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Calvet G, Ogrzewalska M, Tassinari W, Guaraldo L, Resende P, Fuller T, Penetra S, Borges M, Pina-Costa A, Martins E, Moraes I, Santos H, Damasceno L, Medeiros-Filho F, Espindola O, Mota F, Nacife V, Pauvolid-Corrêa A, Whitworth J, Smith C, Siqueira M, Brasil P. Accuracy of saliva for SARS-CoV-2 detection in outpatients and their household contacts during the circulation of the Omicron variant of concern. BMC Infect Dis 2023; 23:295. [PMID: 37147601 PMCID: PMC10161980 DOI: 10.1186/s12879-023-08271-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND While nasopharyngeal (NP) swabs are considered the gold standard for severe acute respiratory coronavirus 2 (SARS-CoV-2) real-time reverse transcriptase-polymerase chain reaction (RT-PCR) detection, several studies have shown that saliva is an alternative specimen for COVID-19 diagnosis and screening. METHODS To analyze the utility of saliva for the diagnosis of COVID-19 during the circulation of the Omicron variant, participants were enrolled in an ongoing cohort designed to assess the natural history of SARS-CoV-2 infection in adults and children. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Cohen's kappa coefficient were calculated to assess diagnostic performance. RESULTS Overall, 818 samples were collected from 365 outpatients from January 3 to February 2, 2022. The median age was 32.8 years (range: 3-94 years). RT-PCR for SARS-CoV-2 was confirmed in 97/121 symptomatic patients (80.2%) and 62/244 (25.4%) asymptomatic patients. Substantial agreement between saliva and combined nasopharyngeal/oropharyngeal samples was observed with a Cohen's kappa value of 0.74 [95% confidence interval (CI): 0.67-0.81]. Sensitivity was 77% (95% CI: 70.9-82.2), specificity 95% (95% CI: 91.9-97), PPV 89.8% (95% CI: 83.1-94.4), NPV 87.9% (95% CI: 83.6-91.5), and accuracy 88.5% (95% CI: 85.0-91.4). Sensitivity was higher among samples collected from symptomatic children aged three years and older and adolescents [84% (95% CI: 70.5-92)] with a Cohen's kappa value of 0.63 (95% CI: 0.35-0.91). CONCLUSIONS Saliva is a reliable fluid for detecting SARS-CoV-2, especially in symptomatic children and adolescents during the circulation of the Omicron variant.
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Affiliation(s)
- Guilherme Calvet
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil.
| | - Maria Ogrzewalska
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Wagner Tassinari
- Federal Rural University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lusiele Guaraldo
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Paola Resende
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Trevon Fuller
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Stephanie Penetra
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Michele Borges
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Anielle Pina-Costa
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Ezequias Martins
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Isabella Moraes
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Heloisa Santos
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Luana Damasceno
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Fernando Medeiros-Filho
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Otavio Espindola
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Fernando Mota
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Valéria Nacife
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Alex Pauvolid-Corrêa
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Jimmy Whitworth
- Departments of Clinical Research and Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Chris Smith
- Departments of Clinical Research and Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Marilda Siqueira
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Patrícia Brasil
- Acute Febrile Illnesses Laboratory, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
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Ávila LMS, Galvis MLD, Campos MAJ, Lozano-Parra A, Villamizar LAR, Arenas MO, Martínez-Vega RA, Cala LMV, Bautista LE. Validation of RT-qPCR test for SARS-CoV-2 in saliva specimens. J Infect Public Health 2022; 15:1403-1408. [PMID: 36371937 PMCID: PMC9628233 DOI: 10.1016/j.jiph.2022.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/19/2022] [Accepted: 10/30/2022] [Indexed: 11/05/2022] Open
Abstract
Background Saliva samples may be an easier, faster, safer, and cost-saving alternative to NPS samples, and can be self-collected by the patient. Whether SARS-CoV-2 RT-qPCR in saliva is more accurate than in nasopharyngeal swaps (NPS) is uncertain. We evaluated the accuracy of the RT-qPCR in both types of samples, assuming both approaches were imperfect. Methods We assessed the limit of detection (LoD) of RT-qPCR in each type of sample. We collected paired NPS and saliva samples and tested them using the Berlin Protocol to detect SARS-CoV-2 envelope protein (E). We used a Bayesian latent class analysis (BLCA) to estimate the sensitivity and specificity of each test, while accounting for their conditional dependence. Results The LoD were 10 copies/mL in saliva and 100 copies/mL in NPS. Paired samples of saliva and NPS were collected in 412 participants. Out of 68 infected cases, 14 were positive only in saliva. RT-qPCR sensitivity ranged from 82.7% (95% CrI: 54.8, 94.8) in NPS to 84.5% (50.9, 96.5) in saliva. Corresponding specificities were 99.1 (95% CrI: 95.3, 99.8) and 98.4 (95% CrI: 92.8, 99.7). Conclusions SARS-CoV-2 RT-qPCR test in saliva specimens has a similar or better accuracy than RT-qPCR test in NPS. Saliva specimens may be ideal for surveillance in general population, particularly in children, and in healthcare or other personnel in need of serial testing.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Leonelo E. Bautista
- University of Wisconsin-Madison, 610 Walnut Street, WARF 703, Madison, United States,Correspondence to: Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, 610 Walnut Street, WARF 703, Madison, WI 53711
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Moraleda C, Domínguez-Rodríguez S, Mesa JM, García-Sánchez P, de la Serna M, Alonso-Cadenas JA, Bermejo A, Sabrido G, Martínez-Campos L, González-Posada AF, Illán-Ramos M, Cobos-Carrascosa E, Ballesteros Á, Galán JC, Llorente F, Aguilera-Alonso D, Jiménez AB, Catalán P, Dahdouh E, Navarro I, Fernández-Garoz B, Mendoza P, Pérez-Jorge C, Cabezas-Fernández T, Blázquez-Gamero D, Rivas G, Gonzalez-Donapetry P, Sáez E, Fernández-Pinero J, Lucas-Fernández J, Pérez-Ramírez E, Merino P, Miragaya S, Lorente J, Iglesias I, Tagarro A. Oral saliva swab reverse transcription PCR for Covid-19 in the paediatric population. Arch Dis Child 2022; 107:1051-1058. [PMID: 35688603 PMCID: PMC9240444 DOI: 10.1136/archdischild-2021-323712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/12/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To evaluate the performance of oral saliva swab (OSS) reverse transcription PCR (RT-PCR) compared with RT-PCR and antigen rapid diagnostic test (Ag-RDT) on nasopharyngeal swabs (NPS) for SARS-CoV-2 in children. DESIGN Cross-sectional multicentre diagnostic study. SETTING Study nested in a prospective, observational cohort (EPICO-AEP) performed between February and March 2021 including 10 hospitals in Spain. PATIENTS Children from 0 to 18 years with symptoms compatible with Covid-19 of ≤5 days of duration were included. Two NPS samples (Ag-RDT and RT-PCR) and one OSS sample for RT-PCR were collected. MAIN OUTCOME Performance of Ag-RDT and RT-PCR on NPS and RT-PCR on OSS sample for SARS-CoV-2. RESULTS 1174 children were included, aged 3.8 years (IQR 1.7-9.0); 73/1174 (6.2%) patients tested positive by at least one of the techniques. Sensitivity and specificity of OSS RT-PCR were 72.1% (95% CI 59.7 to 81.9) and 99.6% (95% CI 99 to 99.9), respectively, versus 61.8% (95% CI 49.1 to 73) and 99.9% (95% CI 99.4 to 100) for the Ag-RDT. Kappa index was 0.79 (95% CI 0.72 to 0.88) for OSS RT-PCR and 0.74 (95% CI 0.65 to 0.84) for Ag-RDT versus NPS RT-PCR. CONCLUSIONS RT-PCR on the OSS sample is an accurate option for SARS-CoV-2 testing in children. A less intrusive technique for younger patients, who usually are tested frequently, might increase the number of patients tested.
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Affiliation(s)
- Cinta Moraleda
- Pediatric Infectious Diseases Unit. Department of Pediatrics, Hospital Universitario 12 de Octubre. Pediatric Research and Clinical Trials Unit (UPIC). RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain
- Instituto de Investigación 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain
| | - Sara Domínguez-Rodríguez
- Instituto de Investigación 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain
| | - Juan Miguel Mesa
- Paediatrics Department. Pediatrics Research Group, Hospital Universitario Infanta Sofia, San Sebastian de los Reyes, Madrid, Spain
| | - Paula García-Sánchez
- Emergency Pediatric Department. Instituto Investigación Hospital La Paz (IDIPaz), Hospital Universitario La Paz, Madrid, Spain
| | - María de la Serna
- Paediatrics Department. Pediatrics Research Group, Hospital Universitario Infanta Sofia, San Sebastian de los Reyes, Madrid, Spain
| | - José Antonio Alonso-Cadenas
- Emergency Pediatric Department. Instituto Investigación La Princesa, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Amanda Bermejo
- Pediatric Department, Hospital Universitario de Móstoles, Móstoles, Madrid, Spain
| | - Gema Sabrido
- Pediatric Department, Hospital Universitario Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Leticia Martínez-Campos
- Pediatric Infectious Diseases, Materno Infantil. Hospital Universitario Torrecárdenas, Almeria, Spain
| | | | - Marta Illán-Ramos
- Pediatrics Department, Hospital Universitario Clínico San Carlos, Madrid, Spain
| | - Elena Cobos-Carrascosa
- Instituto de Investigación 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain
| | - Álvaro Ballesteros
- Instituto de Investigación 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain
| | - Juan Carlos Galán
- Microbiology Department, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS). Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Francisco Llorente
- Centro de Investigacion en Sanidad Animal INIA-CSIC, Valdeolmos, Madrid, Spain
| | - David Aguilera-Alonso
- Pediatric Infectious Diseases Unit. Department of Pediatrics, Hospital Universitario Gregorio Marañón. Unidad de Investigación Maternoinfantil Fundación Familia Alonso (UDIMIFFA), Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM). CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Ana Belén Jiménez
- Pediatrics Department, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiologia Clinica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Elias Dahdouh
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz. IdiPAZ, Madrid, Spain
| | - Ignacio Navarro
- Paediatrics Department. Pediatrics Research Group, Hospital Universitario Infanta Sofia, San Sebastian de los Reyes, Madrid, Spain
| | | | - Pablo Mendoza
- Microbiology Department, Hospital Universitario de Móstoles, Mostoles, Madrid, Spain
| | - Concepción Pérez-Jorge
- Microbiology Department, Hospital Universitario Rey Juan Carlos, Mostoles, Madrid, Spain
| | | | - Daniel Blázquez-Gamero
- Pediatric Infectious Diseases Unit. Department of Pediatrics, Hospital Universitario 12 de Octubre. Pediatric Research and Clinical Trials Unit (UPIC). RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain
- Instituto de Investigación 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
| | - Gonzalo Rivas
- Microbiology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | - Elena Sáez
- Microbiology Department, UR Salud. Hospital Universitario Infanta Sofía. Paediatrics Research Group, San Sebastian de los Reyes, Madrid, Spain
| | | | - Jesús Lucas-Fernández
- Microbiology Department, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS). Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Elisa Pérez-Ramírez
- Centro de Investigacion en Sanidad Animal INIA-CSIC, Valdeolmos, Madrid, Spain
| | - Paloma Merino
- Microbiology Department, Hospital Universitario Clínico San Carlos, Madrid, Spain
| | - Sandra Miragaya
- Clinic Analysis Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Jorge Lorente
- Emergency Pediatric Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Irene Iglesias
- Centro de Investigacion en Sanidad Animal INIA-CSIC, Valdeolmos, Madrid, Spain
| | - Alfredo Tagarro
- Instituto de Investigación 12 de Octubre (imas12), Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain
- Paediatrics Department. Pediatrics Research Group, Hospital Universitario Infanta Sofia, San Sebastian de los Reyes, Madrid, Spain
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Chen H, Feng S, Zhou W, Li Z, Richard-Greenblatt M, Wang P. Pretreatment Methods for Human Nasopharyngeal Swabs to Increase the Signal to Noise Ratio of High Sensitivity Immunoassays. ACS MEASUREMENT SCIENCE AU 2022; 2:414-421. [PMID: 36785662 PMCID: PMC9885992 DOI: 10.1021/acsmeasuresciau.2c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Mucous samples collected through nasopharyngeal (NP) swabs are considered gold standard specimens for the detection of respiratory pathogens. Matrices of these highly viscous samples often cause significant background noises in immunoassays, especially immunoassays with high sensitivity. We demonstrated such nonspecific background signals in both a chemiluminescence enzyme-linked immunosorbent assay (ELISA) and a novel highly sensitive immunoassay called Microbubbling SARS-CoV-2 Antigen Assay (MSAA). We developed and demonstrated the effectiveness of two quick sample pretreatment methods, filtration and preadsorption, to decrease nonspecific signals and increase the signal-to-noise ratio (SNR). Using these pretreatment methods, the SNR (at 3.6 × 104 copies/mL of inactivated SARS-CoV-2) was increased by 42.4-fold (95% CI 41.0-43.8) and 67.1-fold (95% CI 57.9-76.3) in the MSAA, and 1.3-fold (95% CI 0.9-1.7) and 1.8-fold (95% CI 1.6-2.0) in the chemiluminescence ELISA assay. Sample pretreatment methods developed in this study are broadly adaptable for the development of immunoassays for highly viscous samples.
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El Sharif HF, Dennison SR, Tully M, Crossley S, Mwangi W, Bailey D, Graham SP, Reddy SM. Evaluation of electropolymerized molecularly imprinted polymers (E-MIPs) on disposable electrodes for detection of SARS-CoV-2 in saliva. Anal Chim Acta 2022; 1206:339777. [PMID: 35473858 PMCID: PMC8974637 DOI: 10.1016/j.aca.2022.339777] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 02/07/2023]
Abstract
We investigate electropolymerized molecularly imprinted polymers (E-MIPs) for the selective recognition of SARS-CoV-2 whole virus. E-MIPs imprinted with SARS-CoV-2 pseudoparticles (pps) were electrochemically deposited onto screen printed electrodes by reductive electropolymerization, using the water-soluble N-hydroxmethylacrylamide (NHMA) as functional monomer and crosslinked with N,N'-methylenebisacrylamide (MBAm). E-MIPs for SARS-CoV-2 showed selectivity for template SARS-CoV-2 pps, with an imprinting factor of 3:1, and specificity (significance = 0.06) when cross-reacted with other respiratory viruses. E-MIPs detected the presence of SARS-CoV-2 pps in <10 min with a limit of detection of 4.9 log10 pfu/mL, suggesting their suitability for detection of SARS-CoV-2 with minimal sample preparation. Using electrochemical impedance spectroscopy (EIS) and principal component analysis (PCA), the capture of SARS-CoV-2 from real patient saliva samples was also evaluated. Fifteen confirmed COVID-19 positive and nine COVID-19 negative saliva samples were compared against the established loop-mediated isothermal nucleic acid amplification (LAMP) technique used by the UK National Health Service. EIS data demonstrated a PCA discrimination between positive and negative LAMP samples. A threshold real impedance signal (ZRe) ≫ 4000 Ω and a corresponding charge transfer resistance (RCT) ≫ 6000 Ω was indicative of absence of virus (COVID-19 negative) in agreement with values obtained for our control non-imprinted polymer control. A ZRe at or below a threshold value of 600 Ω with a corresponding RCT of <1200 Ω was indicative of a COVID-19 positive sample. The presence of virus was confirmed by treatment of E-MIPs with a SARS-CoV-2 specific monoclonal antibody.
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Affiliation(s)
- H F El Sharif
- Department of Chemistry, UCLan Centre for Smart Materials, School of Natural Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom
| | - S R Dennison
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom
| | - M Tully
- The Pirbright Institute, Pirbright, Woking, Surrey, GU24 0NF, United Kingdom
| | - S Crossley
- The Pirbright Institute, Pirbright, Woking, Surrey, GU24 0NF, United Kingdom
| | - W Mwangi
- The Pirbright Institute, Pirbright, Woking, Surrey, GU24 0NF, United Kingdom
| | - D Bailey
- The Pirbright Institute, Pirbright, Woking, Surrey, GU24 0NF, United Kingdom
| | - S P Graham
- The Pirbright Institute, Pirbright, Woking, Surrey, GU24 0NF, United Kingdom
| | - S M Reddy
- Department of Chemistry, UCLan Centre for Smart Materials, School of Natural Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom.
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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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Campbell JR, Dion C, Uppal A, Yansouni CP, Menzies D. Systematic on-site testing for SARS-CoV-2 infection among asymptomatic essential workers in Montréal, Canada: a prospective observational and cost-assessment study. CMAJ Open 2022; 10:E409-E419. [PMID: 35537749 PMCID: PMC9259431 DOI: 10.9778/cmajo.20210290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Essential workers are at increased risk for SARS-CoV-2 infection. We aimed to estimate the yield, acceptability and cost of systematic workplace-based testing of asymptomatic essential workers for SARS-CoV-2 infection. METHODS From Jan. 27 to Mar. 12, 2021, we prospectively recruited non-health care essential businesses in Montréal, Canada, through email or telephone contact. Two trained mobile teams, each composed of 2 non-health care professionals, visited businesses. Consenting asymptomatic employees provided saline gargle samples under supervision. Samples were analyzed by means of reverse transcription polymerase chain reaction (RT-PCR). At businesses with outbreaks (≥ 2 participants with a positive result), we retested all participants with a negative result on initial testing. Our primary outcomes were yield (proportion of test results that were positive), acceptability (proportion of participants estimated to be present at the business who agreed to participate) and costs (including training, sample collection and analysis, and communicating results). Our secondary outcome was identification of factors associated with a positive test result on multivariable logistic regression. RESULTS Of the 366 businesses contacted, 69 (18.8%) agreed to participate. Nineteen businesses (28%) were manufacturers or suppliers, 12 (17%) were in auto sales or repair, and 11 (16%) were in childcare; the corresponding number of employees was 1225, 242 and 113. The median number of participants per business was 13 (interquartile range [IQR] 8-22). Of an estimated 2348 employees on site, 2128 (90.6%) participated (808 [38.0%] female, median age 48 [IQR 37-57] yr). Of the 2626 tests performed, 53 (2.0%) gave a positive result. Self-reported nonwhite ethnicity (adjusted odds ratio [OR] 3.7, 95% confidence interval [CI] 1.4-9.9) and a negative SARS-CoV-2 test result before the study (adjusted OR 0.4, 95% CI 0.2-0.8) were associated with a positive test result. Five businesses were experiencing an outbreak; at these businesses, 40/917 participants (4.4%) had a positive result on the initial test. We repeated testing for employees with initially negative results at 3 of these businesses over 2-3 weeks: 8/350 participants (2.3%) had a positive result on the second test, and none had a positive result on the third and fourth tests; no employer reported new positive results after our final visit (up to Mar. 26, 2021). At the remaining 64 businesses, 1211 participants were tested once, of whom 5 (0.4%) had a positive result. The per-person RT-PCR cost was $34, and all other costs, $8.67. INTERPRETATION On-site saline gargle sampling of essential workers for SARS-CoV-2 testing was acceptable and of modest cost, and appears most useful in the context of outbreaks. This sampling strategy should be evaluated further as a component of efforts to prevent SARS-CoV-2 transmission. PREPRINT: medRxiv - doi:10.1101/2021.05.12.21256956.
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Affiliation(s)
- Jonathon R Campbell
- Research Institute of the McGill University Health Centre (Campbell, Menzies, Dion, Yansouni, Uppal); Faculty of Medicine (Campbell, Menzies, Yansouni), McGill University; McGill International TB Centre (Campbell, Menzies); J.D. MacLean Centre for Tropical Diseases (Yansouni), Montréal, Que.
| | - Cynthia Dion
- Research Institute of the McGill University Health Centre (Campbell, Menzies, Dion, Yansouni, Uppal); Faculty of Medicine (Campbell, Menzies, Yansouni), McGill University; McGill International TB Centre (Campbell, Menzies); J.D. MacLean Centre for Tropical Diseases (Yansouni), Montréal, Que
| | - Aashna Uppal
- Research Institute of the McGill University Health Centre (Campbell, Menzies, Dion, Yansouni, Uppal); Faculty of Medicine (Campbell, Menzies, Yansouni), McGill University; McGill International TB Centre (Campbell, Menzies); J.D. MacLean Centre for Tropical Diseases (Yansouni), Montréal, Que
| | - Cedric P Yansouni
- Research Institute of the McGill University Health Centre (Campbell, Menzies, Dion, Yansouni, Uppal); Faculty of Medicine (Campbell, Menzies, Yansouni), McGill University; McGill International TB Centre (Campbell, Menzies); J.D. MacLean Centre for Tropical Diseases (Yansouni), Montréal, Que
| | - Dick Menzies
- Research Institute of the McGill University Health Centre (Campbell, Menzies, Dion, Yansouni, Uppal); Faculty of Medicine (Campbell, Menzies, Yansouni), McGill University; McGill International TB Centre (Campbell, Menzies); J.D. MacLean Centre for Tropical Diseases (Yansouni), Montréal, Que
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8
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Comparison between Nasal and Nasopharyngeal Swabs for SARS-CoV-2 Rapid Antigen Detection in an Asymptomatic Population, and Direct Confirmation by RT-PCR from the Residual Buffer. Microbiol Spectr 2022; 10:e0245521. [PMID: 35171010 PMCID: PMC8849095 DOI: 10.1128/spectrum.02455-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Containment measures employed during the COVID-19 pandemic included prompt recognition of cases, isolation, and contact tracing. Bilateral nasal (NA) swabs applied to a commercial antigen-based rapid diagnostic test (Ag-RDT) offer a simpler and more comfortable alternative to nasopharyngeal (NP) collection; however, little is known about the sensitivity of this method in an asymptomatic population. Participants in community-based asymptomatic testing sites were screened for SARS-CoV-2 using an Ag-RDT with NP sampling. Positive individuals returned for confirmatory molecular testing and consented to repeating the Ag-RDT using a bilateral NA swab for comparison. Residual test buffer (RTB) from Ag-RDTs was subjected to real-time reverse transcription-PCR (RT-PCR). Of 123,617 asymptomatic individuals, 197 NP Ag-RDT-positive participants were included, with 175 confirmed positive by RT-PCR. Of these cases, 154 were identified from the NA swab collection with Ag-RDT, with a sensitivity of 88.0% compared to the NP swab collection. Stratifying results by RT-PCR cycle threshold demonstrated that sensitivity of the nasal collection method varied based on the cycle threshold (CT) value of the paired RT-PCR sample. RT-PCR testing on the RTB from the Ag-RDT using NP and NA swab collections resulted in 100.0% and 98.7% sensitivity, respectively. NA swabs provide an adequate alternative to NP swab collection for use with Ag-RDT, with the recognition that the test is most sensitive in specimens with high viral loads. With the high sensitivity of RT-PCR testing on RTB from Ag-RDT, a more streamlined approach to confirmatory testing is possible without recollection or use of paired collections strategies. IMPORTANCE Nasal swabbing for SARS-CoV-2 (COVID-19) comes with many benefits but is slightly less sensitive than traditional nasopharyngeal swabbing; however, confirmatory lab-based testing could be performed directly from the residual buffer from either sample type.
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9
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Costa MM, Martin H, Estellon B, Dupé FX, Saby F, Benoit N, Tissot-Dupont H, Million M, Pradines B, Granjeaud S, Almeras L. Exploratory Study on Application of MALDI-TOF-MS to Detect SARS-CoV-2 Infection in Human Saliva. J Clin Med 2022; 11:295. [PMID: 35053990 PMCID: PMC8781148 DOI: 10.3390/jcm11020295] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/16/2021] [Accepted: 12/31/2021] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 has caused a large outbreak since its emergence in December 2019. COVID-19 diagnosis became a priority so as to isolate and treat infected individuals in order to break the contamination chain. Currently, the reference test for COVID-19 diagnosis is the molecular detection (RT-qPCR) of the virus from nasopharyngeal swab (NPS) samples. Although this sensitive and specific test remains the gold standard, it has several limitations, such as the invasive collection method, the relative high cost and the duration of the test. Moreover, the material shortage to perform tests due to the discrepancy between the high demand for tests and the production capacities puts additional constraints on RT-qPCR. Here, we propose a PCR-free method for diagnosing SARS-CoV-2 based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling and machine learning (ML) models from salivary samples. Kinetic saliva samples were collected at enrollment and ten and thirty days later (D0, D10 and D30), to assess the classification performance of the ML models compared to the molecular tests performed on NPS specimens. Spectra were generated using an optimized protocol of saliva collection and successive quality control steps were developed to ensure the reliability of spectra. A total of 360 averaged spectra were included in the study. At D0, the comparison of MS spectra from SARS-CoV-2 positive patients (n = 105) with healthy healthcare controls (n = 51) revealed nine peaks that significantly distinguished the two groups. Among the five ML models tested, support vector machine with linear kernel (SVM-LK) provided the best performance on the training dataset (accuracy = 85.2%, sensitivity = 85.1%, specificity = 85.3%, F1-Score = 85.1%). The application of the SVM-LK model on independent datasets confirmed its performances with 88.9% and 80.8% of correct classification for samples collected at D0 and D30, respectively. Conversely, at D10, the proportion of correct classification had fallen to 64.3%. The analysis of saliva samples by MALDI-TOF MS and ML appears as an interesting supplementary tool for COVID-19 diagnosis, despite the mitigated results obtained for convalescent patients (D10).
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Affiliation(s)
- Monique Melo Costa
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
| | - Hugo Martin
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
| | - Bertrand Estellon
- Laboratoire d’Informatique et Systèmes, Aix-Marseille University, CNRS, University de Toulon, 13013 Marseille, France; (B.E.); (F.-X.D.)
| | - François-Xavier Dupé
- Laboratoire d’Informatique et Systèmes, Aix-Marseille University, CNRS, University de Toulon, 13013 Marseille, France; (B.E.); (F.-X.D.)
| | - Florian Saby
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
| | - Nicolas Benoit
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Aix-Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Aix-Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Samuel Granjeaud
- CRCM Integrative Bioinformatics Platform, Centre de Recherche en Cancérologie de Marseille, INSERM, U1068, Institut Paoli-Calmettes, CNRS, UMR7258, Aix-Marseille Université UM 105, 13009 Marseille, France;
| | - Lionel Almeras
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
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