paediatric Infectious Diseases (QPID) Research Group, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia
- Infectious Diseases Laboratory, Prevention Division, Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Amanda Bordin
- The Queensland Paediatric Infectious Diseases (QPID) Research Group, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia
- Infectious Diseases Laboratory, Prevention Division, Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Cameron Buckley
- Infectious Diseases Laboratory, Prevention Division, Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Steven Badman
- Kirby Institute for Infection and Immunity in Society, University of New South Wales (UNSW) Medicine, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Patrick Harris
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia
- Prevention Division, Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Ian Mackay
- Infectious Diseases Laboratory, Prevention Division, Pathology Queensland, Brisbane, QLD 4006, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, QLD 4029, Australia
| | - David Whiley
- The Queensland Paediatric Infectious Diseases (QPID) Research Group, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia
- Infectious Diseases Laboratory, Prevention Division, Pathology Queensland, Brisbane, QLD 4006, Australia
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9
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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: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Oh C, Sashittal P, Zhou A, Wang L, El-Kebir M, Nguyen TH. Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Appl Environ Microbiol 2022; 88:e0228921. [PMID: 35285246 PMCID: PMC9004361 DOI: 10.1128/aem.02289-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Monitoring the prevalence of SARS-CoV-2 variants is necessary to make informed public health decisions during the COVID-19 pandemic. PCR assays have received global attention, facilitating a rapid understanding of variant dynamics because they are more accessible and scalable than genome sequencing. However, as PCR assays target only a few mutations, their accuracy could be reduced when these mutations are not exclusive to the target variants. Here we introduce PRIMES, an algorithm that evaluates the sensitivity and specificity of SARS-CoV-2 variant-specific PCR assays across different geographical regions by incorporating sequences deposited in the GISAID database. Using PRIMES, we determined that the accuracy of several PCR assays decreased when applied beyond the geographic scope of the study in which the assays were developed. Subsequently, we used this tool to design Alpha and Delta variant-specific PCR assays for samples from Illinois, USA. In silico analysis using PRIMES determined the sensitivity/specificity to be 0.99/0.99 for the Alpha variant-specific PCR assay and 0.98/1.00 for the Delta variant-specific PCR assay in Illinois, respectively. We applied these two variant-specific PCR assays to six local sewage samples and determined the dominant SARS-CoV-2 variant of either the wild type, the Alpha variant, or the Delta variant. Using next-generation sequencing (NGS) of the spike (S) gene amplicons of the Delta variant-dominant samples, we found six mutations exclusive to the Delta variant (S:T19R, S:Δ156/157, S:L452R, S:T478K, S:P681R, and S:D950N). The consistency between the variant-specific PCR assays and the NGS results supports the applicability of PRIMES. IMPORTANCE Monitoring the introduction and prevalence of variants of concern (VOCs) and variants of interest (VOIs) in a community can help the local authorities make informed public health decisions. PCR assays can be designed to keep track of SARS-CoV-2 variants by measuring unique mutation markers that are exclusive to the target variants. However, the mutation markers may not be exclusive to the target variants because of regional and temporal differences in variant dynamics. We introduce PRIMES, an algorithm that enables the design of reliable PCR assays for variant detection. Because PCR is more accessible, scalable, and robust for sewage samples than sequencing technology, our findings will contribute to improving global SARS-CoV-2 variant surveillance.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Palash Sashittal
- Department of Computer Science, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Mohammed El-Kebir
- Department of Computer Science, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Kohmer N, Eckermann L, Böddinghaus B, Götsch U, Berger A, Herrmann E, Kortenbusch M, Tinnemann P, Gottschalk R, Hoehl S, Ciesek S. Self-Collected Samples to Detect SARS-CoV-2: Direct Comparison of Saliva, Tongue Swab, Nasal Swab, Chewed Cotton Pads and Gargle Lavage. J Clin Med 2021; 10:jcm10245751. [PMID: 34945047 PMCID: PMC8709431 DOI: 10.3390/jcm10245751] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/20/2022] Open
Abstract
Testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by RT-PCR is a vital public health tool in the pandemic. Self-collected samples are increasingly used as an alternative to nasopharyngeal swabs. Several studies suggested that they are sufficiently sensitive to be a useful alternative. However, there are limited data directly comparing several different types of self-collected materials to determine which material is preferable. A total of 102 predominantly symptomatic adults with a confirmed SARS-CoV-2 infection self-collected native saliva, a tongue swab, a mid-turbinate nasal swab, saliva obtained by chewing a cotton pad and gargle lavage, within 48 h of initial diagnosis. Sample collection was unsupervised. Both native saliva and gargling with tap water had high diagnostic sensitivity of 92.8% and 89.1%, respectively. Nasal swabs had a sensitivity of 85.1%, which was not significantly inferior to saliva (p = 0.092), but 16.6% of participants reported they had difficult in self-collection of this sample. A tongue swab and saliva obtained by chewing a cotton pad had a significantly lower sensitivity of 74.2% and 70.2%, respectively. Diagnostic sensitivity was not related to the presence of clinical symptoms or to age. When comparing self-collected specimens from different material, saliva, gargle lavage or mid-turbinate nasal swabs may be considered for most symptomatic patients. However, complementary experiments are required to verify that differences in performance observed among the five sampling modes were not attributed to collection impairment.
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Affiliation(s)
- Niko Kohmer
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt, Germany; (N.K.); (L.E.); (A.B.); (M.K.); (R.G.); (S.C.)
| | - Lisa Eckermann
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt, Germany; (N.K.); (L.E.); (A.B.); (M.K.); (R.G.); (S.C.)
| | - Boris Böddinghaus
- Health Protection Authority, City of Frankfurt, 60313 Frankfurt, Germany; (B.B.); (U.G.); (P.T.)
| | - Udo Götsch
- Health Protection Authority, City of Frankfurt, 60313 Frankfurt, Germany; (B.B.); (U.G.); (P.T.)
| | - Annemarie Berger
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt, Germany; (N.K.); (L.E.); (A.B.); (M.K.); (R.G.); (S.C.)
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modelling, Goethe University Frankfurt, 60596 Frankfurt, Germany;
| | - Marhild Kortenbusch
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt, Germany; (N.K.); (L.E.); (A.B.); (M.K.); (R.G.); (S.C.)
| | - Peter Tinnemann
- Health Protection Authority, City of Frankfurt, 60313 Frankfurt, Germany; (B.B.); (U.G.); (P.T.)
| | - Rene Gottschalk
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt, Germany; (N.K.); (L.E.); (A.B.); (M.K.); (R.G.); (S.C.)
- Health Protection Authority, City of Frankfurt, 60313 Frankfurt, Germany; (B.B.); (U.G.); (P.T.)
| | - Sebastian Hoehl
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt, Germany; (N.K.); (L.E.); (A.B.); (M.K.); (R.G.); (S.C.)
- Correspondence: ; Tel.: +49-69-6301-0
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, 60596 Frankfurt, Germany; (N.K.); (L.E.); (A.B.); (M.K.); (R.G.); (S.C.)
- German Centre for Infection Research, External Partner Site, 60323 Frankfurt, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, 60596 Frankfurt, Germany
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