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Zhang YB, Arizti-Sanz J, Bradley A, Huang Y, Kosoko-Thoroddsen TSF, Sabeti PC, Myhrvold C. CRISPR-Based Assays for Point-of-Need Detection and Subtyping of Influenza. J Mol Diagn 2024; 26:599-612. [PMID: 38901927 DOI: 10.1016/j.jmoldx.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 02/26/2024] [Accepted: 04/02/2024] [Indexed: 06/22/2024] Open
Abstract
The high disease burden of influenza virus poses a significant threat to human health. Optimized diagnostic technologies that combine speed, sensitivity, and specificity with minimal equipment requirements are urgently needed to detect the many circulating species, subtypes, and variants of influenza at the point of need. Here, we introduce such a method using Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), a clustered regularly interspaced short palindromic repeats (CRISPR)-based RNA detection platform. Four SHINE assays were designed and validated for the detection and differentiation of clinically relevant influenza species (A and B) and subtypes (H1N1 and H3N2). When tested on clinical samples, these optimized assays achieved 100% concordance with quantitative RT-PCR. Duplex Cas12a/Cas13a SHINE assays were also developed to detect two targets simultaneously. This study demonstrates the utility of this duplex assay in discriminating two alleles of an oseltamivir resistance (H275Y) mutation as well as in simultaneously detecting influenza A and human RNAse P in patient samples. These assays have the potential to expand influenza detection outside of clinical laboratories for enhanced influenza diagnosis and surveillance.
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Affiliation(s)
- Yibin B Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | - Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts
| | - A'Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts
| | - Yujia Huang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | | | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts; Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, New Jersey; Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey; Department of Chemistry, Princeton University, Princeton, New Jersey.
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2
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da Silva SM, Amaral C, Malta-Luís C, Grilo D, Duarte AG, Morais I, Afonso G, Faria N, Antunes W, Gomes I, Sá-Leão R, Miragaia M, Serrano M, Pimentel C. A one-step low-cost molecular test for SARS-CoV-2 detection suitable for community testing using minimally processed saliva. Biol Methods Protoc 2024; 9:bpae035. [PMID: 38835855 PMCID: PMC11147803 DOI: 10.1093/biomethods/bpae035] [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: 03/22/2024] [Revised: 05/03/2024] [Accepted: 05/17/2024] [Indexed: 06/06/2024] Open
Abstract
The gold standard for coronavirus disease 2019 diagnostic testing relies on RNA extraction from naso/oropharyngeal swab followed by amplification through reverse transcription-polymerase chain reaction (RT-PCR) with fluorogenic probes. While the test is extremely sensitive and specific, its high cost and the potential discomfort associated with specimen collection made it suboptimal for public health screening purposes. In this study, we developed an equally reliable, but cheaper and less invasive alternative test based on a one-step RT-PCR with the DNA-intercalating dye SYBR Green, which enables the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from saliva samples or RNA isolated from nasopharyngeal (NP) swabs. Importantly, we found that this type of testing can be fine-tuned to discriminate SARS-CoV-2 variants of concern. The saliva RT-PCR SYBR Green test was successfully used in a mass-screening initiative targeting nearly 4500 asymptomatic children under the age of 12. Testing was performed at a reasonable cost, and in some cases, the saliva test outperformed NP rapid antigen tests in identifying infected children. Whole genome sequencing revealed that the antigen testing failure could not be attributed to a specific lineage of SARS-CoV-2. Overall, this work strongly supports the view that RT-PCR saliva tests based on DNA-intercalating dyes represent a powerful strategy for community screening of SARS-CoV-2. The tests can be easily applied to other infectious agents and, therefore, constitute a powerful resource for an effective response to future pandemics.
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Affiliation(s)
- Sofia M da Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Catarina Amaral
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Cláudia Malta-Luís
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Diana Grilo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Inês Morais
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Gonçalo Afonso
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Nuno Faria
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Wilson Antunes
- Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Av. Dr Alfredo Bensaúde, Lisboa, 1849-012, Portugal
| | - Inês Gomes
- Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Av. Dr Alfredo Bensaúde, Lisboa, 1849-012, Portugal
| | - Raquel Sá-Leão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Maria Miragaia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
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3
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Silva ETT, Furtado FB, da Silveira RA, Tasca KI, Silva CN, Godoy AT, de Moraes LN, Hong MV, Alves CG, Simões RP, Kubo AMS, Fortaleza CMCB, Pereira-Lima MC, Valente GT, Grotto RMT. Saliva as a Biological Fluid in SARS-CoV-2 Detection. Diagnostics (Basel) 2024; 14:922. [PMID: 38732336 PMCID: PMC11083664 DOI: 10.3390/diagnostics14090922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND The polymerase chain reaction of upper respiratory tract swab samples was established as the gold standard procedure for diagnosing SARS-CoV-2 during the COVID pandemic. However, saliva collection has attracted attention as an alternative diagnostic collection method. The goal of this study was to compare the use of saliva and nasopharyngeal swab (NPS) samples for the detection of SARS-CoV-2. METHODS Ninety-nine paired samples were evaluated for the detection of SARS-CoV-2 by saliva and swab for a qualitative diagnosis and quantitative comparison of viral particles. Furthermore, the detection limits for each sample collection technique were determined. The cycle threshold (CT) values of the saliva samples, the vaccination status, and the financial costs associated with each collection technique were compared. RESULTS The results showed qualitative equivalence in diagnosis (96.96%) comparing saliva and swab collection, although there was low quantitative agreement. Furthermore, the detection limit test demonstrated equivalence for both collection methods. We did not observe a statistically significant association between CT values and vaccination status, indicating that the vaccine had no influence on viral load at diagnosis. Finally, we observed that the use of saliva incurs lower financial costs and requires less use of plastic materials, making it more sustainable. CONCLUSIONS These findings support the adoption of saliva collection as a feasible and sustainable alternative to the diagnosis of COVID-19.
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Affiliation(s)
- Emily Thalia Teixeira Silva
- Laboratory of Applied Biotechnology, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (E.T.T.S.); (F.B.F.); (R.A.d.S.); (C.N.S.); (A.T.G.); (L.N.d.M.); (A.M.S.K.)
| | - Fabiana Barcelos Furtado
- Laboratory of Applied Biotechnology, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (E.T.T.S.); (F.B.F.); (R.A.d.S.); (C.N.S.); (A.T.G.); (L.N.d.M.); (A.M.S.K.)
| | - Rosana Antunes da Silveira
- Laboratory of Applied Biotechnology, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (E.T.T.S.); (F.B.F.); (R.A.d.S.); (C.N.S.); (A.T.G.); (L.N.d.M.); (A.M.S.K.)
| | - Karen Ingrid Tasca
- Department of Infectious Diseases, Dermatology, Imaging Diagnosis, and Radiotherapy, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (K.I.T.); (M.V.H.); (C.G.A.); (C.M.C.B.F.)
| | - Cristiane Nonato Silva
- Laboratory of Applied Biotechnology, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (E.T.T.S.); (F.B.F.); (R.A.d.S.); (C.N.S.); (A.T.G.); (L.N.d.M.); (A.M.S.K.)
| | - Amanda Thais Godoy
- Laboratory of Applied Biotechnology, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (E.T.T.S.); (F.B.F.); (R.A.d.S.); (C.N.S.); (A.T.G.); (L.N.d.M.); (A.M.S.K.)
| | - Leonardo Nazario de Moraes
- Laboratory of Applied Biotechnology, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (E.T.T.S.); (F.B.F.); (R.A.d.S.); (C.N.S.); (A.T.G.); (L.N.d.M.); (A.M.S.K.)
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (Unesp), Botucatu 18618-689, Brazil;
| | - Michelle Venancio Hong
- Department of Infectious Diseases, Dermatology, Imaging Diagnosis, and Radiotherapy, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (K.I.T.); (M.V.H.); (C.G.A.); (C.M.C.B.F.)
| | - Camila Gonçalves Alves
- Department of Infectious Diseases, Dermatology, Imaging Diagnosis, and Radiotherapy, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (K.I.T.); (M.V.H.); (C.G.A.); (C.M.C.B.F.)
| | - Rafael Plana Simões
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (Unesp), Botucatu 18618-689, Brazil;
| | - Agatha Mayume Silva Kubo
- Laboratory of Applied Biotechnology, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (E.T.T.S.); (F.B.F.); (R.A.d.S.); (C.N.S.); (A.T.G.); (L.N.d.M.); (A.M.S.K.)
| | - Carlos Magno Castelo Branco Fortaleza
- Department of Infectious Diseases, Dermatology, Imaging Diagnosis, and Radiotherapy, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (K.I.T.); (M.V.H.); (C.G.A.); (C.M.C.B.F.)
| | - Maria Cristina Pereira-Lima
- Department of Neurology, Psychology and Psychiatry, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil;
| | - Guilherme Targino Valente
- Laboratory of Applied Biotechnology, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (E.T.T.S.); (F.B.F.); (R.A.d.S.); (C.N.S.); (A.T.G.); (L.N.d.M.); (A.M.S.K.)
| | - Rejane Maria Tommasini Grotto
- Laboratory of Applied Biotechnology, Medical School, São Paulo State University (Unesp), Botucatu 18618-689, Brazil; (E.T.T.S.); (F.B.F.); (R.A.d.S.); (C.N.S.); (A.T.G.); (L.N.d.M.); (A.M.S.K.)
- Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (Unesp), Botucatu 18618-689, Brazil;
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Rossetti M, Srisomwat C, Urban M, Rosati G, Maroli G, Yaman Akbay HG, Chailapakul O, Merkoçi A. Unleashing inkjet-printed nanostructured electrodes and battery-free potentiostat for the DNA-based multiplexed detection of SARS-CoV-2 genes. Biosens Bioelectron 2024; 250:116079. [PMID: 38295580 DOI: 10.1016/j.bios.2024.116079] [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: 11/29/2023] [Revised: 01/20/2024] [Accepted: 01/25/2024] [Indexed: 02/02/2024]
Abstract
Following the global COVID-19 pandemic triggered by SARS-CoV-2, the need for rapid, specific and cost-effective point-of-care diagnostic solutions remains paramount. Even though COVID-19 is no longer a public health emergency, the disease still poses a global threat leading to deaths, and it continues to change with the risk of new variants emerging causing a new surge in cases and deaths. Here, we address the urgent need for rapid, cost-effective and point-of-care diagnostic solutions for SARS-CoV-2. We propose a multiplexed DNA-based sensing platform that utilizes inkjet-printed nanostructured gold electrodes and an inkjet-printed battery-free near-field communication (NFC) potentiostat for the simultaneous quantitative detection of two SARS-CoV-2 genes, the ORF1ab and the N gene. The detection strategy based on the formation of an RNA-DNA sandwich structure leads to a highly specific electrochemical output. The inkjet-printed nanostructured gold electrodes providing a large surface area enable efficient binding and increase the sensitivity. The inkjet-printed battery-free NFC potentiostat enables rapid measurements and real-time data analysis via a smartphone application, making the platform accessible and portable. With the advantages of speed (5 min), simplicity, sensitivity (low pM range, ∼450% signal gain) and cost-effectiveness, the proposed platform is a promising alternative for point-of-care diagnostics and high-throughput analysis that complements the COVID-19 diagnostic toolkit.
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Affiliation(s)
- Marianna Rossetti
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain.
| | - Chawin Srisomwat
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Massimo Urban
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain; Universitat Autònoma de Barcelona, Campus de la UAB, Bellaterra, Barcelona, 08193, Spain
| | - Giulio Rosati
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain.
| | - Gabriel Maroli
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain; Universitat Autònoma de Barcelona, Campus de la UAB, Bellaterra, Barcelona, 08193, Spain; Instituto de Investigaciones en Ingeniería Eléctrica Alfredo Desages (IIIE), Universidad Nacional del Sur, CONICET, Avenida Colón 80 Bahía Blanca, Buenos Aires, Argentina
| | - Hatice Gödze Yaman Akbay
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain
| | - Orawon Chailapakul
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Arben Merkoçi
- Catalan Institute of Nanoscience and Nanotechnology, UAB Campus, 08193, Bellaterra, Barcelona, Spain; ICREA Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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5
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Kim MJ, Park PG, Hwang SJ, Bang SJ, Jung JH, Kown EB, Sul EK, Song KC, Choi JS, Han KR, Lee HY, Kim DH, Lee JM. Saliva-based Proteinase K method: A rapid and reliable diagnostic tool for the detection of SARS-COV-2 in children. J Med Virol 2024; 96:e29361. [PMID: 38178612 DOI: 10.1002/jmv.29361] [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: 08/21/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Early and accurate detection of viruses in children might help prevent transmission and severe diseases. In this study, the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) detection in children was evaluated using saliva specimens with a Proteinase K (PTK)-based RNA preparation, as saliva collection is a simple and noninvasive procedure, even in young children, with fewer concerns about sample contamination. The saliva-based PTK and the conventional paired nasopharyngeal aspiration (NPA)-based detection methods were compared between COVID-19-positive and -negative children. In addition, the detection rate for SARS-COV-2 and the difference between admission and discharge by the saliva-based PTK method was tested in COVID-19 patients. The diagnostic accuracy of the saliva-based PTK method was 98.8% compared to NP swab-based reverse transcriptase polymerase chain reaction. Saliva samples showed high sensitivity (94.1%) and specificity (100%) when using the PTK method. Furthermore, the saliva-based PTK method significantly reduced the test processing time by 2 h. Notably, Ct values at discharge increased in saliva samples compared with those at admission, which might indicate patients' clinical conditions or virus activity. In conclusion, the saliva-based PTK implemented in this study streamlines RNA extraction, making the process faster, safer, and more cost-effective, demonstrating that this method is a rapid and reliable diagnostic tool for SARS-CoV-2 detection in children.
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Affiliation(s)
- Min Jung Kim
- Department of Pediatrics, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Korea
| | - Pil-Gu Park
- Department of Microbiology, Gachon University, Incheon, Korea
| | - Su Jin Hwang
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Jun Bang
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
| | - Jae Hwa Jung
- Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Bin Kown
- Department of Pediatrics, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Korea
| | - Eun Kyung Sul
- Department of Pediatrics, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Korea
| | - Kyung Chul Song
- Department of Pediatrics, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Korea
| | - Joon-Sik Choi
- Department of Pediatrics, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Korea
| | - Kyeo Re Han
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hye Young Lee
- Department of Biomedical Laboratory Science, College of Software and Digital Healthcare Convergence, Yonsei University, Wonju, Korea
| | - Dong Hyun Kim
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
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Zhang S, Luo Y, Zhuang W, Zhong G, Su L, Xu T, Zhang X. Fully Integrated Ratiometric Fluorescence Enrichment Platform for High-Sensitivity POC Testing of Salivary Cancer Biomarkers. Anal Chem 2023; 95:18739-18747. [PMID: 38079568 DOI: 10.1021/acs.analchem.3c03170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
The point-of-care (POC) testing of cancer biomarkers in saliva with both high sensitivity and accuracy remains a serious challenge in modern clinical medicine. Herein, we develop a new fully integrated ratiometric fluorescence enrichment platform that utilizes acoustic radiation forces to enrich dual-emission sandwich immune complexes for a POC visual assay. As a result, the color signals from red and green fluorescence (capture probe and report probe, respectively) are enhanced by nearly 10 times, and colorimetric sensitivity is effectively improved. When illuminated using a portable UV lamp, the fluorescence color changing from red to green can be clearly seen with the naked eye, which allows a semiqualitative assessment of the carcinoembryonic antigen (CEA) level. In combination with a homemade smartphone-based portable device, cancer biomarkers like CEA are quantified, achieving a limit of detection as low as 0.012 ng/mL. We also directly quantify CEA in human saliva samples to investigate the reliability of this fully integrated platform, thus validating the usefulness of the proposed strategy for clinical diagnosis and home monitoring of physical conditions.
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Affiliation(s)
- Shuxin Zhang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yong Luo
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Wenxuan Zhuang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Geng Zhong
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Lei Su
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Tailin Xu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Xueji Zhang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
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7
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Schwarz C, Balean O, Dumitrescu R, Ciordas PD, Marian C, Georgescu M, Bolchis V, Sava-Rosianu R, Fratila AD, Alexa I, Jumanca D, Galuscan A. Total Antioxidant Capacity of Saliva and Its Correlation with pH Levels among Dental Students under Different Stressful Conditions. Diagnostics (Basel) 2023; 13:3648. [PMID: 38132232 PMCID: PMC10743087 DOI: 10.3390/diagnostics13243648] [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: 11/14/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
(1) Background: This cross-sectional study conducted at the Faculty of Dental Medicine, Timisoara, Romania, between December 2022 and February 2023 aims to assess salivary total antioxidant capacity and pH levels in dental students experiencing non-stressful and stressful situations and explore potential correlations between these factors. (2) Methods: Saliva samples were collected during two different periods: before an Oral Health course and before the Oral Health exam, under stressful conditions. Ethical principles were followed, and informed consent was obtained. Data on age, gender, health status, drug use, smoking habits, and anxiety levels were recorded. Saliva was collected using the draining method and pH was measured using indicator paper strips. Total antioxidant capacity (TAC) was determined using a commercial assay kit. Statistical analysis involved descriptive statistics, Student's t-test to compare pH and TAC between study groups, and Pearson's correlation coefficient to analyze the correlation between salivary pH and TAC within each group, with p < 0.05 indicating significance. (3) Results: This study involved 80 participants, comprising 26 males and 54 females, all enrolled in the 5th year of the Oral Health course, with ages ranging from 20 to 53 and a mean age of 23.62 (±4.19) years. Pearson's correlation results show a statistically significant negative relationship between the STAI test and TAC during the stress-free period (-0.02 **, N = 80, p < 0.01). (4) Conclusions: There are variations in saliva's antioxidant capacity in response to different stress conditions. Dental students experienced a higher level of stress before academic assessments compared to the non-stress period during the course.
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Affiliation(s)
- Christoph Schwarz
- Translational and Experimental Clinical Research Centre in Oral Health, Department of Preventive, Community Dentistry and Oral Health, University of Medicine and Pharmacy “Victor Babes”, 300040 Timisoara, Romania; (C.S.); (O.B.); (R.D.); (V.B.); (D.J.); (A.G.)
| | - Octavia Balean
- Translational and Experimental Clinical Research Centre in Oral Health, Department of Preventive, Community Dentistry and Oral Health, University of Medicine and Pharmacy “Victor Babes”, 300040 Timisoara, Romania; (C.S.); (O.B.); (R.D.); (V.B.); (D.J.); (A.G.)
- Clinic of Preventive, Community Dentistry and Oral Health, Department I, University of Medicine and Pharmacy “Victor Babes”, Eftimie Murgu Sq. no 2, 300041 Timisoara, Romania
| | - Ramona Dumitrescu
- Translational and Experimental Clinical Research Centre in Oral Health, Department of Preventive, Community Dentistry and Oral Health, University of Medicine and Pharmacy “Victor Babes”, 300040 Timisoara, Romania; (C.S.); (O.B.); (R.D.); (V.B.); (D.J.); (A.G.)
- Clinic of Preventive, Community Dentistry and Oral Health, Department I, University of Medicine and Pharmacy “Victor Babes”, Eftimie Murgu Sq. no 2, 300041 Timisoara, Romania
| | - Paula Diana Ciordas
- Department of Biochemistry and Pharmacology, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania; (P.D.C.); (C.M.)
| | - Catalin Marian
- Department of Biochemistry and Pharmacology, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania; (P.D.C.); (C.M.)
| | - Marius Georgescu
- Functional Sciences Department, Physiology Discipline, Victor Babes University of Medicine and Pharmacy of Timisoara, 2 Eftimie Murgu Sq., 300041 Timisoara, Romania;
| | - Vanessa Bolchis
- Translational and Experimental Clinical Research Centre in Oral Health, Department of Preventive, Community Dentistry and Oral Health, University of Medicine and Pharmacy “Victor Babes”, 300040 Timisoara, Romania; (C.S.); (O.B.); (R.D.); (V.B.); (D.J.); (A.G.)
| | - Ruxandra Sava-Rosianu
- Translational and Experimental Clinical Research Centre in Oral Health, Department of Preventive, Community Dentistry and Oral Health, University of Medicine and Pharmacy “Victor Babes”, 300040 Timisoara, Romania; (C.S.); (O.B.); (R.D.); (V.B.); (D.J.); (A.G.)
- Clinic of Preventive, Community Dentistry and Oral Health, Department I, University of Medicine and Pharmacy “Victor Babes”, Eftimie Murgu Sq. no 2, 300041 Timisoara, Romania
| | - Aurora Doris Fratila
- Faculty of Dental Medicine, Ludwig-Maximilian-University Munich, Goethestraße 70, 80336 München, Germany;
| | - Iulia Alexa
- Department of Dentistry, Faculty of Dental Medicine, “Vasile Goldis” Western University of Arad, 310045 Arad, Romania;
| | - Daniela Jumanca
- Translational and Experimental Clinical Research Centre in Oral Health, Department of Preventive, Community Dentistry and Oral Health, University of Medicine and Pharmacy “Victor Babes”, 300040 Timisoara, Romania; (C.S.); (O.B.); (R.D.); (V.B.); (D.J.); (A.G.)
- Clinic of Preventive, Community Dentistry and Oral Health, Department I, University of Medicine and Pharmacy “Victor Babes”, Eftimie Murgu Sq. no 2, 300041 Timisoara, Romania
| | - Atena Galuscan
- Translational and Experimental Clinical Research Centre in Oral Health, Department of Preventive, Community Dentistry and Oral Health, University of Medicine and Pharmacy “Victor Babes”, 300040 Timisoara, Romania; (C.S.); (O.B.); (R.D.); (V.B.); (D.J.); (A.G.)
- Clinic of Preventive, Community Dentistry and Oral Health, Department I, University of Medicine and Pharmacy “Victor Babes”, Eftimie Murgu Sq. no 2, 300041 Timisoara, Romania
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Mouzinga FH, Heinzel C, Lissom A, Kreidenweiss A, Batchi‐Bouyou AL, Mbama Ntabi JD, Djontu JC, Ngumbi E, Kremsner PG, Fendel R, Ntoumi F. Mucosal response of inactivated and recombinant COVID-19 vaccines in Congolese individuals. Immun Inflamm Dis 2023; 11:e1116. [PMID: 38156395 PMCID: PMC10751728 DOI: 10.1002/iid3.1116] [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: 07/21/2023] [Revised: 11/07/2023] [Accepted: 12/09/2023] [Indexed: 12/30/2023] Open
Abstract
BACKGROUND The efficacy of immunization against an airborne pathogen depends in part on its ability to induce antibodies at the major entry site of the virus, the mucosa. Recent studies have revealed that mucosal immunity is poorly activated after vaccination with messenger RNA vaccines, thus failing in blocking virus acquisition upon its site of initial exposure. Little information is available about the induction of mucosal immunity by inactivated and recombinant coronavirus disease 2019 (COVID-19) vaccines. This study aims to investigate this topic. METHODS Saliva and plasma samples from 440 healthy Congolese were collected including (1) fully vaccinated 2 month postvaccination with either an inactivated or a recombinant COVID-19 vaccine and (2) nonvaccinated control group. Total anti-severe acute respiratory syndrome coronavirus 2 receptor-binding domain IgG and IgA antibodies were assessed using in-house enzyme-linked immunosorbent assays for both specimens. FINDINGS Altogether, the positivity of IgG was significantly higher in plasma than in saliva samples both in vaccinated and nonvaccinated control groups. Inversely, IgA positivity was slightly higher in saliva than in plasma of vaccinated group. The overall IgG and IgA levels were respectively over 103 and 14 times lower in saliva than in plasma samples. We found a strong positive correlation between IgG in saliva and plasma also between IgA in both specimens (r = .70 for IgG and r = .52 for IgA). Interestingly, contrary to IgG, the level of salivary IgA was not different between seropositive control group and seropositive vaccinated group. No significant difference was observed between recombinant and inactivated COVID-19 vaccines in total IgG and IgA antibody concentration release 2 months postvaccination both in plasma and saliva. CONCLUSION Inactivated and recombinant COVID-19 vaccines in use in the Republic of Congo poorly activated mucosal IgA-mediated antibody response 2 months postvaccination.
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Affiliation(s)
- Freisnel H. Mouzinga
- Fondation Congolaise pour la Recherche MédicaleBrazzavilleRepublic of Congo
- Faculté des Sciences et TechniquesUniversité Marien NgouabiBrazzavilleRepublic of Congo
| | | | - Abel Lissom
- Fondation Congolaise pour la Recherche MédicaleBrazzavilleRepublic of Congo
- Department of Zoology, Faculty of ScienceUniversity of BamendaBamendaCameroon
| | - Andrea Kreidenweiss
- Institute of Tropical MedicineUniversity of TübingenTübingenGermany
- Centre de Recherches Médicales de Lambaréné (CERMEL)LambareneGabon
- German Center for Infectious Diseases (DZIF)Partner Site TübingenTübingenGermany
| | - Armel L. Batchi‐Bouyou
- Fondation Congolaise pour la Recherche MédicaleBrazzavilleRepublic of Congo
- Faculté des Sciences et TechniquesUniversité Marien NgouabiBrazzavilleRepublic of Congo
- Global Clinical Scholars Research Training ProgramHarvard Medical SchoolBostonMassachusettsUSA
| | - Jacques D. Mbama Ntabi
- Fondation Congolaise pour la Recherche MédicaleBrazzavilleRepublic of Congo
- Faculté des Sciences et TechniquesUniversité Marien NgouabiBrazzavilleRepublic of Congo
| | - Jean C. Djontu
- Fondation Congolaise pour la Recherche MédicaleBrazzavilleRepublic of Congo
| | - Etienne Ngumbi
- Faculté des Sciences et TechniquesUniversité Marien NgouabiBrazzavilleRepublic of Congo
| | - Peter G. Kremsner
- Institute of Tropical MedicineUniversity of TübingenTübingenGermany
- Centre de Recherches Médicales de Lambaréné (CERMEL)LambareneGabon
- German Center for Infectious Diseases (DZIF)Partner Site TübingenTübingenGermany
| | - Rolf Fendel
- Institute of Tropical MedicineUniversity of TübingenTübingenGermany
- Centre de Recherches Médicales de Lambaréné (CERMEL)LambareneGabon
- German Center for Infectious Diseases (DZIF)Partner Site TübingenTübingenGermany
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche MédicaleBrazzavilleRepublic of Congo
- Institute of Tropical MedicineUniversity of TübingenTübingenGermany
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Moreno-Contreras J, Espinoza MA, Cantú-Cuevas MA, Madrid-González DA, Barón-Olivares H, Ortiz-Orozco OD, Guzmán-Rodríguez C, Arias CF, Lopez S. Saliva sampling and its direct lysis is an excellent option for SARS-CoV-2 diagnosis in paediatric patients: comparison with the PanBio COVID-19 antigen rapid test in symptomatic and asymptomatic children. J Med Microbiol 2023; 72. [PMID: 38014762 DOI: 10.1099/jmm.0.001779] [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: 11/29/2023] Open
Abstract
Introduction. Lateral flow test (LFTs) have been used as an alternative to reverse transcription quantitative PCR (RT-qPCR) in point-of-care testing. Despite their benefits, the sensitivity of LFTs may be low and is affected by several factors. We have previously reported the feasibility of using direct lysis of individual or pools of saliva samples from symptomatic and asymptomatic patients as a source of viral genomes for detection by RT-qPCR.Hypothesis. Direct lysed saliva is more sensitive than antigen tests to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in samples from children.Aim. Our goals here were to valuate the specificity and sensitivity of the PanBio COVID-19 antigen rapid test device (Ag-RTD) compared with RT-qPCR of direct lysed saliva.Methodology. We evaluated the performance of the PanBio COVID-19 Ag-RTD in comparison to RT-qPCR direct lysed saliva from paired samples of 256 symptomatic and 242 asymptomatic paediatric patients.Results. Overall, although there were no differences in the specificity (96.6%), we found a lower sensitivity (64.3%) of the PanBio Ag-test RTD compared to saliva in both symptomatic and asymptomatic patients. In addition, the sensitivity of PanBio was not correlated with the viral load present in the samples.Conclusion. Our data highlight the benefits of using RT-qPCR and saliva samples for SARS-CoV-2 detection, particularly in paediatric patients.
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Affiliation(s)
- Joaquín Moreno-Contreras
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Marco A Espinoza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Marco A Cantú-Cuevas
- Secretaría de Salud del Edo. de Morelos, Ajusco #2 Col. Buena Vista, Cuernavaca, Morelos, Mexico
| | - Daniel A Madrid-González
- Secretaría de Salud del Edo. de Morelos, Ajusco #2 Col. Buena Vista, Cuernavaca, Morelos, Mexico
| | - Héctor Barón-Olivares
- Servicios de Salud del Edo. de Morelos, Callejón Borda 3 Col. Centro, Cuernavaca, Morelos, Mexico
| | - Oscar D Ortiz-Orozco
- Servicios de Salud del Edo. de Morelos, Callejón Borda 3 Col. Centro, Cuernavaca, Morelos, Mexico
| | - Cecilia Guzmán-Rodríguez
- Servicios de Salud del Edo. de Morelos, Callejón Borda 3 Col. Centro, Cuernavaca, Morelos, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Susana Lopez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
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10
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Ochoa M, Peña B, Flores O, Gil AI, Ecker L, Cornejo R, Howard LM, Grijalva CG, Lanata CF. Pooling of six respiratory samples for the detection of SARS-CoV-2: A validation and cost study in a cohort in Lima, Peru. Heliyon 2023; 9:e18904. [PMID: 37600387 PMCID: PMC10432201 DOI: 10.1016/j.heliyon.2023.e18904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023] Open
Abstract
Background The continuous evolution of the SARS-CoV-2 pandemic has led to a high demand for diagnostic testing and major shortages in testing materials, especially in low- and middle-income countries. As an alternative to testing individual samples, pooling of respiratory samples has been suggested. Previous studies have assessed performance of pooling, mainly using nasopharyngeal samples for the detection of SARS-CoV-2, but few studies have examined the performance of pooling the more practical nasal swabs or saliva samples. Objective To evaluate the sensitivity, specificity, and potential cost reduction of pooling of nasal swab (NS) and saliva (SL) samples for detection of SARS-CoV-2 in a community-based cohort study in Lima, Peru. Study design A prospective cohort study was conducted in a community setting in San Juan de Lurigancho, Lima-Peru. NS and SL samples were collected from 132 participants twice-a-week for a 2-month period. Pools of 2 to 12 samples of the same type, from participants of the same household, were tested by RT-PCR. After pooled testing, all individual samples from positive pools and all individual samples from randomly chosen negative pools were evaluated. For assessment of diagnostic performance, pool testing results were compared with results from individual testing, which served as reference, and concordance in pooled and individual test detections was evaluated. Laboratory costs for both types of samples and testing were compared. Results A total of 2008 NS and 2002 SL samples were collected from 132 study participants. We tested 329 NS and 333 SL pools. The mean pool size for NS and SL pools was 6.22 (SD = 0.92) and 6.39 (SD = 1.71), respectively. Using individual testing as reference, NS pooling of 6 had a sensitivity and specificity of 94% and 100%, respectively, with kappa of 0.97 (CI 95%: 0.93-1.00). The corresponding values for SL pooling of 6 were 83%, 100%, and 0.90 (CI 95%: 0.83-0.97). Compared with individual testing, pooling resulted in a cost reduction of 74.8% for NS and 72.4% for SL samples. Conclusions Pooling easy-to-collect respiratory samples, especially NS, demonstrated very high diagnostic performance for detection of SARS-CoV-2 with substantial cost savings. This approach could be considered in large population screening programs, especially in LMIC.
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Affiliation(s)
- Mayra Ochoa
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | - Bia Peña
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | - Omar Flores
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | - Ana I. Gil
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | - Lucie Ecker
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | | | - Leigh M. Howard
- Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Carlos G. Grijalva
- Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Claudio F. Lanata
- Instituto de Investigación Nutricional, Lima 15024, Peru
- Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232, USA
- London School of Hygiene and Tropical Medicine, London WC1E, UK
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11
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Liu Y, Kumblathan T, Tao J, Xu J, Feng W, Xiao H, Hu J, Huang CV, Wu Y, Zhang H, Li XF, Le XC. Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle. Trends Analyt Chem 2023; 165:117107. [PMID: 37317683 PMCID: PMC10204347 DOI: 10.1016/j.trac.2023.117107] [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: 01/01/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Molecular detection of SARS-CoV-2 in gargle and saliva complements the standard analysis of nasopharyngeal swabs (NPS) specimens. Although gargle and saliva specimens can be readily obtained non-invasively, appropriate collection and processing of gargle and saliva specimens are critical to the accuracy and sensitivity of the overall analytical method. This review highlights challenges and recent advances in the treatment of gargle and saliva samples for subsequent analysis using reverse transcription polymerase chain reaction (RT-PCR) and isothermal amplification techniques. Important considerations include appropriate collection of gargle and saliva samples, on-site inactivation of viruses in the sample, preservation of viral RNA, extraction and concentration of viral RNA, removal of substances that inhibit nucleic acid amplification reactions, and the compatibility of sample treatment protocols with the subsequent nucleic acid amplification and detection techniques. The principles and approaches discussed in this review are applicable to molecular detection of other microbial pathogens.
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Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jingyang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Huyan Xiao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Camille V Huang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yiping Wu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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12
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Georgas A, Georgas K, Hristoforou E. Advancements in SARS-CoV-2 Testing: Enhancing Accessibility through Machine Learning-Enhanced Biosensors. MICROMACHINES 2023; 14:1518. [PMID: 37630054 PMCID: PMC10456522 DOI: 10.3390/mi14081518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
The COVID-19 pandemic highlighted the importance of widespread testing for SARS-CoV-2, leading to the development of various new testing methods. However, traditional invasive sampling methods can be uncomfortable and even painful, creating barriers to testing accessibility. In this article, we explore how machine learning-enhanced biosensors can enable non-invasive sampling for SARS-CoV-2 testing, revolutionizing the way we detect and monitor the virus. By detecting and measuring specific biomarkers in body fluids or other samples, these biosensors can provide accurate and accessible testing options that do not require invasive procedures. We provide examples of how these biosensors can be used for non-invasive SARS-CoV-2 testing, such as saliva-based testing. We also discuss the potential impact of non-invasive testing on accessibility and accuracy of testing. Finally, we discuss potential limitations or biases associated with the machine learning algorithms used to improve the biosensors and explore future directions in the field of machine learning-enhanced biosensors for SARS-CoV-2 testing, considering their potential impact on global healthcare and disease control.
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Affiliation(s)
- Antonios Georgas
- School of Electrical and Computer Engineering, National Technical University of Athens, 15780 Athens, Greece; (K.G.); (E.H.)
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13
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Jiang X, Zhao C, Chen Y, Gao X, Zhang Q, Chen Z, Li C, Zhao X, Liu Z, Huang W, Xie W, Yue Y. Probable Evidence of Aerosol Transmission of SARS-COV-2 in a COVID-19 Outbreak of a High-Rise Building. ENVIRONMENTAL HEALTH INSIGHTS 2023; 17:11786302231188269. [PMID: 37522029 PMCID: PMC10372516 DOI: 10.1177/11786302231188269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/29/2023] [Indexed: 08/01/2023]
Abstract
Although it is well established that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be transmitted through aerosols, the mode of long-range aerosol transmission in high-rise buildings remains unclear. In this study, we analyzed an outbreak of coronavirus disease 2019 (COVID-19) that occurred in a high-rise building in China. Our objective was to investigate the plausibility of aerosol transmission of SARS-CoV-2 by testing relevant environmental variables and measuring the dispersion of a tracer gas in the drainage system of the building. The outbreak involved 7 infected families, of which 6 were from vertically aligned flats on different floors. Environmenìtal data revealed that 3 families' bathrooms were contaminated by SARS-CoV-2. In our tracer experiment, we injected tracer gas (CO2) into the dry floor drains and into water-filled toilets in the index case' s bathroom. Our findings showed that the gas could travel through vertical pipes by the dry floor drains, but not through the water of the toilets. This indicates that dry floor drains might facilitate the transmission of viral aerosols through the sewage system. On the basis of circumstantial evidence, long-range aerosol transmission may have contributed to the community outbreak of COVID-19 in this high-rise building. The vertical transmission of diseases through aerosols in high-rise buildings demands urgent attention.
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Affiliation(s)
- Xiaoman Jiang
- Chengdu Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Science, Chengdu, China
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Chenlu Zhao
- Chengdu Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Science, Chengdu, China
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Yuezhu Chen
- Chengdu Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Science, Chengdu, China
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Xufang Gao
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Qinlong Zhang
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Zhenhua Chen
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Changxiong Li
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Xiaoyan Zhao
- Chenghua Center for Disease Control and Prevention, Chengdu, China
| | - Zhijian Liu
- Chenghua Center for Disease Control and Prevention, Chengdu, China
| | - Weiwei Huang
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Wenjun Xie
- Chengdu Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Science, Chengdu, China
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Yong Yue
- Chengdu Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Science, Chengdu, China
- Chengdu Center for Disease Control and Prevention, Chengdu, China
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Suzuki T, Aizawa K, Shibuya K, Yamanaka S, Anzai Y, Kurokawa K, Nagai R. Prevalence of Asymptomatic SARS-CoV-2 Infection in Japan. JAMA Netw Open 2022; 5:e2247704. [PMID: 36574249 PMCID: PMC9856923 DOI: 10.1001/jamanetworkopen.2022.47704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
IMPORTANCE Real-world evidence of SARS-CoV-2 transmission is needed to understand the prevalence of infection in the Japanese population. OBJECTIVE To conduct sentinel screening of the Japanese population to determine the prevalence of SARS-CoV-2 infection in asymptomatic individuals, with complementary analysis for symptomatic patients as reported by active epidemiologic surveillance used by the government. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional study of a sentinel screening program investigated approximately 1 million asymptomatic individuals with polymerase chain reaction (PCR) testing for SARS-CoV-2 infection between February 22 and December 8, 2021. Participants included children, students, employed adults, and older individuals, as well as volunteers to broadly reflect the general Japanese population in the 14 prefectures of Japan that declared a state of emergency. Saliva samples and a cycle threshold (Ct) value of approximately 40 as standard in Japan were used. Polymerase chain reaction testing for symptomatic patients was separately done by public health authorities, and the results were obtained from the Ministry of Health, Labour, and Welfare of Japan to complement data on asymptomatic infections from the present study. MAIN OUTCOMES AND MEASURES Temporal trends in positivity and prevalence (including surges of different variants) and demographic associations (eg, age, geographic location, and vaccination status) were assessed. RESULTS The positive rate of SARS-CoV-2 infection in 1 082 976 asymptomatic individuals (52.08% males; mean [SD] age 39.4 [15.7] years) was 0.03% (95% CI, 0.02%-0.05%) during periods without surges and a maximum of 0.33% (95% CI, 0.25%-0.43%) during peak surges at the Japanese standard Ct value of approximately 40; however, the positive rate would have been 10-fold less at a Ct value of 25 as used elsewhere in the world (eg, UK). There was an increase in patients with a positive PCR test result with a Ct value of 25 or 30 preceding surges in infection and hotspots of asymptomatic infections. CONCLUSIONS AND RELEVANCE In this cross-sectional study of asymptomatic SARS-CoV-2 infection in the general population of Japan in 2021, as investigated by sentinel surveillance, a low rate of infection was seen in the Japanese population compared with reported levels elsewhere in the world. This finding provides real-world data on the state of infection in Japan.
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Affiliation(s)
- Toru Suzuki
- Jichi Medical University, Tochigi, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- University of Leicester, NIHR Leicester Biomedical Research Centre, Leicester, United Kingdom
| | - Kenichi Aizawa
- Division of Clinical Pharmacology, Department of Pharmacology, Jichi Medical University, Tochigi, Japan
| | | | - Shinya Yamanaka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- The Advisory Board of the COVID-19 Artificial Intelligence Simulation Project promoted by the Office for COVID-19 and Other Emerging Infectious Disease Control, Cabinet Secretariat, Government of Japan
| | - Yuichiro Anzai
- Tokyo Foundation for Policy Research, Tokyo, Japan
- The Advisory Board of the COVID-19 Artificial Intelligence Simulation Project promoted by the Office for COVID-19 and Other Emerging Infectious Disease Control, Cabinet Secretariat, Government of Japan
| | - Kiyoshi Kurokawa
- The Advisory Board of the COVID-19 Artificial Intelligence Simulation Project promoted by the Office for COVID-19 and Other Emerging Infectious Disease Control, Cabinet Secretariat, Government of Japan
- Health and Global Policy Institute, Tokyo, Japan
| | - Ryozo Nagai
- Jichi Medical University, Tochigi, Japan
- The Advisory Board of the COVID-19 Artificial Intelligence Simulation Project promoted by the Office for COVID-19 and Other Emerging Infectious Disease Control, Cabinet Secretariat, Government of Japan
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Ávila LMS, Galvis MLD, Campos MAJ, Lozano-Parra A, Villamizar LAR, Arenas MO, Martínez-Vega RA, Cala LMV, Bautista LE. Validation of RT-qPCR test for SARS-CoV-2 in saliva specimens. J Infect Public Health 2022; 15:1403-1408. [PMID: 36371937 PMCID: PMC9628233 DOI: 10.1016/j.jiph.2022.10.028] [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: 08/19/2022] [Revised: 10/19/2022] [Accepted: 10/30/2022] [Indexed: 11/05/2022] Open
Abstract
Background Saliva samples may be an easier, faster, safer, and cost-saving alternative to NPS samples, and can be self-collected by the patient. Whether SARS-CoV-2 RT-qPCR in saliva is more accurate than in nasopharyngeal swaps (NPS) is uncertain. We evaluated the accuracy of the RT-qPCR in both types of samples, assuming both approaches were imperfect. Methods We assessed the limit of detection (LoD) of RT-qPCR in each type of sample. We collected paired NPS and saliva samples and tested them using the Berlin Protocol to detect SARS-CoV-2 envelope protein (E). We used a Bayesian latent class analysis (BLCA) to estimate the sensitivity and specificity of each test, while accounting for their conditional dependence. Results The LoD were 10 copies/mL in saliva and 100 copies/mL in NPS. Paired samples of saliva and NPS were collected in 412 participants. Out of 68 infected cases, 14 were positive only in saliva. RT-qPCR sensitivity ranged from 82.7% (95% CrI: 54.8, 94.8) in NPS to 84.5% (50.9, 96.5) in saliva. Corresponding specificities were 99.1 (95% CrI: 95.3, 99.8) and 98.4 (95% CrI: 92.8, 99.7). Conclusions SARS-CoV-2 RT-qPCR test in saliva specimens has a similar or better accuracy than RT-qPCR test in NPS. Saliva specimens may be ideal for surveillance in general population, particularly in children, and in healthcare or other personnel in need of serial testing.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Leonelo E. Bautista
- University of Wisconsin-Madison, 610 Walnut Street, WARF 703, Madison, United States,Correspondence to: Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, 610 Walnut Street, WARF 703, Madison, WI 53711
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Lowe DM, Brown LAK, Chowdhury K, Davey S, Yee P, Ikeji F, Ndoutoumou A, Shah D, Lennon A, Rai A, Agyeman AA, Checkley A, Longley N, Dehbi HM, Freemantle N, Breuer J, Standing JF. Favipiravir, lopinavir-ritonavir, or combination therapy (FLARE): A randomised, double-blind, 2 × 2 factorial placebo-controlled trial of early antiviral therapy in COVID-19. PLoS Med 2022; 19:e1004120. [PMID: 36260627 PMCID: PMC9629589 DOI: 10.1371/journal.pmed.1004120] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 11/02/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Early antiviral treatment is effective for Coronavirus Disease 2019 (COVID-19) but currently available agents are expensive. Favipiravir is routinely used in many countries, but efficacy is unproven. Antiviral combinations have not been systematically studied. We aimed to evaluate the effect of favipiravir, lopinavir-ritonavir or the combination of both agents on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral load trajectory when administered early. METHODS AND FINDINGS We conducted a Phase 2, proof of principle, randomised, placebo-controlled, 2 × 2 factorial, double-blind trial of ambulatory outpatients with early COVID-19 (within 7 days of symptom onset) at 2 sites in the United Kingdom. Participants were randomised using a centralised online process to receive: favipiravir (1,800 mg twice daily on Day 1 followed by 400 mg 4 times daily on Days 2 to 7) plus lopinavir-ritonavir (400 mg/100 mg twice daily on Day 1, followed by 200 mg/50 mg 4 times daily on Days 2 to 7), favipiravir plus lopinavir-ritonavir placebo, lopinavir-ritonavir plus favipiravir placebo, or both placebos. The primary outcome was SARS-CoV-2 viral load at Day 5, accounting for baseline viral load. Between 6 October 2020 and 4 November 2021, we recruited 240 participants. For the favipiravir+lopinavir-ritonavir, favipiravir+placebo, lopinavir-ritonavir+placebo, and placebo-only arms, we recruited 61, 59, 60, and 60 participants and analysed 55, 56, 55, and 58 participants, respectively, who provided viral load measures at Day 1 and Day 5. In the primary analysis, the mean viral load in the favipiravir+placebo arm had changed by -0.57 log10 (95% CI -1.21 to 0.07, p = 0.08) and in the lopinavir-ritonavir+placebo arm by -0.18 log10 (95% CI -0.82 to 0.46, p = 0.58) compared to the placebo arm at Day 5. There was no significant interaction between favipiravir and lopinavir-ritonavir (interaction coefficient term: 0.59 log10, 95% CI -0.32 to 1.50, p = 0.20). More participants had undetectable virus at Day 5 in the favipiravir+placebo arm compared to placebo only (46.3% versus 26.9%, odds ratio (OR): 2.47, 95% CI 1.08 to 5.65; p = 0.03). Adverse events were observed more frequently with lopinavir-ritonavir, mainly gastrointestinal disturbance. Favipiravir drug levels were lower in the combination arm than the favipiravir monotherapy arm, possibly due to poor absorption. The major limitation was that the study population was relatively young and healthy compared to those most affected by the COVID-19 pandemic. CONCLUSIONS At the current doses, no treatment significantly reduced viral load in the primary analysis. Favipiravir requires further evaluation with consideration of dose escalation. Lopinavir-ritonavir administration was associated with lower plasma favipiravir concentrations. TRIAL REGISTRATION Clinicaltrials.gov NCT04499677 EudraCT: 2020-002106-68.
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Affiliation(s)
- David M. Lowe
- Institute of Immunity and Transplantation, University College London, London, United Kingdom
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, United Kingdom
- * E-mail:
| | - Li-An K. Brown
- Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Kashfia Chowdhury
- Comprehensive Clinical Trials Unit, University College London, London, United Kingdom
| | - Stephanie Davey
- Department of Rheumatology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Philip Yee
- Department of Rheumatology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Felicia Ikeji
- Comprehensive Clinical Trials Unit, University College London, London, United Kingdom
| | - Amalia Ndoutoumou
- Comprehensive Clinical Trials Unit, University College London, London, United Kingdom
| | - Divya Shah
- Department of Virology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Alexander Lennon
- Department of Virology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Abhulya Rai
- Department of Virology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Akosua A. Agyeman
- Infection, Immunity and Inflammation Research and Teaching Department, Institute of Child Health, University College London, London, United Kingdom
| | - Anna Checkley
- University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Nicola Longley
- University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Hakim-Moulay Dehbi
- Comprehensive Clinical Trials Unit, University College London, London, United Kingdom
| | - Nick Freemantle
- Comprehensive Clinical Trials Unit, University College London, London, United Kingdom
| | - Judith Breuer
- Department of Virology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
- Infection, Immunity and Inflammation Research and Teaching Department, Institute of Child Health, University College London, London, United Kingdom
| | - Joseph F. Standing
- Infection, Immunity and Inflammation Research and Teaching Department, Institute of Child Health, University College London, London, United Kingdom
- Department of Pharmacy, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
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17
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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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18
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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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19
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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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20
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Różański M, Walczak-Drzewiecka A, Witaszewska J, Wójcik E, Guziński A, Zimoń B, Matusiak R, Kazimierczak J, Borowiec M, Kania K, Paradowska E, Pawełczyk J, Dziadek J, Dastych J. RT-qPCR-based tests for SARS-CoV-2 detection in pooled saliva samples for massive population screening to monitor epidemics. Sci Rep 2022; 12:8082. [PMID: 35577836 PMCID: PMC9109753 DOI: 10.1038/s41598-022-12179-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 04/28/2022] [Indexed: 01/09/2023] Open
Abstract
Swab, RT-qPCR tests remain the gold standard of diagnostics of SARS-CoV-2 infections. These tests are costly and have limited throughput. We developed a 3-gene, seminested RT-qPCR test with SYBR green-based detection designed to be oversensitive rather than overspecific for high-throughput diagnostics of populations. This two-tier approach depends on decentralized self-collection of saliva samples, pooling, 1st-tier testing with highly sensitive screening test and subsequent 2nd-tier testing of individual samples from positive pools with the IVD test. The screening test was able to detect five copies of the viral genome in 10 µl of isolated RNA with 50% probability and 18.8 copies with 95% probability and reached Ct values that were highly linearly RNA concentration-dependent. In the side-by-side comparison, the screening test attained slightly better results than the commercially available IVD-certified RT-qPCR diagnostic test DiaPlexQ (100% specificity and 89.8% sensitivity vs. 100% and 73.5%, respectively). Testing of 1475 individual clinical samples pooled in 374 pools of four revealed 0.8% false positive pools and no false negative pools. In weekly prophylactic testing of 113 people within 6 months, a two-tier testing approach enabled the detection of 18 infected individuals, including several asymptomatic individuals, with substantially lower cost than individual RT-PCR testing.
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Affiliation(s)
- Michał Różański
- Laboratory of Cellular Immunology, Institute of Medical Biology of PAS, Lodz, Poland
| | | | | | - Ewelina Wójcik
- Proteon Pharmaceuticals S.A., Tylna 3A, 90-364, Lodz, Poland
| | | | - Bogumił Zimoń
- Proteon Pharmaceuticals S.A., Tylna 3A, 90-364, Lodz, Poland
| | - Rafał Matusiak
- Proteon Pharmaceuticals S.A., Tylna 3A, 90-364, Lodz, Poland
| | | | - Maciej Borowiec
- Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland
| | - Katarzyna Kania
- Laboratory of Virology, Institute of Medical Biology of PAS, Lodz, Poland
| | - Edyta Paradowska
- Laboratory of Virology, Institute of Medical Biology of PAS, Lodz, Poland
| | - Jakub Pawełczyk
- Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology of PAS, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology of PAS, Lodz, Poland
| | - Jarosław Dastych
- Laboratory of Cellular Immunology, Institute of Medical Biology of PAS, Lodz, Poland.
- Proteon Pharmaceuticals S.A., Tylna 3A, 90-364, Lodz, Poland.
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21
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Kost GJ. The Coronavirus Disease 2019 Spatial Care Path: Home, Community, and Emergency Diagnostic Portals. Diagnostics (Basel) 2022; 12:diagnostics12051216. [PMID: 35626375 PMCID: PMC9140623 DOI: 10.3390/diagnostics12051216] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 12/28/2022] Open
Abstract
This research uses mathematically derived visual logistics to interpret COVID-19 molecular and rapid antigen test (RAgT) performance, determine prevalence boundaries where risk exceeds expectations, and evaluate benefits of recursive testing along home, community, and emergency spatial care paths. Mathematica and open access software helped graph relationships, compare performance patterns, and perform recursive computations. Tiered sensitivity/specificity comprise: (T1) 90%/95%; (T2) 95%/97.5%; and (T3) 100%/≥99%, respectively. In emergency medicine, median RAgT performance peaks at 13.2% prevalence, then falls below T1, generating risky prevalence boundaries. RAgTs in pediatric ERs/EDs parallel this pattern with asymptomatic worse than symptomatic performance. In communities, RAgTs display large uncertainty with median prevalence boundary of 14.8% for 1/20 missed diagnoses, and at prevalence > 33.3−36.9% risk 10% false omissions for symptomatic subjects. Recursive testing improves home RAgT performance. Home molecular tests elevate performance above T1 but lack adequate validation. Widespread RAgT availability encourages self-testing. Asymptomatic RAgT and PCR-based saliva testing present the highest chance of missed diagnoses. Home testing twice, once just before mingling, and molecular-based self-testing, help avoid false omissions. Community and ER/ED RAgTs can identify contagiousness in low prevalence. Real-world trials of performance, cost-effectiveness, and public health impact could identify home molecular diagnostics as an optimal diagnostic portal.
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Affiliation(s)
- Gerald J Kost
- Fulbright Scholar 2020-2022, ASEAN Program, Point-of-Care Testing Center for Teaching and Research (POCT•CTR), Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA 95616, USA
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22
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Oba J, Taniguchi H, Sato M, Takanashi M, Yokemura M, Sato Y, Nishihara H. SARS-CoV-2 RT-qPCR testing of pooled saliva samples: A case study of 824 asymptomatic individuals and a questionnaire survey in Japan. PLoS One 2022; 17:e0263700. [PMID: 35550622 PMCID: PMC9098043 DOI: 10.1371/journal.pone.0263700] [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: 01/24/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022] Open
Abstract
From the beginning of the COVID-19 pandemic, the demand for diagnostic and screening tests has exceeded supply. Although the proportion of vaccinated people has increased in wealthier countries, breakthrough infections have occurred amid the emergence of new variants. Pooled-sample COVID-19 testing using saliva has been proposed as an efficient, inexpensive, and non-invasive method to allow larger-scale testing, especially in a screening setting. In this study, we aimed to evaluate pooled RT-qPCR saliva testing and to compare the results with individual tests. Employees of Philips Japan, Ltd. were recruited to participate in COVID-19 screening from October to December 2020. Asymptomatic individuals (n = 824) submitted self-collected saliva samples. Samples were tested for the presence of SARS-CoV-2 by RT-qPCR in both 10-sample pools and individual tests. We also surveyed participants regarding their thoughts and behaviors after the PCR screening project. Two of the 824 individuals were positive by RT-qPCR. In the pooled testing, one of these two had no measurable Ct value, but showed an amplification trend at the end of the PCR cycle. Both positive individuals developed cold-like symptoms, but neither required hospitalization. Of the 824 participants, 471 responded to our online questionnaire. Overall, while respondents agreed that PCR screening should be performed regularly, the majority were willing to undergo PCR testing only when it was provided for free or at low cost. In conclusion, pooled testing of saliva samples can support frequent large-scale screening that is rapid, efficient, and inexpensive.
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Affiliation(s)
- Junna Oba
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hiroaki Taniguchi
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- Research and Development Center for Precision Medicine, University of Tsukuba, Innovation Medical Research Institute, Tsukuba-shi, Ibaraki, Japan
- Keio University Hospital Clinical and Translational Research Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- * E-mail:
| | - Masae Sato
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masaki Takanashi
- LSI Medience Corporation Central Laboratory Center, Itabashi-ku, Tokyo, Japan
| | - Moe Yokemura
- LSI Medience Corporation Central Laboratory Center, Itabashi-ku, Tokyo, Japan
| | - Yasunori Sato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hiroshi Nishihara
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- Research and Development Center for Precision Medicine, University of Tsukuba, Innovation Medical Research Institute, Tsukuba-shi, Ibaraki, Japan
- Keio University Hospital Clinical and Translational Research Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
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23
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Development and Testing of a Low-Cost Inactivation Buffer That Allows for Direct SARS-CoV-2 Detection in Saliva. Vaccines (Basel) 2022; 10:vaccines10050730. [PMID: 35632485 PMCID: PMC9143422 DOI: 10.3390/vaccines10050730] [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: 02/15/2022] [Revised: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 11/28/2022] Open
Abstract
Massive testing is a cornerstone in efforts to effectively track infections and stop COVID-19 transmission, including places with good vaccination coverage. However, SARS-CoV-2 testing by RT-qPCR requires specialized personnel, protection equipment, commercial kits, and dedicated facilities, which represent significant challenges for massive testing in resource-limited settings. It is therefore important to develop testing protocols that are inexpensive, fast, and sufficiently sensitive. Here, we optimized the composition of a buffer (PKTP), containing a protease, a detergent, and an RNase inhibitor, which is compatible with the RT-qPCR chemistry, allowing for direct SARS-CoV-2 detection from saliva without extracting RNA. PKTP is compatible with heat inactivation, reducing the biohazard risk of handling samples. We assessed the PKTP buffer performance in comparison to the RNA-extraction-based protocol of the US Centers for Disease Control and Prevention in saliva samples from 70 COVID-19 patients finding a good sensitivity (85.7% for the N1 and 87.1% for the N2 target) and correlations (R = 0.77, p < 0.001 for N1, and R = 0.78, p < 0.001 for N2). We also propose an auto-collection protocol for saliva samples and a multiplex reaction to minimize the PCR reaction number per patient and further reduce costs and processing time of several samples, while maintaining diagnostic standards in favor of massive testing.
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Wang Y, Upadhyay A, Pillai S, Khayambashi P, Tran SD. Saliva as a diagnostic specimen for SARS-CoV-2 detection: a scoping review. Oral Dis 2022; 28 Suppl 2:2362-2390. [PMID: 35445491 PMCID: PMC9115496 DOI: 10.1111/odi.14216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 03/22/2022] [Accepted: 04/12/2022] [Indexed: 12/03/2022]
Abstract
Objectives This scoping review aims to summarize the diagnostic value of saliva assessed from current studies that (1) compare its performance in reverse transcriptase‐polymerase chain reaction testing to nasopharyngeal swabs, (2) evaluate its performance in rapid and point‐of‐care COVID‐19 diagnostic tests, and (3) explore its use as a specimen for detecting anti‐SARS‐CoV‐2 antibodies. Materials and Methods A systematic search was performed on the following databases: Medline and Embase (Ovid), World Health Organization, Centers for Disease Control and Prevention, and Global Health (Ovid) from January 2019 to September 2021. Of the 657 publications identified from the searches, n = 146 articles were included in the final scoping review. Results Our findings showcase that salivary samples exceed nasopharyngeal swabs in detecting SARS‐CoV‐2 using reverse transcriptase‐polymerase chain reaction testing in several studies. A select number of rapid antigen and point‐of‐care tests from the literature were also identified capable of high detection rates using saliva. Moreover, anti‐SARS‐CoV‐2 antibodies have been shown to be detectable in saliva through biochemical assays. Conclusion We highlight the potential of saliva as an all‐rounded specimen in detecting SARS‐CoV‐2. However, future large‐scale clinical studies will be needed to support its widespread use as a non‐invasive clinical specimen for COVID‐19 testing.
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25
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Kolodziej LM, van Lelyveld SFL, Haverkort ME, Mariman R, Sluiter-Post JGC, Badoux P, de Koff EM, Koole JCD, Miellet WR, Swart AN, Coipan EC, Meijer A, Sanders EAM, Trzciński K, Euser SM, Eggink D, van Houten MA. High SARS-CoV-2 household transmission rates detected by dense saliva sampling. Clin Infect Dis 2022; 75:e10-e19. [PMID: 35385575 PMCID: PMC9047155 DOI: 10.1093/cid/ciac261] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Understanding the dynamics of SARS-CoV-2 household transmission is important for adequate infection control measures in this ongoing pandemic. METHODS Households were enrolled upon a PCR-confirmed index case between October and December 2020, prior to the COVID-19 vaccination program. Saliva samples were obtained by self-sampling at day 1, 3, 5, 7, 10, 14, 21, 28, 35, and 42 from study inclusion. Nasopharyngeal swabs (NPS) and oropharyngeal swabs (OPS) were collected by the research team at day 7 and capillary blood samples at day 42. Household secondary attack rate (SAR) and per-person SAR were calculated based on at least one positive saliva, NPS, OPS, or serum sample. Whole genome sequencing was performed to investigate the possibility of multiple independent SARS-CoV-2 introductions within a household. RESULTS Eighty-five households were included consisting of 326 (unvaccinated) individuals. Comparable numbers of secondary cases were identified by saliva (133/241; 55.2%) and serum (127/213; 59.6%). The household SAR was 88.2%. The per-person SAR was 64.3%. The majority of the secondary cases tested positive in saliva at day 1 (103/150; 68.7%). Transmission from index case to household member was not affected by age or the nature of their relationship. Phylogenetic analyses suggested a single introduction for the investigated households. CONCLUSION Households have a pivotal role in SARS-CoV-2 transmission. By repeated saliva self-sampling combined with NPS, OPS, and serology, we found the highest SARS-CoV-2 household transmission rates reported to date. Salivary (self-)sampling of adults and children is suitable and attractive for near real-time monitoring of SARS-CoV-2 transmission in this setting.
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Affiliation(s)
- L M Kolodziej
- Spaarne Gasthuis Academy, Hoofddorp, The Netherlands
| | - S F L van Lelyveld
- Department of Internal Medicine, Spaarne Gasthuis Hospital, Haarlem/Hoofddorp, The Netherlands
| | - M E Haverkort
- Public Health Services Kennemerland, Haarlem, The Netherlands
| | - R Mariman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - P Badoux
- Spaarne Gasthuis Academy, Hoofddorp, The Netherlands
| | - E M de Koff
- Spaarne Gasthuis Academy, Hoofddorp, The Netherlands
| | - J C D Koole
- Spaarne Gasthuis Academy, Hoofddorp, The Netherlands.,(current affiliation) Public Health Services Amsterdam, Amsterdam, The Netherlands
| | - W R Miellet
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.,Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, The Netherlands
| | - A N Swart
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - E C Coipan
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - A Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - E A M Sanders
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - K Trzciński
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, The Netherlands
| | - S M Euser
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - D Eggink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - M A van Houten
- Spaarne Gasthuis Academy, Hoofddorp, The Netherlands.,Department of Paediatrics, Spaarne Gasthuis, Haarlem/Hoofddorp, The Netherlands
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Pajon R, Paila YD, Girard B, Dixon G, Kacena K, Baden LR, El Sahly HM, Essink B, Mullane KM, Frank I, Denhan D, Kerwin E, Zhao X, Ding B, Deng W, Tomassini JE, Zhou H, Leav B, Schödel F. Initial analysis of viral dynamics and circulating viral variants during the mRNA-1273 Phase 3 COVE trial. Nat Med 2022; 28:823-830. [PMID: 35145311 PMCID: PMC9018421 DOI: 10.1038/s41591-022-01679-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022]
Abstract
The mRNA-1273 vaccine for coronavirus disease 2019 (COVID-19) demonstrated 93.2% efficacy in reduction of symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in the blinded portion of the Phase 3 Coronavirus Efficacy (COVE) trial. While mRNA-1273 demonstrated high efficacy in prevention of COVID-19, including severe disease, its effect on the viral dynamics of SARS-CoV-2 infections is not understood. Here, in exploratory analyses, we assessed the impact of mRNA-1273 vaccination in the ongoing COVE trial (number NCT04470427) on SARS-CoV-2 copy number and shedding, burden of disease and infection, and viral variants. Viral variants were sequenced in all COVID-19 and adjudicated COVID-19 cases (n = 832), from July 2020 in the blinded part A of the study to May 2021 of the open-label part B of the study, in which participants in the placebo arm started to receive the mRNA-1273 vaccine after US Food and Drug Administration emergency use authorization of mRNA-1273 in December 2020. mRNA-1273 vaccination significantly reduced SARS-CoV-2 viral copy number (95% confidence interval) by 100-fold on the day of diagnosis compared with placebo (4.1 (3.4-4.8) versus 6.2 (6.0-6.4) log10 copies per ml). Median times to undetectable viral copies were 4 days for mRNA-1273 and 7 days for placebo. Vaccination also substantially reduced the burden of disease and infection scores. Vaccine efficacies (95% confidence interval) against SARS-CoV-2 variants circulating in the United States during the trial assessed in this post hoc analysis were 82.4% (40.4-94.8%) for variants Epsilon and Gamma and 81.2% (36.1-94.5%) for Epsilon. The detection of other, non-SARS-CoV-2, respiratory viruses during the trial was similar between groups. While additional study is needed, these data show that in SARS-CoV-2-infected individuals, vaccination reduced both the viral copy number and duration of detectable viral RNA, which may be markers for the risk of virus transmission.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ian Frank
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Edward Kerwin
- Criscor Clinical Research Institute, Medford, OR, USA
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Hardt M, Föderl-Höbenreich E, Freydl S, Kouros A, Loibner M, Zatloukal K. Pre-analytical sample stabilization by different sampling devices for PCR-based COVID-19 diagnostics. N Biotechnol 2022; 70:19-27. [PMID: 35398581 PMCID: PMC8990442 DOI: 10.1016/j.nbt.2022.04.001] [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: 02/08/2022] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 11/04/2022]
Abstract
The outbreak of the SARS-CoV-2 pandemic created an unprecedented requirement for diagnostic testing, challenging not only healthcare workers and laboratories, but also providers. Quantitative RT-PCR of various specimen types is considered the diagnostic gold standard for the detection of SARS-CoV-2, both in terms of sensitivity and specificity. The pre-analytical handling of patient specimens is a critical factor to ensure reliable and valid test results. Therefore, the effect of storage duration and temperature on SARS-CoV-2 RNA copy number stability was examined in various commercially available specimen collection, transport and storage devices for naso/oropharyngeal swabs and saliva. The swab specimen transport and storage devices tested showed no significant alteration of viral RNA copy numbers when stored at room temperature, except for one system when stored for up to 96 h. However, at 37 °C a significant reduction of detectable RNA was found in 3 out of 4 of the swab solutions tested. It was also found that detectability of viral RNA remained unchanged in all 7 saliva devices as well as in unstabilized saliva when stored for 96 h at room temperature, but one device showed marked RNA copy number loss at 37 °C. All tested saliva collection devices inhibited SARS-CoV-2 infectivity immediately, whereas SARS-CoV-2 remained infectious in the swab transport systems examined, which are designed to be used for viral or bacterial growth in cell culture systems.
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28
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End-point RT-PCR based on a conservation landscape for SARS-COV-2 detection. Sci Rep 2022; 12:4759. [PMID: 35306521 PMCID: PMC8933765 DOI: 10.1038/s41598-022-07756-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 02/24/2022] [Indexed: 11/09/2022] Open
Abstract
End-point RT-PCR is a suitable alternative diagnostic technique since it is cheaper than RT-qPCR tests and can be implemented on a massive scale in low- and middle-income countries. In this work, a bioinformatic approach to guide the design of PCR primers was developed, and an alternative diagnostic test based on end-point PCR was designed. End-point PCR primers were designed through conservation analysis based on kmer frequency in SARS-CoV-2 and human respiratory pathogen genomes. Highly conserved regions were identified for primer design, and the resulting PCR primers were used to amplify 871 nasopharyngeal human samples with a previous RT-qPCR based SARS-CoV-2 diagnosis. The diagnostic test showed high accuracy in identifying SARS-CoV-2-positive samples including B.1.1.7, P.1, B.1.427/B.1.429 and B.1.617.2/ AY samples with a detection limit of 7.2 viral copies/µL. In addition, this test could discern SARS-CoV-2 infection from other viral infections with COVID-19-like symptomatology. The designed end-point PCR diagnostic test to detect SARS-CoV-2 is a suitable alternative to RT-qPCR. Since the proposed bioinformatic approach can be easily applied in thousands of viral genomes and over highly divergent strains, it can be used as a PCR design tool as new SARS-CoV-2 variants emerge. Therefore, this end-point PCR test could be employed in epidemiological surveillance to detect new SARS-CoV-2 variants as they emerge and propagate.
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29
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Investigation of discordant SARS-CoV-2 RT-PCR results using minimally processed saliva. Sci Rep 2022; 12:2806. [PMID: 35181678 PMCID: PMC8857222 DOI: 10.1038/s41598-022-06642-5] [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: 09/29/2021] [Accepted: 02/03/2022] [Indexed: 11/08/2022] Open
Abstract
Saliva is an attractive sample for coronavirus disease 2019 testing due its ease of collection and amenability to detect viral RNA with minimal processing. Using a direct-to-RT-PCR method with saliva self-collected from confirmed COVID-19 positive volunteers, we observed 32% false negative results. Confirmed negative and healthy volunteer samples spiked with 106 genome copies/mL of heat-inactivated severe acute respiratory syndrome coronavirus 2 showed false negative results of 10% and 13%, respectively. Additional sample heating or dilution of the false negative samples conferred only modest improvements. These results highlight the potential to significantly underdiagnose COVID-19 infections when testing directly from minimally processed heterogeneous saliva samples.
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30
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Esteves E, Mendes AK, Barros M, Figueiredo C, Andrade J, Capelo J, Novais A, Rebelo C, Soares R, Nunes A, Ferreira A, Lemos J, Duarte AS, Silva RM, Inácio Bernardino L, Correia MJ, Esteves AC, Rosa N. Population wide testing pooling strategy for SARS-CoV-2 detection using saliva. PLoS One 2022; 17:e0263033. [PMID: 35089942 PMCID: PMC8797214 DOI: 10.1371/journal.pone.0263033] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/10/2022] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 pandemic has forced frequent testing of populations. It is necessary to identify the most cost-effective strategies for the detection of COVID-19 outbreaks. Nasopharyngeal samples have been used for SARS-CoV-2 detection but require a healthcare professional to collect the sample and cause discomfort and pain to the individual. Saliva has been suggested as an appropriate fluid for the diagnosis of COVID-19. We have investigated the possibility of using pools of saliva samples to detect SARS-CoV-2 in symptomatic and asymptomatic patients. Two hundred and seventy-nine saliva samples were analyzed through RT-PCR of Envelope, Nucleocapsid and Open Reading Frame 1ab genes. Reproducibility assays showed an almost perfect agreement as well as high sensitivity (96.6%), specificity (96.8%), positive predicted value (96.6%), and negative predicted value (96.8%). The average Cycle Threshold of the genes detected was 29.7. No significant differences (p > 0.05) were detected when comparing the cycle threshold average of two consecutive reactions on the same positive saliva samples. Saliva samples have a higher median viral load (32.6) than in nasopharyngeal samples (28.9), although no significant differences were detected (p > 0.05). Saliva-pool samples allowed effective SARS-CoV-2 screening, with a higher sensibility (96.9%) on 10-sample pools than in 20-sample pools (87.5%). Regardless of pools size specificity was high (99.9%) and an almost perfect agreement was observed. Our strategy was successfully applied in population wide testing of more than 2000 individuals, showing that it is possible to use pooled saliva as diagnostic fluid for SARS-CoV-2 infection.
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Affiliation(s)
- Eduardo Esteves
- Universidade Católica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
- Faculty of Health Sciences, University of Beira Interior, Covilhã, Portugal
| | - Ana Karina Mendes
- Universidade Católica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Marlene Barros
- Universidade Católica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | | | | | - Joana Capelo
- Centro Hospitalar Tondela Viseu, Viseu, Portugal
| | | | - Carla Rebelo
- Centro Hospitalar Tondela Viseu, Viseu, Portugal
| | - Rita Soares
- Centro Hospitalar Tondela Viseu, Viseu, Portugal
| | - Ana Nunes
- Centro Hospitalar Tondela Viseu, Viseu, Portugal
| | | | - Joana Lemos
- Centro Hospitalar Tondela Viseu, Viseu, Portugal
| | - Ana Sofia Duarte
- Universidade Católica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Raquel M. Silva
- Universidade Católica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | | | - Maria José Correia
- Universidade Católica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | | | - Nuno Rosa
- Universidade Católica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
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Moreno-Contreras J, Espinoza MA, Sandoval-Jaime C, Cantú-Cuevas MA, Madrid-González DA, Barón-Olivares H, Ortiz-Orozco OD, Muñoz-Rangel AV, Guzmán-Rodríguez C, Hernández-de la Cruz M, Eroza-Osorio CM, Arias CF, López S. Pooling saliva samples as an excellent option to increase the surveillance for SARS-CoV-2 when re-opening community settings. PLoS One 2022; 17:e0263114. [PMID: 35077513 PMCID: PMC8789121 DOI: 10.1371/journal.pone.0263114] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022] Open
Abstract
In many countries a second wave of infections caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has occurred, triggering a shortage of reagents needed for diagnosis and compromising the capacity of laboratory testing. There is an urgent need to develop methods to accelerate the diagnostic procedures. Pooling samples represents a strategy to overcome the shortage of reagents, since several samples can be tested using one reaction, significantly increasing the number and speed with which tests can be carried out. We have reported the feasibility to use a direct lysis procedure of saliva as source for RNA to SARS-CoV-2 genome detection by reverse transcription quantitative-PCR (RT-qPCR). Here, we show that the direct lysis of saliva pools, of either five or ten samples, does not compromise the detection of viral RNA. In addition, it is a sensitive, fast, and inexpensive method that can be used for massive screening, especially considering the proximity of the reincorporation of activities in universities, offices, and schools.
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Affiliation(s)
- Joaquín Moreno-Contreras
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, México
| | - Marco A. Espinoza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, México
| | - Carlos Sandoval-Jaime
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, México
| | | | | | | | | | | | | | | | | | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, México
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, México
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Wang Q, Li Y, Lung DC, Chan PT, Dung CH, Jia W, Miao T, Huang J, Chen W, Wang Z, Leung KM, Lin Z, Wong D, Tse H, Wong SCY, Choi GKY, Lam JYW, To KKW, Cheng VCC, Yuen KY. Aerosol transmission of SARS-CoV-2 due to the chimney effect in two high-rise housing drainage stacks. JOURNAL OF HAZARDOUS MATERIALS 2022; 421:126799. [PMID: 34396958 PMCID: PMC8327615 DOI: 10.1016/j.jhazmat.2021.126799] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 05/22/2023]
Abstract
Stack aerosols are generated within vertical building drainage stacks during the discharge of wastewater containing feces and exhaled mucus from toilets and washbasins. Fifteen stack aerosol-related outbreaks of coronavirus disease 2019 (COVID-19) in high-rise buildings have been observed in Hong Kong and Guangzhou. Currently, we investigated two such outbreaks of COVID-19 in Hong Kong, identified the probable role of chimney effect-induced airflow in a building drainage system in the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We injected tracer gas (SF6) into the drainage stacks via the water closet of the index case and monitored tracer gas concentrations in the bathrooms and along the facades of infected and non-infected flats and in roof vents. The air temperature, humidity, and pressure in vertical stacks were also monitored. The measured tracer gas distribution agreed with the observed distribution of the infected cases. Phylogenetic analysis of the SARS-CoV-2 genome sequences demonstrated clonal spread from a point source in cases along the same vertical column. The stack air pressure and temperature distributions suggested that stack aerosols can spread to indoors through pipe leaks which provide direct evidence for the long-range aerosol transmission of SARS-CoV-2 through drainage pipes via the chimney effect.
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Affiliation(s)
- Qun Wang
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Yuguo Li
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China.
| | - David Christopher Lung
- Department of Pathology, Hong Kong Children's Hospital, Hong Kong, China; Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - Pak-To Chan
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Chung-Hin Dung
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Wei Jia
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Te Miao
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Jianxiang Huang
- Department of Urban Planning and Design, Faculty of Architecture, The University of Hong Kong, Hong Kong, China
| | - Wenzhao Chen
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Zixuan Wang
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | | | - Zhang Lin
- Division of Building Science and Technology, City University of Hong Kong, Hong Kong, China
| | - Daniel Wong
- Estates Office, The University of Hong Kong, Hong Kong, China
| | - Herman Tse
- Department of Pathology, Hong Kong Children's Hospital, Hong Kong, China
| | | | | | - Jimmy Yiu-Wing Lam
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China
| | | | | | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Noverón NR, Peralta LP, Compte DV, Montalvo LAH, Pineda SRG, Gómez AAG, Vega OAR, Gutiérrez RC, Miranda AH, Vargas AM, Martínez DDLR, Juárez PC, García AAM. SARS-CoV-2 positivity rates in asymptomatic workers at a cancer referral center in Mexico City: A prospective observational study in the context of adapting hospitals back to regular practice. Am J Infect Control 2021; 49:1469-1473. [PMID: 34551335 PMCID: PMC8452087 DOI: 10.1016/j.ajic.2021.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 10/30/2022]
Abstract
BACKGROUND Healthcare workers are at increased risk of SARS-CoV-2 infection. The positivity rates in hospitals that do not receive patients with COVID-19, such as the National Cancer Institute (INCan) in Mexico, and the associated factors are unknown. OBJECTIVE To assess the incidence and factors associated with SARS-CoV-2 infection in health workers at INCan. METHODS A cohort study of 531 workers who were followed for 6 months. RT-PCR analysis of saliva and nasopharyngeal swab samples were used in the baseline and to confirm cases during follow-up The incidence rate ratio was calculated according to the measured characteristics and the associated factors were calculated using logistic regression models. RESULTS Out of 531 workers, 9.6% tested positive for SARS-CoV-2, Being male (RR: 2.07, 95% CI: 1.1-3.8, P = .02), performing administrative tasks (RR: 1.99, 95% CI: 1.0-3.9, P = .04), and having relatives also working at INCan (RR: 3.7, 95% CI: 1.4-9.5, P < .01) were associated with higher positivity rates. DISCUSSION Incidence of positive cases in health workers were similar to that reported in non-COVID hospitals from other countries. CONCLUSIONS Even though active surveillance helped to detect a significant number of asymptomatic infections, it is still necessary to reinforce preventive measures in non-medical staff to prevent nosocomial transmission.
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Affiliation(s)
| | - Liliana Pérez Peralta
- Instituto de Oftalmología Fundación Conde de Valenciana (CONVAL), Mexico City, Mexico; Centro de Atención Integral del Paciente con Diabetes del Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Mexico City, Mexico
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34
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Martinez-Cuazitl A, Vazquez-Zapien GJ, Sanchez-Brito M, Limon-Pacheco JH, Guerrero-Ruiz M, Garibay-Gonzalez F, Delgado-Macuil RJ, de Jesus MGG, Corona-Perezgrovas MA, Pereyra-Talamantes A, Mata-Miranda MM. ATR-FTIR spectrum analysis of saliva samples from COVID-19 positive patients. Sci Rep 2021; 11:19980. [PMID: 34620977 PMCID: PMC8497525 DOI: 10.1038/s41598-021-99529-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) is the latest biological hazard for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Even though numerous diagnostic tests for SARS-CoV-2 have been proposed, new diagnosis strategies are being developed, looking for less expensive methods to be used as screening. This study aimed to establish salivary vibrational modes analyzed by attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy to detect COVID-19 biological fingerprints that allow the discrimination between COVID-19 and healthy patients. Clinical dates, laboratories, and saliva samples of COVID-19 patients (N = 255) and healthy persons (N = 1209) were obtained and analyzed through ATR-FTIR spectroscopy. Then, a multivariate linear regression model (MLRM) was developed. The COVID-19 patients showed low SaO2, cough, dyspnea, headache, and fever principally. C-reactive protein, lactate dehydrogenase, fibrinogen, D-dimer, and ferritin were the most important altered laboratory blood tests, which were increased. In addition, changes in amide I and immunoglobulin regions were evidenced in the FTIR spectra analysis, and the MLRM showed clear discrimination between both groups. Specific salivary vibrational modes employing ATR-FTIR spectroscopy were established; moreover, the COVID-19 biological fingerprint in saliva was characterized, allowing the COVID-19 detection using an MLRM, which could be helpful for the development of new diagnostic devices.
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Affiliation(s)
- Adriana Martinez-Cuazitl
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, 11200, Mexico City, Mexico
| | - Gustavo J Vazquez-Zapien
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, 11200, Mexico City, Mexico
| | | | - Jorge H Limon-Pacheco
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, 11200, Mexico City, Mexico
| | - Melissa Guerrero-Ruiz
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, 11200, Mexico City, Mexico
| | - Francisco Garibay-Gonzalez
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, 11200, Mexico City, Mexico
| | | | | | | | | | - Monica M Mata-Miranda
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, 11200, Mexico City, Mexico.
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35
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Pratelli A, Lucente MS, Mari V, Cordisco M, Sposato A, Capozza P, Lanave G, Martella V, Buonavoglia A. A simple pooling salivary test for SARS-CoV-2 diagnosis: A Columbus' egg? Virus Res 2021; 305:198575. [PMID: 34560181 PMCID: PMC8454190 DOI: 10.1016/j.virusres.2021.198575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/30/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022]
Abstract
Saliva is an appropriate specimen for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) diagnosis. The possibility of pooling samples of saliva, using non-invasive bibula strips for sampling, was explored employing Bovine coronavirus (BCoV) spiked saliva. In laboratory, up to 30 saliva-soaked strips were pooled in a single tube with 2 mL of medium. After quick adsorption with the medium and vortexing, the liquid was collected and tested with a quantitative molecular assay to quantify viral RNA genome copies. On testing of single and pooled strips, the difference between the median threshold cycles (Ct) value of test performed on the single positive saliva sample and the median Ct value obtained on the pool of 30 strips, was 3.21 cycles. Saliva pooling with bibula strips could allow monitoring of COVID-19 on a large scale, reducing costs for the health bodies in terms of medical material and skilled personnel. Finally, saliva sampling is noninvasive and less traumatic than nasopharyngeal swabs and can be self-collected.
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Affiliation(s)
- Annamaria Pratelli
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano (Ba) 70010, Italy.
| | - Maria Stella Lucente
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano (Ba) 70010, Italy
| | - Viviana Mari
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano (Ba) 70010, Italy
| | - Marco Cordisco
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano (Ba) 70010, Italy
| | - Alessio Sposato
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano (Ba) 70010, Italy
| | - Paolo Capozza
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano (Ba) 70010, Italy
| | - Gianvito Lanave
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano (Ba) 70010, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano (Ba) 70010, Italy
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Abstract
The gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection diagnosis is reverse transcription (RT)-PCR from a nasopharyngeal swab specimen (NPS). Its collection involves close contact between patients and health care workers, requiring a significant amount of workforce and putting them at risk of infection. We evaluated self-collection of alternative specimens and compared their sensitivity and cycle threshold (CT) values to those of NPS. We visited acute coronavirus disease 2019 (COVID-19) outpatients to collect concomitant NPS and gargle specimens and had patients self-collect gargle and either sputum or spit specimens the next morning. We included 40 patients and collected 40 concomitant NPS and gargle specimens, as well as 40 gargle, 22 spit, and 16 sputum specimens the next day (2 patients could not produce sputum). All specimens were as sensitive as NPS. Gargle specimens had a sensitivity of 0.97 (95% confidence interval [CI], 0.92 to 1.00), whether collected concomitantly with NPS or the next morning. Next-morning spit and sputum specimens showed sensitivities of 1.00 (95% CI, 1.00 to 1.00) and 0.94 (95% CI, 0.87 to 1.00]), respectively. The gargle specimens had significantly higher mean CT values of 29.89 (standard deviation [SD], 4.63; P < 0.001) and 29.25 (SD, 3.99; P < 0.001) when collected concomitantly and the next morning, respectively, compared to NPS (22.07 [SD, 4.63]). CT values obtained with spit (23.51 [SD, 4.57]; P = 0.11) and sputum (25.82 [SD, 9.21]; P = 0.28) specimens were close to those of NPS. All alternative specimen collection methods were as sensitive as NPS, but spit collection appeared more promising, with a low CT value and ease of collection. Our findings warrant further investigation. IMPORTANCE Control of the COVID-19 pandemic relies heavily on a test-trace-isolate strategy. The most commonly used specimen for diagnosis of SARS-CoV-2 infection is a nasopharyngeal swab. However, this method is quite uncomfortable for the patient, requires specific equipment (nose swabs and containers), and requires close proximity to health care workers, putting them at risk of infection. Developing alternative sampling strategies could decrease the burden for health care workers, help overcome potential shortages of equipment, and improve acceptability of testing by reducing patient discomfort.
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Mendoza RP, Bi C, Cheng HT, Gabutan E, Pagaspas GJ, Khan N, Hoxie H, Hanna S, Holmes K, Gao N, Lewis R, Wang H, Neumann D, Chan A, Takizawa M, Lowe J, Chen X, Kelly B, Asif A, Barnes K, Khan N, May B, Chowdhury T, Pollonini G, Gouda N, Guy C, Gordon C, Ayoluwa N, Colon E, Miller-Medzon N, Jones S, Hossain R, Dodson A, Weng M, McGaskey M, Vasileva A, Lincoln AE, Sikka R, Wyllie AL, Berke EM, Libien J, Pincus M, Premsrirut PK. Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections in K-12 schools and universities. EClinicalMedicine 2021; 38:101028. [PMID: 34308321 DOI: 10.1101/2021.02.09.21251464v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND The negative impact of continued school closures during the height of the COVID-19 pandemic warrants the establishment of cost-effective strategies for surveillance and screening to safely reopen and monitor for potential in-school transmission. Here, we present a novel approach to increase the availability of repetitive and routine COVID-19 testing that may ultimately reduce the overall viral burden in the community. METHODS We implemented a testing program using the SalivaClear࣪ pooled surveillance method that included students, faculty and staff from K-12 schools (student age range 5-18 years) and universities (student age range >18 years) across the country (Mirimus Clinical Labs, Brooklyn, NY). The data analysis was performed using descriptive statistics, kappa agreement, and outlier detection analysis. FINDINGS From August 27, 2020 until January 13, 2021, 253,406 saliva specimens were self-collected from students, faculty and staff from 93 K-12 schools and 18 universities. Pool sizes of up to 24 samples were tested over a 20-week period. Pooled testing did not significantly alter the sensitivity of the molecular assay in terms of both qualitative (100% detection rate on both pooled and individual samples) and quantitative (comparable cycle threshold (Ct) values between pooled and individual samples) measures. The detection of SARS-CoV-2 in saliva was comparable to the nasopharyngeal swab. Pooling samples substantially reduced the costs associated with PCR testing and allowed schools to rapidly assess transmission and adjust prevention protocols as necessary. In one instance, in-school transmission of the virus was determined within the main office and led to review and revision of heating, ventilating and air-conditioning systems. INTERPRETATION By establishing low-cost, weekly testing of students and faculty, pooled saliva analysis for the presence of SARS-CoV-2 enabled schools to determine whether transmission had occurred, make data-driven decisions, and adjust safety protocols. We provide strong evidence that pooled testing may be a fundamental component to the reopening of schools by minimizing the risk of in-school transmission among students and faculty. FUNDING Skoll Foundation generously provided funding to Mobilizing Foundation and Mirimus for these studies.
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Affiliation(s)
- Rachelle P Mendoza
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
- Department of Pathology, SUNY Downstate Health Sciences University, 450 Clarkson Ave., Brooklyn, NY 11226, USA
| | - Chongfeng Bi
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Hui-Ting Cheng
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Elmer Gabutan
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | | | - Nadia Khan
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Helen Hoxie
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Stephen Hanna
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Kelly Holmes
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Nicholas Gao
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Raychel Lewis
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Huaien Wang
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Daniel Neumann
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Angela Chan
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Meril Takizawa
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - James Lowe
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Xiao Chen
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Brianna Kelly
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Aneeza Asif
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Keena Barnes
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Nusrat Khan
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Brandon May
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Tasnim Chowdhury
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | | | - Nourelhoda Gouda
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Chante Guy
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Candice Gordon
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Nana Ayoluwa
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Elvin Colon
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | | | - Shanique Jones
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Rauful Hossain
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Arabia Dodson
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Meimei Weng
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Miranda McGaskey
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Ana Vasileva
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, 450 Clarkson Ave., Brooklyn, NY 11226, USA
| | - Andrew E Lincoln
- MedStar Sports Medicine Research Center, MedStar Health Research Institute, 2900 S Hanover St., Baltimore, MD 21225, USA
- Department of Rehabilitation Medicine, Georgetown University Medical Center, 3800 Reservoir Rd NW, Washington, DC 20007, USA
| | - Robby Sikka
- Minnesota Timberwolves, 600 Hennepin Ave, Minneapolis, MN 55403, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, CT 06510, USA
| | - Ethan M Berke
- OptumLabs, UnitedHealth Group, 12700 Whitewater Dr, Minnetonka, MN 55343 USA
| | - Jenny Libien
- Department of Pathology, SUNY Downstate Health Sciences University, 450 Clarkson Ave., Brooklyn, NY 11226, USA
| | - Matthew Pincus
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
- Department of Pathology, SUNY Downstate Health Sciences University, 450 Clarkson Ave., Brooklyn, NY 11226, USA
| | - Prem K Premsrirut
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, 450 Clarkson Ave., Brooklyn, NY 11226, USA
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38
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Mendoza RP, Bi C, Cheng HT, Gabutan E, Pagapas GJ, Khan N, Hoxie H, Hanna S, Holmes K, Gao N, Lewis R, Wang H, Neumann D, Chan A, Takizawa M, Lowe J, Chen X, Kelly B, Asif A, Barnes K, Khan N, May B, Chowdhury T, Pollonini G, Gouda N, Guy C, Gordon C, Ayoluwa N, Colon E, Miller-Medzon N, Jones S, Hossain R, Dodson A, Weng M, McGaskey M, Vasileva A, Lincoln AE, Sikka R, Wyllie AL, Berke EM, Libien J, Pincus M, Premsrirut PK. Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections in K-12 schools and universities. EClinicalMedicine 2021; 38:101028. [PMID: 34308321 PMCID: PMC8286123 DOI: 10.1016/j.eclinm.2021.101028] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The negative impact of continued school closures during the height of the COVID-19 pandemic warrants the establishment of cost-effective strategies for surveillance and screening to safely reopen and monitor for potential in-school transmission. Here, we present a novel approach to increase the availability of repetitive and routine COVID-19 testing that may ultimately reduce the overall viral burden in the community. METHODS We implemented a testing program using the SalivaClear࣪ pooled surveillance method that included students, faculty and staff from K-12 schools (student age range 5-18 years) and universities (student age range >18 years) across the country (Mirimus Clinical Labs, Brooklyn, NY). The data analysis was performed using descriptive statistics, kappa agreement, and outlier detection analysis. FINDINGS From August 27, 2020 until January 13, 2021, 253,406 saliva specimens were self-collected from students, faculty and staff from 93 K-12 schools and 18 universities. Pool sizes of up to 24 samples were tested over a 20-week period. Pooled testing did not significantly alter the sensitivity of the molecular assay in terms of both qualitative (100% detection rate on both pooled and individual samples) and quantitative (comparable cycle threshold (Ct) values between pooled and individual samples) measures. The detection of SARS-CoV-2 in saliva was comparable to the nasopharyngeal swab. Pooling samples substantially reduced the costs associated with PCR testing and allowed schools to rapidly assess transmission and adjust prevention protocols as necessary. In one instance, in-school transmission of the virus was determined within the main office and led to review and revision of heating, ventilating and air-conditioning systems. INTERPRETATION By establishing low-cost, weekly testing of students and faculty, pooled saliva analysis for the presence of SARS-CoV-2 enabled schools to determine whether transmission had occurred, make data-driven decisions, and adjust safety protocols. We provide strong evidence that pooled testing may be a fundamental component to the reopening of schools by minimizing the risk of in-school transmission among students and faculty. FUNDING Skoll Foundation generously provided funding to Mobilizing Foundation and Mirimus for these studies.
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Affiliation(s)
- Rachelle P. Mendoza
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
- Department of Pathology, SUNY Downstate Health Sciences University, 450 Clarkson Ave., Brooklyn, NY 11226, USA
| | - Chongfeng Bi
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Hui-Ting Cheng
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Elmer Gabutan
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | | | - Nadia Khan
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Helen Hoxie
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Stephen Hanna
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Kelly Holmes
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Nicholas Gao
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Raychel Lewis
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Huaien Wang
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Daniel Neumann
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Angela Chan
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Meril Takizawa
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - James Lowe
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Xiao Chen
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Brianna Kelly
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Aneeza Asif
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Keena Barnes
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Nusrat Khan
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Brandon May
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Tasnim Chowdhury
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | | | - Nourelhoda Gouda
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Chante Guy
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Candice Gordon
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Nana Ayoluwa
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Elvin Colon
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | | | - Shanique Jones
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Rauful Hossain
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Arabia Dodson
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Meimei Weng
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Miranda McGaskey
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
| | - Ana Vasileva
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, 450 Clarkson Ave., Brooklyn, NY 11226, USA
| | - Andrew E. Lincoln
- MedStar Sports Medicine Research Center, MedStar Health Research Institute, 2900 S Hanover St., Baltimore, MD 21225, USA
- Department of Rehabilitation Medicine, Georgetown University Medical Center, 3800 Reservoir Rd NW, Washington, DC 20007, USA
| | - Robby Sikka
- Minnesota Timberwolves, 600 Hennepin Ave, Minneapolis, MN 55403, USA
| | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, CT 06510, USA
| | - Ethan M. Berke
- OptumLabs, UnitedHealth Group, 12700 Whitewater Dr, Minnetonka, MN 55343 USA
| | - Jenny Libien
- Department of Pathology, SUNY Downstate Health Sciences University, 450 Clarkson Ave., Brooklyn, NY 11226, USA
| | - Matthew Pincus
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
- Department of Pathology, SUNY Downstate Health Sciences University, 450 Clarkson Ave., Brooklyn, NY 11226, USA
| | - Prem K. Premsrirut
- Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, 450 Clarkson Ave., Brooklyn, NY 11226, USA
- Corresponding author at: Mirimus Inc, 760 Parkside Ave. Suite 206, Brooklyn, NY 11226, USA.
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Palikša S, Lopeta M, Belevičius J, Kurmauskaitė V, Ašmenavičiūtė I, Pereckaitė L, Vitkauskienė A, Baliūtytė I, Valentaitė M, Mickienė A, Gagilas J. Saliva Testing is a Robust Non-Invasive Method for SARS-CoV-2 RNA Detection. Infect Drug Resist 2021; 14:2943-2951. [PMID: 34349529 PMCID: PMC8326287 DOI: 10.2147/idr.s314491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/07/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose The precise diagnostic testing is of high importance in fighting the coronavirus pandemic. While nasopharyngeal (NP) swab testing is currently the gold standard, the SARS-CoV-2 virus could be also detected in some other body fluids. In this study, we aimed to compare the SARS-CoV-2 RNA detection results, obtained using saliva samples and NP swab samples, collected from infected patients and healthy volunteers. Patients and Methods A total of 111 individuals were enrolled in this study: 53 healthy volunteers, participating in routine testing and 58 COVID-19 patients. Diagnosis for both groups was confirmed using a set of diagnostic CE-IVD labeled RT-qPCR kits. Most of the saliva samples were collected within 48 hours after the NP swabs were taken. RNA was purified from saliva samples and analyzed using a laboratory-developed kit (Diagnolita). Detection results for both sample types were compared and analyzed in terms of result agreement, Ct variation, and quantity of internal control, as well as population analysis. Results We found a good concordance between the NP swab and saliva samples. The positive percent agreement was 98.28% (CI 90.76–99.96%) and negative percent agreement was 98.11% (CI 89.93–99.95%). Additionally, we observed a statistically significant (p<0.05) and moderately strong (R = 0.53) correlation between Ct values in saliva and NP swab samples. The saliva collection method is more robust since the Ct variation of internal control ribonuclease P mRNA detection is lower in saliva samples. Conclusion Saliva sample testing is a robust and reliable non-invasive alternative to the NP swab method for SARS-CoV-2 RNA detection, as well as a promising tool for COVID-19 screening.
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Affiliation(s)
| | | | | | | | | | - Laura Pereckaitė
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, 50161, Lithuania
| | - Astra Vitkauskienė
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, 50161, Lithuania
| | - Ieva Baliūtytė
- Department of Infectious Diseases, Lithuanian University of Health Sciences, Kaunas Hospital, Kaunas, 47116, Lithuania
| | - Monika Valentaitė
- Department of Infectious Diseases, Lithuanian University of Health Sciences, Kaunas Hospital, Kaunas, 47116, Lithuania
| | - Auksė Mickienė
- Department of Infectious Diseases, Lithuanian University of Health Sciences, Kaunas Hospital, Kaunas, 47116, Lithuania
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40
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Bouam A, Vincent JJ, Le Glass E, Almeras L, Levy PY, Tissot-Dupont H, Lagier JC, Fournier PE, Raoult D, Drancourt M. Rapid Isothermal Amplification for the Buccal Detection SARS-CoV-2 in the Context of Out-Patient COVID-19 Screening. J Clin Med 2021; 10:jcm10122643. [PMID: 34208430 PMCID: PMC8234220 DOI: 10.3390/jcm10122643] [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: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/10/2021] [Indexed: 12/04/2022] Open
Abstract
A commercially available isothermal amplification of SARS-CoV-2 RNA was applied to self-collected saliva samples using dry dental cotton rolls, which were held in the mouth for two minutes. Of 212 tests, isothermal amplification yielded three (0.14%) invalid results, 120 (56.6%) positive results and 89 (42%) negative results. Compared to reference RT-PCR assays routinely performed simultaneously on nasopharyngeal swabs, excluding the three invalid isothermal amplification assays and one RT-PCR invalid assay, these figures indicated that 119/123 (96.7%) samples were positive in both methods and 85/85 samples were negative in both methods. Four positive buccal swabs which were missed by the isothermal amplification, exhibited Ct values of 26–34 in reference RT-PCR assays. Positive isothermal amplification detection was achieved in less than 10 min. Supervision of the self-sampling procedure was key to achieve these performances. These data support the proposal to use the protocol reported in this paper, including supervised buccal self-sampling, to screen people suspected of having COVID-19 at the point of care.
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Affiliation(s)
- Amar Bouam
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (A.B.); (H.T.-D.); (J.-C.L.); (D.R.)
- POCRAMé, 13005 Marseille, France
| | - Jean-Jacques Vincent
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Elisabeth Le Glass
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Lionel Almeras
- Aix-Marseille-Université, IRD, VITROME, IHU Méditerranée Infection, 13005 Marseille, France;
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
| | - Pierre-Yves Levy
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Hervé Tissot-Dupont
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (A.B.); (H.T.-D.); (J.-C.L.); (D.R.)
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Jean-Christophe Lagier
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (A.B.); (H.T.-D.); (J.-C.L.); (D.R.)
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Pierre-Edward Fournier
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
- Aix-Marseille-Université, IRD, VITROME, IHU Méditerranée Infection, 13005 Marseille, France;
| | - Didier Raoult
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (A.B.); (H.T.-D.); (J.-C.L.); (D.R.)
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Michel Drancourt
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (A.B.); (H.T.-D.); (J.-C.L.); (D.R.)
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
- Correspondence:
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Seitz T, Schindler S, Winkelmeyer P, Zach B, Wenisch C, Zoufaly A, Allerberger F. Evaluation of rapid antigen tests based on saliva for the detection of SARS-CoV-2. J Med Virol 2021; 93:4161-4162. [PMID: 33788280 PMCID: PMC8251355 DOI: 10.1002/jmv.26983] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/03/2021] [Accepted: 03/29/2021] [Indexed: 11/10/2022]
Affiliation(s)
- Tamara Seitz
- Department of Infectious Diseases and Tropical Medicine, Clinic Favoriten, Vienna, Austria
| | | | | | - Bernhard Zach
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Christoph Wenisch
- Department of Infectious Diseases and Tropical Medicine, Clinic Favoriten, Vienna, Austria
| | - Alexander Zoufaly
- Department of Infectious Diseases and Tropical Medicine, Clinic Favoriten, Vienna, Austria
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