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Van Poelvoorde LAE, Gobbo A, Nauwelaerts SJD, Verhaegen B, Lesenfants M, Janssens R, Hutse V, Fraiture MA, De Keersmaecker S, Herman P, Van Hoorde K, Roosens N. Development of a reverse transcriptase digital droplet polymerase chain reaction-based approach for SARS-CoV-2 variant surveillance in wastewater. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e10999. [PMID: 38414298 DOI: 10.1002/wer.10999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/29/2024]
Abstract
An urgent need for effective surveillance strategies arose due to the global emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although vaccines and antivirals are available, concerns persist about the evolution of new variants with potentially increased infectivity, transmissibility, and immune evasion. Therefore, variant monitoring is crucial for public health decision-making. Wastewater-based surveillance has proven to be an effective tool to monitor SARS-CoV-2 variants within populations. Specific SARS-CoV-2 variants are detected and quantified in wastewater in this study using a reverse transcriptase digital droplet polymerase chain reaction (RT-ddPCR) approach. The 11 designed assays were first validated in silico using a substantial dataset of high-quality SARS-CoV-2 genomes to ensure comprehensive variant coverage. The assessment of the sensitivity and specificity with reference material showed the capability of the developed assays to reliably identify target mutations while minimizing false positives and false negatives. The applicability of the assays was evaluated using wastewater samples from a wastewater treatment plant in Ghent, Belgium. The quantification of the specific mutations linked to the variants of concern present in these samples was calculated using these assays based on the detection of single mutations, which confirms their use for real-world variant surveillance. In conclusion, this study provides an adaptable protocol to monitor SARS-CoV-2 variants in wastewater with high sensitivity and specificity. Its potential for broader application in other viral surveillance contexts highlights its added value for rapid response to emerging infectious diseases. PRACTITIONER POINTS: Robust RT-ddPCR methodology for specific SARS-CoV-2 variants of concern detection in wastewater. Rigorous validation that demonstrates high sensitivity and specificity. Demonstration of real-world applicability using wastewater samples. Valuable tool for rapid response to emerging infectious diseases.
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Affiliation(s)
| | - Andrea Gobbo
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Marie Lesenfants
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Raphael Janssens
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Veronik Hutse
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | | | | | | | | | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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Oh C, Xun G, Lane ST, Petrov VA, Zhao H, Nguyen TH. Portable, single nucleotide polymorphism-specific duplex assay for virus surveillance in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168701. [PMID: 37992833 DOI: 10.1016/j.scitotenv.2023.168701] [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: 08/30/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
The Argonaute protein from the archaeon Pyrococcus furiosus (PfAgo) is a DNA-guided nuclease that targets DNA with any sequence. We designed a virus detection assay in which the PfAgo enzyme cleaves the reporter probe, thus generating fluorescent signals when amplicons from a reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay contain target sequences. We confirmed that the RT-LAMP-PfAgo assay for the SARS-CoV-2 Delta variant produced significantly higher fluorescent signals (p < 0.001) when a single nucleotide polymorphism (SNP), exclusive to the Delta variant, was present, compared to the samples without the SNP. Additionally, the duplex assay for Pepper mild mottle virus (PMMOV) and SARS-CoV-2 detection produced specific fluorescent signals (FAM or ROX) only when the corresponding sequences were present. Furthermore, the RT-LAMP-PfAgo assay does not require dilution to reduce the impact of environmental inhibitors. The limit of detection of the PMMOV assay, determined with 30 wastewater samples, was 28 gc/μL, with a 95 % confidence interval of [11,103]. Finally, using a point-of-use device, the RT-LAMP-PfAgo assay successfully detected PMMOV in wastewater samples. Based on our findings, we conclude that the RT-LAMP-PfAgo assay can be used as a portable, SNP-specific duplex assay, which will significantly improve virus surveillance in wastewater.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA.
| | - Guanhua Xun
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Stephan Thomas Lane
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
| | - Vassily Andrew Petrov
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
| | - Huimin Zhao
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States; Departments of Chemical and Biomolecular Engineering, Chemistry, and Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States; Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
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3
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Li J, Zhang K, Lin G, Li J. CRISPR-Cas system: A promising tool for rapid detection of SARS-CoV-2 variants. J Med Virol 2024; 96:e29356. [PMID: 38180237 DOI: 10.1002/jmv.29356] [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: 06/04/2023] [Revised: 12/05/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
COVID-19, caused by SARS-CoV-2, remains a global health crisis. The emergence of multiple variants with enhanced characteristics necessitates their detection and monitoring. Genome sequencing, the gold standard, faces implementation challenges due to complexity, cost, and limited throughput. The CRISPR-Cas system offers promising potential for rapid variant detection, with advantages such as speed, sensitivity, specificity, and programmability. This review provides an in-depth examination of the applications of CRISPR-Cas in mutation detection specifically for SARS-CoV-2. It begins by introducing SARS-CoV-2 and existing variant detection platforms. The principles of the CRISPR-Cas system are then clarified, followed by an exploration of three CRISPR-Cas-based mutation detection platforms, which are evaluated from different perspectives. The review discusses strategies for mutation site selection and the utilization of CRISPR-Cas, offering valuable insights for the development of mutation detection methods. Furthermore, a critical analysis of the clinical applications, advantages, disadvantages, challenges, and prospects of the CRISPR-Cas system is provided.
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Affiliation(s)
- Jing Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
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Oh C, Zhou A, O'Brien K, Schmidt AR, Geltz J, Shisler JL, Schmidt AR, Keefer L, Brown WM, Nguyen TH. Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance. Appl Environ Microbiol 2023; 89:e0033123. [PMID: 37791775 PMCID: PMC10654041 DOI: 10.1128/aem.00331-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/07/2023] [Indexed: 10/05/2023] Open
Abstract
Nucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of their genetic diversity. Here, we calculated the variability of nucleotides within the genomes of 10 human viral species in silico and found that endemic viruses exhibit a high percentage of variable nucleotides (e.g., 51.4% for norovirus genogroup II). This genetic diversity led to the variable probability of detection of PCR assays (the proportion of viral sequences that contain the assay's target sequences divided by the total number of viral sequences). We then experimentally confirmed that the probability of the target sequence detection is indicative of the number of mismatches between PCR assays and norovirus genomes. Next, we developed a degenerate PCR assay that detects 97% of known norovirus genogroup II genome sequences and recognized norovirus in eight clinical samples. By contrast, previously developed assays with 31% and 16% probability of detection had 1.1 and 2.5 mismatches on average, respectively, which negatively impacted RNA quantification. In addition, the two PCR assays with a lower probability of detection also resulted in false negatives for wastewater-based epidemiology. Our findings suggest that the probability of detection serves as a simple metric for evaluating nucleic acid-based assays for genetically diverse virus surveillance.IMPORTANCENucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are employed widely as a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of the rapid evolution and genetic variation of viruses. The study analyzed clinical and wastewater samples using multiple PCR assays and found significant performance variation among the PCR assays for genetically diverse norovirus surveillance. This finding suggests that some PCR assays may miss detecting certain virus strains, leading to a compromise in detection sensitivity. To address this issue, we propose a metric called the probability of detection, which can be simply calculated in silico using a code developed in this study, to evaluate nucleic acid-based assays for genetically diverse virus surveillance. This new approach can help improve the sensitivity and accuracy of virus detection, which is crucial for effective infectious disease surveillance and control.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kate O'Brien
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Arthur R. Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Joshua Geltz
- Division of Laboratories, Illinois Department of Public Health, Springfield, Illinois, USA
| | - Joanna L. Shisler
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Arthur R. Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Laura Keefer
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - William M. Brown
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Navas MC, Cerón JD, Aguilar-Jiménez W, Rugeles MT, Díaz FJ. Outbreak report of SARS-CoV-2 infection by airborne transmission: Epidemiologic and molecular evidence. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:121-130. [PMID: 37167462 PMCID: PMC10501502 DOI: 10.7705/biomedica.6695] [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: 08/12/2022] [Accepted: 03/04/2023] [Indexed: 05/13/2023]
Abstract
INTRODUCTION It has been shown that the transmission of SARS-CoV-2 occurs mainly by air, and the risk of infection is greater in closed spaces. OBJECTIVE To describe the epidemiology, virology and molecular characterization of a COVID-19 outbreak at a closed vaccination point during the third wave of SARS-CoV-2 in Colombia. MATERIALS AND METHODS Diagnostic tests, interviews, sampling, cell cultures and viral sequencing were carried out, the latter being molecular characterization and lineage identification. RESULTS Seven workers were positive for SARS-CoV-2; among these, 3 samples were analyzed, plus an additional sample belonging to the mother of the presumed index case; all samples were identified with lineage B.1.625, with a maximum of 2 nucleotides difference between them. CONCLUSIONS Variant B.1.625 was identified as the cause of the COVID-19 outbreak, and a co-worker was also identified as the index case. Unexpectedly, attending a vaccination day became a risk factor for acquiring the infection.
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Affiliation(s)
- María-Cristina Navas
- Grupo Gastrohepatología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| | - Juan D Cerón
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| | | | - María T Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| | - Francisco J Díaz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
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Prado T, Rey-Benito G, Miagostovich MP, Sato MIZ, Rajal VB, Filho CRM, Pereira AD, Barbosa MRF, Mannarino CF, da Silva AS. Wastewater-based epidemiology for preventing outbreaks and epidemics in Latin America - Lessons from the past and a look to the future. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161210. [PMID: 36581294 DOI: 10.1016/j.scitotenv.2022.161210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Wastewater-based epidemiology (WBE) is an approach with the potential to complement clinical surveillance systems. Using WBE, it is possible to carry out an early warning of a possible outbreak, monitor spatial and temporal trends of infectious diseases, produce real-time results and generate representative epidemiological information in a territory, especially in areas of social vulnerability. Despite the historical uses of this approach, particularly in the Global Polio Eradication Initiative, and for other pathogens, it was during the COVID-19 pandemic that occurred an exponential increase in environmental surveillance programs for SARS-CoV-2 in wastewater, with many experiences and developments in the field of public health using data for decision making and prioritizing actions to control the pandemic. In Latin America, WBE was applied in heterogeneous contexts and with emphasis on populations that present many socio-environmental inequalities, a condition shared by all Latin American countries. This manuscript addresses the concepts and applications of WBE in public health actions, as well as different experiences in Latin American countries, and discusses a model to implement this surveillance system at the local or national level. We emphasize the need to implement this sentinel surveillance system in countries that want to detect the early entry and spread of new pathogens and monitor outbreaks or epidemics of infectious agents in their territories as a complement of public health surveillance systems.
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Affiliation(s)
- Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil.
| | - Gloria Rey-Benito
- Pan American Health Organization (PAHO/WHO), 525 23rd St NW, Washington, DC 20037, United States of America.
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Maria Inês Zanoli Sato
- Department of Environmental Analysis, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil
| | - Veronica Beatriz Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Facultad de Ingeniería, UNSa, Av. Bolivia 5150, Salta 4400, Argentina; Singapore Centre for Environmental Life Science Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Cesar Rossas Mota Filho
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Alyne Duarte Pereira
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Mikaela Renata Funada Barbosa
- Department of Environmental Analysis, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil
| | - Camille Ferreira Mannarino
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Agnes Soares da Silva
- Pan American Health Organization (PAHO/WHO), 525 23rd St NW, Washington, DC 20037, United States of America.
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Oh C, Zhou A, O'Brien K, Jamal Y, Wennerdahl H, Schmidt AR, Shisler JL, Jutla A, Schmidt AR, Keefer L, Brown WM, Nguyen TH. Application of neighborhood-scale wastewater-based epidemiology in low COVID-19 incidence situations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158448. [PMID: 36063927 PMCID: PMC9436825 DOI: 10.1016/j.scitotenv.2022.158448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/08/2022] [Accepted: 08/28/2022] [Indexed: 05/17/2023]
Abstract
Wastewater-based epidemiology (WBE), an emerging approach for community-wide COVID-19 surveillance, was primarily characterized at large sewersheds such as wastewater treatment plants serving a large population. Although informed public health measures can be better implemented for a small population, WBE for neighborhood-scale sewersheds is less studied and not fully understood. This study applied WBE to seven neighborhood-scale sewersheds (average population of 1471) from January to November 2021. Community testing data showed an average of 0.004 % incidence rate in these sewersheds (97 % of monitoring periods reported two or fewer daily infections). In 92 % of sewage samples, SARS-CoV-2 N gene fragments were below the limit of quantification. We statistically determined 10-2.6 as the threshold of the SARS-CoV-2 N gene concentration normalized to pepper mild mottle virus (N/PMMOV) to alert high COVID-19 incidence rate in the studied sewershed. This threshold of N/PMMOV identified neighborhood-scale outbreaks (COVID-19 incidence rate higher than 0.2 %) with 82 % sensitivity and 51 % specificity. Importantly, neighborhood-scale WBE can discern local outbreaks that would not otherwise be identified by city-scale WBE. Our findings suggest that neighborhood-scale WBE is an effective community-wide disease surveillance tool when COVID-19 incidence is maintained at a low level.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States.
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States
| | - Kate O'Brien
- School of Integrative Biology, University of Illinois Urbana-Champaign, United States
| | - Yusuf Jamal
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, United States
| | - Hayden Wennerdahl
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, United States
| | - Arthur R Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States
| | - Joanna L Shisler
- Department of Microbiology, University of Illinois Urbana-Champaign, United States
| | - Antarpreet Jutla
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, United States
| | - Arthur R Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States
| | - Laura Keefer
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, United States
| | - William M Brown
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, United States
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States; Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
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8
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Zhu Y, Zhang M, Jie Z, Tao S. Nucleic acid testing of SARS-CoV-2: A review of current methods, challenges, and prospects. Front Microbiol 2022; 13:1074289. [PMID: 36569096 PMCID: PMC9780671 DOI: 10.3389/fmicb.2022.1074289] [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: 10/19/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has brought a huge threat to public health and the global economy. Rapid identification and isolation of SARS-CoV-2-infected individuals are regarded as one of the most effective measures to control the pandemic. Because of its high sensitivity and specificity, nucleic acid testing has become the major method of SARS-CoV-2 detection. A deep understanding of different diagnosis methods for COVID-19 could help researchers make an optimal choice in detecting COVID-19 at different symptom stages. In this review, we summarize and evaluate the latest developments in current nucleic acid detection methods for SARS-CoV-2. In particular, we discuss biosensors and CRISPR-based diagnostic systems and their characteristics and challenges. Furthermore, the emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis are systematically introduced and discussed. Considering the disease dynamics, we also recommend optional diagnostic tests for different symptom stages. From sample preparation to results readout, we conclude by pointing out the pain points and future directions of COVID-19 detection.
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Affiliation(s)
- Yuanshou Zhu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China,School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China,Center of Community-Based Health Research, Fudan University, Shanghai, China,*Correspondence: Zhijun Jie,
| | - Shengce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China,School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China,Shengce Tao,
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9
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Aralis Z, Comer S, Ansorg H, Palmer C, Smith J, Feinstein SC, Fitzgibbons LN, Arias C. Efficient Tracing of the SARS-CoV-2 Omicron Variants in Santa Barbara County Using a Rapid Quantitative Reverse Transcription PCR Assay. Diagnostics (Basel) 2022; 12:2805. [PMID: 36428863 PMCID: PMC9689663 DOI: 10.3390/diagnostics12112805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/18/2022] Open
Abstract
The emergence of the SARS-CoV-2 Omicron variant in 2021 is associated with a global surge of cases in late 2021 and early 2022. Identifying the introduction of novel SARS-CoV-2 variants to a population is imperative to inform decisions by clinicians and public health officials. Here, we describe a quantitative reverse transcription PCR-based assay (RT-qPCR) targeting unique mutations in the Omicron BA.1/BA1.1 and BA.2 viral genomes. This assay accurately and precisely detect the presence of these Omicron variants in patient samples in less than four hours. Using this assay, we tested 270 clinical samples and detected the introduction of Omicron BA.1/BA1.1 and BA.2 in the Santa Barbara County (SBC) population in December 2021 and February 2022, respectively. Identifying Omicron variants using this RT-qPCR assay showed complete concordance with whole viral genome sequencing; both assays indicated that Omicron was the dominant variant in SB County. Our data substantiate that RT-qPCR-based virus detection assays offer a fast and inexpensive alternative to NGS for virus variant-specific detection approach, which allows streamlining the detection of Omicron variants in patient samples.
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Affiliation(s)
- Zach Aralis
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
- Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Stewart Comer
- Santa Barbara County Public Health Department, Santa Barbara, CA 93106, USA
- Department of Pathology, Santa Barbara Cottage Hospital, Santa Barbara, CA 93106, USA
- Pacific Diagnostic Laboratories, Santa Barbara, CA 93106, USA
| | - Henning Ansorg
- Santa Barbara County Public Health Department, Santa Barbara, CA 93106, USA
| | - Carl Palmer
- LegacyWorks Group, Santa Barbara, CA 93106, USA
| | - Jennifer Smith
- California NanoSystems Institute, University of California, Santa Barbara, CA 93106, USA
| | - Stuart C. Feinstein
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Lynn N. Fitzgibbons
- Department of Medical Education, Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, CA 93106, USA
| | - Carolina Arias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
- Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
- Infectious Disease Initiative, Chan Zuckerberg BioHub, San Francisco, CA 93106, USA
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