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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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3
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Uddin MKM, Hossain ME, Ami JQ, Hasan R, Hasan MM, Islam A, Hasan MJ, Shaly NJ, Ahmed S, Samina P, Rahman MZ, Rahman M, Banu S. SalivaDirect: an alternative to a conventional RNA extraction protocol for molecular detection of SARS-CoV-2 in a clinical setting. Microbiol Spectr 2024; 12:e0327223. [PMID: 38014980 PMCID: PMC10783095 DOI: 10.1128/spectrum.03272-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Affordable and accessible tests for COVID-19 allow for timely disease treatment and pandemic management. SalivaDirect is a faster and easier method to implement than NPS sampling. Patients can self-collect saliva samples at home or in other non-clinical settings without the help of a healthcare professional. Sample processing in SalivaDirect is less complex and more adaptable than in conventional nucleic acid extraction methods. We found that SalivaDirect has good diagnostic performance and is ideal for large-scale testing in settings where supplies may be limited or trained healthcare professionals are unavailable.
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Affiliation(s)
| | - Mohammad Enayet Hossain
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jenifar Quaiyum Ami
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Rashedul Hasan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Md. Mahmudul Hasan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Ashabul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Md. Jahid Hasan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Nusrat Jahan Shaly
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Shahriar Ahmed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Pushpita Samina
- Centre for Health Economics and Policy Analysis, McMaster University, Hamilton, Ontario, Canada
| | - Mohammed Ziaur Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Mustafizur Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Sayera Banu
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
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Krause E, Michel J, Puyskens A, Hofmann N, Rinner T, Biere B, Dorner BG, Skiba M, Schaade L, Nitsche A. Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic. Virol J 2023; 20:139. [PMID: 37408040 DOI: 10.1186/s12985-023-02088-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Over the course of the COVID-19 pandemic, laboratories worldwide have been facing an unprecedented increase in demand for PCR testing because of the high importance of diagnostics for prevention and control of virus spread. Moreover, testing demand has been varying considerably over time, depending on the epidemiological situation, rendering efficient resource allocation difficult. Here, we present a scalable workflow which we implemented in our laboratory to increase PCR testing capacity while maintaining high flexibility regarding the number of samples to be processed. METHODS We compared the performance of five automated extraction instruments, using dilutions of SARS-CoV-2 cell culture supernatant as well as clinical samples. To increase PCR throughput, we combined the two duplex PCR reactions of our previously published SARS-CoV-2 PCR assay into one quadruplex reaction and compared their limit of detection as well as their performance on the detection of low viral loads in clinical samples. Furthermore, we developed a sample pooling protocol with either two or four samples per pool, combined with a specifically adapted SARS-CoV-2 quadruplex PCR assay, and compared the diagnostic sensitivity of pooled testing and individual testing. RESULTS All tested automated extraction instruments yielded comparable results regarding the subsequent sensitivity of SARS-CoV-2 detection by PCR. While the limit of detection of the quadruplex SARS-CoV-2 PCR assay (E-Gene assay: 28.7 genome equivalents (ge)/reaction, orf1ab assay: 32.0 ge/reaction) was slightly higher than that of our previously published duplex PCR assays (E-Gene assay: 9.8 ge/reaction, orf1ab assay: 6.6 ge/reaction), the rate of correctly identified positive patient samples was comparable for both assays. Sample pooling with optimized downstream quadruplex PCR showed no loss in diagnostic sensitivity compared to individual testing. CONCLUSION Specific adaptation of PCR assays can help overcome the potential loss of sensitivity due to higher levels of PCR multiplexing or sample dilution in pooled testing. Combining these adapted PCR assays with different sample processing strategies provides a simple and highly adjustable workflow for resource-efficient SARS-CoV-2 diagnostics. The presented principles can easily be adopted in a variety of laboratory settings as well as be adapted to pathogens other than SARS-CoV-2, making it feasible for any laboratory that conducts PCR diagnostics.
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Affiliation(s)
- Eva Krause
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany.
| | - Janine Michel
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Andreas Puyskens
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Natalie Hofmann
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Thomas Rinner
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Barbara Biere
- Department for Infectious Diseases, Unit Influenza and Other Respiratory Viruses (FG 17), Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Brigitte G Dorner
- Centre for Biological Threats and Special Pathogens, Unit Biological Toxins (ZBS 3), WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Martin Skiba
- Centre for Biological Threats and Special Pathogens, Unit Biological Toxins (ZBS 3), WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
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5
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De Santi C, Cavalleri GL, Kerrigan SW, Fitzpatrick F, McGrogan K, Gilroy J, Baxter R, Quadu V, Ryan K, Humphreys H. Screening medical students for SARS-CoV-2 to facilitate face-to-face clinical teaching and prevent onward spread to patients. J Hosp Infect 2023; 135:1-3. [PMID: 36775068 PMCID: PMC9916130 DOI: 10.1016/j.jhin.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/13/2023] [Accepted: 02/04/2023] [Indexed: 02/12/2023]
Affiliation(s)
- C De Santi
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland
| | - G L Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland; Science Foundation Ireland FutureNeuro Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - S W Kerrigan
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland
| | - F Fitzpatrick
- Department of Clinical Microbiology, RCSI University of Medicine and Healthcare Sciences, Dublin, Ireland; Department of Microbiology, Beaumont Hospital, Dublin, Ireland
| | - K McGrogan
- Mercer's Medical Centre, RCSI University of Medicine and Healthcare Sciences, Dublin, Ireland
| | - J Gilroy
- Student Academic and Regulatory Affairs, RCSI University of Medicine and Healthcare Sciences, Dublin, Ireland
| | - R Baxter
- Estate and Support Services, RCSI University of Medicine and Healthcare Sciences, Dublin, Ireland
| | - V Quadu
- Mercer's Medical Centre, RCSI University of Medicine and Healthcare Sciences, Dublin, Ireland
| | - K Ryan
- Department of Surgical Affairs, RCSI University of Medicine and Healthcare Sciences, Dublin, Ireland
| | - H Humphreys
- Department of Clinical Microbiology, RCSI University of Medicine and Healthcare Sciences, Dublin, Ireland.
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6
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McPhillips L, MacSharry J. Saliva as an alternative specimen to nasopharyngeal swabs for COVID-19 diagnosis: Review. Access Microbiol 2022; 4:acmi000366. [PMID: 36003360 PMCID: PMC9394527 DOI: 10.1099/acmi.0.000366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 04/25/2022] [Indexed: 12/12/2022] Open
Abstract
Almost 2 years ago, the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was discovered to be the causative agent of the disease COVID-19. Subsequently, SARS-CoV-2 has spread across the world infecting millions of people, resulting in the ongoing COVID-19 pandemic. The current 'gold standard' for COVID-19 diagnosis involves obtaining a nasopharyngeal swab (NPS) from the patient and testing for the presence of SARS-CoV-2 RNA in the specimen using real-time reverse transcription PCR (RT-qPCR). However, obtaining a NPS specimen is an uncomfortable and invasive procedure for the patient and is limited in its applicability to mass testing. Interest in saliva as an alternative diagnostic specimen is of increasing global research interest due to its malleability to mass testing, greater patient acceptability and overall ease of specimen collection. However, the current literature surrounding the sensitivity of saliva compared to NPS is conflicting. The aim of this review was to analyse the recent literature to assess the viability of saliva in COVID-19 diagnosis. We hypothesize that the discrepancies in the current literature are likely due to the variations in the saliva collection and processing protocols used between studies. The universal adaptation of an optimised protocol could alleviate these discrepancies and see saliva specimens be as sensitive, if not more, than NPS for COVID-19 diagnosis. Whilst saliva specimens are more complimentary to mass-testing, with the possibility of samples being collected from home, the RT-qPCR diagnostic process remains to be the rate-limiting step and therefore interest in salivary rapid antigen tests, which negate the wait-times of RT-qPCR with results available within 15-30 min, may be an answer to this.
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Affiliation(s)
- Leah McPhillips
- School of Microbiology, University College Cork, Cork, Ireland
- Present address: Department of Molecular Microbiology, The John Innes Centre, Norwich, UK
| | - John MacSharry
- School of Microbiology, University College Cork, Cork, Ireland
- School of Medicine, University College Cork, Cork, Ireland
- The APC Microbiome Ireland, University College Cork, Cork, Ireland
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7
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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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8
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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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9
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Savela ES, Viloria Winnett A, Romano AE, Porter MK, Shelby N, Akana R, Ji J, Cooper MM, Schlenker NW, Reyes JA, Carter AM, Barlow JT, Tognazzini C, Feaster M, Goh YY, Ismagilov RF. Quantitative SARS-CoV-2 Viral-Load Curves in Paired Saliva Samples and Nasal Swabs Inform Appropriate Respiratory Sampling Site and Analytical Test Sensitivity Required for Earliest Viral Detection. J Clin Microbiol 2022; 60:e0178521. [PMID: 34911366 PMCID: PMC8849374 DOI: 10.1128/jcm.01785-21] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and presymptomatic transmission, curb the spread of variants, and maximize treatment efficacy. Low-analytical-sensitivity nasal-swab testing is commonly used for surveillance and symptomatic testing, but the ability of these tests to detect the earliest stages of infection has not been established. In this study, conducted between September 2020 and June 2021 in the greater Los Angeles County, California, area, initially SARS-CoV-2-negative household contacts of individuals diagnosed with COVID-19 prospectively self-collected paired anterior-nares nasal-swab and saliva samples twice daily for viral-load quantification by high-sensitivity reverse-transcription quantitative PCR (RT-qPCR) and digital-RT-PCR assays. We captured viral-load profiles from the incidence of infection for seven individuals and compared diagnostic sensitivities between respiratory sites. Among unvaccinated persons, testing saliva with a high-analytical-sensitivity assay detected infection up to 4.5 days before viral loads in nasal swabs reached concentrations detectable by low-analytical-sensitivity nasal-swab tests. For most participants, nasal swabs reached higher peak viral loads than saliva but were undetectable or at lower loads during the first few days of infection. High-analytical-sensitivity saliva testing was most reliable for earliest detection. Our study illustrates the value of acquiring early (within hours after a negative high-sensitivity test) viral-load profiles to guide the appropriate analytical sensitivity and respiratory site for detecting earliest infections. Such data are challenging to acquire but critical to designing optimal testing strategies with emerging variants in the current pandemic and to respond to future viral pandemics.
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Affiliation(s)
- Emily S. Savela
- California Institute of Technology, Pasadena, California, USA
| | | | - Anna E. Romano
- California Institute of Technology, Pasadena, California, USA
| | | | - Natasha Shelby
- California Institute of Technology, Pasadena, California, USA
| | - Reid Akana
- California Institute of Technology, Pasadena, California, USA
| | - Jenny Ji
- California Institute of Technology, Pasadena, California, USA
| | | | | | | | | | - Jacob T. Barlow
- California Institute of Technology, Pasadena, California, USA
| | - Colten Tognazzini
- City of Pasadena Public Health Department, Pasadena, California, USA
| | - Matthew Feaster
- City of Pasadena Public Health Department, Pasadena, California, USA
| | - Ying-Ying Goh
- City of Pasadena Public Health Department, Pasadena, California, USA
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10
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De Santi C, Jacob B, Kroich P, Doyle S, Ward R, Li B, Donnelly O, Dykes A, Neelakant T, Neary D, McGuinness R, Cafferkey J, Ryan K, Quadu V, McGrogan K, Garcia Leon A, Mallon P, Fitzpatrick F, Humphreys H, De Barra E, Kerrigan SW, Cavalleri GL. Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing. HRB Open Res 2021; 4:85. [PMID: 34522839 PMCID: PMC8408542 DOI: 10.12688/hrbopenres.13353.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2021] [Indexed: 11/04/2023] Open
Abstract
Introduction: Saliva represents a less invasive alternative to nasopharyngeal swab (NPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid extraction-free method for detecting SARS-CoV2 in saliva specimens. Studies evaluating the concordance of gold standard NPS and newly developed SalivaDirect protocols are limited. The aim of our study was to to assess SalivaDirect as an alternative method for COVID-19 testing. Methods: Matching NPS and saliva samples were analysed from a cohort of symptomatic (n=127) and asymptomatic (n=181) participants recruited from hospital and university settings, respectively. RNA was extracted from NPS while saliva samples were subjected to the SalivaDirect protocol before RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using RdRP and N1 gene targets in NPS and saliva, respectively. Results: Overall we observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95% CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis of concordance demonstrated 95.5% accuracy overall for the saliva test relative to NPS, and a very high level of agreement (κ coefficient = 0.889, 95% CI 0.833-0.946) between the two sets of specimens. Fourteen of 308 samples were discordant, all from symptomatic patients. Ct values were >30 in 13/14 and >35 in 6/14 samples. No significant difference was found in the Ct values of matching NPS and saliva sample ( p=0.860). A highly significant correlation (r = 0.475, p<0.0001) was also found between the Ct values of the concordant positive saliva and NPS specimens. Conclusions: Use of saliva processed according to the SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Accurate and less invasive saliva screening is an attractive alternative to current testing methods based on NPS and would afford greater capacity to test asymptomatic populations especially in the context of frequent testing.
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Affiliation(s)
- Chiara De Santi
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Benson Jacob
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Patricia Kroich
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sean Doyle
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Rebecca Ward
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Brian Li
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Owain Donnelly
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Amy Dykes
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Trisha Neelakant
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - David Neary
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ross McGuinness
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Kieran Ryan
- Department of Surgical Affairs, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Veronica Quadu
- Mercer's Medical Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Killian McGrogan
- Mercer's Medical Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alejandro Garcia Leon
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Dublin, Ireland
| | - Patrick Mallon
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Dublin, Ireland
| | - Fidelma Fitzpatrick
- Department of Microbiology, Beaumont Hospital, Dublin, Ireland
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Hilary Humphreys
- Department of Microbiology, Beaumont Hospital, Dublin, Ireland
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Eoghan De Barra
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Infectious Diseases, Beaumont Hospital, Dublin, Ireland
| | - Steve W. Kerrigan
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
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