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Sharma S, Caputi M, Asghar W. Development of a Diagnostic Microfluidic Chip for SARS-CoV-2 Detection in Saliva and Nasopharyngeal Samples. Viruses 2024; 16:1190. [PMID: 39205164 PMCID: PMC11360425 DOI: 10.3390/v16081190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 09/04/2024] Open
Abstract
The novel coronavirus SARS-CoV-2 was first isolated in late 2019; it has spread to all continents, infected over 700 million people, and caused over 7 million deaths worldwide to date. The high transmissibility of the virus and the emergence of novel strains with altered pathogenicity and potential resistance to therapeutics and vaccines are major challenges in the study and treatment of the virus. Ongoing screening efforts aim to identify new cases to monitor the spread of the virus and help determine the danger connected to the emergence of new variants. Given its sensitivity and specificity, nucleic acid amplification tests (NAATs) such as RT-qPCR are the gold standard for SARS-CoV-2 detection. However, due to high costs, complexity, and unavailability in low-resource and point-of-care (POC) settings, the available RT-qPCR assays cannot match global testing demands. An alternative NAAT, RT-LAMP-based SARS-CoV-2 detection offers scalable, low-cost, and rapid testing capabilities. We have developed an automated RT-LAMP-based microfluidic chip that combines the RNA isolation, purification, and amplification steps on the same device and enables the visual detection of SARS-CoV-2 within 40 min from saliva and nasopharyngeal samples. The entire assay is executed inside a uniquely designed, inexpensive disposable microfluidic chip, where assay components and reagents have been optimized to provide precise and qualitative results and can be effectively deployed in POC settings. Furthermore, this technology could be easily adapted for other novel emerging viruses.
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Affiliation(s)
- Sandhya Sharma
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
| | - Massimo Caputi
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA;
| | - Waseem Asghar
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
- Department of Biological Sciences (Courtesy Appointment), Florida Atlantic University, Boca Raton, FL 33431, USA
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2
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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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LaBute B, Fong J, Ziaee F, Gombar R, Stover M, Beaudin T, Badalova M, Geng Q, Corchis-Scott R, Podadera A, Lago K, Xu Z, Lim F, Chiu F, Fu M, Nie X, Wu Y, Quan C, Hamm C, McKay RM, Ng K, Porter LA, Tong Y. Evaluating and optimizing Acid-pH and Direct Lysis RNA extraction for SARS-CoV-2 RNA detection in whole saliva. Sci Rep 2024; 14:7017. [PMID: 38527999 DOI: 10.1038/s41598-024-54183-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024] Open
Abstract
COVID-19 has been a global public health and economic challenge. Screening for the SARS-CoV-2 virus has been a key part of disease mitigation while the world continues to move forward, and lessons learned will benefit disease detection beyond COVID-19. Saliva specimen collection offers a less invasive, time- and cost-effective alternative to standard nasopharyngeal swabs. We optimized two different methods of saliva sample processing for RT-qPCR testing. Two methods were optimized to provide two cost-efficient ways to do testing for a minimum of four samples by pooling in a 2.0 mL tube and decrease the need for more highly trained personnel. Acid-pH-based RNA extraction method can be done without the need for expensive kits. Direct Lysis is a quick one-step reaction that can be applied quickly. Our optimized Acid-pH and Direct Lysis protocols are reliable and reproducible, detecting the beta-2 microglobulin (B2M) mRNA in saliva as an internal control from 97 to 96.7% of samples, respectively. The cycle threshold (Ct) values for B2M were significantly higher in the Direct Lysis protocol than in the Acid-pH protocol. The limit of detection for N1 gene was higher in Direct Lysis at ≤ 5 copies/μL than Acid-pH. Saliva samples collected over the course of several days from two COVID-positive individuals demonstrated Ct values for N1 that were consistently higher from Direct Lysis compared to Acid-pH. Collectively, this work supports that each of these techniques can be used to screen for SARS-CoV-2 in saliva for a cost-effective screening platform.
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Affiliation(s)
- Brayden LaBute
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Jackie Fong
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
| | - Farinaz Ziaee
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Robert Gombar
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Mathew Stover
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Terry Beaudin
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Maria Badalova
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ana Podadera
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Kyle Lago
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
| | - ZhenHuan Xu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Fievel Lim
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Felix Chiu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Minghua Fu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Xiaofeng Nie
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Yuanmin Wu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | | | - Caroline Hamm
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
- Windsor Regional Hospital, Windsor, ON, Canada
| | - R Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Kenneth Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
| | - Lisa A Porter
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada.
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada.
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada.
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada.
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4
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Henin D, Fappani C, Carmagnola D, Gori M, Pellegrini G, Colzani D, Amendola A, Perrotta M, Tanzi E, Dellavia C. COVID-19 monitoring of school personnel through molecular salivary test and dried blood spot analysis. J Glob Health 2024; 14:05004. [PMID: 38330189 PMCID: PMC10852534 DOI: 10.7189/jogh.14.05004] [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: 02/10/2024] Open
Abstract
Background When the coronavirus disease 2019 (COVID-19) pandemic broke out, most countries enforced school closures as a precautionary measure. Although COVID-19 is still present three years later, schools have been reopened. We aimed to test the association of molecular salivary testing (MST) and dried blood spot (DBS) analysis for community surveillance by investigating the immunological profile of a group of school staff during and following COVID-19 vaccination. Methods We conducted the study in a school in Milan from April 2021, when school staff were administered the first dose of vaccine against SARS-CoV-2, until the school year ended in June 2022. Each participant provided samples for MST and DBS one month (T1, W1) after receiving their first dose of vaccine. Subsequently, they collected weekly MST samples for five weeks (W2-W6), plus a DBS sample in the last week (T2). Both samples were collected one (T3), four (T4), and seven months (T5) after the administration of the second vaccine dose in May 2021. A final DBS sample was collected one year (T6) after T3. Results Sixty participants provided 327 MSTs and 251 DBSs. None of the MST samples tested positive for SARS-CoV-2 RNA during the study period. A total of 201 DBS samples tested positive for the IgG semiquantitative analysis. Negative samples were found only at T1 (20.45%) and T2 (7.32%). We observed borderline results at T1 (4.55%), T2 (7.32%), and T4 (2.70%). The anti-SARS-CoV-2 average antibody ratio increased after the second dose between T2 and T3, and the trend peaked after the third dose between T4 and T6. We performed an immunoenzymatic assay of antibodies against nucleocapsid protein on samples collected at T1 from five participants who reported having been infected before the study and from four subjects with an abnormal increase in the antibody values at T4. Two samples tested positive in the first group and two in the second one. Conclusions Our findings show that MST and DBS could be effective tools in the active surveillance of school personnel and that schools could be considered safe settings in view of SARS-CoV-2 infection. Vaccines might have contributed to case and/or symptom reduction.
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Affiliation(s)
- Dolaji Henin
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Clara Fappani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Daniela Carmagnola
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Maria Gori
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
| | - Gaia Pellegrini
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Daniela Colzani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Antonella Amendola
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre MACH (Centre for Multidisciplinary Research in Health Sciences), Università degli Studi di Milano, Milan, Italy
| | - Mariachiara Perrotta
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Tanzi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre MACH (Centre for Multidisciplinary Research in Health Sciences), Università degli Studi di Milano, Milan, Italy
| | - Claudia Dellavia
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
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5
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Jacob AA, C C C, Mohan G, Mathew R, Matteethra GC, M A, B MM, David A. Evaluation of the efficacy of tongue swab and saliva as samples for testing COVID-19 infection in symptomatic cases in comparison with nasopharyngeal swab. J Med Microbiol 2023; 72. [PMID: 37589671 DOI: 10.1099/jmm.0.001743] [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: 08/18/2023] Open
Abstract
Introduction. COVID-19 caused by SARS CoV-2 continues to be a major health concern globally. Methods for detection of the disease are necessary for public health efforts to monitor the spread of this disease as well as for detecting the emergence of new variants.Gap statement. Collection of Nasopharyngeal swab (NPS), the gold standard sample for the detection of COVID-19 infection by RT-qPCR is invasive and requires the expertise of a trained medical provider. This highlights the need for validating less invasive samples that can be self-collected without the need for trained medical provider.Aim. To validate saliva and tongue swab as potential samples for the diagnosis of COVID-19.Methodology. Adult and paediatric cases who had acute influenza like illness were enrolled in the study. The study involved comparison of Nucleic Acid Amplification Tests (NAAT) results for the detection of COVID-19 obtained by using saliva and tongue swab with that of NPS.Result and Conclusion. The sensitivity and specificity of saliva as sample for COVID-19 detection were found to be 71 and 88% respectively whereas those of tongue swab as sample were 78 and 90 %. Further validation was based on the positive and negative predictive values, the likelihood ratio, agreement percentage and the kappa statistic. The findings of the study point towards tongue swab and saliva as suitable alternative samples for the diagnosis of COVID-19 with a slightly higher accuracy and agreement for tongue swab than saliva. However considering the fatality of COVID-19, they are better suited for mass screening of people than for diagnosis.
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Affiliation(s)
- Anjali Anne Jacob
- Department of Microbiology, Believers Church Medical College Hospital, Thiruvalla, Kerala, India
- Central Research Laboratory, Believers Church Medical College Hospital, Thiruvalla, Kerala, India
| | - Cleetus C C
- Central Research Laboratory, Believers Church Medical College Hospital, Thiruvalla, Kerala, India
| | - Girija Mohan
- Department of Paediatrics, Believers Church Medical College Hospital, Thiruvalla, Kerala, India
| | - Renu Mathew
- Department of Microbiology, Believers Church Medical College Hospital, Thiruvalla, Kerala, India
| | - George Chandy Matteethra
- Central Research Laboratory, Believers Church Medical College Hospital, Thiruvalla, Kerala, India
| | - Afferedi M
- Central Research Laboratory, Believers Church Medical College Hospital, Thiruvalla, Kerala, India
| | - Manju M B
- Central Research Laboratory, Believers Church Medical College Hospital, Thiruvalla, Kerala, India
| | - Alice David
- Department of Medical Research (Epidemiology & Biostatistics), Believers Church Medical College Hospital, Thiruvalla, Kerala, India
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6
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Cardoso AG, Viltres H, Ortega GA, Phung V, Grewal R, Mozaffari H, Ahmed SR, Rajabzadeh AR, Srinivasan S. Electrochemical sensing of analytes in saliva: Challenges, progress, and perspectives. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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Raimondi S, Gandini S, Rubio Quintanares GH, Abecasis A, Lopalco PL, D’Ecclesiis O, Chiocca S, Tomezzoli E, Cutica I, Mazzoni D, Amparo N, Pingarilho M, Carmagnola D, Dallavia C, Zuccotti G, Ronchini C, Bellerba F, Dewald F, Kaiser R, Incardona F. European Cohorts of patients and schools to Advance Response to Epidemics (EuCARE): a cluster randomised interventional and observational study protocol to investigate the relationship between schools and SARS-CoV-2 infection. BMC Infect Dis 2023; 23:1. [PMID: 36597074 PMCID: PMC9808677 DOI: 10.1186/s12879-022-07947-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/13/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Contradictory results were reported on the role of school closure/reopening on the overall SARS-CoV-2 transmission rate, as well as on which kind and level of mitigation measures implemented in schools may be effective in limiting its diffusion. Some recent studies were reassuring, showing that opening did not increase the community spread, although teachers and families are worried about the high class density. On the other hand, distance learning was associated with a negative impact on learning, sociability and psychological health, especially in vulnerable children. As it becomes clear that the SARS-CoV-2 pandemic will last for a long time, there is a high need for studies and solutions to support safe schools opening based on scientific evidence of harms and benefits. The Lolli-Methode (LM) is a strategy for epidemiological surveillance and early intervention aiming at SARS-CoV-2 outbreaks' reduction in schools, relying on polymerase chain reaction analysis of saliva samples. METHODS In this cluster randomised trial protocol, we aim to determine whether the LM is useful to support schools opening and to reduce clusters and attack rates in schools, compared with the standard of care (SoC) surveillance by public health departments. This multicenter study will enrol 440 classes (around 8800 students, teachers and other personnel) from two countries, cluster randomised to LM or SoC. The samples from the pools will be collected and tested using PCR-based techniques. Test results will be combined with questionnaires filled in by children, parents, schoolteachers, and principals, concerning ongoing mitigation measures, their perceived psychological impact and other health and socio-economic information. An ancillary observational study will be carried out to study the prevalence of SARS-CoV-2 in schools, frequencies and size of clusters and attack rates, to compare the effectiveness of the different preventive measures adopted and to evaluate psychological issues in students and teachers in relation to the pandemic's containment measures. DISCUSSION By the end of this study, we will have defined and characterised the applicability of the LM for SARS-CoV-2 surveillance, as well as the impact of pandemic preventive measures on children and teachers. Trial registration International Standard Randomised Controlled Trial Number: NCT05396040, 27.05.2022.
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Affiliation(s)
- Sara Raimondi
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Sara Gandini
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gibran Horemheb Rubio Quintanares
- Institute of Virology, University Clinics of Cologne, Cologne, Germany. .,Paul Ehrlich Institut, Langen, Germany. .,Infectious Diseases Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
| | - Ana Abecasis
- grid.10772.330000000121511713Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, Lisbon, Portugal
| | - Pier Luigi Lopalco
- grid.9906.60000 0001 2289 7785Department of Biological and Environmental Sciences and Technology, University of Salento, Lecce, Italy
| | - Oriana D’Ecclesiis
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Susanna Chiocca
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Elisa Tomezzoli
- grid.15667.330000 0004 1757 0843Applied Research Division for Cognitive and Psychological Science, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Ilaria Cutica
- grid.4708.b0000 0004 1757 2822Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Davide Mazzoni
- grid.4708.b0000 0004 1757 2822Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nuno Amparo
- grid.10772.330000000121511713Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, Lisbon, Portugal ,Public Health Clusters’ Public Health Unit of Central Alentejo, Lisbon, Portugal
| | - Marta Pingarilho
- grid.10772.330000000121511713Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, Lisbon, Portugal
| | - Daniela Carmagnola
- grid.4708.b0000 0004 1757 2822Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Claudia Dallavia
- grid.4708.b0000 0004 1757 2822Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Gianvincenzo Zuccotti
- grid.414189.10000 0004 1772 7935Pediatric Department, “Vittore Buzzi” Children’s Hospital, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Biomedical and Clinical Science, University of Milan, Milan, Italy
| | - Chiara Ronchini
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Federica Bellerba
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Felix Dewald
- Institute of Virology, University Clinics of Cologne, Cologne, Germany
| | - Rolf Kaiser
- Institute of Virology, University Clinics of Cologne, Cologne, Germany
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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] [MESH Headings] [Grants] [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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Byanyima P, Kaswabuli S, Musisi E, Nabakiibi C, Zawedde J, Sanyu I, Sessolo A, Andama A, Worodria W, Huang L, Davis JL. Feasibility and Sensitivity of Saliva GeneXpert MTB/RIF Ultra for Tuberculosis Diagnosis in Adults in Uganda. Microbiol Spectr 2022; 10:e0086022. [PMID: 36154664 PMCID: PMC9603304 DOI: 10.1128/spectrum.00860-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/30/2022] [Indexed: 12/30/2022] Open
Abstract
The objective of this prospective observational study carried out at China-Uganda Friendship Hospital-Naguru in Kampala, Uganda, was to determine the performance of GeneXpert MTB/RIF Ultra (Xpert Ultra) molecular testing on saliva for active tuberculosis (TB) disease among consecutive adults undergoing TB diagnostic evaluation who were Xpert Ultra positive on sputum. We calculated sensitivity to determine TB diagnostic performance in comparison to a composite reference standard of Mycobacterium tuberculosis liquid and solid cultures on two spot sputum specimens. Xpert Ultra on a single saliva sample had a sensitivity of 90% (95% confidence interval [CI], 81 to 95%) relative to the composite sputum culture-based reference standard, similar to the composite sensitivity of 87% (95% CI, 77 to 94%) for fluorescence microscopy (FM) for acid-fast bacilli on two sputum smears. The sensitivity of salivary Xpert Ultra was 24% lower (95% CI for difference, 2 to 48%; P = 0.003) among persons living with HIV (71%; 95% CI, 44 to 90%) than among persons living without HIV (95%; 95% CI, 86 to 99%) and 46% higher (95% CI, 14 to 77%; P < 0.0001) among FM-positive (96%; 95% CI, 87 to 99%) than among FM-negative (50%; 95% CI, 19 to 81%) patients. The semiquantitative Xpert Ultra grade was systematically higher in sputum than in a paired saliva sample from the same patient. In conclusion, molecular testing of saliva for active TB diagnosis was feasible and almost as sensitive as molecular testing of sputum in a high TB burden setting. IMPORTANCE Tuberculosis is among the leading causes of morbidity and mortality worldwide, in large part because >3 million people go undiagnosed and untreated each year. Sputum has been the mainstay for TB diagnosis for over a century but can be difficult for patients to produce. In addition, the vigorous coughing required during sputum collection can lead to infection of nearby individuals and health workers. In this case-only study, applying the ultra-sensitive GeneXpert MTB/RIF Ultra molecular diagnostic assay to saliva detected 90% of culture-confirmed TB cases among 81 adults who were undergoing TB evaluation at the outpatient department of a general hospital in Uganda and tested sputum GeneXpert MTB/RIF Ultra positive. These results suggest that saliva may be a feasible and sensitive alternative to sputum for TB diagnosis, thereby meeting two key metrics proposed by the World Health Organization in its target performance profile for a nonsputum test for TB.
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Affiliation(s)
| | | | - Emmanuel Musisi
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, United Kingdom
| | | | | | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Abdul Sessolo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Alfred Andama
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - William Worodria
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, USA
- Division of HIV, Infectious Diseases, and Global Medicine, University of California San Francisco, San Francisco, California, USA
| | - J. Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, Connecticut, USA
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Kundrod KA, Natoli ME, Chang MM, Smith CA, Paul S, Ogoe D, Goh C, Santhanaraj A, Price A, Eldin KW, Patel KP, Baker E, Schmeler KM, Richards-Kortum R. Sample-to-answer, extraction-free, real-time RT-LAMP test for SARS-CoV-2 in nasopharyngeal, nasal, and saliva samples: Implications and use for surveillance testing. PLoS One 2022; 17:e0264130. [PMID: 35213596 PMCID: PMC8880874 DOI: 10.1371/journal.pone.0264130] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 02/03/2022] [Indexed: 12/19/2022] Open
Abstract
The global COVID-19 pandemic has highlighted the need for rapid, accurate and accessible nucleic acid tests to enable timely identification of infected individuals. We optimized a sample-to-answer nucleic acid test for SARS-CoV-2 that provides results in <1 hour using inexpensive and readily available reagents. The test workflow includes a simple lysis and viral inactivation protocol followed by direct isothermal amplification of viral RNA using RT-LAMP. The assay was validated using two different instruments, a portable isothermal fluorimeter and a standard thermocycler. Results of the RT-LAMP assay were compared to traditional RT-qPCR for nasopharyngeal swabs, nasal swabs, and saliva collected from a cohort of patients hospitalized due to COVID-19. For all three sample types, positive agreement with RT-LAMP performed using the isothermal fluorimeter was 100% for samples with Ct <30 and 69-91% for samples with Ct <40. Following validation, the test was successfully scaled to test the saliva of up to 400 asymptomatic individuals per day as part of the campus surveillance program at Rice University. Successful development, validation, and scaling of this sample-to-answer, extraction-free real-time RT-LAMP test for SARS-CoV-2 adds a highly adaptable tool to efforts to control the COVID-19 pandemic, and can inform test development strategies for future infectious disease threats.
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Affiliation(s)
- Kathryn A. Kundrod
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Mary E. Natoli
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Megan M. Chang
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Chelsey A. Smith
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Sai Paul
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Dereq Ogoe
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Christopher Goh
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Akshaya Santhanaraj
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Anthony Price
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Karen W. Eldin
- McGovern Medical School, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ellen Baker
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Kathleen M. Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
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Bean Extract-Based Gargle for Efficient Diagnosis of Active COVID-19 Infection Using Rapid Antigen Tests. Microbiol Spectr 2022; 10:e0161421. [PMID: 35171037 PMCID: PMC8849053 DOI: 10.1128/spectrum.01614-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The antigen-based rapid diagnostic test (Ag-RDT) using saliva specimens is fast, noninvasive, and suitable for SARS-CoV-2 self-testing, unlike nasopharyngeal swab (NPS) testing. We evaluated a novel Beanguard gargle (BG)-based virus collection method that can be applied to Ag-RDT as an alternative to the current RT-PCR with an NPS for early diagnosis of COVID-19. This clinical trial comprised 102 COVID-19-positive patients hospitalized after a governmental screening process and 100 healthy individuals. Paired NPS and BG-based saliva specimens from COVID-19 patients and healthy individuals were analyzed using NPS-RT-PCR, BG-RT-PCR, and BG-Ag-RDTs, whose diagnostic performance for detecting SARS-CoV-2 was compared. BG-Ag-RDTs showed high sensitivity (97.8%) and specificity (100%) in 45 patients within 6 days of illness and detected all cases of SARS-CoV-2 Alpha and Delta variants. In 11 asymptomatic active COVID-19 cases, both BG-Ag-RDTs and BG-RT-PCR showed sensitivities and specificities of 100%. Sensitivities of BG-Ag-RDT and BG-RT-PCR toward salivary viral detection were highly concordant, with no discrimination between symptomatic (97.0%), asymptomatic (100%), or SARS-CoV-2 variant (100%) cases. The intermolecular interactions between SARS-CoV-2 spike proteins and truncated canavalin, an active ingredient from the bean extract (BE), were observed in terms of physicochemical properties. The detachment of the SARS-CoV-2 receptor-binding domain from hACE2 increased as the BE concentration increased, allowing the release of the virus from hACE2 for early diagnosis. Using BG-based saliva specimens remarkably enhances the Ag-RDT diagnostic performance as an alternative to NPS and enables noninvasive, rapid, and accurate COVID-19 self-testing and mass screening, supporting efficient COVID-19 management. IMPORTANCE An Ag-RDT is less likely to be accepted as an initial test method for early diagnosis owing to its low sensitivity. However, our self-collection method, Ag-RDT using BG-based saliva specimens, showed significantly enhanced detection sensitivity and specificity toward SARS-CoV-2 including the Alpha and Delta variants in all patients tested within 6 days of illness. The method represents an attractive alternative to nasopharyngeal swabs for the early diagnosis of symptomatic and asymptomatic COVID-19 cases. The evidence suggests that the method could have a potential for mass screening and monitoring of COVID-19 cases.
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