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Sluimer J, van den Akker WMR, Goderski G, Swart A, van der Veer B, Cremer J, Chung NH, Molenkamp R, Voermans J, Guldemeester J, Eggink D, Presser LD, Meijer A. High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment. Sci Rep 2024; 14:1378. [PMID: 38228693 DOI: 10.1038/s41598-023-50912-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 12/27/2023] [Indexed: 01/18/2024] Open
Abstract
A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.
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Grants
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
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Affiliation(s)
- John Sluimer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Willem M R van den Akker
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Gabriel Goderski
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Arno Swart
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Bas van der Veer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jeroen Cremer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ngoc Hoa Chung
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jolanda Voermans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Judith Guldemeester
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dirk Eggink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Lance D Presser
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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Ding H, Zhang W, Wang SA, Li C, Li W, Liu J, Yu F, Tao Y, Cheng S, Xie H, Chen Y. A semi-quantitative upconversion nanoparticle-based immunochromatographic assay for SARS-CoV-2 antigen detection. Front Microbiol 2023; 14:1289682. [PMID: 38149276 PMCID: PMC10750388 DOI: 10.3389/fmicb.2023.1289682] [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: 09/06/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023] Open
Abstract
The unprecedented public health and economic impact of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been met with an equally unprecedented scientific response. Sensitive point-of-care methods to detect SARS-CoV-2 antigens in clinical specimens are urgently required for the rapid screening of individuals with viral infection. Here, we developed an upconversion nanoparticle-based lateral flow immunochromatographic assay (UCNP-LFIA) for the high-sensitivity detection of SARS-CoV-2 nucleocapsid (N) protein. A pair of rabbit SARS-CoV-2 N-specific monoclonal antibodies was conjugated to UCNPs, and the prepared UCNPs were then deposited into the LFIA test strips for detecting and capturing the N protein. Under the test conditions, the limit of detection (LOD) of UCNP-LFIA for the N protein was 3.59 pg/mL, with a linear range of 0.01-100 ng/mL. Compared with that of the current colloidal gold-based LFIA strips, the LOD of the UCNP-LFIA-based method was increased by 100-fold. The antigen recovery rate of the developed method in the simulated pharyngeal swab samples ranged from 91.1 to 117.3%. Furthermore, compared with the reverse transcription-polymerase chain reaction, the developed UCNP-LFIA method showed a sensitivity of 94.73% for 19 patients with COVID-19. Thus, the newly established platform could serve as a promising and convenient fluorescent immunological sensing approach for the efficient screening and diagnosis of COVID-19.
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Affiliation(s)
- Hai Ding
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wanying Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shu-an Wang
- Department of Clinic Nutrition, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Chuang Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wanting Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Liu
- Polariton Life Technologies Ltd., Soochow, Jiangsu, China
| | - Fang Yu
- Polariton Life Technologies Ltd., Soochow, Jiangsu, China
| | - Yanru Tao
- Polariton Life Technologies Ltd., Soochow, Jiangsu, China
| | - Siyun Cheng
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hui Xie
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
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3
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Hart JJ, Jamison MN, McNair JN, Szlag DC. Frequency and degradation of SARS-CoV-2 markers N1, N2, and E in sewage. JOURNAL OF WATER AND HEALTH 2023; 21:514-524. [PMID: 37119151 DOI: 10.2166/wh.2023.314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease that is mainly spread through aerosolized droplets containing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is excreted in feces by infected individuals. Sewage surveillance has been applied widely to obtain data on the prevalence of COVID-19 in whole communities. We used SARS-CoV-2 gene targets N1, N2, and E to determine the prevalence of COVID-19 at both municipal and building levels. Frequency analysis of wastewater testing indicated that single markers detected only 85% or less of samples that were detected as positive for SARS-CoV-2 with the three markers combined, indicating the necessity of pairing markers to lower the false-negative rate. The best pair of markers in both municipal and building level monitoring was N1 and N2, which correctly identified 98% of positive samples detected with the three markers combined. The degradation rates of all three targets were assessed at two different temperatures (25 and 35 °C) as a possible explanation for observed differences between markers in frequency. Results indicated that all three RNA targets degrade at nearly the same rate, indicating that differences in degradation rate are not responsible for the observed differences in marker frequency.
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Affiliation(s)
- John J Hart
- Oakland University, Department of Chemistry, 146 Library Dr, Rochester, MI 48309, USA E-mail: ; Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI 49441, USA
| | - Megan N Jamison
- Oakland University, Department of Chemistry, 146 Library Dr, Rochester, MI 48309, USA E-mail: ; The Ohio State University, 281 W Lane Ave, Columbus, OH 43210, USA
| | - James N McNair
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI 49441, USA
| | - David C Szlag
- Oakland University, Department of Chemistry, 146 Library Dr, Rochester, MI 48309, USA E-mail:
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Sun YS, Sun H, Zhu HP, Li GL, Xu F, Lu HJ, Tang A, Wu BB, Li YD, Yao PP, Jiang JM. Comparative transcriptomic analyzes of human lung epithelial cells infected with wild-type SARS-CoV-2 and its variant with a 12-bp missing in the E gene. Front Microbiol 2023; 13:1079764. [PMID: 36699595 PMCID: PMC9868179 DOI: 10.3389/fmicb.2022.1079764] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that caused a global outbreak of coronavirus disease 2019 (COVID-19) pandemic. To elucidate the mechanism of SARS-CoV-2 replication and immunogenicity, we performed a comparative transcriptome profile of mRNA and long non-coding RNAs (lncRNAs) in human lung epithelial cells infected with the SARS-CoV-2 wild-type strain (8X) and the variant with a 12-bp deletion in the E gene (F8). In total, 3,966 differentially expressed genes (DEGs) and 110 differentially expressed lncRNA (DE-lncRNA) candidates were identified. Of these, 94 DEGs and 32 DE-lncRNAs were found between samples infected with F8 and 8X. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyzes revealed that pathways such as the TNF signaling pathway and viral protein interaction with cytokine and cytokine receptor were involved. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to the immune response, which might explain the different replication and immunogenicity properties of the 8X and F8 strains. These results provide a useful resource for studying the pathogenesis of SARS-CoV-2 variants.
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Affiliation(s)
- Yi-Sheng Sun
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Hao Sun
- Department of Biological Engineering, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Han-Ping Zhu
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Gao-Lei Li
- Department of Biological Engineering, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Fang Xu
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Hang-Jing Lu
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - An Tang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, Zhejiang, China
| | - Bei-Bei Wu
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yu-Dong Li
- Department of Biological Engineering, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China,*Correspondence: Yu-Dong Li, ✉
| | - Ping-Ping Yao
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China,Ping-Ping Yao, ✉
| | - Jian-Min Jiang
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China,Jian-Min Jiang, ✉
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