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Samsunder N, Sivro A, Hassan-Moosa R, Lewis L, Kara Z, Baxter C, Karim QA, Karim SA, Kharsany ABM, Naidoo K, Ngcapu S. Evaluating diagnostic accuracy of an RT-PCR test for the detection of SARS-CoV-2 in saliva. Diagn Progn Res 2024; 8:9. [PMID: 39044271 PMCID: PMC11267770 DOI: 10.1186/s41512-024-00176-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 07/01/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND AND OBJECTIVE Saliva has been proposed as a potential more convenient, cost-effective, and easier sample for diagnosing SARS-CoV-2 infections, but there is limited knowledge of the impact of saliva volumes and stages of infection on its sensitivity and specificity. METHODS In this study, we assessed the performance of SARS-CoV-2 testing in 171 saliva samples from 52 mostly mildly symptomatic patients (aged 18 to 70 years) with a positive reference standard result at screening. The samples were collected at different volumes (50, 100, 300, and 500 µl of saliva) and at different stages of the disease (at enrollment, day 7, 14, and 28 post SARS-CoV-2 diagnosis). Imperfect nasopharyngeal (NP) swab nucleic acid amplification testing was used as a reference. We used a logistic regression with generalized estimating equations to estimate sensitivity, specificity, PPV, and NPV, accounting for the correlation between repeated observations. RESULTS The sensitivity and specificity values were consistent across saliva volumes. The sensitivity of saliva samples ranged from 70.2% (95% CI, 49.3-85.0%) for 100 μl to 81.0% (95% CI, 51.9-94.4%) for 300 μl of saliva collected. The specificity values ranged between 75.8% (95% CI, 55.0-88.9%) for 50 μl and 78.8% (95% CI, 63.2-88.9%) for 100 μl saliva compared to NP swab samples. The overall percentage of positive results in NP swabs and saliva specimens remained comparable throughout the study visits. We observed no significant difference in cycle number values between saliva and NP swab specimens, irrespective of saliva volume tested. CONCLUSIONS The saliva collection offers a promising approach for population-based testing.
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Affiliation(s)
- Natasha Samsunder
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 719 Umbilo Road, Durban, 4001, South Africa
| | - Aida Sivro
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 719 Umbilo Road, Durban, 4001, South Africa
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Razia Hassan-Moosa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 719 Umbilo Road, Durban, 4001, South Africa
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 719 Umbilo Road, Durban, 4001, South Africa
| | - Zahra Kara
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 719 Umbilo Road, Durban, 4001, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 719 Umbilo Road, Durban, 4001, South Africa
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Salim Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 719 Umbilo Road, Durban, 4001, South Africa
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Ayesha B M Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 719 Umbilo Road, Durban, 4001, South Africa
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 719 Umbilo Road, Durban, 4001, South Africa
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Sinaye Ngcapu
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 719 Umbilo Road, Durban, 4001, South Africa.
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa.
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Reis de Andrade J, Scourfield E, Peswani-Sajnani SL, Poulton K, ap Rees T, Khooshemehri P, Doherty G, Ong S, Ivan IF, Goudarzi N, Gardiner I, Caine E, Maguire TJA, Leightley D, Torrico L, Gasulla A, Menendez-Vazquez A, Ortega-Prieto AM, Pickering S, Jimenez-Guardeño JM, Batra R, Rubinchik S, Tan AVF, Griffin A, Sherrin D, Papaioannou S, Trouillet C, Mischo HE, Giralt V, Wilson S, Kirk M, Neil SJD, Galao RP, Martindale J, Curtis C, Zuckerman M, Razavi R, Malim MH, Martinez-Nunez RT. KCL TEST: an open-source inspired asymptomatic SARS-CoV-2 surveillance programme in an academic institution. Biol Methods Protoc 2024; 9:bpae046. [PMID: 38993523 PMCID: PMC11238426 DOI: 10.1093/biomethods/bpae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/10/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
Rapid and accessible testing was paramount in the management of the COVID-19 pandemic. Our university established KCL TEST: a SARS-CoV-2 asymptomatic testing programme that enabled sensitive and accessible PCR testing of SARS-CoV-2 RNA in saliva. Here, we describe our learnings and provide our blueprint for launching diagnostic laboratories, particularly in low-resource settings. Between December 2020 and July 2022, we performed 158277 PCRs for our staff, students, and their household contacts, free of charge. Our average turnaround time was 16 h and 37 min from user registration to result delivery. KCL TEST combined open-source automation and in-house non-commercial reagents, which allows for rapid implementation and repurposing. Importantly, our data parallel those of the UK Office for National Statistics, though we detected a lower positive rate and virtually no delta wave. Our observations strongly support regular asymptomatic community testing as an important measure for decreasing outbreaks and providing safe working spaces. Universities can therefore provide agile, resilient, and accurate testing that reflects the infection rate and trend of the general population. Our findings call for the early integration of academic institutions in pandemic preparedness, with capabilities to rapidly deploy highly skilled staff, as well as develop, test, and accommodate efficient low-cost pipelines.
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Affiliation(s)
- Joana Reis de Andrade
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | - Edward Scourfield
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | | | - Kate Poulton
- Department of Infectious Diseases, King’s College London, London, UK
| | - Thomas ap Rees
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | | | - George Doherty
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
| | - Stephanie Ong
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
| | - Iustina-Francisca Ivan
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
| | - Negin Goudarzi
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
| | - Isaac Gardiner
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | - Estelle Caine
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | - Thomas J A Maguire
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
| | - Daniel Leightley
- Department of Population Health Sciences, School of Life Course & Population Sciences, Faculty of Life Sciences & Medicine, King’s College London, London, UK
| | | | | | | | | | - Suzanne Pickering
- Department of Infectious Diseases, King’s College London, London, UK
| | | | - Rahul Batra
- Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Sona Rubinchik
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | - Aaron V F Tan
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | - Amy Griffin
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | - David Sherrin
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | | | - Celine Trouillet
- Department of Infectious Diseases, King’s College London, London, UK
| | - Hannah E Mischo
- Department of Infectious Diseases, King’s College London, London, UK
| | - Victoriano Giralt
- Area de Sistemas, Servicio Central de Informática, University of Malaga, Malaga, Spain
| | - Samantha Wilson
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | - Martin Kirk
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, King’s College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, King’s College London, London, UK
| | - Jo Martindale
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | - Charles Curtis
- Research Management and Innovation Directorate, KCL TEST, King’s College London, London, UK
| | - Mark Zuckerman
- South London Specialist Virology Centre, King’s College Hospital, London, UK
| | - Reza Razavi
- School of Biomedical Engineering and Imaging Sciences, King’s College London, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, King’s College London, London, UK
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3
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Powell EA, Greninger AL, Marlowe EM, Naccache SN, Doern CD. Proceedings of the Clinical Microbiology Open 2023: discussions about pandemic preparedness. J Clin Microbiol 2024; 62:e0014424. [PMID: 38775470 PMCID: PMC11237618 DOI: 10.1128/jcm.00144-24] [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: 05/31/2024] Open
Abstract
The 4th Clinical Microbiology Open (CMO) took place in Carlsbad, California, on 10 and 11 February 2023. This event facilitated discussion between clinical and public health laboratory directors, government agencies, and industry representatives from the companies that make up ASM's Corporate Council. While many topics were discussed, much of the discussion focused on pandemic preparedness. There were four major questions addressed: (i) When is the perfect the enemy of good in pandemic testing? (ii) What other types of pathogens might cause another pandemic and how would this affect laboratory response? (iii) What research is needed to better understand the effectiveness of the pandemic response? (iv) What have we learned about the utility of self and at-home testing in future pandemics? This review serves as a summary of these discussions.
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Affiliation(s)
- Eleanor A. Powell
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA
| | | | | | - Christopher D. Doern
- Department of Pathology, Virginia Commonwealth University Health System, Richmond, Virginia, USA
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4
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Tornberg EC, Tomlinson A, Oshiro NTT, Derfalie E, Ali RA, Curlin ME. Comparative Performance of COVID-19 Test Methods in Healthcare Workers during the Omicron Wave. Diagnostics (Basel) 2024; 14:986. [PMID: 38786285 PMCID: PMC11120500 DOI: 10.3390/diagnostics14100986] [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: 02/28/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The COVID-19 pandemic presents unique requirements for accessible, reliable testing, and many testing platforms and sampling techniques have been developed over the course of the pandemic. Not all test methods have been systematically compared to each other or a common gold standard, and the performance of tests developed in the early epidemic have not been consistently re-evaluated in the context of new variants. We conducted a repeated measures study with adult healthcare workers presenting for SARS-CoV-2 testing. Participants were tested using seven testing modalities. Test sensitivity was compared using any positive PCR test as the gold standard. A total of 325 individuals participated in the study. PCR tests were the most sensitive (saliva PCR 0.957 ± 0.048, nasopharyngeal PCR 0.877 ± 0.075, oropharyngeal PCR 0.849 ± 0.082). Standard nasal rapid antigen tests were less sensitive but roughly equivalent (BinaxNOW 0.613 ± 0.110, iHealth 0.627 ± 0.109). Oropharyngeal rapid antigen tests were the least sensitive (BinaxNOW 0.400 ± 0.111, iHealth brands 0.311 ± 0.105). PCR remains the most sensitive testing modality for the diagnosis of COVID-19 and saliva PCR is significantly more sensitive than oropharyngeal PCR and equivalent to nasopharyngeal PCR. Nasal AgRDTs are less sensitive than PCR but have benefits in convenience and accessibility. Saliva-based PCR testing is a viable alternative to traditional swab-based PCR testing for the diagnosis of COVID-19.
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Affiliation(s)
- Emma C. Tornberg
- Department of Medicine, Division of Infectious Diseases, Oregon Health and Sciences University, Portland, OR 97239, USA (M.E.C.)
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5
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Piubelli C, Treggiari D, Lavezzari D, Deiana M, Dishnica K, Tosato EMS, Mazzi C, Cattaneo P, Mori A, Pomari E, Nicolini L, Leonardi M, Perandin F, Formenti F, Giorgetti A, Conti A, Capobianchi MR, Gobbi FG, Castilletti C. Wide Real-Life Data Support Reduced Sensitivity of Antigen Tests for Omicron SARS-CoV-2 Infections. Viruses 2024; 16:657. [PMID: 38793539 PMCID: PMC11125898 DOI: 10.3390/v16050657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
With the continuous spread of new SARS-CoV-2 variants of concern (VOCs), the monitoring of diagnostic test performances is mandatory. We evaluated the changes in antigen diagnostic tests' (ADTs) accuracy along the Delta to Omicron VOCs transition, exploring the N protein mutations possibly affecting ADT sensitivity and assessing the best sampling site for the diagnosis of Omicron infections. In total, 5175 subjects were enrolled from 1 October 2021 to 15 July 2022. The inclusion criteria were SARS-CoV-2 ADT combined with a same-day RT-PCR swab test. For the sampling site analysis, 61 patients were prospectively recruited during the Omicron period for nasal and oral swab analyses by RT-PCR. Next-Generation Sequencing data were obtained to evaluate the different sublineages. Using RT-PCR as a reference, 387 subjects resulted in becoming infected and the overall sensitivity of the ADT decreased from 63% in the Delta period to 33% in the Omicron period. This decrease was highly statistically significant (p < 0.001), and no decrease in viral load was detected at the RNA level. The nasal site presented a significantly higher viral load than the oral site during the Omicron wave. The reduced detection rate of Omicron infections by ADT should be considered in the global testing strategy to preserve accurate diagnoses across the changing SARS-CoV-2 variants.
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Affiliation(s)
- Chiara Piubelli
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Davide Treggiari
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Denise Lavezzari
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Michela Deiana
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Klevia Dishnica
- Department of Biotechnology, University of Verona, 37124 Verona, Italy
| | | | - Cristina Mazzi
- Centre for Clinical Research, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy;
| | - Paolo Cattaneo
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Antonio Mori
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Elena Pomari
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Lavinia Nicolini
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Martina Leonardi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Francesca Perandin
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Fabio Formenti
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | | | - Antonio Conti
- Clinical Analysis Laboratory and Transfusional Service, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy
| | - Maria Rosaria Capobianchi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Federico Giovanni Gobbi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
| | - Concetta Castilletti
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore—Don Calabria Hospital, Negrar di Valpolicella, 37124 Verona, Italy (L.N.)
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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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7
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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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8
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Samsunder N, Devnarain N, Sivro A, Kharsany ABM. The Performance of Diagnostic Tests for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the South African Population: A Scoping Review. Trop Med Infect Dis 2023; 8:514. [PMID: 38133446 PMCID: PMC10748306 DOI: 10.3390/tropicalmed8120514] [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: 10/16/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
To determine the performance and reliability of diagnostic tests for the identification of SARS-CoV-2 infection in South Africa, we conducted a scoping review to identify published studies undertaken in the English language from March 2020 to August 2022 that evaluated the performance of antigen- and antibody-based diagnostic tests for SARS-CoV-2 in South Africa. We identified 17 relevant peer-reviewed articles; six reported on SARS-CoV-2 gene and/or antigen detection whilst 11 reported on antibody detection. Of the SARS-CoV-2 gene and/or antigen-based tests, sensitivity ranged from 40% to 100%, whilst for the antibody-based tests, sensitivity ranged from 13% to 100%. All tests evaluated were highly dependent on the stage of infection and the timing of sample collection. This scoping review demonstrated that no single SARS-CoV-2 gene and/or antigen- or antibody-based assay was sufficiently sensitive and specific simultaneously. The sensitivity of the tests was highly dependent on the timing of sample collection with respect to SARS-CoV-2 infection. In the case of SARS-CoV-2 gene and/or antigen detection, the earlier the collection of samples, the greater the sensitivity, while antibody detection tests showed better sensitivity using samples from later stages of infection.
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Affiliation(s)
- Natasha Samsunder
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa; (N.S.); (N.D.); (A.S.)
| | - Nikita Devnarain
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa; (N.S.); (N.D.); (A.S.)
- School of Health Science, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Aida Sivro
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa; (N.S.); (N.D.); (A.S.)
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4013, South Africa
- JC Wilt Infectious Disease Research Centre, National Microbiology laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ayesha B. M. Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa; (N.S.); (N.D.); (A.S.)
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4013, South Africa
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9
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Faruque MRJ, Bikker FJ, Laine ML. Comparing SARS-CoV-2 Viral Load in Human Saliva to Oropharyngeal Swabs, Nasopharyngeal Swabs, and Sputum: A Systematic Review and Meta-Analysis. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:5807370. [PMID: 37600753 PMCID: PMC10435302 DOI: 10.1155/2023/5807370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/04/2022] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
Abstract
A systematic review and meta-analysis were conducted to investigate the SARS-CoV-2 viral load in human saliva and compared it with the loads in oropharyngeal swabs, nasopharyngeal swabs, and sputum. In addition, the salivary viral loads of symptomatic and asymptomatic COVID-19 patients were compared. Searches were conducted using four electronic databases: PubMed, Embase, Scopus, and Web of Science, for studies published on SARS-CoV-2 loads expressed by CT values or copies/mL RNA. Three reviewers evaluated the included studies to confirm eligibility and assessed the risk of bias. A total of 37 studies were included. Mean CT values in saliva ranged from 21.5 to 39.6 and mean copies/mL RNA ranged from 1.91 × 101 to 6.98 × 1011. Meta-analysis revealed no significant differences in SARS-CoV-2 load in saliva compared to oropharyngeal swabs, nasopharyngeal swabs, and sputum. In addition, no significant differences were observed in the salivary viral load of symptomatic and asymptomatic COVID-19 patients. We conclude that saliva specimen can be used as an alternative for SARS-CoV-2 detection in oropharyngeal swabs, nasopharyngeal swabs, and sputum.
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Affiliation(s)
- Mouri R. J. Faruque
- Department of Periodontology, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
| | - Floris J. Bikker
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
| | - Marja L. Laine
- Department of Periodontology, Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, Netherlands
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10
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Merling MR, Williams A, Mahfooz NS, Ruane-Foster M, Smith J, Jahnes J, Ayers LW, Bazan JA, Norris A, Norris Turner A, Oglesbee M, Faith SA, Quam MB, Robinson RT. The emergence of SARS-CoV-2 lineages and associated saliva antibody responses among asymptomatic individuals in a large university community. PLoS Pathog 2023; 19:e1011596. [PMID: 37603565 PMCID: PMC10470930 DOI: 10.1371/journal.ppat.1011596] [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: 02/15/2023] [Revised: 08/31/2023] [Accepted: 08/02/2023] [Indexed: 08/23/2023] Open
Abstract
SARS-CoV-2 (CoV2) infected, asymptomatic individuals are an important contributor to COVID transmission. CoV2-specific immunoglobulin (Ig)-as generated by the immune system following infection or vaccination-has helped limit CoV2 transmission from asymptomatic individuals to susceptible populations (e.g. elderly). Here, we describe the relationships between COVID incidence and CoV2 lineage, viral load, saliva Ig levels (CoV2-specific IgM, IgA and IgG), and ACE2 binding inhibition capacity in asymptomatic individuals between January 2021 and May 2022. These data were generated as part of a large university COVID monitoring program in Ohio, United States of America, and demonstrate that COVID incidence among asymptomatic individuals occurred in waves which mirrored those in surrounding regions, with saliva CoV2 viral loads becoming progressively higher in our community until vaccine mandates were established. Among the unvaccinated, infection with each CoV2 lineage (pre-Omicron) resulted in saliva Spike-specific IgM, IgA, and IgG responses, the latter increasing significantly post-infection and being more pronounced than N-specific IgG responses. Vaccination resulted in significantly higher Spike-specific IgG levels compared to unvaccinated infected individuals, and uninfected vaccinees' saliva was more capable of inhibiting Spike function. Vaccinees with breakthrough Delta infections had Spike-specific IgG levels comparable to those of uninfected vaccinees; however, their ability to inhibit Spike binding was diminished. These data are consistent with COVID vaccines having achieved hoped-for effects in our community, including the generation of mucosal antibodies that inhibit Spike and lower community viral loads, and suggest breakthrough Delta infections were not due to an absence of vaccine-elicited Ig, but instead limited Spike binding activity in the face of high community viral loads.
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Affiliation(s)
- Marlena R. Merling
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Amanda Williams
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, Ohio, United States of America
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Najmus S. Mahfooz
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Marisa Ruane-Foster
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Jacob Smith
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Jeff Jahnes
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Leona W. Ayers
- Department of Pathology, The Ohio State University, Columbus, Ohio, United States of America
| | - Jose A. Bazan
- Division of Infectious Disease, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Alison Norris
- Division of Infectious Disease, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Department of Epidemiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Abigail Norris Turner
- Division of Infectious Disease, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Michael Oglesbee
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Seth A. Faith
- Infectious Disease Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Mikkel B. Quam
- Department of Epidemiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Richard T. Robinson
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, Ohio, United States of America
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11
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Ahti J, Österback R, Keskitalo A, Mokkala K, Vidbäck S, Veikkolainen V, Vuorinen T, Peltola V, Hakanen AJ, Waris M, Laine M. Diagnostic Performance and Tolerability of Saliva and Nasopharyngeal Swab Specimens in the Detection of SARS-CoV-2 by RT-PCR. Microbiol Spectr 2023; 11:e0532422. [PMID: 37093085 PMCID: PMC10269602 DOI: 10.1128/spectrum.05324-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023] Open
Abstract
Saliva is a promising alternative for a nasopharyngeal swab (NPS) in specimen collection to detect SARS-CoV-2. We compared the diagnostic performance and tolerability of saliva collection versus NPS in a clinical setting. Paired NPS and saliva specimens were collected sequentially from participants (n = 250) at the Turku University Hospital drive-in coronavirus testing station in the spring of 2022, with Omicron BA.2 as the dominant SARS-CoV-2 variant. Discomfort and preference for the sampling method were assessed. The specimens were analyzed for SARS-CoV-2 using real-time multiplex reverse transcriptase PCR (RT-PCR) with a laboratory-developed test (LDT) and two commercial kits (PerkinElmer SARS-CoV-2 and PerkinElmer SARS-CoV-2 Plus) for several target genes. Among the 250 participants, 246 had respiratory symptoms. With LDT, SARS-CoV-2 was detected in 135 and 134 participants from NPS and saliva, respectively. Of the 250 specimens, 11 gave a discordant outcome, resulting in excellent agreement between the specimen types (Cohen's kappa coefficient of 0.911; P = 0.763). The cycle threshold (CT) values of LDT and commercial kit target genes were significantly lower from NPS than from saliva. A total of 172 (69%) participants assessed saliva sampling as more tolerable than NPS (P < 0.0001). Our findings present saliva as an applicable alternative for SARS-CoV-2 diagnostics. However, the lower CT values obtained from NPS indicate that NPS may be a slightly more sensitive specimen type. Participants preferred saliva sampling, although delivering an adequate volume of saliva was challenging for some participants. IMPORTANCE The extensive testing of SARS-CoV-2 is vital in controlling the spread of COVID-19. The reference standard for specimen collection is a nasopharyngeal swab (NPS). However, the discomfort of NPS sampling, the risk of nosocomial infections, and global material shortages have accelerated the development of alternative testing methods. Our study demonstrates that patients tolerate saliva sampling better than NPS. Of importance, although the RT-PCR qualitative test results seem to correspond between NPS and saliva, we show significantly lower CT values for NPS, compared to saliva, thus contradicting the suggested superiority of the saliva specimen over NPS in the detection of the Omicron variants of SARS-CoV-2. Future research is still required to enable individual planning for specimen collection and to determine the effects of different SARS-CoV-2 variants on the sensitivity of the saliva matrix.
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Affiliation(s)
- Jaakko Ahti
- Department of Paediatrics and Adolescent Medicine, University of Turku, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Riikka Österback
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anniina Keskitalo
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | | | | | - Tytti Vuorinen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ville Peltola
- Department of Paediatrics and Adolescent Medicine, University of Turku, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Antti J. Hakanen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Matti Waris
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Miia Laine
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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12
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Bordi L, Sberna G, Lalle E, Fabeni L, Mazzotta V, Lanini S, Corpolongo A, Garbuglia AR, Nicastri E, Girardi E, Vaia F, Antinori A, Maggi F. Comparison of SARS-CoV-2 Detection in Nasopharyngeal Swab and Saliva Samples from Patients Infected with Omicron Variant. Int J Mol Sci 2023; 24:ijms24054847. [PMID: 36902277 PMCID: PMC10003189 DOI: 10.3390/ijms24054847] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
To compare the detection of the SARS-CoV-2 Omicron variant in nasopharyngeal-swab (NPS) and oral saliva samples. 255 samples were obtained from 85 Omicron-infected patients. SARS-CoV-2 load was measured in the NPS and saliva samples by using Simplexa™ COVID-19 direct and Alinity m SARS-CoV-2 AMP assays. Results obtained with the two diagnostic platforms showed very good inter-assay concordance (91.4 and 82.4% for saliva and NPS samples, respectively) and a significant correlation among cycle threshold (Ct) values. Both platforms revealed a highly significant correlation among Ct obtained in the two matrices. Although the median Ct value was lower in NPS than in saliva samples, the Ct drop was comparable in size for both types of samples after 7 days of antiviral treatment of the Omicron-infected patients. Our result demonstrates that the detection of the SARS-CoV-2 Omicron variant is not influenced by the type of sample used for PCR analysis, and that saliva can be used as an alternative specimen for detection and follow-up of Omicron-infected patients.
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Affiliation(s)
- Licia Bordi
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
- Correspondence: ; Tel.: +39-0655170693
| | - Giuseppe Sberna
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Eleonora Lalle
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Valentina Mazzotta
- Clinical and Research Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Simone Lanini
- Clinical and Research Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Angela Corpolongo
- Clinical and Research Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Anna Rosa Garbuglia
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Emanuele Nicastri
- Clinical and Research Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Francesco Vaia
- General and Health Management Direction, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Andrea Antinori
- Clinical and Research Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
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13
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SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with COVID-19. Diagnostics (Basel) 2023; 13:diagnostics13030559. [PMID: 36766664 PMCID: PMC9913917 DOI: 10.3390/diagnostics13030559] [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: 01/06/2023] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on 26 November 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. The reverse transcription-polymerase chain reaction (RT-PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. Mounting evidence has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC.
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14
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Migueres M, Mansuy JM, Vasseur S, Claverie N, Lougarre C, Soulier F, Trémeaux P, Izopet J. Omicron Wave SARS-CoV-2 Diagnosis: Evaluation of Saliva, Anterior Nasal, and Nasopharyngeal Swab Samples. Microbiol Spectr 2022; 10:e0252122. [PMID: 36318040 PMCID: PMC9769796 DOI: 10.1128/spectrum.02521-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
The Omicron variant differs from earlier strains of SARS-CoV-2 in the way it enters host cells and grows in vitro. We therefore reevaluated its diagnosis using saliva, nasopharyngeal swab (NPs), and anterior nasal swab (ANs) specimens from 202 individuals (64.9% symptomatic) tested at the Toulouse University Hospital SARS-CoV-2 drive-through testing center. All tests were done with the Thermo Fisher TaqPath COVID-19 reverse transcription-PCR (RT-PCR) kit. Overall, 92 subjects (45.5%) had one or more positive specimens. Global sensitivities of saliva, NPs, and ANs were 94.6%, 90.2%, and 82.6%, respectively. Saliva provided significantly greater sensitivity among symptomatic patients tested within 5 days of symptom onset (100%) than did ANs (83.1%) or NPs (89.8%). We obtained follow-up samples for 7/20 individuals with discordant results. Among them, 5 symptomatic patients were diagnosed positive on saliva sample only, soon after symptom onset; NPs and ANs became positive only later. Thus, saliva samples are effective tools for the detection of the Omicron variant. In addition to its many advantages, such as improved patient acceptance and reduced cost, saliva sampling could help limit viral spread through earlier viral detection. IMPORTANCE Diagnostic testing for SARS-CoV-2 is an essential component of the global strategy for the prevention and control of COVID-19. Since the beginning of the pandemic, numerous studies have evaluated the diagnostic sensitivity of different respiratory and oral specimens for SARS-CoV-2 detection. The pandemic has been since dominated by the emergence of new variants, the latest being the Omicron variant characterized by numerous mutations and changes in host tropism in vitro that might affect the diagnostic performance of tests depending on the sampling location. In this prospective study, we evaluated the clinical performance of NPs, ANs, and saliva for SARS-CoV-2 diagnosis during the Omicron wave. Our results highlight the effectiveness of saliva-based RT-PCR for the early detection of the Omicron variant. These findings may help to refine guidelines and support the use of a highly sensitive diagnostic method that allows earlier diagnosis, when transmission is the most critical.
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Affiliation(s)
- Marion Migueres
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jean-Michel Mansuy
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
| | - Sandrine Vasseur
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Nicolas Claverie
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Catherine Lougarre
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Françoise Soulier
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Pauline Trémeaux
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
| | - Jacques Izopet
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
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15
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Salmona M, Chaix ML, Feghoul L, Mahjoub N, Maylin S, Schnepf N, Jacquier H, Walle EM, Helary M, Mellon G, Osinski N, Zebiche W, Achili Y, Amarsy R, Mahé V, Le Goff J, Delaugerre C. Detection of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs According to Viral Variants. Microbiol Spectr 2022; 10:e0213322. [PMID: 36346252 PMCID: PMC9769595 DOI: 10.1128/spectrum.02133-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
The genome of the Omicron variant of concern (VOC) contains more than 50 mutations, many of which have been associated with increased transmissibility, differing disease severity, and the potential to elute immune responses acquired after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination or infection with previous VOCs. Due to a better tropism for the upper respiratory tract, it was suggested that the detection of the Omicron variant could be preferred in saliva, compared to nasopharyngeal swabs (NPS). Our objective was to compare the SARS-CoV-2 levels in saliva fluid and NPS to estimated Ct values, according to the main SARS-CoV-2 variants circulating in France since the beginning of 2021. We analyzed 1,289 positive reverse transcription-polymerase chain reaction (RT-PCR) results during the three major waves: Alpha, Delta, and Omicron. NPS and saliva sampling were performed for 909 (71%) and 380 (29%) cases, respectively. The Ct values were significantly lower in the NPS samples than in the saliva samples for the three main VOCs. Still, the difference was less pronounced with the Omicron variant than for the Alpha and Delta variants. In contrast, in the saliva samples, Ct values were significantly lower for the Omicron variant than for the Delta (difference of -2.7 Ct) and the Alpha (difference of -3.0 Ct) variants, confirming a higher viral load in saliva. To conclude, the higher viral load in saliva was evidenced for the Omicron variant, compared to the Alpha and Delta variants, suggesting that established diagnostic methods might require revalidation with the emergence of novel variants. IMPORTANCE Established methods for SARS-CoV-2 diagnostics might require revalidation with the emergence of novel variants. This is important for screening strategy programs and for the investigation of the characteristics of new variants in terms of tropism modification and increased viral burden leading to its spread. SARS-CoV-2 RT-PCR screening on saliva samples reported lower but acceptable performance, compared to nasopharyngeal samples. Due to a better tropism for the upper respiratory tract, it was suggested that the detection of the Omicron variant could be preferred in saliva, compared to nasopharyngeal swabs. Our study analyzed 1,289 positive RT-PCR results during the three major waves in France: Alpha, Delta, and Omicron. Our findings also showed a higher viral load in saliva for the Omicron variant, compared to the Alpha and Delta variants.
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Affiliation(s)
- Maud Salmona
- Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
- Université Paris Cité, INSERM U976, Equipe INSIGHT, Paris, France
| | - Marie-Laure Chaix
- Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
- Université Paris Cité, INSERM, Paris, France
| | - Linda Feghoul
- Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
- Université Paris Cité, INSERM U976, Equipe INSIGHT, Paris, France
| | - Nadia Mahjoub
- Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
| | - Sarah Maylin
- Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
| | - Nathalie Schnepf
- Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
| | - Hervé Jacquier
- Service de Bactériologie-Hygiène, Hôpitaux Universitaires Saint-Louis - Lariboisière - Fernand Widal, Paris, France
- Université Paris Cité, IAME UMR 1137, INSERM, Paris, France
| | - Eve-Marie Walle
- Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
| | - Marion Helary
- Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
| | - Guillaume Mellon
- Équipe Opérationnelle d’Hygiène, AP-HP, Hôpital Saint Louis, Paris, France
| | - Nathalie Osinski
- Équipe Opérationnelle d’Hygiène, AP-HP, Hôpital Saint Louis, Paris, France
| | - Widad Zebiche
- Équipe Opérationnelle d’Hygiène, AP-HP, Hôpital Saint Louis, Paris, France
| | - Yacine Achili
- Service Central de Santé au Travail, AP-HP, Hôpital Saint Louis, Paris, France
| | - Rishma Amarsy
- Equipe Opérationnelle d’Hygiène, AP-HP, Hôpitaux Lariboisière-Fernand Widal, Paris, France
| | - Véronique Mahé
- Service Central de Santé au Travail, AP-HP, Hôpital Saint Louis, Paris, France
| | - Jérôme Le Goff
- Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
- Université Paris Cité, INSERM U976, Equipe INSIGHT, Paris, France
| | - Constance Delaugerre
- Laboratoire de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
- Université Paris Cité, INSERM, Paris, France
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16
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Clinical performance of SARS-CoV-2 detection on the cobas Liat using water gargle samples. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100108. [PMID: 36117531 PMCID: PMC9468300 DOI: 10.1016/j.jcvp.2022.100108] [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: 08/04/2022] [Revised: 09/04/2022] [Accepted: 09/12/2022] [Indexed: 11/22/2022] Open
Abstract
Spring water gargle (SWG) is a suitable, non-invasive, alternative specimen for SARS-CoV-2 detection by RT-PCR. This study sought to evaluate the performance of the cobas Liat point-of-care system for the detection of SARS-CoV-2 in SWG samples. SWG samples and standard oral and nasopharyngeal swab (ONPS) were collected simultaneously from participants in a COVID-19 screening clinic, in November and December 2020. Both sample types were analyzed in parallel on the cobas Liat platform and with the Seegene Allplex 2019-nCoV assay. Among the 110 participants, 53% had compatible symptoms and 71% had a contact with a confirmed COVID-19 case. Only two (1.8%) individuals had neither symptoms nor contact. Amongst 110 paired samples, 25 (23%) were positive for SARS-CoV-2 on the cobas Liat for a least one sample type, with a kappa coefficient of 0.92. Agreement between the cobas Liat platform and the Seegene assay was also excellent (kappa coefficient values of 0.94 and 0.95). Two SWG samples failed to provide a positive result when their ONPS pair was positive, but their cycle threshold (Ct) values were >35 on the Seegene assay, reflecting a low viral load. Overall, the performance of the cobas Liat platform is excellent for the detection of SARS-CoV-2 in SWG samples in a high pre-test probability population.
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Mohammadi M, Antoine D, Vitt M, Dickie JM, Sultana Jyoti S, Wall JG, Johnson PA, Wawrousek KE. A fast, ultrasensitive SERS immunoassay to detect SARS-CoV-2 in saliva. Anal Chim Acta 2022; 1229:340290. [PMID: 36156215 PMCID: PMC9395977 DOI: 10.1016/j.aca.2022.340290] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 01/13/2023]
Abstract
The COVID-19 pandemic has emphasized the need for accurate, rapid, point-of-care diagnostics to control disease transmission. We have developed a simple, ultrasensitive single-particle surface-enhanced Raman spectroscopy (SERS) immunoassay to detect the SARS-CoV-2 spike protein in saliva. This assay relies on the use of single chain Fv (scFv) recombinant antibody expressed in E. coli to bind the SARS-CoV-2 spike protein. Recombinant scFv labeled with a SERS-active dye in solution is mixed with unlabeled scFv conjugated to gold-coated magnetic nanoparticles and a sample to be tested. In the presence of the SARS-CoV-2 spike protein, immunocomplexes form and concentrate the labeled scFv close to the gold surface of the nanoparticles, causing an increased SERS signal. The assay detects inactivated SARS-CoV-2 virus and spike protein in saliva at concentrations of 1.94 × 103 genomes mL-1 and 4.7 fg mL-1, respectively, making this direct detection antigen test only 2-3 times less sensitive than some qRT-PCR tests. All tested SARS-CoV-2 spike proteins, including those from alpha, beta, gamma, delta, and omicron variants, were detected without recognition of the closely related SARS and MERS spike proteins. This 30 min, no-wash assay requires only mixing, a magnetic separation step, and signal measurements using a hand-held, battery-powered Raman spectrometer, making this assay ideal for ultrasensitive detection of the SARS-CoV-2 virus at the point-of-care.
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Affiliation(s)
- Moein Mohammadi
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA
| | - Delphine Antoine
- Microbiology, School of Biological and Chemical Sciences, and SFI Centre for Medical Devices (CÚRAM), University of Galway, Galway H91 TK33, Ireland
| | - Madison Vitt
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA
| | - Julia Marie Dickie
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA
| | - Sharmin Sultana Jyoti
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA
| | - J Gerard Wall
- Microbiology, School of Biological and Chemical Sciences, and SFI Centre for Medical Devices (CÚRAM), University of Galway, Galway H91 TK33, Ireland
| | - Patrick A Johnson
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA
| | - Karen E Wawrousek
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA.
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