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Banholzer N, Bittel P, Jent P, Furrer L, Zürcher K, Egger M, Hascher T, Fenner L. Molecular detection of SARS-CoV-2 and other respiratory viruses in saliva and classroom air: a two winters tale. Clin Microbiol Infect 2024; 30:829.e1-829.e4. [PMID: 38467247 DOI: 10.1016/j.cmi.2024.03.002] [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: 01/11/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
OBJECTIVES To compare the prevalence of SARS-CoV-2 and other respiratory viruses in saliva and bioaerosols between two winters and to model the probability of virus detection in classroom air for different viruses. METHODS We analysed saliva, air, and air cleaner filter samples from studies conducted in two Swiss secondary schools (students aged 14-17 years) over 7 weeks during the winters of 2021/22 and 2022/23. Two bioaerosol sampling devices and high efficiency particulate air (HEPA) filters from air cleaners were used to collect airborne virus particles in four classrooms. Daily bioaerosol samples were pooled for each sampling device before PCR analysis of a panel of 19 respiratory viruses and viral subtypes. The probability of detection of airborne viruses was modelled using an adjusted Bayesian logistic regression model. RESULTS Three classes (58 students) participated in 2021/22, and two classes (38 students) in 2022/23. During winter 2021/22, SARS-CoV-2 dominated in saliva (19 of 21 positive samples) and bioaerosols (9 of 10). One year later, there were 50 positive saliva samples, mostly influenza B, rhinovirus, and adenovirus, and two positive bioaerosol samples, one rhinovirus and one adenovirus. The weekly probability of airborne detection was 34% (95% credible interval [CrI] 22-47%) for SARS-CoV-2 and 10% (95% CrI 5-16%) for other respiratory viruses. DISCUSSION There was a distinct shift in the distribution of respiratory viruses from SARS-CoV-2 during the omicron wave to other respiratory viruses one year later. SARS-CoV-2 is more likely to be detected in the air than other endemic respiratory viruses, possibly reflecting differences in viral characteristics and the composition of virus-carrying particles that facilitate airborne long-range transmission.
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Affiliation(s)
- Nicolas Banholzer
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Pascal Bittel
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland; Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Philipp Jent
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland; Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Lavinia Furrer
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Kathrin Zürcher
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Population Health Sciences, University of Bristol, Bristol, UK; Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
| | - Tina Hascher
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland; Institute of Educational Science, University of Bern, Bern, Switzerland
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
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Zhou C, Cai Z, Jin B, Lin H, Xu L, Jin Z. Saliva-based detection of SARS-CoV-2: a bibliometric analysis of global research. Mol Cell Biochem 2024; 479:761-777. [PMID: 37178376 PMCID: PMC10182745 DOI: 10.1007/s11010-023-04760-w] [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: 03/13/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
Saliva has emerged as a promising noninvasive biofluid for the diagnosis of oral and systemic diseases, including viral infections. During the coronavirus disease 2019 (COVID-19) pandemic, a growing number of studies focused on saliva-based detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Taking advantage of the WoS core collection (WoSCC) and CiteSpace, we retrieved 1021 articles related to saliva-based detection of SARS-CoV-2 and conducted a comprehensive bibliometric analysis. We analyzed countries, institutions, authors, cited authors, and cited journals to summarize their contribution and influence and analyzed keywords to explore research hotspots and trends. From 2020 to 2021, research focused on viral transmission via saliva and verification of saliva as a reliable specimen, whereas from 2021 to the present, the focus of research has switched to saliva-based biosensors for SARS-CoV-2 detection. By far, saliva has been verified as a reliable specimen for SARS-CoV-2 detection, although a standardized procedure for saliva sampling and processing is needed. Studies on saliva-based detection of SARS-CoV-2 will promote the development of saliva-based diagnostics and biosensors for viral detection. Collectively, our findings could provide valuable information to help scientists perceive the basic knowledge landscapes on saliva-based detection of SARS-CoV-2, the past and current research hotspots, and future opportunities.
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Affiliation(s)
- Chun Zhou
- Jinhua People's Hospital Joint Center for Biomedical Research, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
- Department of Science and Education, the Affiliated Jinhua Hospital of Wenzhou Medical University, Jinhua, 321000, Zhejiang, China
| | - Zhaopin Cai
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China
| | - Boxing Jin
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China
| | - Huisong Lin
- Zhejiang Institute of Medical Device Testing, Hangzhou, Zhejiang, China
| | - Lingling Xu
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China
| | - Zhigang Jin
- Jinhua People's Hospital Joint Center for Biomedical Research, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China.
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China.
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Wang Z, Liu YL, Chen Y, Siegel L, Cappelleri JC, Chu H. Double-Negative Results Matter: A Reevaluation of Sensitivities for Detecting SARS-CoV-2 Infection Using Saliva Versus Nasopharyngeal Swabs. Am J Epidemiol 2024; 193:548-560. [PMID: 37939113 DOI: 10.1093/aje/kwad212] [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: 10/06/2022] [Accepted: 10/27/2023] [Indexed: 11/10/2023] Open
Abstract
In a recent systematic review, Bastos et al. (Ann Intern Med. 2021;174(4):501-510) compared the sensitivities of saliva sampling and nasopharyngeal swabs in the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by assuming a composite reference standard defined as positive if either test is positive and negative if both tests are negative (double negative). Even under a perfect specificity assumption, this approach ignores the double-negative results and risks overestimating the sensitivities due to residual misclassification. In this article, we first illustrate the impact of double-negative results in the estimation of the sensitivities in a single study, and then propose a 2-step latent class meta-analysis method for reevaluating both sensitivities using the same published data set as that used in Bastos et al. by properly including the observed double-negative results. We also conduct extensive simulation studies to compare the performance of the proposed method with Bastos et al.'s method for varied levels of prevalence and between-study heterogeneity. The results demonstrate that the sensitivities are overestimated noticeably using Bastos et al.'s method, and the proposed method provides a more accurate evaluation with nearly no bias and close-to-nominal coverage probability. In conclusion, double-negative results can significantly impact the estimated sensitivities when a gold standard is absent, and thus they should be properly incorporated.
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Sritong N, Ngo WW, Ejendal KFK, Linnes JC. Development of an integrated sample amplification control for salivary point-of-care pathogen testing. Anal Chim Acta 2024; 1287:342072. [PMID: 38182338 DOI: 10.1016/j.aca.2023.342072] [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: 10/03/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND The COVID-19 pandemic has led to a rise in point-of-care (POC) and home-based tests, but concerns over usability, accuracy, and effectiveness have arisen. The incorporation of internal amplification controls (IACs), essential control for translational POC diagnostics, could mitigate false-negative and false-positive results due to sample matrix interference or inhibition. Although emerging POC nucleic acid amplification tests (NAATs) for detecting SARS-CoV-2 show impressive analytical sensitivity in the lab, the assessment of clinical accuracy with IACs is often overlooked. In some cases, the IACs were run spatially, complicating assay workflow. Therefore, the multiplex assay for pathogen and IAC is needed. RESULTS We developed a one-pot duplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for saliva samples, a non-invasive and simple collected specimen for POC NAATs. The ORF1ab gene of SARS-CoV-2 was used as a target and a human 18S ribosomal RNA in human saliva was employed as an IAC to ensure clinical reliability of the RT-LAMP assay. The optimized assay could detect SARS-CoV-2 viral particles down to 100 copies/μL of saliva within 30 min without RNA extraction. The duplex RT-LAMP for SARS-CoV-2 and IAC is successfully amplified in the same reaction without cross-reactivity. The valid results were easily visualized in triple-line lateral flow immunoassay, in which two lines (flow control and IAC lines) represent valid negative results and three lines (flow control, IAC, and test line) represent valid positive results. This duplex assay demonstrated a clinical sensitivity of 95%, specificity of 100%, and accuracy of 96% in 30 clinical saliva samples. SIGNIFICANCE IACs play a crucial role in ensuring user confidence with respect to the accuracy and reliability of at-home and POC molecular diagnostics. We demonstrated the multiplex capability of SARS-COV-2 and human18S ribosomal RNA RT-LAMP without complicating assay design. This generic platform can be extended in a similar manner to include human18S ribosomal RNA IACs into different clinical sample matrices.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Winston Wei Ngo
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Karin F K Ejendal
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA; Department of Public Health, Purdue University, West Lafayette, IN, USA.
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de Araujo WR, Lukas H, Torres MDT, Gao W, de la Fuente-Nunez C. Low-Cost Biosensor Technologies for Rapid Detection of COVID-19 and Future Pandemics. ACS NANO 2024; 18:1757-1777. [PMID: 38189684 DOI: 10.1021/acsnano.3c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Many systems have been designed for the detection of SARS-CoV-2, which is the virus that causes COVID-19. SARS-CoV-2 is readily transmitted, resulting in the rapid spread of disease in human populations. Frequent testing at the point of care (POC) is a key aspect for controlling outbreaks caused by SARS-CoV-2 and other emerging pathogens, as the early identification of infected individuals can then be followed by appropriate measures of isolation or treatment, maximizing the chances of recovery and preventing infectious spread. Diagnostic tools used for high-frequency testing should be inexpensive, provide a rapid diagnostic response without sophisticated equipment, and be amenable to manufacturing on a large scale. The application of these devices should enable large-scale data collection, help control viral transmission, and prevent disease propagation. Here we review functional nanomaterial-based optical and electrochemical biosensors for accessible POC testing for COVID-19. These biosensors incorporate nanomaterials coupled with paper-based analytical devices and other inexpensive substrates, traditional lateral flow technology (antigen and antibody immunoassays), and innovative biosensing methods. We critically discuss the advantages and disadvantages of nanobiosensor-based approaches compared to widely used technologies such as PCR, ELISA, and LAMP. Moreover, we delineate the main technological, (bio)chemical, translational, and regulatory challenges associated with developing functional and reliable biosensors, which have prevented their translation into the clinic. Finally, we highlight how nanobiosensors, given their unique advantages over existing diagnostic tests, may help in future pandemics.
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Affiliation(s)
- William Reis de Araujo
- Portable Chemical Sensors Lab, Department of Analytical Chemistry, Institute of Chemistry, State University of Campinas - UNICAMP, Campinas, SP 13083-970, Brazil
| | - Heather Lukas
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, United States
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Wei Gao
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, United States
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Nazar NSBM, Ramanathan A, Ghani WMN, Rokhani FB, Jacob PS, Sabri NEB, Hassan MS, Kadir K, Dharmarajan L. Salivary metabolomics in oral potentially malignant disorders and oral cancer patients-a systematic review with meta-analysis. Clin Oral Investig 2024; 28:98. [PMID: 38225483 DOI: 10.1007/s00784-023-05481-6] [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: 08/10/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024]
Abstract
OBJECTIVES The aim of this systematic review and meta-analysis is to assess the diagnostic potential of salivary metabolomics in the detection of oral potentially malignant disorders (OPMDs) and oral cancer (OC). MATERIALS AND METHODS A systematic review was performed in accordance with the 3rd edition of the Centre for Reviews and Dissemination (CRD) and Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement. Electronic searches for articles were carried out in the PubMed, Web of Science, and Scopus databases. The quality assessment of the included studies was evaluated using the Newcastle-Ottawa Quality Assessment Scale (NOS) and the new version of the QUADOMICS tool. Meta-analysis was conducted whenever possible. The effect size was presented using the Forest plot, whereas the presence of publication bias was examined through Begg's funnel plot. RESULTS A total of nine studies were included in the systematic review. The metabolite profiling was heterogeneous across all the studies. The expression of several salivary metabolites was found to be significantly altered in OPMDs and OCs as compared to healthy controls. Meta-analysis was able to be conducted only for N-acetylglucosamine. There was no significant difference (SMD = 0.15; 95% CI - 0.25-0.56) in the level of N-acetylglucosamine between OPMDs, OC, and the control group. CONCLUSION Evidence for N-acetylglucosamine as a salivary biomarker for oral cancer is lacking. Although several salivary metabolites show changes between healthy, OPMDs, and OC, their diagnostic potential cannot be assessed in this review due to a lack of data. Therefore, further high-quality studies with detailed analysis and reporting are required to establish the diagnostic potential of the salivary metabolites in OPMDs and OC. CLINICAL RELEVANCE While some salivary metabolites exhibit significant changes in oral potentially malignant disorders (OPMDs) and oral cancer (OC) compared to healthy controls, the current evidence, especially for N-acetylglucosamine, is inadequate to confirm their reliability as diagnostic biomarkers. Additional high-quality studies are needed for a more conclusive assessment of salivary metabolites in oral disease diagnosis.
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Affiliation(s)
- Nur Syahirah Binti Mohd Nazar
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, Malaysia
- Department of Oral and Maxillofacial Surgery, Medicine and Pathology, Faculty of Dentistry, Universiti Sains Islam Malaysia, Kuala Lumpur, Malaysia
| | - Anand Ramanathan
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, Malaysia.
- Oral Cancer Research & Coordinating Center, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, Malaysia.
| | - Wan Maria Nabillah Ghani
- Oral Cancer Research & Coordinating Center, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Faezah Binti Rokhani
- Department of Oral and Maxillofacial Surgery, Medicine and Pathology, Faculty of Dentistry, Universiti Sains Islam Malaysia, Kuala Lumpur, Malaysia
| | - Pulikkotil Shaju Jacob
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - Nurul Elma Binti Sabri
- Department of Agrotechnology and Bioscience, Malaysian Nuclear Agency, Bangi, Selangor, Malaysia
| | - Mohd Sukri Hassan
- Faculty of Science and Technology, Universiti Sains Islam Malaysia, Kuala Lumpur, Malaysia
| | - Kathreena Kadir
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, Malaysia
- Oral Cancer Research & Coordinating Center, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, Malaysia
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Khyati, Manchanda V, Pumma P, Chawla R, Garg S, Saxena S. Diagnostic performance of saliva RT-PCR test as a diagnostic tool and its utility in the detection of SARS-CoV-2 shedding with different patient characteristics: Prospective observational study. Indian J Med Microbiol 2024; 47:100490. [PMID: 37890412 DOI: 10.1016/j.ijmmb.2023.100490] [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: 04/16/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Salivary shedding of SARS-CoV-2 is a known entity and its role has been established in transmission of the disease. The present study was performed to evaluate the duration of viral shedding in saliva in COVID-19 patients and its variation among symptomatic and asymptomatic patients with or without co-morbidities. METHODS The present prospective observational study was conducted at the COVID-19 care hospital associated with primary to tertiary care in New Delhi, India. A total of 124 COVID-19 confirmed cases enrolled in two phases (January-March 2021; April-June 2021) who consented for 48hrly saliva and nasopharyngeal swab (NPS) specimens till discharge from the hospital for SARS-CoV-2 detection were included. The specimens obtained were tested for SARS-CoV-2 by Real-Time PCR. RESULTS The sensitivity and the specificity of RT-PCR on saliva were 81.7 % and 85.0 %, respectively. The sensitivity of saliva-based PCR was comparable in symptomatic and asymptomatic patients (81.6 % vs 82.1 %). The sensitivity of saliva-based PCR markedly increased in the second phase of enrollment as compared to the first phase (92.6 % vs 78.5 %) indicating higher level of salivary shedding by the delta variant of SARS-CoV-2. The sensitivity of PCR on saliva was the highest up to day seven of illness. The median duration of RNA shedding in saliva was comparable among the symptomatic and asymptomatic patients. The severity of the disease was not associated with the duration of SARS-CoV-2 shedding in saliva. CONCLUSIONS SARS-CoV-2 shedding in saliva continued till seven days in large number of patients including asymptomatic patients. Saliva is non-inferior to NPS specimen in the diagnosis of SARS-CoV-2. Saliva specimen is recommended as a good alternate to NPS for SARS-CoV-2 testing.
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Affiliation(s)
- Khyati
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
| | - V Manchanda
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India.
| | - P Pumma
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
| | - R Chawla
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
| | - S Garg
- Department of Medicine, Maulana Azad Medical College, 110002, New Delhi, India
| | - S Saxena
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
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Ray R, Rakesh A, Singh S, Madhyastha H, Mani NK. Hair and Nail-On-Chip for Bioinspired Microfluidic Device Fabrication and Biomarker Detection. Crit Rev Anal Chem 2023:1-27. [PMID: 38133962 DOI: 10.1080/10408347.2023.2291825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
The advent of biosensors has tremendously increased our potential of identifying and solving important problems in various domains, ranging from food safety and environmental analysis, to healthcare and medicine. However, one of the most prominent drawbacks of these technologies, especially in the biomedical field, is to employ conventional samples, such as blood, urine, tissue extracts and other body fluids for analysis, which suffer from the drawbacks of invasiveness, discomfort, and high costs encountered in transportation and storage, thereby hindering these products to be applied for point-of-care testing that has garnered substantial attention in recent years. Therefore, through this review, we emphasize for the first time, the applications of switching over to noninvasive sampling techniques involving hair and nails that not only circumvent most of the aforementioned limitations, but also serve as interesting alternatives in understanding the human physiology involving minimal costs, equipment and human interference when combined with rapidly advancing technologies, such as microfluidics and organ-on-a-chip to achieve miniaturization on an unprecedented scale. The coalescence between these two fields has not only led to the fabrication of novel microdevices involving hair and nails, but also function as robust biosensors for the detection of biomarkers, chemicals, metabolites and nucleic acids through noninvasive sampling. Finally, we have also elucidated a plethora of futuristic innovations that could be incorporated in such devices, such as expanding their applications in nail and hair-based drug delivery, their potential in serving as next-generation wearable sensors and integrating these devices with machine-learning for enhanced automation and decentralization.
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Affiliation(s)
- Rohitraj Ray
- Department of Bioengineering (BE), Indian Institute of Science Bangalore, Bengaluru, Karnataka, India
| | - Amith Rakesh
- Microfluidics, Sensors and Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576 104, India
| | - Sheetal Singh
- Microfluidics, Sensors and Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576 104, India
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Naresh Kumar Mani
- Microfluidics, Sensors and Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576 104, India
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Shuai Y, Ma Z, Ju J, Wei T, Gao S, Kang Y, Yang Z, Wang X, Yue J, Yuan P. Liquid-based biomarkers in breast cancer: looking beyond the blood. J Transl Med 2023; 21:809. [PMID: 37957623 PMCID: PMC10644618 DOI: 10.1186/s12967-023-04660-z] [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: 05/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
In recent decades, using circulating tumor cell (CTC), circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), exosomes and etc. as liquid biomarkers has received enormous attention in various tumors, including breast cancer (BC). To date, efforts in the area of liquid biopsy predominantly focus on the analysis of blood-based markers. It is worth noting that the identifications of markers from non-blood sources provide unique advantages beyond the blood and these alternative sources may be of great significance in offering supplementary information in certain settings. Here, we outline the latest advances in the analysis of non-blood biomarkers, predominantly including urine, saliva, cerebrospinal fluid, pleural fluid, stool and etc. The unique advantages of such testings, their current limitations and the appropriate use of non-blood assays and blood assays in different settings are further discussed. Finally, we propose to highlight the challenges of these alternative assays from basic to clinical implementation and explore the areas where more investigations are warranted to elucidate its potential utility.
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Affiliation(s)
- You Shuai
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhonghua Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Endoscopy, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jie Ju
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tong Wei
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Songlin Gao
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yikun Kang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zixuan Yang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Moulahoum H, Ghorbanizamani F, Beduk T, Beduk D, Ozufuklar O, Guler Celik E, Timur S. Emerging trends in nanomaterial design for the development of point-of-care platforms and practical applications. J Pharm Biomed Anal 2023; 235:115623. [PMID: 37542827 DOI: 10.1016/j.jpba.2023.115623] [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: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/07/2023]
Abstract
Nanomaterials and nanotechnology offer promising opportunities in point-of-care (POC) diagnostics and therapeutics due to their unique physical and chemical properties. POC platforms aim to provide rapid and portable diagnostic and therapeutic capabilities at the site of patient care, offering cost-effective solutions. Incorporating nanomaterials with distinct optical, electrical, and magnetic properties can revolutionize the POC industry, significantly enhancing the effectiveness and efficiency of diagnostic and theragnostic devices. By leveraging nanoparticles and nanofibers in POC devices, nanomaterials have the potential to improve the accuracy and speed of diagnostic tests, making them more practical for POC settings. Technological advancements, such as smartphone integration, imagery instruments, and attachments, complement and expand the application scope of POCs, reducing invasiveness by enabling analysis of various matrices like saliva and breath. These integrated testing platforms facilitate procedures without compromising diagnosis quality. This review provides a summary of recent trends in POC technologies utilizing nanomaterials and nanotechnologies for analyzing disease biomarkers. It highlights advances in device development, nanomaterial design, and their applications in POC. Additionally, complementary tools used in POC and nanomaterials are discussed, followed by critical analysis of challenges and future directions for these technologies.
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Affiliation(s)
- Hichem Moulahoum
- Biochemistry Department, Faculty of Science, Ege University, 35100 Bornova, Izmir, Turkey
| | - Faezeh Ghorbanizamani
- Biochemistry Department, Faculty of Science, Ege University, 35100 Bornova, Izmir, Turkey
| | - Tutku Beduk
- Silicon Austria Labs GmbH: Sensor Systems, Europastrasse 12, Villach 9524, Austria
| | - Duygu Beduk
- Central Research Testing and Analysis Laboratory Research and Application Center, Ege University, 35100 Bornova, Izmir, Turkey
| | - Ozge Ozufuklar
- Department of Biotechnology, Institute of Natural Sciences, Ege University, Izmir 35100, Turkey
| | - Emine Guler Celik
- Bioengineering Department, Faculty of Engineering, 35100 Bornova, Izmir, Turkey
| | - Suna Timur
- Biochemistry Department, Faculty of Science, Ege University, 35100 Bornova, Izmir, Turkey; Central Research Testing and Analysis Laboratory Research and Application Center, Ege University, 35100 Bornova, Izmir, Turkey.
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11
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Sritong N, Ngo WW, Ejendal KFK, Linnes JC. Development of an Integrated Sample Amplification Control for Salivary Point-of-Care Pathogen Testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.03.23296477. [PMID: 37873363 PMCID: PMC10593008 DOI: 10.1101/2023.10.03.23296477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The COVID-19 pandemic has led to a rise in point-of-care (POC) and home-based tests, but concerns over usability, accuracy, and effectiveness have arisen. The incorporation of internal amplification controls (IACs), essential control for translational POC diagnostics, could mitigate false-negative and false-positive results due to sample matrix interference or inhibition. Although emerging POC nucleic acid amplification tests (NAATs) for detecting SARS-CoV-2 show impressive analytical sensitivity in the lab, the assessment of clinical accuracy with IACs is often overlooked. In some cases, the IACs were run spatially, complicating assay workflow. Therefore, the multiplex assay for pathogen and IAC is needed. Results We developed a one-pot duplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for saliva samples, a non-invasive and simple collected specimen for POC NAATs. The ORF1ab gene of SARS-CoV-2 was used as a target and a human 18S ribosomal RNA in human saliva was employed as an IAC to ensure clinical reliability of the RT-LAMP assay. The optimized assay could detect SARS-CoV-2 viral particles down to 100 copies/μL of saliva within 30 minutes without RNA extraction. The duplex RT-LAMP for SARS-CoV-2 and IAC is successfully amplified in the same reaction without cross-reactivity. The valid results were easily visualized in triple-line lateral flow immunoassay, in which two lines (flow control and IAC lines) represent valid negative results and three lines (flow control, IAC, and test line) represent valid positive results. This duplex assay demonstrated a clinical sensitivity of 95%, specificity of 100%, and accuracy of 96% in 30 clinical saliva samples. Significance IACs play a crucial role in ensuring user confidence with respect to the accuracy and reliability of at-home and POC molecular diagnostics. We demonstrated the multiplex capability of SARS-COV-2 and human18S ribosomal RNA RT-LAMP without complicating assay design. This generic platform can be extended in a similar manner to include human18S ribosomal RNA IACs into different clinical sample matrices.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Winston Wei Ngo
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Karin F. K. Ejendal
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Jacqueline C. Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Department of Public Health, Purdue University, West Lafayette, IN, USA
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12
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Bakshi SS, Mangayarkarasi V, Dash D, Das S, Ramesh S, Jayam C, Kalidoss VK. Comparative study on Saliva and Nasopharyngeal swabs and the outcome of RT-PCR test in patients with mild symptoms of SARS-CoV-2. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2023; 74:315-319. [PMID: 36965822 DOI: 10.1016/j.otoeng.2023.03.004] [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: 08/06/2022] [Revised: 11/01/2022] [Accepted: 12/06/2022] [Indexed: 03/27/2023]
Abstract
AIM A simple and reliable method for diagnosing COVID 19 infections is the needed. The role of saliva in the transmission of the infection has already been established. METHOD Saliva and nasopharyngeal swabs from patients suspected to have COVID 19 infections were taken simultaneously, and the results of the RT-PCR were compared. RESULT Total 405 samples were collected, of which 250 males and 155 females. In the 391 samples included for analysis, 370 (94.63%) samples were found to have concordance results, and 21 (5.37%) samples had discordant results. CONCLUSION The use of saliva to diagnose COVID 19 infection is reliable, and its use can be recommended.
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Affiliation(s)
- Satvinder Singh Bakshi
- Department of ENT and Head & Neck Surgery, All India Institute of Medical Sciences Mangalagiri, Guntur, Andhra Pradesh, India.
| | - V Mangayarkarasi
- Department of Microbiology, AIIMS Mangalagiri, Guntur, Andhra Pradesh, India.
| | - Debabrata Dash
- Department of Microbiology, AIIMS Mangalagiri, Guntur, Andhra Pradesh, India.
| | - Soumyajit Das
- Department of ENT and Head & Neck Surgery, All India Institute of Medical Sciences Mangalagiri, Guntur, Andhra Pradesh, India.
| | - Seepana Ramesh
- Department of ENT and Head & Neck Surgery, All India Institute of Medical Sciences Mangalagiri, Guntur, Andhra Pradesh, India.
| | - Cheeranjeevi Jayam
- Department of Dentistry, AIIMS Mangalagiri, Guntur, Andhra Pradesh, India.
| | - Vinoth Kumar Kalidoss
- Department of Community and Family Medicine, AIIMS Mangalagiri, Guntur, Andhra Pradesh, India.
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13
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Faruque MRJ, Bikker FJ, Laine ML. Comparing SARS-CoV-2 Viral Load in Human Saliva to Oropharyngeal Swabs, Nasopharyngeal Swabs, and Sputum: A Systematic Review and Meta-Analysis. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:5807370. [PMID: 37600753 PMCID: PMC10435302 DOI: 10.1155/2023/5807370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/04/2022] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
Abstract
A systematic review and meta-analysis were conducted to investigate the SARS-CoV-2 viral load in human saliva and compared it with the loads in oropharyngeal swabs, nasopharyngeal swabs, and sputum. In addition, the salivary viral loads of symptomatic and asymptomatic COVID-19 patients were compared. Searches were conducted using four electronic databases: PubMed, Embase, Scopus, and Web of Science, for studies published on SARS-CoV-2 loads expressed by CT values or copies/mL RNA. Three reviewers evaluated the included studies to confirm eligibility and assessed the risk of bias. A total of 37 studies were included. Mean CT values in saliva ranged from 21.5 to 39.6 and mean copies/mL RNA ranged from 1.91 × 101 to 6.98 × 1011. Meta-analysis revealed no significant differences in SARS-CoV-2 load in saliva compared to oropharyngeal swabs, nasopharyngeal swabs, and sputum. In addition, no significant differences were observed in the salivary viral load of symptomatic and asymptomatic COVID-19 patients. We conclude that saliva specimen can be used as an alternative for SARS-CoV-2 detection in oropharyngeal swabs, nasopharyngeal swabs, and sputum.
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Affiliation(s)
- Mouri R. J. Faruque
- Department of Periodontology, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
| | - Floris J. Bikker
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
| | - Marja L. Laine
- Department of Periodontology, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
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14
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Millward GG, Popelka SM, Gutierrez AG, Kowallis WJ, von Tersch RL, Yerramilli SV. A novel strategy to avoid sensitivity loss in pooled testing for SARS-CoV-2 surveillance: validation using nasopharyngeal swab and saliva samples. Front Public Health 2023; 11:1190308. [PMID: 37637813 PMCID: PMC10450028 DOI: 10.3389/fpubh.2023.1190308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
At the peak of the COVID-19 pandemic, pooled surveillance strategies were employed to alleviate the overwhelming demand for clinical testing facilities. A major drawback of most pooled-testing methods is the dilution of positive samples, which leads to a loss of detection sensitivity and the potential for false negatives. We developed a novel pooling strategy that compensates for the initial dilution with an appropriate concentration during nucleic acid extraction and real-time PCR. We demonstrated the proof of principle using laboratory-created 10-sample pools with one positive and corresponding individual positive samples by spiking a known amount of heat-inactivated SARS-CoV-2 into viral transport medium (VTM) or pooled negative saliva. No Ct difference was observed between a 10-sample pool with one positive vs. the corresponding individually analyzed positive sample by this method, suggesting that there is no detectable loss of sensitivity. We further validated this approach by using nasopharyngeal swab (NPS) specimens and showed that there is no loss of sensitivity. Serial dilutions of the virus were spiked into VTM and pooled with negative saliva in simulated 10-sample pools containing one positive to determine the LOD and process efficiency of this pooling methodology. The LOD of this approach was 10 copies/PCR, and the process efficiencies are ~95%-103% for N1 and ~87%-98% for N2 with samples in different matrices and with two different master mixes tested. Relative to TaqPath 1-step master mix, the TaqMan Fast Virus 1-Step master mix showed better sensitivity for the N2 assay, while the N1 assay showed no Ct difference. Our pooled testing strategy can facilitate large-scale, cost-effective SARS-CoV-2 surveillance screening and maintain the same level of sensitivity when analyzed individually or in a pool. This approach is highly relevant for public health surveillance efforts aimed at mitigating SARS-CoV-2 spread.
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Affiliation(s)
| | | | | | | | | | - Subrahmanyam V. Yerramilli
- Emerging Biological Threats Branch, Molecular Biology Division, Laboratory Sciences, Defense Centers for Public Health - Aberdeen “Formerly the Army Public Health Center”, Aberdeen Proving Ground, Edgewood, MD, United States
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15
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Kritika S, Mahalaxmi S, Srinivasan N, Krithikadatta J. Deciphering the role of Saliva in COVID 19: A global cross-sectional study on the knowledge, awareness and perception among dentists. BMC Oral Health 2023; 23:424. [PMID: 37365550 DOI: 10.1186/s12903-023-03152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023] Open
Abstract
OBJECTIVES The global pandemic outbreak of the coronavirus has instilled the quest amongst researchers on the expedited need for the early detection of viral load. Saliva is a complex oral biological fluid which not only causes the disease transmission but can be an effective alternative sample for detection of SARS-CoV2. This provides an ideal opportunity for dentists to be the frontline healthcare professionals who can collect the salivary samples; however the awareness of this amongst dentists is uncertain. Hence the aim of this survey was to evaluate the knowledge, perception and awareness of the role of saliva in detecting the SARS-CoV2 among dentists worldwide. METHODS The online questionnaire comprising of 19 questions was shared to 1100 dentists worldwide and a total of 720 responses was collected. The data was tabulated, statistically analysed using the non- parametric Kruskal-Wallis test (p < 0.05). Based on the principal component analysis, 4 components (knowledge about virus transmission, perception about SARS-CoV2 virus, awareness on the sample collection and knowledge about prevention of the virus) were obtained which was compared with the 3 independent variables (years of clinical experience, occupation and region). RESULTS A statistically significant difference was observed in the awareness quotient amongst the dentists with 0-5 years and greater than 20 years of clinical experience. In terms of the occupation, a significant difference was noted when comparing the postgraduate students to practitioners knowledge about the virus transmission. A highly significant difference was seen on comparing academicians and postgraduate students and also between academicians and practitioners. No significant difference was evidenced amongst the different regions, however the mean score was in the range of 3-3.44. CONCLUSION This survey highlights the deficiency in the knowledge, perception and awareness among dentists worldwide.
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Affiliation(s)
- Selvakumar Kritika
- Department of Conservative Dentistry and Endodontics, SRM Dental College, Ramapuram, SRM Institute of Science & Technology, Ramapuram Campus, Bharathi Salai, Ramapuram, Chennai, Tamil Nadu, 600089, India.
| | - Sekar Mahalaxmi
- Department of Conservative Dentistry and Endodontics, SRM Dental College, Ramapuram, SRM Institute of Science & Technology, Ramapuram Campus, Bharathi Salai, Ramapuram, Chennai, Tamil Nadu, 600089, India
| | - N Srinivasan
- Specialist Endodontist, Hamad Dental Center, Hamad Medical Corporation, Doha, Qatar
| | - Jogikalmat Krithikadatta
- Department of Cariology and Department of Conservative Dentistry and Endodontics, Saveetha Dental College and Hospitals, Chennai, Tamil Nadu, 600077, India
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Kostinov M, Svitich O, Chuchalin A, Abramova N, Osiptsov V, Khromova E, Pakhomov D, Tatevosov V, Vlasenko A, Gainitdinova V, Mashilov K, Kryukova N, Baranova I, Kostinov A. Changes in nasal, pharyngeal and salivary secretory IgA levels in patients with COVID-19 and the possibility of correction of their secretion using combined intranasal and oral administration of a pharmaceutical containing antigens of opportunistic microorganisms. Drugs Context 2023; 12:2022-10-4. [PMID: 37342460 PMCID: PMC10278444 DOI: 10.7573/dic.2022-10-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/08/2023] [Indexed: 06/23/2023] Open
Abstract
Background Although extensive research has been conducted on the role of local immunity in patients with SARS-CoV-2, little is known about the production and concentrations of secretory IgA (SIgA) in different mucosal compartments. This article aims to assess the secretion of SIgA in the nasal and pharyngeal compartments and saliva of patients with COVID-19 and to investigate the possibility and efficiency of correction of their secretion using combined intranasal and oral administration of a pharmaceutical containing antigens of opportunistic microorganisms. Methods This study included 78 inpatients, aged between 18 and 60 years, who had confirmed COVID-19 with moderate lung involvement. The control group (n=45) received basic therapy, and the treatment group (n=33) was additionally administered the bacteria-based pharmaceutical Immunovac VP4 from day 1 to day 10 of hospitalization. SIgA levels were measured by ELISA at baseline and on days 14 and 30. Results No systemic or local reactions associated with Immunovac VP4 were reported. We observed a statistically significant reduction in the duration of fever and hospitalization in patients who received Immunovac VP4 compared with those from the control group (p=0.03 and p=0.05, respectively). Changes over time in SIgA levels in nasal swabs were found to be significantly different in the two treatment groups (F=7.9, p[78.0]<0.001). On day 14 of observation, patients in the control group showed a statistically significant reduction in SIgA levels from baseline (p=0.02), whereas patients in the Immunovac VP4 group had stable SIgA levels (p=0.07). On day 30 after the start of treatment, there was a statistically significant increase in SIgA levels in the Immunovac VP4 group compared with baseline (from 77.7 (40.5-98.7) μg/L to 113.4 (39.8-156.7) μg/L; p=0.05) and the levels measured on day 14 (from 60.2 (23.3-102.9) μg/L to 113.4 (39.8-156.7) μg/L; p=0.03). The control group showed a statistically significant decrease in levels of nasal SIgA (to 37.3) on day 30 (p=0.007 for comparison with baseline values and p=0.04 for comparison with levels measured on day 14). Changes over time in SIgA levels measured in pharyngeal swabs were also different between the two treatment groups, and this difference reached statistical significance (F=6.5, p[73.0]=0.003). In the control group, this parameter did not change throughout the study (p=0.17 for a comparison between the levels measured on day 14 and the baseline values, and p=0.12 for a comparison between the levels measured on day 30 and the baseline values). In the Immunovac VP4 group, there was a statistically significant increase from baseline in SIgA levels on study day 30: from 1.5 (0.2-16.5) μg/L to 29.8 (3.6-106.8) μg/L (p=0.02). Changes over time in salivary SIgA did not show a significant difference between study groups (F=0.3, p[66.3]=0.75). Conclusion As part of combination therapy, the bacteria-based immunostimulant agent Immunovac VP4 increases SIgA levels in the nasal and pharyngeal compartments and induces clinical improvement. Induced mucosal immunity is central to the prevention of respiratory infections, particularly in patients with post-COVID-19 syndrome.
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Affiliation(s)
- Mikhail Kostinov
- Laboratory of Preventive Vaccination and Immunotherapy of Allergic Diseases, I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russian Federation
- Department of Epidemiology and Modern Technologies of Vaccination, I.M. Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Oksana Svitich
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russian Federation
| | - Alexander Chuchalin
- Department of Hospital Therapy of the Faculty of Pediatrics, Pirogov Russian National Research Medical University (Pirogov Medical University), Moscow, Russian Federation
- Research Institute of Pulmonology, Moscow, Russian Federation
| | - Natalya Abramova
- Laboratory of Molecular Immunology, I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russian Federation
| | - Valery Osiptsov
- The Main Military Clinical Hospital of the National Guard Troops of the Russian Federation, Moscow, Russian Federation
| | - Ekaterina Khromova
- Laboratory of Preventive Vaccination and Immunotherapy of Allergic Diseases, I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russian Federation
| | - Dmitry Pakhomov
- Laboratory of Preventive Vaccination and Immunotherapy of Allergic Diseases, I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russian Federation
| | - Vitaly Tatevosov
- The Main Military Clinical Hospital of the National Guard Troops of the Russian Federation, Moscow, Russian Federation
| | - Anna Vlasenko
- Medical Cybernetics and Informatics Department, Novokuznetsk State Institute of Advanced Training of Physicians – Branch of the “Russian Medical Academy of Continuous Professional Education”, Novokuznetsk, Russian Federation
| | - Vilia Gainitdinova
- Pulmonology Department of the I.M. Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Kirill Mashilov
- Laboratory of Preventive Vaccination and Immunotherapy of Allergic Diseases, I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russian Federation
| | - Nadezhda Kryukova
- Department of Hospital Therapy of the Faculty of Pediatrics, Pirogov Russian National Research Medical University (Pirogov Medical University), Moscow, Russian Federation
| | - Irina Baranova
- Department of Hospital Therapy of the Faculty of Pediatrics, Pirogov Russian National Research Medical University (Pirogov Medical University), Moscow, Russian Federation
| | - Anton Kostinov
- Allergodiagnostics Laboratory, I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russian Federation
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Nakgul L, Pasomsub E, Thongpradit S, Chanprasertyothin S, Prasongtanakij S, Thadanipon K, Jadmuang C, Kunanan D, Ongphiphadhanakul B, Phuphuakrat A. Saliva and wastewater surveillance for SARS-CoV-2 during school reopening amid COVID-19 pandemic in Thailand. PUBLIC HEALTH IN PRACTICE 2023; 5:100378. [PMID: 36937099 PMCID: PMC10010048 DOI: 10.1016/j.puhip.2023.100378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
Objectives School closure during the coronavirus disease 2019 (COVID-19) pandemic resulted in a negative impact on children. Serial testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been proposed as a measure for safety school reopening. We aimed to study the usefulness of SARS-CoV-2 surveillance by saliva testing and performing wastewater surveillance for SARS-CoV-2 in a day school in a resource-limited setting. Methods We conducted a cluster randomized study to investigate the potential use of saliva antigen testing compared to saliva pooling for nucleic acid detection in a primary school in Thailand from December 2021 to March 2022. Wastewater surveillance in the school was also performed. Results A total of 484 participants attended the study. SARS-CoV-2 was detected in two participants from the tests provided by the study (one in the pool nucleic acid test arm, and another in the quantitative antigen test arm). Additional ten participants reported positive results on an additional rapid antigen test (RAT) performed by nasal swab when they had symptoms or household contact. There was no difference among arms in viral detection by intention-to-treat and per protocol analysis (p = 0.304 and 0.894, respectively). We also investigated the feasibility of wastewater surveillance to detect the virus in this setting. However, wastewater surveillance could not detect the virus. Conclusions In a low COVID-19 prevalence, serial saliva testing and wastewater surveillance for SARS-CoV-2 rarely detected the virus in a day school setting. Performing RAT on nasal swabs when students, teachers or staff have symptoms or household contact might be more reasonable.
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Affiliation(s)
- Laor Nakgul
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Supranee Thongpradit
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | - Somsak Prasongtanakij
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kunlawat Thadanipon
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chokchai Jadmuang
- Anubansamsen School (the Government Lottery Office Support), Bangkok, Thailand
| | - Daranee Kunanan
- Anubansamsen School (the Government Lottery Office Support), Bangkok, Thailand
| | | | - Angsana Phuphuakrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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18
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Filgueiras PS, Corsini CA, Almeida NBF, Pedrosa MLC, Miranda DAPD, Gomes SVC, Assis JVD, Silva RA, Medeiros MIVDARCD, Lourenço AJ, Bicalho CMF, Vilela RVR, Jeremias WDJ, Fernandes GDR, Queiroz RFGE. Rapid antigen test as a tool for the identification of SARS-CoV-2 infection and its potential as a self-testing device. Rev Soc Bras Med Trop 2023; 56:e01672022. [PMID: 37222349 DOI: 10.1590/0037-8682-0167-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 03/01/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND SARS-CoV-2 virus originated in Wuhan (China) in December (2019) and quickly spread worldwide. Antigen tests are rapid diagnostic tests (RDT) that produce results in 15-30 min and are an important tool for the scale-up of COVID-19 testing. COVID-19 diagnostic tests are authorized for self-testing at home in some countries, including Brazil. Widespread COVID-19 diagnostic testing is required to guide public health policies and control the speed of transmission and economic recovery. METHODS Patients with suspected COVID-19 were recruited at the Hospital da Baleia (Belo Horizonte, Brazil). The SARS-CoV-2 antigen-detecting rapid diagnostic tests were evaluated from June 2020 to June 2021 using saliva, nasal, and nasopharyngeal swab samples from 609 patients. Patient samples were simultaneously tested using a molecular assay (RT-qPCR). Sensitivity, specificity, accuracy, and positive and negative predictive values were determined using the statistical program, MedCalc, and GraphPad Prism 8.0. RESULTS The antigen-detecting rapid diagnostic tests displayed 98% specificity, 60% sensitivity, 96% positive predictive value, and moderate concordance with RT-qPCR. Substantial agreement was found between the two methods for patients tested < 7 days of symptom onset. CONCLUSIONS Our findings support the use of Ag-RDT as a valuable and safe diagnostic method. Ag-RDT was also demonstrated to be an important triage tool for suspected COVID-19 patients in emergencies. Overall, Ag-RDT is an effective strategy for reducing the spread of SARS-CoV-2 and contributing to COVID-19 control.
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Affiliation(s)
- Priscilla Soares Filgueiras
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Patologia, Belo Horizonte, MG, Brasil
| | - Camila Amormino Corsini
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
| | - Nathalie Bonatti Franco Almeida
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
- Universidade da Geórgia, Faculdade de Medicina Veterinária, Departamento de Doenças Infecciosas, Athens, GA, Estados Unidos da América
| | - Maria Luysa Camargos Pedrosa
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
| | - Daniel Alvim Pena de Miranda
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
| | - Sarah Vieira Contin Gomes
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
| | - Jéssica Vieira de Assis
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Patologia, Belo Horizonte, MG, Brasil
| | | | | | | | | | | | - Wander de Jesus Jeremias
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
- Universidade Federal de Ouro Preto, Departamento de Farmácia, Ouro Preto, MG, Brasil
| | | | - Rafaella Fortini Grenfell E Queiroz
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Patologia, Belo Horizonte, MG, Brasil
- Universidade da Geórgia, Faculdade de Medicina Veterinária, Departamento de Doenças Infecciosas, Athens, GA, Estados Unidos da América
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19
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Calvet G, Ogrzewalska M, Tassinari W, Guaraldo L, Resende P, Fuller T, Penetra S, Borges M, Pina-Costa A, Martins E, Moraes I, Santos H, Damasceno L, Medeiros-Filho F, Espindola O, Mota F, Nacife V, Pauvolid-Corrêa A, Whitworth J, Smith C, Siqueira M, Brasil P. Accuracy of saliva for SARS-CoV-2 detection in outpatients and their household contacts during the circulation of the Omicron variant of concern. BMC Infect Dis 2023; 23:295. [PMID: 37147601 PMCID: PMC10161980 DOI: 10.1186/s12879-023-08271-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND While nasopharyngeal (NP) swabs are considered the gold standard for severe acute respiratory coronavirus 2 (SARS-CoV-2) real-time reverse transcriptase-polymerase chain reaction (RT-PCR) detection, several studies have shown that saliva is an alternative specimen for COVID-19 diagnosis and screening. METHODS To analyze the utility of saliva for the diagnosis of COVID-19 during the circulation of the Omicron variant, participants were enrolled in an ongoing cohort designed to assess the natural history of SARS-CoV-2 infection in adults and children. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Cohen's kappa coefficient were calculated to assess diagnostic performance. RESULTS Overall, 818 samples were collected from 365 outpatients from January 3 to February 2, 2022. The median age was 32.8 years (range: 3-94 years). RT-PCR for SARS-CoV-2 was confirmed in 97/121 symptomatic patients (80.2%) and 62/244 (25.4%) asymptomatic patients. Substantial agreement between saliva and combined nasopharyngeal/oropharyngeal samples was observed with a Cohen's kappa value of 0.74 [95% confidence interval (CI): 0.67-0.81]. Sensitivity was 77% (95% CI: 70.9-82.2), specificity 95% (95% CI: 91.9-97), PPV 89.8% (95% CI: 83.1-94.4), NPV 87.9% (95% CI: 83.6-91.5), and accuracy 88.5% (95% CI: 85.0-91.4). Sensitivity was higher among samples collected from symptomatic children aged three years and older and adolescents [84% (95% CI: 70.5-92)] with a Cohen's kappa value of 0.63 (95% CI: 0.35-0.91). CONCLUSIONS Saliva is a reliable fluid for detecting SARS-CoV-2, especially in symptomatic children and adolescents during the circulation of the Omicron variant.
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Affiliation(s)
- Guilherme Calvet
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil.
| | - Maria Ogrzewalska
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Wagner Tassinari
- Federal Rural University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lusiele Guaraldo
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Paola Resende
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Trevon Fuller
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Stephanie Penetra
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Michele Borges
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Anielle Pina-Costa
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Ezequias Martins
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Isabella Moraes
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Heloisa Santos
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Luana Damasceno
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Fernando Medeiros-Filho
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Otavio Espindola
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Fernando Mota
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Valéria Nacife
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Alex Pauvolid-Corrêa
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Jimmy Whitworth
- Departments of Clinical Research and Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Chris Smith
- Departments of Clinical Research and Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Marilda Siqueira
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Patrícia Brasil
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
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20
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Devina C, Nasution BB, Kusumawati RL, Daulay RS, Trisnawati Y, Lubis IND. Sensitivity of nasopharyngeal swab and saliva specimens in the detection of SARS-CoV-2 virus among boarding school girls. IJID REGIONS 2023:S2772-7076(23)00023-1. [PMID: 37363192 PMCID: PMC10157386 DOI: 10.1016/j.ijregi.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 06/28/2023]
Abstract
Objectives With the reopening of schools, the detection of coronavirus disease 2019 (COVID-19) in children is very important in order to prevent outbreaks in schools and to reduce the risk of more severe post-COVID-19 complications. Various specimens can be used to detect the SARS-CoV-2 virus, and saliva has been considered as an alternative specimen in adults. However, data in children are lacking, especially among the female population. This study compared the efficacy of saliva specimens with nasopharyngeal swab specimens for the detection of severe acute respiratory syndrome coronavirus-2 using reverse transcriptase polymerase chain reaction. Methods This study evaluated the diagnostic performance of saliva among boarding school girls at three time points: diagnosis, and days 7 and 14 since first confirmation using a nasopharyngeal swab specimen. Eighty-four paired samples from 36 individuals were compared. Nasopharyngeal samplings were carried out by trained health officers, while saliva samplings were performed independently by children. Results The overall percentage agreement (OPA) between saliva and nasopharyngeal swabs was 50.2%. The OPA was 52.8% at diagnosis, and this increased slightly to 54.2% at day 7, and subsequently decreased to 45.8% at day 14. Saliva specimens had sensitivity of 44.6%, specificity of 80.0%, positive predictive value of 94.2% and negative predictive value of 16.3% compared with nasopharyngeal swab specimens for the diagnosis of COVID-19. Conclusions The use of saliva as an alternative specimen for the diagnosis of COVID-19 in children should be considered carefully. Thorough sampling instructions should be given in order to minimize bias in the findings.
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Affiliation(s)
- Clara Devina
- Department of Paediatrics, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Badai Buana Nasution
- Department of Paediatrics, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - R Lia Kusumawati
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Rini Savitri Daulay
- Department of Paediatrics, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Yunnie Trisnawati
- Department of Paediatrics, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Inke Nadia Diniyanti Lubis
- Department of Paediatrics, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
- Menzies School of Health Research, Darwin, Australia
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21
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Adl A, Sedigh-Shams M, Jamalidoust M, Rajabzadeh Z. Evaluating the effect of gargling with hydrogen peroxide and povidone-iodine on salivary viral load of SARS-CoV-2: A pilot randomized clinical trial. Niger J Clin Pract 2023; 26:391-396. [PMID: 37203101 DOI: 10.4103/njcp.njcp_320_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Background and Aim This study evaluates the salivary viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in hospitalized patients and outpatients before and after gargling with 1% hydrogen peroxide and 0.25% povidone-iodine in comparison with normal saline. Patients and Methods This clinical trial was conducted on 120 participants with laboratory-confirmed coronavirus disease 2019 (COVID-19) in two groups: outpatients (n = 60) and hospitalized patients (n = 60). In each group, the patients were randomly divided into three subgroups of 20 based on their given mouthwash for gargling (hydrogen peroxide, povidone-iodine, or normal saline). Two saliva samples were taken from each patient: the first one before gargling and the second one 10 minutes after gargling 10 ml of the respected mouthwashes for 30 seconds. The TaqMan real-time polymerase chain reaction (PCR) amplification of SARS-CoV-2 was used to measure the viral load. Results Saliva samples from 46% of patients were positive for coronavirus before gargling the mouthwashes. The percentage of patients with an initial positive saliva sample was significantly higher in the outpatient group (83.3%) than in the hospitalized group (5.4%) (P = 0.01). According to the findings, gargling any mouthwash similar to saline did not reduce the viral load (P > 0.05). Conclusion The saliva of COVID-19 patients in the initial stage of the disease was more likely to contain SARS-CoV-2 than the saliva of the hospitalized patients. Gargling hydrogen peroxide or povidone-iodine did not reduce the salivary SARS-CoV-2 viral load.
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Affiliation(s)
- A Adl
- Department of Endodontics, Biomaterials Research Center, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - M Sedigh-Shams
- Department of Endodontics, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - M Jamalidoust
- Department of Virology, Clinical Microbiology Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Z Rajabzadeh
- Student Research Committee, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran
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22
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Li Y, Zhao S, Xu Z, Qiao X, Li M, Li Y, Luo X. Peptide nucleic acid and antifouling peptide based biosensor for the non-fouling detection of COVID-19 nucleic acid in saliva. Biosens Bioelectron 2023; 225:115101. [PMID: 36708624 DOI: 10.1016/j.bios.2023.115101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/24/2022] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
The electrochemical biosensor with outstanding sensitivity and low cost is regarded as a viable alternative to current clinical diagnostic techniques for various disease biomarkers. However, their actual analytical use in complex biological samples is severely hampered due to the biofouling, as they are also highly sensitive to nonspecific adsorption on the sensing interfaces. Herein, we have constructed a non-fouling electrochemical biosensor based on antifouling peptides and the electroneutral peptide nucleic acid (PNA), which was used as the recognizing probe for the specific binding of the viral RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Different from the negatively charged DNA probes that will normally weaken the biosensors' antifouling capabilities owing to the charge attraction of positively charged biomolecules, the neutral PNA probe will generate no side-effects on the biosensor. The biosensor demonstrated remarkable sensitivity in detecting SARS-CoV-2 viral RNA, possessing a broad linear range (1.0 fM - 1.0 nM) and a detection limit down to 0.38 fM. Furthermore, the sensing performance of the constructed electrochemical biosensor in human saliva was nearly similar to that in pure buffer, indicating satisfying antifouling capability. The combination of PNA probes with antifouling peptides offered a new strategy for the development of non-fouling sensing systems capable of assaying trace disease biomarkers in complicated biological media.
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Affiliation(s)
- Yanxin Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Shuju Zhao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Zhenying Xu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Xiujuan Qiao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Mingxuan Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Youke Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China.
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23
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SARS-CoV-2 viral RNA detection using the novel CoVradar device associated with the CoVreader smartphone app. Biosens Bioelectron 2023; 230:115268. [PMID: 37030262 PMCID: PMC10060197 DOI: 10.1016/j.bios.2023.115268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 03/25/2023] [Indexed: 04/01/2023]
Abstract
The COVID-19 pandemic has highlighted the need for innovative approaches to its diagnosis. Here we present CoVradar, a novel and simple colorimetric method that combines nucleic acid analysis with dynamic chemical labeling (DCL) technology and the Spin-Tube device to detect SARS-CoV-2 RNA in saliva samples. The assay includes a fragmentation step to increase the number of RNA templates for analysis, using abasic peptide nucleic acid probes (DGL probes) immobilized to nylon membranes in a specific dot pattern to capture RNA fragments. Duplexes are formed by labeling complementary RNA fragments with biotinylated SMART bases, which act as templates for DCL. Signals are generated by recognizing biotin with streptavidin alkaline phosphatase and incubating with a chromogenic substrate to produce a blue precipitate. CoVradar results are analysed by CoVreader, a smartphone-based image processing system that can display and interpret the blotch pattern. CoVradar and CoVreader provide a unique molecular assay capable of detecting SARS-CoV-2 viral RNA without the need for extraction, preamplification, or prelabeling steps, offering advantages in terms of time (∼3 h/test), cost (∼€1/test manufacturing cost) and simplicity (does not require large equipment). This solution is also promising for the development of assays for other infectious diseases.
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24
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Gadkar VJ, Goldfarb DM, Al-Rawahi GN, Srigley JA, Smailus DE, Coope RJN, Pleasance S, Watson N, Chen T, Lam S, Hoang L, Tilley PAG. Extraction-free clinical detection of SARS-CoV-2 virus from saline gargle samples using Hamilton STARlet liquid handler. Sci Rep 2023; 13:4241. [PMID: 36918604 PMCID: PMC10013237 DOI: 10.1038/s41598-023-30993-2] [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: 05/12/2022] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
As part of the COVID-19 pandemic, clinical laboratories have been faced with massive increases in testing, resulting in sample collection systems, reagent, and staff shortages. We utilized self-collected saline gargle samples to optimize high throughput SARS-CoV-2 multiplex polymerase chain reaction (PCR) testing in order to minimize cost and technologist time. This was achieved through elimination of nucleic acid extraction and automation of sample handling on a widely available robotic liquid handler, Hamilton STARlet. A customized barcode scanning script for reading the sample ID by the Hamilton STARlet's software system was developed to allow primary tube sampling. Use of pre-frozen SARS-CoV-2 assay reaction mixtures reduced assay setup time. In both validation and live testing, the assay produced no false positive or false negative results. Of the 1060 samples tested during validation, 3.6% (39/1060) of samples required retesting as they were either single gene positive, had internal control failure or liquid aspiration error. Although the overall turnaround time was only slightly faster in the automated workflow (185 min vs 200 min), there was a 76% reduction in hands-on time, potentially reducing staff fatigue and burnout. This described process from sample self-collection to automated direct PCR testing significantly reduces the total burden on healthcare systems in terms of human resources and reagent requirements.
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Affiliation(s)
- Vijay J Gadkar
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada.
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada.
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital, Room No 2K9, 4500 Oak St, Vancouver, V6H 3N1, Canada.
| | - David M Goldfarb
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Ghada N Al-Rawahi
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Jocelyn A Srigley
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Duane E Smailus
- Canada's Michael Smith Genome Science Centre at BC Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Robin J N Coope
- Canada's Michael Smith Genome Science Centre at BC Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Stephen Pleasance
- Canada's Michael Smith Genome Science Centre at BC Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Nicole Watson
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
| | - Tammy Chen
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
| | - Sunny Lam
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
| | - Linda Hoang
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, Canada
| | - Peter A G Tilley
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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25
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Ferreira MDP, Yamada-Ogatta SF, Teixeira Tarley CR. Electrochemical and Bioelectrochemical Sensing Platforms for Diagnostics of COVID-19. BIOSENSORS 2023; 13:336. [PMID: 36979548 PMCID: PMC10046778 DOI: 10.3390/bios13030336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/15/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Rapid transmission and high mortality rates caused by the SARS-CoV-2 virus showed that the best way to fight against the pandemic was through rapid, accurate diagnosis in parallel with vaccination. In this context, several research groups around the world have endeavored to develop new diagnostic methods due to the disadvantages of the gold standard method, reverse transcriptase polymerase chain reaction (RT-PCR), in terms of cost and time consumption. Electrochemical and bioelectrochemical platforms have been important tools for overcoming the limitations of conventional diagnostic platforms, including accuracy, accessibility, portability, and response time. In this review, we report on several electrochemical sensors and biosensors developed for SARS-CoV-2 detection, presenting the concepts, fabrication, advantages, and disadvantages of the different approaches. The focus is devoted to highlighting the recent progress of electrochemical devices developed as next-generation field-deployable analytical tools as well as guiding future researchers in the manufacture of devices for disease diagnosis.
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Affiliation(s)
| | | | - César Ricardo Teixeira Tarley
- Department of Chemistry, State University of Londrina (UEL), Londrina 86051-990, Brazil
- National Institute of Science and Technology in Bioanalysis (INCTBio), Institute of Chemistry, State University of Campinas (UNICAMP), Campinas 13083-970, Brazil
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26
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Ali DY, Hussein RA, ELshafie SM, Mohamed RA, Abd El Reheem F. Comparable detection of nasopharyngeal swabs and induced sputum specimens for viral nucleic acid detection of suspected novel coronavirus (SARS-Cov-2) patients in Fayoum governorate, Egypt. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2023; 12:43. [PMID: 37151720 PMCID: PMC10153783 DOI: 10.1186/s43088-023-00379-4] [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: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023] Open
Abstract
Background The most commonly utilized samples for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection using real-time quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) are nasopharyngeal swabs (NPS) and oropharyngeal swabs. However, there are some drawbacks. For SARS-CoV-2 detection, induced sputum might be analyzed and may be equivalent to pharyngeal swabs. This study was done to assess the potential superiority of induced sputum over NPS for SARS-CoV-2 detection. Sixty symptomatic COVID-19 patients who attended Fayoum University Hospitals in Fayoum Governorate, Egypt, were included in this cross-sectional descriptive study. Paired NPS and induced sputum samples were collected from each subject on the third and tenth days after symptoms began for RT-qPCR SARS-COV2 diagnosis. Results At day 3, 52 (86.7%) of NPS and 48 (80.00%) of induced sputum specimens had positive RT-qPCR results with a significant statistical difference (P = 0.001). At day 10, 41 induced sputum samples (68.3%) were negative, while 19 (31.7%) were positive. Only three (5.0%) of the 19 positive induced sputum samples tested positive for NPS. NPS samples had a higher viral load than induced sputum samples at day 3 [25 (41.7%) vs. 23 (38.3%)]. At day 10, induced sputum samples had a higher viral load than NPS [9 (15.0%) vs. 6 (10.0%)]. A statistically significant positive correlation between the viral load value of the NPS and the induced sputum sample at day 3 (r = 0.497, p = 0.00) denoting similarity in the results of the two types of samples. By ROC analysis, the highest area under the curve for the overall CT value of the induced sputum was (0.604), with a statistically significant difference (p value = 0.0418). Conclusion In the early stages of the disease, induced sputum and NPS tests had comparable results, but NPS yielded more false negative results later in the disease course than an induced sputum sample, which yielded higher sample positivity and viral load than NPS. Furthermore, induced sputum collection is a straightforward, non-invasive, and risk-free method. As a result, induced sputum could be useful for COVID-19 confirmation in patients with radiologically or epidemiologically suspected COVID-19 who have a negative NPS or in difficult-to-diagnose COVID-19 patients.
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Affiliation(s)
- Doaa Y. Ali
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Rasha A. Hussein
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Shahira Morsy ELshafie
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Reem Amgad Mohamed
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Fadwa Abd El Reheem
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
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27
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Tahir B, Weldegebreal F, Ayele F, Ayana DA. Comparative evaluation of saliva and nasopharyngeal swab for SARS-CoV-2 detection using RT-qPCR among COVID-19 suspected patients at Jigjiga, Eastern Ethiopia. PLoS One 2023; 18:e0282976. [PMID: 36913377 PMCID: PMC10010556 DOI: 10.1371/journal.pone.0282976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/28/2023] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND Nasopharyngeal swab (NPS) remains the recommended sample type for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) diagnosis. However, the collection procedure causes discomfort and irritation to the patients, lowering the quality of the sample and exposing healthcare workers to risk. Furthermore, there is also a shortage of flocked swabs and personnel protective equipment in low-income settings. Therefore, this necessitates an alternative diagnostic specimen. The purpose of this study was to evaluate the performance of saliva against NPS for SARS-CoV-2 detection using RT-qPCR among COVID-19 suspected patients at Jigjiga, Eastern Ethiopia. METHODS Comparative cross-sectional study was conducted from June 28 to July 30, 2022. A total of 227 paired saliva and NPS samples were collected from 227 COVID-19 suspected patients. Saliva and NPS samples were collected and transported to the Somali Regional Molecular Laboratory. Extraction was conducted using DaAn kit (DaAn Gene Co., Ltd China). Veri-Q RT-qPCR was used for amplification and detection (Mico BioMed Co, Ltd, Republic of Korea). The data were entered into Epi-data version 4.6 and analyzed using SPSS 25. McNemar's test was used to compare the detection rate. Agreement between NPS and saliva was performed using Cohen's Kappa. The mean and median of cycle threshold values were compared using paired t-tests and the correlation between cycle threshold values was measured using Pearson correlation coefficient. P value < 0.05 was considered statistically significant. RESULTS The overall positivity rate of SARS-CoV-2 RNA was 22.5% (95% CI 17-28%). Saliva showed higher sensitivity (83.8%, 95% CI, 73-94.5%) than NPS (68.9%, 95% CI 60.8-76.8%). The specificity of saliva was 92.6% (95% CI, 80.6% - 100%) compared to NPS (96.7%, 95% CI, 87% - 100%). The positive, negative, and overall percent agreement between NPS and saliva was 83.8%, 92.6%, and 91.2% respectively (κ = 0.703, 95% CI 0.58-0.825, P = 0.00). The concordance rate between the two samples was 60.8%. NPS showed a higher viral load than saliva. There was low positive correlation between the cycle threshold values of the two samples (r = 0.41, 95% CI -1.69 to -0.98, P >0.05). CONCLUSION Saliva showed a higher detection rate for SARS-CoV-2 molecular diagnosis than NPS and there was significant agreement between the two specimens. Therefore, saliva could be suitable and easily obtainable alternative diagnostic specimen for SARS-CoV-2 molecular diagnosis.
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Affiliation(s)
- Bawlah Tahir
- Department of Medical Laboratory Sciences, Jigjiga University, Jigjiga, Ethiopia
| | - Fitsum Weldegebreal
- School of Medical Laboratory Sciences, College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
| | - Firayad Ayele
- School of Medical Laboratory Sciences, College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
- * E-mail:
| | - Desalegn Admassu Ayana
- School of Medical Laboratory Sciences, College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
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Migueres M, Mansuy JM, Vasseur S, Claverie N, Lougarre C, Soulier F, Trémeaux P, Izopet J. Omicron Wave SARS-CoV-2 Diagnosis: Evaluation of Saliva, Anterior Nasal, and Nasopharyngeal Swab Samples. Microbiol Spectr 2022; 10:e0252122. [PMID: 36318040 PMCID: PMC9769796 DOI: 10.1128/spectrum.02521-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
The Omicron variant differs from earlier strains of SARS-CoV-2 in the way it enters host cells and grows in vitro. We therefore reevaluated its diagnosis using saliva, nasopharyngeal swab (NPs), and anterior nasal swab (ANs) specimens from 202 individuals (64.9% symptomatic) tested at the Toulouse University Hospital SARS-CoV-2 drive-through testing center. All tests were done with the Thermo Fisher TaqPath COVID-19 reverse transcription-PCR (RT-PCR) kit. Overall, 92 subjects (45.5%) had one or more positive specimens. Global sensitivities of saliva, NPs, and ANs were 94.6%, 90.2%, and 82.6%, respectively. Saliva provided significantly greater sensitivity among symptomatic patients tested within 5 days of symptom onset (100%) than did ANs (83.1%) or NPs (89.8%). We obtained follow-up samples for 7/20 individuals with discordant results. Among them, 5 symptomatic patients were diagnosed positive on saliva sample only, soon after symptom onset; NPs and ANs became positive only later. Thus, saliva samples are effective tools for the detection of the Omicron variant. In addition to its many advantages, such as improved patient acceptance and reduced cost, saliva sampling could help limit viral spread through earlier viral detection. IMPORTANCE Diagnostic testing for SARS-CoV-2 is an essential component of the global strategy for the prevention and control of COVID-19. Since the beginning of the pandemic, numerous studies have evaluated the diagnostic sensitivity of different respiratory and oral specimens for SARS-CoV-2 detection. The pandemic has been since dominated by the emergence of new variants, the latest being the Omicron variant characterized by numerous mutations and changes in host tropism in vitro that might affect the diagnostic performance of tests depending on the sampling location. In this prospective study, we evaluated the clinical performance of NPs, ANs, and saliva for SARS-CoV-2 diagnosis during the Omicron wave. Our results highlight the effectiveness of saliva-based RT-PCR for the early detection of the Omicron variant. These findings may help to refine guidelines and support the use of a highly sensitive diagnostic method that allows earlier diagnosis, when transmission is the most critical.
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Affiliation(s)
- Marion Migueres
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jean-Michel Mansuy
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
| | - Sandrine Vasseur
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Nicolas Claverie
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Catherine Lougarre
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Françoise Soulier
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Pauline Trémeaux
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
| | - Jacques Izopet
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
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Castillo-Bravo R, Lucca N, Lai L, Marlborough K, Brychkova G, Sakhteh MS, Lonergan C, O’Grady J, Alikhan NF, Trotter AJ, Page AJ, Smyth B, McKeown PC, Feenstra JDM, Ulekleiv C, Sorel O, Gandhi M, Spillane C. Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals. Microbiol Spectr 2022; 10:e0222922. [PMID: 36409097 PMCID: PMC9769602 DOI: 10.1128/spectrum.02229-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/18/2022] [Indexed: 11/23/2022] Open
Abstract
RT-PCR tests based on RNA extraction from nasopharyngeal swabs (NPS) are promoted as the "gold standard" for SARS-CoV-2 detection. However, the use of saliva samples offers noninvasive self-collection more suitable for high-throughput testing. This study evaluated performance of the TaqPath COVID-19 Fast PCR Combo kit 2.0 assay for detection of SARS-CoV-2 in raw saliva relative to a lab-developed direct RT-PCR test (SalivaDirect-based PCR, SDB-PCR) and an RT-PCR test based on RNA extraction from NPS. Saliva and NPS samples were collected from symptomatic and asymptomatic individuals (N = 615). Saliva samples were tested for SARS-CoV-2 using the TaqPath COVID-19 Fast PCR Combo kit 2.0 and the SDB-PCR, while NPS samples were tested by RT-PCR in RNA extracts according to the Irish national testing system. TaqPath COVID-19 Fast PCR Combo kit 2.0 detected SARS-CoV-2 in 52 saliva samples, of which 51 were also positive with the SDB-PCR. Compared to the NPS "gold standard" biospecimen method, 49 samples displayed concordant results, while three samples (35
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Affiliation(s)
- Rosa Castillo-Bravo
- Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
| | - Noel Lucca
- Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
| | - Linyi Lai
- Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
| | - Killian Marlborough
- Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
| | - Galina Brychkova
- Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
| | - Maryam Shideh Sakhteh
- Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
| | - Charlie Lonergan
- Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
| | - Justin O’Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Nabil-Fareed Alikhan
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Alexander J. Trotter
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Andrew J. Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Breda Smyth
- College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Ireland
- Health Service Executive (HSE) West, Merlin Park University Hospital, Galway, Ireland
| | - Peter C. McKeown
- Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
| | | | | | - Oceane Sorel
- Thermo Fisher Scientific, South San Francisco, California, USA
| | - Manoj Gandhi
- Thermo Fisher Scientific, South San Francisco, California, USA
| | - Charles Spillane
- Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
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Meller S, Al Khatri MSA, Alhammadi HK, Álvarez G, Alvergnat G, Alves LC, Callewaert C, Caraguel CGB, Carancci P, Chaber AL, Charalambous M, Desquilbet L, Ebbers H, Ebbers J, Grandjean D, Guest C, Guyot H, Hielm-Björkman A, Hopkins A, Kreienbrock L, Logan JG, Lorenzo H, Maia RDCC, Mancilla-Tapia JM, Mardones FO, Mutesa L, Nsanzimana S, Otto CM, Salgado-Caxito M, de los Santos F, da Silva JES, Schalke E, Schoneberg C, Soares AF, Twele F, Vidal-Martínez VM, Zapata A, Zimin-Veselkoff N, Volk HA. Expert considerations and consensus for using dogs to detect human SARS-CoV-2-infections. Front Med (Lausanne) 2022; 9:1015620. [PMID: 36569156 PMCID: PMC9773891 DOI: 10.3389/fmed.2022.1015620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Affiliation(s)
- Sebastian Meller
- Department of Small Animal Medicine & Surgery, University of Veterinary Medicine Hannover, Hanover, Germany,*Correspondence: Sebastian Meller,
| | | | - Hamad Khatir Alhammadi
- International Operations Department, Ministry of Interior of the United Arab Emirates, Abu Dhabi, United Arab Emirates
| | - Guadalupe Álvarez
- Faculty of Veterinary Science, University of Buenos Aires, Buenos Aires, Argentina
| | - Guillaume Alvergnat
- International Operations Department, Ministry of Interior of the United Arab Emirates, Abu Dhabi, United Arab Emirates
| | - Lêucio Câmara Alves
- Department of Veterinary Medicine, Federal Rural University of Pernambuco, Recife, Brazil
| | - Chris Callewaert
- Center for Microbial Ecology and Technology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Charles G. B. Caraguel
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Paula Carancci
- Faculty of Veterinary Science, University of Buenos Aires, Buenos Aires, Argentina
| | - Anne-Lise Chaber
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Marios Charalambous
- Department of Small Animal Medicine & Surgery, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Loïc Desquilbet
- École Nationale Vétérinaire d’Alfort, IMRB, Université Paris Est, Maisons-Alfort, France
| | | | | | - Dominique Grandjean
- École Nationale Vétérinaire d’Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Claire Guest
- Medical Detection Dogs, Milton Keynes, United Kingdom
| | - Hugues Guyot
- Clinical Department of Production Animals, Fundamental and Applied Research for Animals & Health Research Unit, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Anna Hielm-Björkman
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Amy Hopkins
- Medical Detection Dogs, Milton Keynes, United Kingdom
| | - Lothar Kreienbrock
- Department of Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover, Hanover, Germany
| | - James G. Logan
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom,Arctech Innovation, The Cube, Dagenham, United Kingdom
| | - Hector Lorenzo
- Faculty of Veterinary Science, University of Buenos Aires, Buenos Aires, Argentina
| | | | | | - Fernando O. Mardones
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal and Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Leon Mutesa
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda,Rwanda National Joint Task Force COVID-19, Kigali, Rwanda
| | | | - Cynthia M. Otto
- Penn Vet Working Dog Center, Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Marília Salgado-Caxito
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal and Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - Esther Schalke
- Bundeswehr Medical Service Headquarters, Koblenz, Germany
| | - Clara Schoneberg
- Department of Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Anísio Francisco Soares
- Department of Animal Morphology and Physiology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Friederike Twele
- Department of Small Animal Medicine & Surgery, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Victor Manuel Vidal-Martínez
- Laboratorio de Parasitología y Patología Acuática, Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN Unidad Mérida, Mérida, Yucatán, Mexico
| | - Ariel Zapata
- Faculty of Veterinary Science, University of Buenos Aires, Buenos Aires, Argentina
| | - Natalia Zimin-Veselkoff
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal and Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Holger A. Volk
- Department of Small Animal Medicine & Surgery, University of Veterinary Medicine Hannover, Hanover, Germany,Center for Systems Neuroscience Hannover, Hanover, Germany
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Cheng TY, Zimmerman JJ, Giménez-Lirola LG. Internal reference genes with the potential for normalizing quantitative PCR results for oral fluid specimens. Anim Health Res Rev 2022; 23:147-156. [PMID: 36330795 DOI: 10.1017/s1466252322000044] [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] [Indexed: 11/06/2022]
Abstract
In basic research, testing of oral fluid specimens by real-time quantitative polymerase chain reaction (qPCR) has been used to evaluate changes in gene expression levels following experimental treatments. In diagnostic medicine, qPCR has been used to detect DNA/RNA transcripts indicative of bacterial or viral infections. Normalization of qPCR using endogenous and exogenous reference genes is a well-established strategy for ensuring result comparability by controlling sample-to-sample variation introduced during sampling, storage, and qPCR testing. In this review, the majority of recent publications in human (n = 136) and veterinary (n = 179) medicine did not describe the use of internal reference genes in qPCRs for oral fluid specimens (52.9% animal studies; 57.0% human studies). However, the use of endogenous reference genes has not been fully explored or validated for oral fluid specimens. The lack of valid internal reference genes inherent to the oral fluid matrix will continue to hamper the reliability, reproducibility, and generalizability of oral fluid qPCR assays until this issue is addressed.
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Affiliation(s)
- Ting-Yu Cheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jeffrey J Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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Moura AV, de Oliveira DC, Silva AAR, da Rosa JR, Garcia PHD, Sanches PHG, Garza KY, Mendes FMM, Lambert M, Gutierrez JM, Granado NM, dos Santos AC, de Lima IL, Negrini LDDO, Antonio MA, Eberlin MN, Eberlin LS, Porcari AM. Urine Metabolites Enable Fast Detection of COVID-19 Using Mass Spectrometry. Metabolites 2022; 12:1056. [PMID: 36355139 PMCID: PMC9697918 DOI: 10.3390/metabo12111056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 08/27/2023] Open
Abstract
The COVID-19 pandemic boosted the development of diagnostic tests to meet patient needs and provide accurate, sensitive, and fast disease detection. Despite rapid advancements, limitations related to turnaround time, varying performance metrics due to different sampling sites, illness duration, co-infections, and the need for particular reagents still exist. As an alternative diagnostic test, we present urine analysis through flow-injection-tandem mass spectrometry (FIA-MS/MS) as a powerful approach for COVID-19 diagnosis, targeting the detection of amino acids and acylcarnitines. We adapted a method that is widely used for newborn screening tests on dried blood for urine samples in order to detect metabolites related to COVID-19 infection. We analyzed samples from 246 volunteers with diagnostic confirmation via PCR. Urine samples were self-collected, diluted, and analyzed with a run time of 4 min. A Lasso statistical classifier was built using 75/25% data for training/validation sets and achieved high diagnostic performances: 97/90% sensitivity, 95/100% specificity, and 95/97.2% accuracy. Additionally, we predicted on two withheld sets composed of suspected hospitalized/symptomatic COVID-19-PCR negative patients and patients out of the optimal time-frame collection for PCR diagnosis, with promising results. Altogether, we show that the benchmarked FIA-MS/MS method is promising for COVID-19 screening and diagnosis, and is also potentially useful after the peak viral load has passed.
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Affiliation(s)
- Alexandre Varao Moura
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Danilo Cardoso de Oliveira
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Alex Ap. R. Silva
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Jonas Ribeiro da Rosa
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Pedro Henrique Dias Garcia
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Pedro Henrique Godoy Sanches
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Kyana Y. Garza
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Flavio Marcio Macedo Mendes
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Mayara Lambert
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Junier Marrero Gutierrez
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Nicole Marino Granado
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Alicia Camacho dos Santos
- Department of Material Engineering and Nanotechnology, Mackenzie Presbyterian University, São Paulo 01302-907, SP, Brazil
| | - Iasmim Lopes de Lima
- Department of Material Engineering and Nanotechnology, Mackenzie Presbyterian University, São Paulo 01302-907, SP, Brazil
| | | | - Marcia Aparecida Antonio
- Integrated Unit of Pharmacology and Gastroenterology, UNIFAG, Bragança Paulista 12916-900, SP, Brazil
| | - Marcos N. Eberlin
- Department of Material Engineering and Nanotechnology, Mackenzie Presbyterian University, São Paulo 01302-907, SP, Brazil
| | - Livia S. Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andreia M. Porcari
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
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Byanyima P, Kaswabuli S, Musisi E, Nabakiibi C, Zawedde J, Sanyu I, Sessolo A, Andama A, Worodria W, Huang L, Davis JL. Feasibility and Sensitivity of Saliva GeneXpert MTB/RIF Ultra for Tuberculosis Diagnosis in Adults in Uganda. Microbiol Spectr 2022; 10:e0086022. [PMID: 36154664 PMCID: PMC9603304 DOI: 10.1128/spectrum.00860-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/30/2022] [Indexed: 12/30/2022] Open
Abstract
The objective of this prospective observational study carried out at China-Uganda Friendship Hospital-Naguru in Kampala, Uganda, was to determine the performance of GeneXpert MTB/RIF Ultra (Xpert Ultra) molecular testing on saliva for active tuberculosis (TB) disease among consecutive adults undergoing TB diagnostic evaluation who were Xpert Ultra positive on sputum. We calculated sensitivity to determine TB diagnostic performance in comparison to a composite reference standard of Mycobacterium tuberculosis liquid and solid cultures on two spot sputum specimens. Xpert Ultra on a single saliva sample had a sensitivity of 90% (95% confidence interval [CI], 81 to 95%) relative to the composite sputum culture-based reference standard, similar to the composite sensitivity of 87% (95% CI, 77 to 94%) for fluorescence microscopy (FM) for acid-fast bacilli on two sputum smears. The sensitivity of salivary Xpert Ultra was 24% lower (95% CI for difference, 2 to 48%; P = 0.003) among persons living with HIV (71%; 95% CI, 44 to 90%) than among persons living without HIV (95%; 95% CI, 86 to 99%) and 46% higher (95% CI, 14 to 77%; P < 0.0001) among FM-positive (96%; 95% CI, 87 to 99%) than among FM-negative (50%; 95% CI, 19 to 81%) patients. The semiquantitative Xpert Ultra grade was systematically higher in sputum than in a paired saliva sample from the same patient. In conclusion, molecular testing of saliva for active TB diagnosis was feasible and almost as sensitive as molecular testing of sputum in a high TB burden setting. IMPORTANCE Tuberculosis is among the leading causes of morbidity and mortality worldwide, in large part because >3 million people go undiagnosed and untreated each year. Sputum has been the mainstay for TB diagnosis for over a century but can be difficult for patients to produce. In addition, the vigorous coughing required during sputum collection can lead to infection of nearby individuals and health workers. In this case-only study, applying the ultra-sensitive GeneXpert MTB/RIF Ultra molecular diagnostic assay to saliva detected 90% of culture-confirmed TB cases among 81 adults who were undergoing TB evaluation at the outpatient department of a general hospital in Uganda and tested sputum GeneXpert MTB/RIF Ultra positive. These results suggest that saliva may be a feasible and sensitive alternative to sputum for TB diagnosis, thereby meeting two key metrics proposed by the World Health Organization in its target performance profile for a nonsputum test for TB.
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Affiliation(s)
| | | | - Emmanuel Musisi
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, United Kingdom
| | | | | | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Abdul Sessolo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Alfred Andama
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - William Worodria
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, USA
- Division of HIV, Infectious Diseases, and Global Medicine, University of California San Francisco, San Francisco, California, USA
| | - J. Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, Connecticut, USA
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Comparison of SARS-CoV-2 Detection from Saliva Sampling and Oropharyngeal Swab. Microbiol Spectr 2022; 10:e0142222. [PMID: 36129278 PMCID: PMC9604035 DOI: 10.1128/spectrum.01422-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We examined the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using reverse transcription-PCR (RT-PCR) of side-by-side saliva and oropharyngeal swab (OPS) samples from 639 symptomatic and asymptomatic subjects, of which 47 subjects were found to be positive for SARS-CoV-2 in the OPS or saliva sample or both. It was found that the detection rate (93.6% for both OPS and saliva) as well as the sensitivity and specificity were comparable between the two sampling methods in this cohort. The sensitivity was 0.932 (95% confidence interval [CI], 0.818 to 0.977) and the specificity was 0.995 (95% CI, 0.985 to 0.998), both for saliva when OPS sampling was used as the reference and for OPS when saliva was used as the reference. Furthermore, the Cohen's kappa value was 0.926 (95% CI, 0.868 to 0.985), indicating strong agreement between the two sampling methods. In addition, the viral RNA stability in pure saliva and saliva mixed with preservation buffers was examined following storage at room temperature and at 4°C. It was found that pure saliva kept the viral RNA stable for 9 days at both temperatures and that the type of preservation buffer can either enhance or reduce the stability of the RNA. We conclude that self-administered saliva sampling is an attractive alternative to oropharyngeal swabbing for SARS-CoV-2 detection, and it might be useful in large-scale testing. IMPORTANCE It is not inconceivable that we will witness recurring surges of COVID-19 before the pandemic finally recedes. It is therefore still relevant to look for feasible, simple, and flexible screening methods so that schools, workplaces, and communities in general can avoid lockdowns. In this work, we analyzed two different sampling methods: oropharyngeal swabs and saliva collection. Oropharyngeal swabs must be collected by trained health personnel at clinics, whereas self-assisted saliva collection can be performed at any given location. It was found that the two sampling methods were comparable. Saliva sampling is a simple method that allows easy mass testing using minimal resources from the existing health care system, and this method may therefore prove to be an effective tool for containing the COVID-19 pandemic.
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Gamage SST, Pahattuge TN, Wijerathne H, Childers K, Vaidyanathan S, Athapattu US, Zhang L, Zhao Z, Hupert ML, Muller RM, Muller-Cohn J, Dickerson J, Dufek D, Geisbrecht BV, Pathak H, Pessetto Z, Gan GN, Choi J, Park S, Godwin AK, Witek MA, Soper SA. Microfluidic affinity selection of active SARS-CoV-2 virus particles. SCIENCE ADVANCES 2022; 8:eabn9665. [PMID: 36170362 PMCID: PMC9519043 DOI: 10.1126/sciadv.abn9665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/10/2022] [Indexed: 06/07/2023]
Abstract
We report a microfluidic assay to select active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral particles (VPs), which were defined as intact particles with an accessible angiotensin-converting enzyme 2 receptor binding domain (RBD) on the spike (S) protein, from clinical samples. Affinity selection of SARS-CoV-2 particles was carried out using injection molded microfluidic chips, which allow for high-scale production to accommodate large-scale screening. The microfluidic contained a surface-bound aptamer directed against the virus's S protein RBD to affinity select SARS-CoV-2 VPs. Following selection (~94% recovery), the VPs were released from the chip's surface using a blue light light-emitting diode (89% efficiency). Selected SARS-CoV-2 VP enumeration was carried out using reverse transcription quantitative polymerase chain reaction. The VP selection assay successfully identified healthy donors (clinical specificity = 100%) and 19 of 20 patients with coronavirus disease 2019 (COVID-19) (95% sensitivity). In 15 patients with COVID-19, the presence of active SARS-CoV-2 VPs was found. The chip can be reprogrammed for any VP or exosomes by simply changing the affinity agent.
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Affiliation(s)
- Sachindra S. T. Gamage
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Thilanga N. Pahattuge
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Harshani Wijerathne
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Katie Childers
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Swarnagowri Vaidyanathan
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Uditha S. Athapattu
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Lulu Zhang
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Zheng Zhao
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | | | | | | | | | | | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | | | - Gregory N. Gan
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Industrial and Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Industrial and Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Andrew K. Godwin
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Malgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
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Endo (遠藤彰) A, Uchida (内田満夫) M, Liu (刘扬) Y, Atkins KE, Kucharski AJ, Funk S. Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools. Proc Natl Acad Sci U S A 2022; 119:e2203019119. [PMID: 36074818 PMCID: PMC9478679 DOI: 10.1073/pnas.2203019119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022] Open
Abstract
The global spread of coronavirus disease 2019 (COVID-19) has emphasized the need for evidence-based strategies for the safe operation of schools during pandemics that balance infection risk with the society's responsibility of allowing children to attend school. Due to limited empirical data, existing analyses assessing school-based interventions in pandemic situations often impose strong assumptions, for example, on the relationship between class size and transmission risk, which could bias the estimated effect of interventions, such as split classes and staggered attendance. To fill this gap in school outbreak studies, we parameterized an individual-based model that accounts for heterogeneous contact rates within and between classes and grades to a multischool outbreak data of influenza. We then simulated school outbreaks of respiratory infectious diseases of ongoing threat (i.e., COVID-19) and potential threat (i.e., pandemic influenza) under a variety of interventions (changing class structures, symptom screening, regular testing, cohorting, and responsive class closures). Our results suggest that interventions changing class structures (e.g., reduced class sizes) may not be effective in reducing the risk of major school outbreaks upon introduction of a case and that other precautionary measures (e.g., screening and isolation) need to be employed. Class-level closures in response to detection of a case were also suggested to be effective in reducing the size of an outbreak.
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Affiliation(s)
- Akira Endo (遠藤彰)
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
- The Alan Turing Institute, London NW1 2DB, United Kingdom
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki 852-8523, Japan
- Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - CMMID COVID-19 Working Group
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | | | - Yang Liu (刘扬)
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Katherine E. Atkins
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH16 4UX, United Kingdom
| | - Adam J. Kucharski
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Sebastian Funk
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
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McLennan K, Barton E, Lang C, Adams IR, McAllister G, Reijns MAM, Templeton K, Johannessen I, Leckie A, Gilbert N. User acceptability of saliva and gargle samples for identifying COVID-19 positive high-risk workers and household contacts. Diagn Microbiol Infect Dis 2022; 104:115732. [PMID: 35728458 PMCID: PMC9132684 DOI: 10.1016/j.diagmicrobio.2022.115732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 11/23/2022]
Abstract
Throughout the COVID-19 pandemic nasopharyngeal or nose and/or throat swabs (NTS) have been the primary approach for collecting patient samples for the subsequent detection of viral RNA. However, this procedure, if undertaken correctly, can be unpleasant and therefore deters individuals from providing high quality samples. To overcome these limitations other modes of sample collection have been explored. In a cohort of frontline health care workers we have compared saliva and gargle samples to gold-standard NTS. 93% of individuals preferred providing saliva or gargle samples, with little sex-dependent variation. Viral titers collected in samples were analyzed using standard methods and showed that gargle and saliva were similarly comparable for identifying COVID-19 positive individuals compared to NTS (92% sensitivity; 98% specificity). We suggest that gargle and saliva collection are viable alternatives to NTS swabs and may encourage testing to provide better disease diagnosis and population surveillance.
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Affiliation(s)
- Kirsty McLennan
- Occupational Health and Safety Service, Astley Ainsley Hospital, NHS Lothian, Edinburgh, UK.
| | - Ellen Barton
- Occupational Health and Safety Service, Astley Ainsley Hospital, NHS Lothian, Edinburgh, UK
| | - Christie Lang
- Occupational Health and Safety Service, Astley Ainsley Hospital, NHS Lothian, Edinburgh, UK
| | - Ian R Adams
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, UK
| | - Gina McAllister
- Clinical Microbiology and Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
| | - Martin A M Reijns
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, UK
| | - Kate Templeton
- Clinical Microbiology and Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
| | - Ingólfur Johannessen
- Clinical Microbiology and Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
| | - Alastair Leckie
- Occupational Health and Safety Service, Astley Ainsley Hospital, NHS Lothian, Edinburgh, UK
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, UK.
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Evaluation of Saliva as a Matrix for RT-PCR Analysis and Two Rapid Antigen Tests for the Detection of SARS-CoV-2. Viruses 2022; 14:v14091931. [PMID: 36146737 PMCID: PMC9502549 DOI: 10.3390/v14091931] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
The use of saliva for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sparks debate due to presumed lower sensitivity and lack of standardization. Our aim was to evaluate the performance characteristics of (i) saliva collected by the ORAcollectTM device as a matrix for SARS-CoV-2 reverse-transcriptase polymerase chain reaction (RT-PCR), and (ii) 2 saliva rapid antigen tests (AgRDT). From 342 ambulatory individuals, both a nasopharyngeal swab and saliva sample via ORAcollectTM were obtained for a SARS-CoV-2 RT-PCR test. Furthermore, 54 and 123 additionally performed the V-ChekTM or WhistlingTM saliva AgRDT. In total, 35% of individuals screened positive for SARS-CoV-2 via nasopharyngeal swab. Saliva, as a matrix for the RT-PCR, had a specificity of 96.5% and a negative predictive value (NPV) of 91.3%. Interestingly, 6 out of 8 patients thought to be false positive in saliva re-tested positive by nasopharyngeal sampling after 2 to 9 days. Both V-ChekTM and WhistlingTM AgRDT had a lack of sensitivity, resulting in an NPV of 66.9 and 67.3%, respectively. Saliva proved to be a sensitive and specific matrix for SARS-CoV-2 detection by the RT-PCR. In this setting, saliva might have an earlier window of detection than the nasopharyngeal swab. By contrast, both AgRDT showed an unacceptably low sensitivity and NPV.
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Tang Z, Cui J, Kshirsagar A, Liu T, Yon M, Kuchipudi SV, Guan W. SLIDE: Saliva-Based SARS-CoV-2 Self-Testing with RT-LAMP in a Mobile Device. ACS Sens 2022; 7:2370-2378. [PMID: 35920555 PMCID: PMC9364980 DOI: 10.1021/acssensors.2c01023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/14/2022] [Indexed: 12/14/2022]
Abstract
Regular, accurate, rapid, and inexpensive self-testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is urgently needed to quell pandemic propagation. The existing at-home nucleic acid testing (NAT) test has high sensitivity and specificity, but it requires users to mail the sample to the central lab, which often takes 3-5 days to obtain the results. On the other hand, rapid antigen tests for the SARS-CoV-2 antigen provide a fast sample to answer the test (15 min). However, the sensitivity of antigen tests is 30 to 40% lower than nucleic acid testing, which could miss a significant portion of infected patients. Here, we developed a fully integrated SARS-CoV-2 reverse transcription loop-mediated isothermal amplification (RT-LAMP) device using a self-collected saliva sample. This platform can automatically handle the complexity and can perform the functions, including (1) virus particles' thermal lysis preparation, (2) sample dispensing, (3) target sequence RT-LAMP amplification, (4) real-time detection, and (5) result report and communication. With a turnaround time of less than 45 min, our device achieved the limit of detection (LoD) of 5 copies/μL of the saliva sample, which is comparable with the LoD (6 copies/μL) using FDA-approved quantitative real-time polymerase chain reaction (qRT-PCR) assays with the same heat-lysis saliva sample preparation method. With clinical samples, our platform showed a good agreement with the results from the gold-standard RT-PCR method. These results show that our platform can perform self-administrated SARS-CoV-2 nucleic acid testing by laypersons with noninvasive saliva samples. We believe that our self-testing platform will have an ongoing benefit for COVID-19 control and fighting future pandemics.
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Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Jiarui Cui
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Michele Yon
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for Infectious Disease Dynamic, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
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Suwarti S, Zanjabila S, Bonifacius, Da Costa Y, Bogh C, Subekti D, Jeny J, Dewi AM, Nuraeni N, Rahardjani M, Elyazar I, Nelwan EJ, Shankar AH, Baird JK, Hamers RL. Evaluating Saliva Sampling with Reverse Transcription Loop-mediated Isothermal Amplification to Improve Access to SARS-CoV-2 Diagnosis in Low-Resource Settings. Am J Trop Med Hyg 2022; 107:284-290. [PMID: 35895405 PMCID: PMC9393441 DOI: 10.4269/ajtmh.22-0230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/21/2022] [Indexed: 11/07/2022] Open
Abstract
Standard diagnosis of SARS-CoV-2 by nasopharyngeal swab (NPS) and real-time reverse transcriptase-polymerase chain reaction (PCR) requires a sophisticated laboratory, skilled staff, and expensive reagents that are difficult to establish and maintain in isolated, low-resource settings. In the remote setting of tropical Sumba Island, eastern Indonesia, we evaluated alternative sampling with fresh saliva (FS) and testing with colorimetric loop-medicated isothermal amplification (LAMP). Between August 2020 and May 2021, we enrolled 159 patients with suspected SARS-CoV-2 infection, of whom 75 (47%) had a positive PCR on NPS (median cycle threshold [Ct] value: 27.6, interquartile range: 12.5-37.6). PCR on FS had a sensitivity of 72.5% (50/69, 95% confidence interval [CI]: 60.4-82.5) and a specificity of 85.7% (66/77, 95% CI: 75.9-92.6), and positive (PPV) and negative (NPV) predictive values of 82.0% (95% CI: 0.0-90.6) and 77.6% (95% CI: 67.3-86.0), respectively. LAMP on NPS had a sensitivity of 68.0% (51/75, 95% CI: 56.2-78.3) and a specificity of 70.8% (63/84, 95% CI: 58.9-81.0), with PPV 70.8% (95% CI: 58.9-81.0) and NPV 72.4% (95% CI: 61.8-81.5%). LAMP on FS had a sensitivity of 62.3% (43/69, 95% CI: 49.8-73.7%) and a specificity of 72.7% (56/77, 95% CI: 61.4-82.3%), with PPV 67.2% (95% CI: 54.3-78.4) and NPV 68.3% (95% CI: 57.1-78.1%). LAMP sensitivity was higher for NPS and FS specimens with high viral loads (87.1% and 75.0% for Ct value < 26, respectively). Dried saliva on filter paper was stable for 4 days at room temperature. LAMP on either NPS or FS could offer an accessible alternative for SARS-CoV-2 diagnosis in low-resource settings, with potential for optimizing sample collection and processing, and selection of gene targets.
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Affiliation(s)
- Suwarti Suwarti
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | | | - Bonifacius
- Karitas Hospital, Sumba Barat Daya, Nusa Tenggara Timur, Indonesia
| | - Yacobus Da Costa
- Pratama Reda Bolo Hospital, Sumba Barat Daya, Sumba, East Nusa Tenggara, Indonesia
| | - Claus Bogh
- Sumba Foundation, Sumba Barat, Nusa Tenggara Timur, Indonesia
| | - Decy Subekti
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Jeny Jeny
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Ayu Madri Dewi
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Nunung Nuraeni
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Mutia Rahardjani
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Iqbal Elyazar
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Erni J. Nelwan
- Tropical Infection Division, Internal Medicine Department, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Anuraj H Shankar
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - J. Kevin Baird
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Raph L. Hamers
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Duncan DB, Mackett K, Ali MU, Yamamura D, Balion C. Performance of saliva compared with nasopharyngeal swab for diagnosis of COVID-19 by NAAT in cross-sectional studies: Systematic review and meta-analysis. Clin Biochem 2022; 117:84-93. [PMID: 35952732 PMCID: PMC9359767 DOI: 10.1016/j.clinbiochem.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 11/03/2022]
Abstract
Nucleic acid amplification testing (NAAT) is the preferred method to diagnose coronavirus disease 2019 (COVID-19). Saliva has been suggested as an alternative to nasopharyngeal swabs (NPS), but previous systematic reviews were limited by the number and types of studies available. The objective of this systematic review and meta-analysis was to assess the diagnostic performance of saliva compared with NPS for COVID-19. We searched Ovid MEDLINE, Embase, Cochrane, and Scopus databases up to 24 April 2021 for studies that directly compared paired NPS and saliva specimens taken at the time of diagnosis. Meta-analysis was performed using an exact binomial rendition of the bivariate mixed-effects regression model. Risk of bias was assessed using the QUADAS-2 tool. Of 2683 records, we included 23 studies with 25 cohorts, comprising 11,582 paired specimens. A wide variety of NAAT assays and collection methods were used. Meta-analysis gave a pooled sensitivity of 87 % (95 % CI = 83-90 %) and specificity of 99 % (95 % CI = 98-99 %). Subgroup analyses showed the highest sensitivity when the suspected individual is tested in an outpatient setting and is symptomatic. Our results support the use of saliva NAAT as an alternative to NPS NAAT for the diagnosis of COVID-19.
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Affiliation(s)
- Donald Brody Duncan
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada; Microbiology Department, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario L8L 2X2, Canada
| | - Katharine Mackett
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Muhammad Usman Ali
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Deborah Yamamura
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada; Microbiology Department, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario L8L 2X2, Canada; Division of Infectious Diseases, Department of Medicine, McMaster University, Hamilton, Ontario L8V 1C3, Canada
| | - Cynthia Balion
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada; Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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42
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Leibovici L, Friedman J. CMI: How did we do in 2021? Clin Microbiol Infect 2022. [DOI: 10.1016/j.cmi.2022.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Tobik ER, Kitfield-Vernon LB, Thomas RJ, Steel SA, Tan SH, Allicock OM, Choate BL, Akbarzada S, Wyllie AL. Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe. Expert Rev Mol Diagn 2022; 22:519-535. [PMID: 35763281 DOI: 10.1080/14737159.2022.2094250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Symptomatic testing and asymptomatic screening for SARS-CoV-2 continue to be essential tools for mitigating virus transmission. Though COVID-19 diagnostics initially defaulted to oropharyngeal or nasopharyngeal sampling, the worldwide urgency to expand testing efforts spurred innovative approaches and increased diversity of detection methods. Strengthening innovation and facilitating widespread testing remains critical for global health, especially as additional variants emerge and other mitigation strategies are recalibrated. AREAS COVERED A growing body of evidence reflects the need to expand testing efforts and further investigate the efficiency, sensitivity, and acceptability of saliva samples for SARS-CoV-2 detection. Countries have made pandemic response decisions based on resources, costs, procedures, and regional acceptability - the adoption and integration of saliva-based testing among them. Saliva has demonstrated high sensitivity and specificity while being less invasive relative to nasopharyngeal swabs, securing saliva's position as a more acceptable sample type. EXPERT OPINION Despite the accessibility and utility of saliva sampling, global implementation remains low compared to swab-based approaches. In some cases, countries have validated saliva-based methods but face challenges with testing implementation or expansion. Here, we review the localities that have demonstrated success with saliva-based SARS-CoV-2 testing approaches and can serve as models for transforming concepts into globally-implemented best practices.
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Affiliation(s)
- Emily R Tobik
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Lily B Kitfield-Vernon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Russell J Thomas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sydney A Steel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Steph H Tan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.,Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, USA
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Brittany L Choate
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sumaira Akbarzada
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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Gómez-Carballa A, Rivero-Calle I, Pardo-Seco J, Gómez-Rial J, Rivero-Velasco C, Rodríguez-Núñez N, Barbeito-Castiñeiras G, Pérez-Freixo H, Cebey-López M, Barral-Arca R, Rodriguez-Tenreiro C, Dacosta-Urbieta A, Bello X, Pischedda S, Currás-Tuala MJ, Viz-Lasheras S, Martinón-Torres F, Salas A. A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity. ENVIRONMENTAL RESEARCH 2022; 210:112890. [PMID: 35202626 PMCID: PMC8861187 DOI: 10.1016/j.envres.2022.112890] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/11/2022] [Accepted: 02/02/2022] [Indexed: 05/08/2023]
Abstract
Coronavirus Disease-19 (COVID-19) symptoms range from mild to severe illness; the cause for this differential response to infection remains unknown. Unravelling the immune mechanisms acting at different levels of the colonization process might be key to understand these differences. We carried out a multi-tissue (nasal, buccal and blood; n = 156) gene expression analysis of immune-related genes from patients affected by different COVID-19 severities, and healthy controls through the nCounter technology. Mild and asymptomatic cases showed a powerful innate antiviral response in nasal epithelium, characterized by activation of interferon (IFN) pathway and downstream cascades, successfully controlling the infection at local level. In contrast, weak macrophage/monocyte driven innate antiviral response and lack of IFN signalling activity were present in severe cases. Consequently, oral mucosa from severe patients showed signals of viral activity, cell arresting and viral dissemination to the lower respiratory tract, which ultimately could explain the exacerbated innate immune response and impaired adaptative immune responses observed at systemic level. Results from saliva transcriptome suggest that the buccal cavity might play a key role in SARS-CoV-2 infection and dissemination in patients with worse prognosis. Co-expression network analysis adds further support to these findings, by detecting modules specifically correlated with severity involved in the abovementioned biological routes; this analysis also provides new candidate genes that might be tested as biomarkers in future studies. We also found tissue specific severity-related signatures mainly represented by genes involved in the innate immune system and cytokine/chemokine signalling. Local immune response could be key to determine the course of the systemic response and thus COVID-19 severity. Our findings provide a framework to investigate severity host gene biomarkers and pathways that might be relevant to diagnosis, prognosis, and therapy.
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Affiliation(s)
- Alberto Gómez-Carballa
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jacobo Pardo-Seco
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - José Gómez-Rial
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Laboratorio de Inmunología. Servicio de Análisis Clínicos. Hospital Clínico Universitario (SERGAS), Galicia, Spain
| | - Carmen Rivero-Velasco
- Intensive Medicine Department, Hospital Clìnico Universitario de Santiago de Compostela, Galicia, Spain
| | - Nuria Rodríguez-Núñez
- Pneumology Department, Hospital Clìnico Universitario de Santiago de Compostela, Galicia, Spain
| | - Gema Barbeito-Castiñeiras
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Hugo Pérez-Freixo
- Preventive Medicine Department, Hospital Clínico Universitario de Santiago de Compostela, Spain
| | - Miriam Cebey-López
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ruth Barral-Arca
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Carmen Rodriguez-Tenreiro
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Dacosta-Urbieta
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Xabier Bello
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Sara Pischedda
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - María José Currás-Tuala
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Sandra Viz-Lasheras
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Salas
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain.
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Tallmadge RL, Laverack M, Cronk B, Venugopalan R, Martins M, Zhang X, Elvinger F, Plocharczyk E, Diel DG. Viral RNA Load and Infectivity of SARS-CoV-2 in Paired Respiratory and Oral Specimens from Symptomatic, Asymptomatic, or Postsymptomatic Individuals. Microbiol Spectr 2022; 10:e0226421. [PMID: 35575498 PMCID: PMC9241670 DOI: 10.1128/spectrum.02264-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 04/17/2022] [Indexed: 11/30/2022] Open
Abstract
In the present study, we assessed the diagnostic sensitivity and determined the viral RNA load and infectivity of SARS-CoV-2 in paired respiratory (nasopharyngeal and anterior nares) and oral samples (saliva and sublingual swab). Samples were collected from 77 individuals of which 75 were diagnosed with COVID-19 and classified as symptomatic (n = 29), asymptomatic (n = 31), or postsymptomatic (n = 15). Specimens were collected at one time point from each individual, between day 1 and 23 after the initial COVID-19 diagnosis, and included self-collected saliva (S), or sublingual (SL) swab, and bilateral anterior nares (AN) swab, followed by health care provider collected nasopharyngeal (NP) swab. Sixty-three specimen sets were tested using five assay/platforms. The diagnostic sensitivity of each assay/platform and specimen type was determined. Of the 63 specimen sets, SARS-CoV-2 was detected in 62 NP specimens, 52 AN specimens, 59 saliva specimens, and 31 SL specimens by at least one platform. Infectious SARS-CoV-2 was isolated from 21 NP, 13 AN, 12 saliva, and one SL specimen out of 50 specimen sets. SARS-CoV-2 isolation was most successful up to 5 days after initial COVID-19 diagnosis using NP specimens from symptomatic patients (16 of 24 positives, 66.67%), followed by specimens from asymptomatic patients (5 of 17 positives, 29.41%), while it was not very successful with specimens from postsymptomatic patients. Benefits of self-collected saliva and AN specimens balance the loss of sensitivity relative to NP specimens. Therefore, saliva and AN specimens are acceptable alternatives for symptomatic SARS-CoV-2 diagnostic testing or surveillance with increased sampling frequency of asymptomatic individuals. IMPORTANCE The dynamics of infection with SARS-CoV-2 have a significant impact on virus infectivity and in the diagnostic sensitivity of molecular and classic virus detection tests. In the present study we determined the diagnostic sensitivity of paired respiratory (nasopharyngeal and anterior nares swabs) and oral secretions (saliva and sublingual swab) and assessed infectious virus shedding patterns by symptomatic, asymptomatic, or postsymptomatic individuals. Understanding the diagnostic performance of these specimens and the patterns of infectious virus shedding in these bodily secretions provides critical information to control COVID-19, and may help to refine guidelines on isolation and quarantine of positive individuals and their close contacts identified through epidemiological investigations.
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Affiliation(s)
- Rebecca L. Tallmadge
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Brittany Cronk
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Roopa Venugopalan
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - XiuLin Zhang
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - François Elvinger
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | | | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Veguilla V, Fowlkes AL, Bissonnette A, Beitel S, Gaglani M, Porucznik CA, Stockwell MS, Tyner HL, Naleway AL, Yoon SK, Caban-Martinez AJ, Wesley MG, Duque J, Jeddy Z, Stanford JB, Daugherty M, Dixon A, Burgess JL, Odean M, Groom HC, Phillips AL, Schaefer-Solle N, Mistry P, Rolfes MA, Thompson M, Dawood FS, Meece J. Detection and Stability of SARS-CoV-2 in Three Self-Collected Specimen Types: Flocked Midturbinate Swab (MTS) in Viral Transport Media, Foam MTS, and Saliva. Microbiol Spectr 2022; 10:e0103322. [PMID: 35665629 PMCID: PMC9241800 DOI: 10.1128/spectrum.01033-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/19/2022] [Indexed: 11/20/2022] Open
Abstract
Respiratory specimen collection materials shortages hampers severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. We compared specimen alternatives and evaluated SARS-CoV-2 RNA stability under simulated shipping conditions. We compared concordance of RT-PCR detection of SARS-CoV-2 from flocked midturbinate swabs (MTS) in viral transport media (VTM), foam MTS without VTM, and saliva. Specimens were collected between August 2020 and April 2021 from three prospective cohorts. We compared RT-PCR cycle quantification (Cq) for Spike (S), Nucleocapsid (N), and the Open Reading Frame 1ab (ORF) genes for flocked MTS and saliva specimens tested before and after exposure to a range of storage temperatures (4-30°C) and times (2, 3, and 7 days). Of 1,900 illnesses with ≥2 specimen types tested, 335 (18%) had SARS-CoV-2 detected in ≥1 specimen; 304 (91%) were concordant across specimen types. Among illnesses with SARS-CoV-2 detection, 97% (95% confidence interval [CI]: 94-98%) were positive on flocked MTS, 99% (95% CI: 97-100%) on saliva, and 89% (95% CI: 84-93%) on foam MTS. SARS-CoV-2 RNA was detected in flocked MTS and saliva stored up to 30°C for 7 days. All specimen types provided highly concordant SARS-CoV-2 results. These findings support a range of viable options for specimen types, collection, and transport methods that may facilitate SARS-CoV-2 testing during supply and personnel shortages. IMPORTANCE Findings from this analysis indicate that (1) self-collection of flocked and foam MTS and saliva samples is feasible in both adults and children, (2) foam MTS with VTM and saliva are both viable and reasonable alternatives to traditional flocked MTS in VTM for SARS-CoV-2 detection, and (3) these sample types may be stored and transported at ambient temperatures for up to 7 days without compromising sample quality. These findings support methods of sample collection for SARS-CoV-2 detection that may facilitate widespread community testing in the setting of supply and personnel shortages during the current pandemic.
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Affiliation(s)
- Vic Veguilla
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Adam Bissonnette
- Integrated Research & Development Laboratory, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Shawn Beitel
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - Manjusha Gaglani
- Baylor Scott and White Health, Temple, Texas, USA
- Texas A&M University College of Medicine, Temple, Texas, USA
| | - Christina A. Porucznik
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Melissa S. Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
- Department of Population and Family Health, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Allison L. Naleway
- Kaiser Permanente Northwest Center for Health Research, Portland, Oregon, USA
| | - Sarang K. Yoon
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | | | | | - Jazmin Duque
- Abt Associates, Inc., Cambridge, Massachusetts, USA
| | - Zuha Jeddy
- Abt Associates, Inc., Cambridge, Massachusetts, USA
| | - Joseph B. Stanford
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | | | - Ashton Dixon
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jefferey L. Burgess
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - Marilyn Odean
- St. Luke’s Regional Health Care System, Duluth, Minnesota, USA
- The Whiteside Institute for Clinical Research, Duluth, Minnesota, USA
| | - Holly C. Groom
- Kaiser Permanente Northwest Center for Health Research, Portland, Oregon, USA
| | - Andrew L. Phillips
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | | | | | | | - Mark Thompson
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Jennifer Meece
- Integrated Research & Development Laboratory, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
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The Matrix Effect in the RT-PCR Detection of SARS-CoV-2 Using Saliva without RNA Extraction. Diagnostics (Basel) 2022; 12:diagnostics12071547. [PMID: 35885453 PMCID: PMC9318260 DOI: 10.3390/diagnostics12071547] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/23/2022] Open
Abstract
The present work focuses on the detection of SARS-CoV-2 in saliva, contributing to understanding the inhibition effect of the matrix and its influence on the results. Detection of viral genes ORF1ab, N, and E was performed by RT-PCR using saliva directly in the reaction without RNA extraction. Different amounts of saliva were spiked with increasing amounts of viral RNA from COVID-19 patients and subjected to RT-PCR detection. In parallel, 64 saliva samples from confirmed COVID-19 patients were used in two different amounts directly in the RT-PCR reaction and their results compared. The presence of saliva in the RT-PCR always causes a positive shift of the Ct values, but a very high between-person variability of its magnitude was obtained, with increases ranging from 0.93 to 11.36. Viral targets are also affected differently depending on the initial number of viral particles. Due to inhibitors present in saliva, the duplication of sample volume causes only 48 to 61% of the expected Ct value decrease depending on the viral target gene. The use of saliva has advantages, but also limitations, due to potential inhibitors present in the matrix. However, the choice of the target and the right amount of sample may significantly influence the results.
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Ranoa DRE, Holland RL, Alnaji FG, Green KJ, Wang L, Fredrickson RL, Wang T, Wong GN, Uelmen J, Maslov S, Weiner ZJ, Tkachenko AV, Zhang H, Liu Z, Ibrahim A, Patel SJ, Paul JM, Vance NP, Gulick JG, Satheesan SP, Galvan IJ, Miller A, Grohens J, Nelson TJ, Stevens MP, Hennessy PM, Parker RC, Santos E, Brackett C, Steinman JD, Fenner MR, Dohrer K, DeLorenzo M, Wilhelm-Barr L, Brauer BR, Best-Popescu C, Durack G, Wetter N, Kranz DM, Breitbarth J, Simpson C, Pryde JA, Kaler RN, Harris C, Vance AC, Silotto JL, Johnson M, Valera EA, Anton PK, Mwilambwe L, Bryan SP, Stone DS, Young DB, Ward WE, Lantz J, Vozenilek JA, Bashir R, Moore JS, Garg M, Cooper JC, Snyder G, Lore MH, Yocum DL, Cohen NJ, Novakofski JE, Loots MJ, Ballard RL, Band M, Banks KM, Barnes JD, Bentea I, Black J, Busch J, Conte A, Conte M, Curry M, Eardley J, Edwards A, Eggett T, Fleurimont J, Foster D, Fouke BW, Gallagher N, Gastala N, Genung SA, Glueck D, Gray B, Greta A, Healy RM, Hetrick A, Holterman AA, Ismail N, Jasenof I, Kelly P, Kielbasa A, Kiesel T, Kindle LM, Lipking RL, Manabe YC, Mayes J́, McGuffin R, McHenry KG, Mirza A, Moseley J, Mostafa HH, Mumford M, Munoz K, Murray AD, Nolan M, Parikh NA, Pekosz A, Pflugmacher J, Phillips JM, Pitts C, Potter MC, Quisenberry J, Rear J, Robinson ML, Rosillo E, Rye LN, Sherwood M, Simon A, Singson JM, Skadden C, Skelton TH, Smith C, Stech M, Thomas R, Tomaszewski MA, Tyburski EA, Vanwingerden S, Vlach E, Watkins RS, Watson K, White KC, Killeen TL, Jones RJ, Cangellaris AC, Martinis SA, Vaid A, Brooke CB, Walsh JT, Elbanna A, Sullivan WC, Smith RL, Goldenfeld N, Fan TM, Hergenrother PJ, Burke MD. Mitigation of SARS-CoV-2 transmission at a large public university. Nat Commun 2022. [DOI: doi.org/10.1038/s41467-022-30833-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
AbstractIn Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health of the university and surrounding communities, and viability of in-person instruction. Here we report a case study at the University of Illinois at Urbana-Champaign, where a multimodal “SHIELD: Target, Test, and Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms and laboratories open. The program included epidemiological modeling and surveillance, fast/frequent testing using a novel low-cost and scalable saliva-based RT-qPCR assay for SARS-CoV-2 that bypasses RNA extraction, called covidSHIELD, and digital tools for communication and compliance. In Fall 2020, we performed >1,000,000 covidSHIELD tests, positivity rates remained low, we had zero COVID-19-related hospitalizations or deaths amongst our university community, and mortality in the surrounding Champaign County was reduced more than 4-fold relative to expected. This case study shows that fast/frequent testing and other interventions mitigated transmission of SARS-CoV-2 at a large public university.
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49
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Ranoa DRE, Holland RL, Alnaji FG, Green KJ, Wang L, Fredrickson RL, Wang T, Wong GN, Uelmen J, Maslov S, Weiner ZJ, Tkachenko AV, Zhang H, Liu Z, Ibrahim A, Patel SJ, Paul JM, Vance NP, Gulick JG, Satheesan SP, Galvan IJ, Miller A, Grohens J, Nelson TJ, Stevens MP, Hennessy PM, Parker RC, Santos E, Brackett C, Steinman JD, Fenner MR, Dohrer K, DeLorenzo M, Wilhelm-Barr L, Brauer BR, Best-Popescu C, Durack G, Wetter N, Kranz DM, Breitbarth J, Simpson C, Pryde JA, Kaler RN, Harris C, Vance AC, Silotto JL, Johnson M, Valera EA, Anton PK, Mwilambwe L, Bryan SP, Stone DS, Young DB, Ward WE, Lantz J, Vozenilek JA, Bashir R, Moore JS, Garg M, Cooper JC, Snyder G, Lore MH, Yocum DL, Cohen NJ, Novakofski JE, Loots MJ, Ballard RL, Band M, Banks KM, Barnes JD, Bentea I, Black J, Busch J, Conte A, Conte M, Curry M, Eardley J, Edwards A, Eggett T, Fleurimont J, Foster D, Fouke BW, Gallagher N, Gastala N, Genung SA, Glueck D, Gray B, Greta A, Healy RM, Hetrick A, Holterman AA, Ismail N, Jasenof I, Kelly P, Kielbasa A, Kiesel T, Kindle LM, Lipking RL, Manabe YC, Mayes J, McGuffin R, McHenry KG, Mirza A, Moseley J, Mostafa HH, Mumford M, Munoz K, Murray AD, Nolan M, Parikh NA, Pekosz A, Pflugmacher J, Phillips JM, Pitts C, Potter MC, Quisenberry J, Rear J, Robinson ML, Rosillo E, Rye LN, Sherwood M, Simon A, Singson JM, Skadden C, Skelton TH, Smith C, Stech M, Thomas R, Tomaszewski MA, Tyburski EA, Vanwingerden S, Vlach E, Watkins RS, Watson K, White KC, Killeen TL, Jones RJ, Cangellaris AC, Martinis SA, Vaid A, Brooke CB, Walsh JT, Elbanna A, Sullivan WC, Smith RL, Goldenfeld N, Fan TM, Hergenrother PJ, Burke MD. Mitigation of SARS-CoV-2 transmission at a large public university. Nat Commun 2022; 13:3207. [PMID: 35680861 PMCID: PMC9184485 DOI: 10.1038/s41467-022-30833-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/19/2022] [Indexed: 11/09/2022] Open
Abstract
In Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health of the university and surrounding communities, and viability of in-person instruction. Here we report a case study at the University of Illinois at Urbana-Champaign, where a multimodal “SHIELD: Target, Test, and Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms and laboratories open. The program included epidemiological modeling and surveillance, fast/frequent testing using a novel low-cost and scalable saliva-based RT-qPCR assay for SARS-CoV-2 that bypasses RNA extraction, called covidSHIELD, and digital tools for communication and compliance. In Fall 2020, we performed >1,000,000 covidSHIELD tests, positivity rates remained low, we had zero COVID-19-related hospitalizations or deaths amongst our university community, and mortality in the surrounding Champaign County was reduced more than 4-fold relative to expected. This case study shows that fast/frequent testing and other interventions mitigated transmission of SARS-CoV-2 at a large public university. Safely opening university campuses has been a major challenge during the COVID-19 pandemic. Here, the authors describe a program of public health measures employed at a university in the United States which, combined with other non-pharmaceutical interventions, allowed the university to stay open in fall 2020 with limited evidence of transmission.
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Affiliation(s)
- Diana Rose E Ranoa
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robin L Holland
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Fadi G Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kelsie J Green
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Richard L Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tong Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - George N Wong
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Johnny Uelmen
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zachary J Weiner
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alexei V Tkachenko
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Hantao Zhang
- Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zhiru Liu
- Department of Physics, Stanford University, Palo Alto, CA, USA
| | - Ahmed Ibrahim
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sanjay J Patel
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John M Paul
- Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Nickolas P Vance
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joseph G Gulick
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Isaac J Galvan
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrew Miller
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joseph Grohens
- Department of English, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Todd J Nelson
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mary P Stevens
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Robert C Parker
- McKinley Health Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | - Julie D Steinman
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Melvin R Fenner
- McKinley Health Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kirstin Dohrer
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Michael DeLorenzo
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Laura Wilhelm-Barr
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Catherine Best-Popescu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gary Durack
- Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Tekmill, Champaign, IL, USA
| | | | - David M Kranz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jessica Breitbarth
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Charlie Simpson
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julie A Pryde
- Champaign-Urbana Public Health District, Champaign, IL, USA
| | - Robin N Kaler
- Public Affairs, College of Media, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chris Harris
- Public Affairs, College of Media, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Allison C Vance
- Public Affairs, College of Media, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jodi L Silotto
- Public Affairs, College of Media, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mark Johnson
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Enrique Andres Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Patricia K Anton
- Housing Division, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lowa Mwilambwe
- Office of the Vice Chancellor for Student Affairs, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Stephen P Bryan
- Office of the Dean of Students, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Deborah S Stone
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Danita B Young
- Office of the Vice Chancellor for Student Affairs, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Wanda E Ward
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John Lantz
- Office of the Dean of Students, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John A Vozenilek
- Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Rashid Bashir
- Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jeffrey S Moore
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mayank Garg
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julian C Cooper
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gillian Snyder
- Interdisciplinary Health Sciences Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Michelle H Lore
- Interdisciplinary Health Sciences Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dustin L Yocum
- Office for the Protection of Human Subjects, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Neal J Cohen
- Office of the Dean of Students, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Psychology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jan E Novakofski
- College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Melanie J Loots
- Office of the Vice Chancellor for Research and Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Randy L Ballard
- Department of Intercollegiate Athletics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mark Band
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kayla M Banks
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joseph D Barnes
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Iuliana Bentea
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Jessica Black
- Illinois Human Resources, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jeremy Busch
- Department of Intercollegiate Athletics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael Curry
- Illinois Human Resources, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jennifer Eardley
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - April Edwards
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Therese Eggett
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Judes Fleurimont
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Delaney Foster
- Division of Campus Recreation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole Gastala
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Scott A Genung
- Office of the Chief Info Officer, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Declan Glueck
- Illinois Human Resources, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Brittani Gray
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Andrew Greta
- University of Illinois System Office, Urbana, IL, USA
| | - Robert M Healy
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ashley Hetrick
- University Health Services, University of Wisconsin-Madison, Madison, WI, USA
| | - Arianna A Holterman
- Office of the Dean of Students, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nahed Ismail
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Ian Jasenof
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Patrick Kelly
- University Health Services, University of Wisconsin-Madison, Madison, WI, USA
| | - Aaron Kielbasa
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Teresa Kiesel
- University Health Services, University of Wisconsin-Madison, Madison, WI, USA
| | - Lorenzo M Kindle
- Technology Services, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rhonda L Lipking
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jade Mayes
- Department of Intercollegiate Athletics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Reubin McGuffin
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kenton G McHenry
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jada Moseley
- Illinois Human Resources, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melody Mumford
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Kathleen Munoz
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Arika D Murray
- Illinois Human Resources, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Moira Nolan
- Office of Corporate Relations, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nil A Parikh
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Janna Pflugmacher
- University Administration, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Janise M Phillips
- McKinley Health Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Collin Pitts
- University Health Services, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark C Potter
- Department of Family and Community Medicine, College of Medicine, University of Illinois at Chicago, Chicago, USA
| | - James Quisenberry
- Division of Student Affairs, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Janelle Rear
- Office of the Vice President for Economic Development and Innovation, University of Illinois System, Urbana, IL, USA
| | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Edith Rosillo
- Library Department, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leslie N Rye
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - MaryEllen Sherwood
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anna Simon
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jamie M Singson
- Division of Student Affairs, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Carly Skadden
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tina H Skelton
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Charlie Smith
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mary Stech
- McKinley Health Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ryan Thomas
- Office of the Chief Info Officer, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Erika A Tyburski
- Atlanta Center for Microsystems Engineered Point-of-Care Technologies, Emory University School of Medicine, Children's Healthcare of Atlanta, and Georgia Institute of Technology, Atlanta, GA, USA.,Georgia Institute of Technology, Institute for Electronics and Nanotechnology, Atlanta, GA, USA
| | - Scott Vanwingerden
- IT Service Delivery, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Evette Vlach
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ronald S Watkins
- University of Illinois System Office, Urbana, IL, USA.,Office of the President, University of Illinois System, Urbana, IL, USA
| | - Karriem Watson
- Mile Square Health Center, University of Illinois Health, Chicago, IL, USA
| | - Karen C White
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Timothy L Killeen
- Gies College of Business, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Robert J Jones
- Office of the Chancellor, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Susan A Martinis
- Office of the Vice Chancellor for Research and Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Awais Vaid
- Champaign-Urbana Public Health District, Champaign, IL, USA
| | - Christopher B Brooke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joseph T Walsh
- Library Department, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ahmed Elbanna
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - William C Sullivan
- Department of Landscape Architecture, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA. .,Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Nigel Goldenfeld
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Physics, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Timothy M Fan
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA. .,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Martin D Burke
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA. .,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Impact of Thermal Pretreatment of Saliva on the RT-PCR Detection of SARS-CoV-2. Adv Virol 2022; 2022:7442907. [PMID: 35693127 PMCID: PMC9177321 DOI: 10.1155/2022/7442907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/25/2022] [Accepted: 05/06/2022] [Indexed: 11/23/2022] Open
Abstract
The use of saliva directly as a specimen to detect viral RNA by RT-PCR has been tested for a long time as its advantages are relevant in terms of convenience and costs. However, as other body fluids, its proven inhibition effect on the amplification reaction can be troublesome and compromise its use in the detection of viral particles. The aim of the present work is to demonstrate that saliva pretreatment may influence the RT-PCR amplification of three gene targets of SARS-CoV-2 significantly. A pool of RNA from confirmed COVID-19 patients was used to test the influence of heat pretreatment of saliva samples at 95°C for 5, 10, 15 and 20 min on the amplification performance of ORF1ab, E, and N SARS-CoV-2 genes. Prolonged heating at 95°C significantly improves the Ct value shift, usually observed in the presence of saliva, increasing the limit of detection of viral genes ORF1ab, E, and N. When tested using a cohort of COVID-19 patients' saliva, the increased time of heat pretreatment resulted in a significant increase in the detection sensitivity.
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