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Abreu H, Royer CA, Poitevin CG, Kohler AF, Rodrigues AC, Raboni SM, Nogueira MB, Cardoso PH, Arruda MB, Baptista PADS, Bonatto AC, Gradia DF, Adamoski D, Maltempi de Souza E, Carvalho de Oliveira J. Influenza A, like Omicron SARS-CoV-2, Is Similarly Detected in Saliva or Nasopharyngeal Samples via RT-qPCR. Viruses 2023; 15:2352. [PMID: 38140593 PMCID: PMC10747790 DOI: 10.3390/v15122352] [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: 10/10/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 12/24/2023] Open
Abstract
After the Coronavirus pandemic, the importance of virus surveillance was highlighted, reinforcing the constant necessity of discussing and updating the methods for collection and diagnoses, including for other respiratory viruses. Although the nasopharyngeal swab is the gold-standard sample for detecting and genotyping SARS-CoV-2 and Influenza viruses, its collection is uncomfortable and requires specialized teams, which can be costly. During the pandemic, non-invasive saliva samples proved to be a suitable alternative for SARS-CoV-2 diagnosis, but for Influenza virus the use of this sample source is not recognized yet. In addition, most SARS-CoV-2 comparisons were conducted before the Omicron variant emerged. Here, we aimed to compare Influenza A and Omicron RT-qPCR analysis of nasopharyngeal swabs and saliva self-collection in paired samples from 663 individuals. We found that both nasopharyngeal swab and saliva collection are efficient for the diagnosis of Omicron (including sub-lineages) and for Influenza A, with high sensitivity and accuracy (>90%). The kappa index is 0.938 for Influenza A and 0.905 for SARS-CoV-2. These results showed excellent agreement between the two samples reinforcing saliva samples as a reliable source for detecting Omicron and highlighting saliva as a valid sample source for Influenza detection, considering this cheaper and more comfortable alternative.
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Affiliation(s)
- Hellen Abreu
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil; (H.A.); (C.A.R.); (C.G.P.); (A.F.K.); (A.C.R.); (A.C.B.); (D.F.G.)
| | - Carla Adriane Royer
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil; (H.A.); (C.A.R.); (C.G.P.); (A.F.K.); (A.C.R.); (A.C.B.); (D.F.G.)
| | - Carolina Gracia Poitevin
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil; (H.A.); (C.A.R.); (C.G.P.); (A.F.K.); (A.C.R.); (A.C.B.); (D.F.G.)
| | - Ana Flávia Kohler
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil; (H.A.); (C.A.R.); (C.G.P.); (A.F.K.); (A.C.R.); (A.C.B.); (D.F.G.)
| | - Ana Carolina Rodrigues
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil; (H.A.); (C.A.R.); (C.G.P.); (A.F.K.); (A.C.R.); (A.C.B.); (D.F.G.)
| | - Sonia Mara Raboni
- Virology and Molecular Biology Research Laboratory, Federal University of Parana, Curitiba 80030-110, Brazil; (S.M.R.); (M.B.N.)
| | - Meri Bordignon Nogueira
- Virology and Molecular Biology Research Laboratory, Federal University of Parana, Curitiba 80030-110, Brazil; (S.M.R.); (M.B.N.)
| | - Pedro Henrique Cardoso
- Institute of Technology in Immunobiology Bio-Manguinhos, Oswaldo Cruz Foundation/Fiocruz, Rio de Janeiro 21040-900, Brazil; (P.H.C.); (M.B.A.); (P.A.d.S.B.)
| | - Monica Barcellos Arruda
- Institute of Technology in Immunobiology Bio-Manguinhos, Oswaldo Cruz Foundation/Fiocruz, Rio de Janeiro 21040-900, Brazil; (P.H.C.); (M.B.A.); (P.A.d.S.B.)
| | - Patrícia Alvarez da Silva Baptista
- Institute of Technology in Immunobiology Bio-Manguinhos, Oswaldo Cruz Foundation/Fiocruz, Rio de Janeiro 21040-900, Brazil; (P.H.C.); (M.B.A.); (P.A.d.S.B.)
| | - Ana Claudia Bonatto
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil; (H.A.); (C.A.R.); (C.G.P.); (A.F.K.); (A.C.R.); (A.C.B.); (D.F.G.)
| | - Daniela Fiori Gradia
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil; (H.A.); (C.A.R.); (C.G.P.); (A.F.K.); (A.C.R.); (A.C.B.); (D.F.G.)
| | - Douglas Adamoski
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, Brazil;
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba 81530-000, Brazil;
| | - Jaqueline Carvalho de Oliveira
- Department of Genetics, Federal University of Parana, Curitiba 81531-980, Brazil; (H.A.); (C.A.R.); (C.G.P.); (A.F.K.); (A.C.R.); (A.C.B.); (D.F.G.)
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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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3
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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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Wagner K, Fox P, Gordon E, Hahn W, Olsen K, Markham A, Buglewicz D, Selemenakis P, Lessard A, Goldstein D, Threatt A, Davis L, Miller-Dawson J, Stockett H, Sanders H, Rugh K, Turner H, Remias M, Williams M, Chavez J, Galindo G, Cialek C, Koch A, Fout A, Fosdick B, Broeckling B, Zabel MD. A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva. Sci Rep 2023; 13:3075. [PMID: 36813822 PMCID: PMC9944410 DOI: 10.1038/s41598-023-29858-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/11/2023] [Indexed: 02/24/2023] Open
Abstract
In response to the SARS-CoV-2 pandemic, we developed a multiplexed, paired-pool droplet digital PCR (MP4) screening assay. Key features of our assay are the use of minimally processed saliva, 8-sample paired pools, and reverse-transcription droplet digital PCR (RT-ddPCR) targeting the SARS-CoV-2 nucleocapsid gene. The limit of detection was determined to be 2 and 12 copies per µl for individual and pooled samples, respectively. Using the MP4 assay, we routinely processed over 1,000 samples a day with a 24-h turnaround time and over the course of 17 months, screened over 250,000 saliva samples. Modeling studies showed that the efficiency of 8-sample pools was reduced with increased viral prevalence and that this could be mitigated by using 4-sample pools. We also present a strategy for, and modeling data supporting, the creation of a third paired pool as an additional strategy to employ under high viral prevalence.
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Affiliation(s)
- Kaitlyn Wagner
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Phil Fox
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Elizabeth Gordon
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Westen Hahn
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Kenzie Olsen
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Alex Markham
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Dylan Buglewicz
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Platon Selemenakis
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Avery Lessard
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Daniella Goldstein
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Alissa Threatt
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Luke Davis
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Jake Miller-Dawson
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Halie Stockett
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | | | - Kristin Rugh
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Houston Turner
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Michelle Remias
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Maggie Williams
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Jorge Chavez
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Gabriel Galindo
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Charlotte Cialek
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Amanda Koch
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Alex Fout
- Department of Statistics, Colorado State University, Fort Collins, CO, 80523, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Bailey Fosdick
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Bettina Broeckling
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Mark D Zabel
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA.
- Colorado State University, Fort Collins, CO, 80523, USA.
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5
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Kritikos A, Caruana G, Lazor-Blanchet C, Currat M, Chiche JD, Vollenweider P, Bart PA, Opota O, Greub G. Comparison of Nasopharyngeal and Saliva Swab Nucleic Acid Amplification and Rapid Antigen Testing To Detect Omicron SARS-CoV-2 Variant of Concern: a Prospective Clinical Trial (OMICRON). Microbiol Spectr 2022; 10:e0392322. [PMID: 36346225 PMCID: PMC9769748 DOI: 10.1128/spectrum.03923-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022] Open
Abstract
In November 2021, the World Health Organization declared the Omicron variant (B.1.1.519) a variant of concern. Since then, worries have been expressed regarding the ability of usual diagnostic tests to detect the Omicron variant. In addition, some recently published data suggested that the salivary reverse transcription (RT)-PCR might perform better than the current gold standard, nasopharyngeal (NP) RT-PCR. In this study, we aimed to compare the sensitivities of nasopharyngeal and saliva RT-PCR and assess the diagnostic performances of rapid antigen testing (RAT) in nasopharyngeal and saliva samples. We conducted a prospective clinical study among symptomatic health care professionals consulting the occupational health service of our hospital for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) screening and hospitalized patients in internal medicine/intensive care wards screened for SARS-CoV-2 with COVID-19-compatible symptoms. A composite outcome considering NP PCR and/or saliva PCR was used as a reference standard to define COVID-19 cases. A total of 475 paired NP/saliva specimens have been collected with a positivity rate of 40% (n = 192). NP and salivary RT-PCR exhibited sensitivities of 98% (95% CI, 94 to 99%) and 87% (95% CI, 81 to 91%), respectively, for outpatients (n = 453) and 94% (95% CI, 72 to 99%) and 69% (95% CI, 44 to 86%), respectively, for hospitalized patients (n = 22). Nasopharyngeal rapid antigen testing exhibited much lower diagnostic performances (sensitivity of 66% and 31% for outpatients and inpatients, respectively), while saliva RAT showed a sensitivity of less than 5% in both groups. Nasopharyngeal RT-PCR testing remains the gold standard for SARS-CoV-2 Omicron variant screening. Salivary RT-PCR can be used as an alternative in case of contraindication to perform NP sampling. The use of RAT should be limited to settings where access to molecular diagnostic methods is lacking. IMPORTANCE The Omicron variant of concern spread rapidly since it was first reported in November 2021 and currently accounts for the vast majority of new infections worldwide. Recent reports suggest that saliva sampling might outweigh nasopharyngeal sampling for the diagnosis of the Omicron variant. Nevertheless, data investigating the best diagnostic strategy specifically for the Omicron variant of concern remain scarce. This study fills this gap in current knowledge and elucidates the question of which strategy to use in which patient. It provides a new basis for further improving COVID-19 screening programs and managing patients suspected to have COVID-19.
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Affiliation(s)
- Antonios Kritikos
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Giorgia Caruana
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Michael Currat
- Occupational Health Service, Lausanne University Hospital, Lausanne, Switzerland
| | - Jean-Daniel Chiche
- Intensive Care Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Peter Vollenweider
- Service of Internal Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Alexandre Bart
- Service of Internal Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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