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Wang Z, Liu YL, Chen Y, Siegel L, Cappelleri JC, Chu H. Double-Negative Results Matter: A Reevaluation of Sensitivities for Detecting SARS-CoV-2 Infection Using Saliva Versus Nasopharyngeal Swabs. Am J Epidemiol 2024; 193:548-560. [PMID: 37939113 DOI: 10.1093/aje/kwad212] [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] [Received: 10/06/2022] [Accepted: 10/27/2023] [Indexed: 11/10/2023] Open
Abstract
In a recent systematic review, Bastos et al. (Ann Intern Med. 2021;174(4):501-510) compared the sensitivities of saliva sampling and nasopharyngeal swabs in the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by assuming a composite reference standard defined as positive if either test is positive and negative if both tests are negative (double negative). Even under a perfect specificity assumption, this approach ignores the double-negative results and risks overestimating the sensitivities due to residual misclassification. In this article, we first illustrate the impact of double-negative results in the estimation of the sensitivities in a single study, and then propose a 2-step latent class meta-analysis method for reevaluating both sensitivities using the same published data set as that used in Bastos et al. by properly including the observed double-negative results. We also conduct extensive simulation studies to compare the performance of the proposed method with Bastos et al.'s method for varied levels of prevalence and between-study heterogeneity. The results demonstrate that the sensitivities are overestimated noticeably using Bastos et al.'s method, and the proposed method provides a more accurate evaluation with nearly no bias and close-to-nominal coverage probability. In conclusion, double-negative results can significantly impact the estimated sensitivities when a gold standard is absent, and thus they should be properly incorporated.
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Loria V, Aparicio A, Hildesheim A, Cortés B, Barrientos G, Retana D, Sun K, Ocampo R, Prevots DR, Zúñiga M, Waterboer T, Wong-McClure R, Morera M, Butt J, Binder M, Abdelnour A, Calderón A, Gail MH, Pfeiffer RM, Solís CB, Fantin R, Vanegas JC, Mercado R, Ávila C, Porras C, Herrero R. Cohort profile: evaluation of immune response and household transmission of SARS-CoV-2 in Costa Rica: the RESPIRA study. BMJ Open 2023; 13:e071284. [PMID: 38070892 PMCID: PMC10729140 DOI: 10.1136/bmjopen-2022-071284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/19/2023] [Indexed: 12/18/2023] Open
Abstract
PURPOSE The RESPIRA cohort aims to describe the nature, magnitude, time course and efficacy of the immune response to SARS-CoV-2 infection and vaccination, population prevalence, and household transmission of COVID-19. PARTICIPANTS From November 2020, we selected age-stratified random samples of COVID-19 cases from Costa Rica confirmed by PCR. For each case, two population-based controls, matched on age, sex and census tract were recruited, supplemented with hospitalised cases and household contacts. Participants were interviewed and blood and saliva collected for antibodies and PCR tests. Participants will be followed for 2 years to assess antibody response and infection incidence. FINDINGS TO DATE Recruitment included 3860 individuals: 1150 COVID-19 cases, 1999 population controls and 719 household contacts from 304 index cases. The age and regional distribution of cases was as planned, including four age strata, 30% rural and 70% urban. The control cohort had similar sex, age and regional distribution as the cases according to the study design. Among the 1999 controls recruited, 6.8% reported at enrolment having had COVID-19 and an additional 12.5% had antibodies against SARS-CoV-2. Compliance with visits and specimens has been close to 70% during the first 18 months of follow-up. During the study, national vaccination was implemented and nearly 90% of our cohort participants were vaccinated during follow-up. FUTURE PLANS RESPIRA will enable multiple analyses, including population prevalence of infection, clinical, behavioural, immunological and genetic risk factors for SARS-CoV-2 acquisition and severity, and determinants of household transmission. We are conducting retrospective and prospective assessment of antibody levels, their determinants and their protective efficacy after infection and vaccination, the impact of long-COVID and a series of ancillary studies. Follow-up continues with bimonthly saliva collection for PCR testing and biannual blood collection for immune response analyses. Follow-up will be completed in early 2024. TRIAL REGISTRATION NUMBER NCT04537338.
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Affiliation(s)
- Viviana Loria
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Amada Aparicio
- Caja Costarricense de Seguro Social, San Jose, Costa Rica
| | - Allan Hildesheim
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Bernal Cortés
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Gloriana Barrientos
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Daniela Retana
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, NIH, Bethesda, Maryland, USA
| | - Rebeca Ocampo
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - D Rebecca Prevots
- Epidemiology and Population Studies Unit, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Zúñiga
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Melvin Morera
- Caja Costarricense de Seguro Social, San Jose, Costa Rica
| | - Julia Butt
- Infections and Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Marco Binder
- Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Arturo Abdelnour
- Hospital Nacional de Niños, Caja Costarricense de Seguro Social, San Jose, Costa Rica
| | | | - Mitchell H Gail
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ruth M Pfeiffer
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Cristina Barboza Solís
- Public Health Dental Department, Universidad de Costa Rica, Sabanilla de Montes de Oca, Costa Rica
| | - Romain Fantin
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Juan Carlos Vanegas
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Rachel Mercado
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Carlos Ávila
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Carolina Porras
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
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Ansil BR, George CE, Chandrasingh S, Viswanathan A, Thattai M, Raghu P, Devadiga S, Harikumar AG, Harsha PK, Nair I, Ramakrishnan U, Mayor S. Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2. Indian J Med Microbiol 2023; 45:100384. [PMID: 37573057 PMCID: PMC10231307 DOI: 10.1016/j.ijmmb.2023.100384] [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: 01/30/2022] [Revised: 11/12/2022] [Accepted: 05/11/2023] [Indexed: 08/14/2023]
Abstract
PURPOSE Compared to nasopharyngeal/oropharyngeal swabs (N/OPS-VTM), non-invasive saliva samples have enormous potential for scalability and routine population screening of SARS-CoV-2. In this study, we investigate the efficacy of saliva samples relative to N/OPS-VTM for use as a direct source for RT-PCR based SARS-CoV-2 detection. METHODS We collected paired nasopharyngeal/oropharyngeal swabs and saliva samples from suspected positive SARS-CoV-2 patients and tested using RT-PCR. We used generalized linear models to investigate factors that explain result agreement. Further, we used simulations to evaluate the effectiveness of saliva-based screening in restricting the spread of infection in a large campus such as an educational institution. RESULTS We observed a 75.4% agreement between saliva and N/OPS-VTM, that increased drastically to 83% in samples stored for less than three days. Such samples processed within two days of collection showed 74.5% test sensitivity. Our simulations suggest that a test with 75% sensitivity, but high daily capacity can be very effective in limiting the size of infection clusters in a workspace. Guided by these results, we successfully implemented a saliva-based screening in the Bangalore Life Sciences Cluster (BLiSC) campus. CONCLUSION These results suggest that saliva may be a viable alternate source for SARS-CoV-2 surveillance if samples are processed immediately. Although saliva shows slightly lower sensitivity levels when compared to N/OPS-VTM, saliva collection is logistically advantageous. We strongly recommend the implementation of saliva-based screening strategies for large workplaces and in schools, as well as for population-level screening and routine surveillance as we learn to live with the SARS-CoV-2 virus.
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Affiliation(s)
- B R Ansil
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India.
| | - Carolin Elizabeth George
- Community Health and Research Division, Bangalore Baptist Hospital, Bangalore, Karnataka, 560024, India.
| | - Sindhulina Chandrasingh
- Department of Microbiology, Bangalore Baptist Hospital, Bangalore, Karnataka, 560024, India.
| | | | - Mukund Thattai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India.
| | - Padinjat Raghu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India.
| | - Santhosha Devadiga
- COVID-19 Testing Laboratory, Institute for Stem Cell Science and Regenerative Medicine, Bangalore Life Science Cluster, Bangalore, Karnataka, 560065, India.
| | - Arun Geetha Harikumar
- COVID-19 Testing Laboratory, Institute for Stem Cell Science and Regenerative Medicine, Bangalore Life Science Cluster, Bangalore, Karnataka, 560065, India.
| | - Pulleri Kandi Harsha
- COVID-19 Testing Laboratory, Institute for Stem Cell Science and Regenerative Medicine, Bangalore Life Science Cluster, Bangalore, Karnataka, 560065, India.
| | - Indu Nair
- Department of Medicine and Infectious Diseases, Bangalore Baptist Hospital, Bangalore, Karnataka, 560024, India.
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India.
| | - Satyajit Mayor
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India.
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Caixeta DC, Paranhos LR, Blumenberg C, Garcia-Júnior MA, Guevara-Vega M, Taveira EB, Nunes MAC, Cunha TM, Jardim ACG, Flores-Mir C, Sabino-Silva R. Salivary SARS-CoV-2 RNA for diagnosis of COVID-19 patients: a systematic revisew and meta-analysis of diagnostic accuracy. JAPANESE DENTAL SCIENCE REVIEW 2023:S1882-7616(23)00016-9. [PMID: 37360001 PMCID: PMC10284464 DOI: 10.1016/j.jdsr.2023.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/22/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
Accurate, self-collected, and non-invasive diagnostics are critical to perform mass-screening diagnostic tests for COVID-19. This systematic review with meta-analysis evaluated the accuracy, sensitivity, and specificity of salivary diagnostics for COVID-19 based on SARS-CoV-2 RNA compared with the current reference tests using a nasopharyngeal swab (NPS) and/or oropharyngeal swab (OPS). An electronic search was performed in seven databases to find COVID-19 diagnostic studies simultaneously using saliva and NPS/OPS tests to detect SARS-CoV-2 by RT-PCR. The search resulted in 10,902 records, of which 44 studies were considered eligible. The total sample consisted of 14,043 participants from 21 countries. The accuracy, specificity, and sensitivity for saliva compared with the NPS/OPS was 94.3% (95%CI= 92.1;95.9), 96.4% (95%CI= 96.1;96.7), and 89.2% (95%CI= 85.5;92.0), respectively. Besides, the sensitivity of NPS/OPS was 90.3% (95%CI= 86.4;93.2) and saliva was 86.4% (95%CI= 82.1;89.8) compared to the combination of saliva and NPS/OPS as the gold standard. These findings suggest a similarity in SARS-CoV-2 RNA detection between NPS/OPS swabs and saliva, and the association of both testing approaches as a reference standard can increase by 3.6% the SARS-CoV-2 detection compared with NPS/OPS alone. This study supports saliva as an attractive alternative for diagnostic platforms to provide a non-invasive detection of SARS-CoV-2.
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Affiliation(s)
- Douglas Carvalho Caixeta
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Luiz Renato Paranhos
- School of Dentistry, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Cauane Blumenberg
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Marcelo Augusto Garcia-Júnior
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Marco Guevara-Vega
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Elisa Borges Taveira
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Marjorie Adriane Costa Nunes
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
- School of Dentistry, CEUMA University, Sao Luiz, MA, Brazil
| | - Thúlio Marquez Cunha
- Department of Pulmonology, School of Medicine, Federal University of Uberlandia, Minas Gerais, Brazil
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Carlos Flores-Mir
- Division of Orthodontics, School of Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
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5
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Sugita S, Takase H, Nakano S. Role of Recent PCR Tests for Infectious Ocular Diseases: From Laboratory-Based Studies to the Clinic. Int J Mol Sci 2023; 24:ijms24098146. [PMID: 37175854 PMCID: PMC10179472 DOI: 10.3390/ijms24098146] [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: 03/20/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Infectious uveitis is a vision-threatening condition that requires prompt clinical diagnosis and proper treatment. However, rapid and proper diagnosis in infectious uveitis remains challenging. Several examination tests, including polymerase chain reaction (PCR) tests, are transitioning from laboratory-based basic research-level tests to bedside clinical tests, and recently tests have changed to where they can be performed right next to clinicians. In this review, we introduce an updated overview of recent studies that are representative of the current trends in clinical microbiological techniques including PCR tests for infectious uveitis.
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Affiliation(s)
- Sunao Sugita
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe 650-0047, Japan
| | - Hiroshi Takase
- Department of Ophthalmology & Visual Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Satoko Nakano
- Department of Ophthalmology, Oita University, Oita 879-5593, Japan
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Katayama Y, Murai R, Moriai M, Nirasawa S, Saeki M, Yakuwa Y, Sato Y, Asanuma K, Fujiya Y, Kuronuma K, Takahashi S. Does the timing of saliva collection affect the diagnosis of SARS-CoV-2 infection? J Infect Chemother 2022; 28:1012-1014. [PMID: 35339382 PMCID: PMC8948004 DOI: 10.1016/j.jiac.2022.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 01/31/2023]
Abstract
We evaluated the optimal timing of saliva sample collection to diagnose the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We obtained 150 saliva samples at four specific time points from 13 patients with confirmed SARS-CoV-2 infection. The time points were (1) early morning (immediately after waking), (2) immediately after breakfast before tooth brushing, (3) 2 h after breakfast, and (4) before lunch. On the 2nd hospital day, patients collected saliva at the four time points by themselves. We collected samples at two time points, (1) and (3), from the 3rd hospital day to day 9 following symptom onset. In 52 samples collected at the four time points, there was no significant difference. Meanwhile, there was no significant difference in the positive proportion or the viral load between the two time points in both analyses by the day from symptom onset and by all samples. In this study, there was no difference in the positive proportions in saliva collected at various time points within 9 days after symptom onset. The timing of saliva collection was not affected by the diagnosis of SARS-CoV-2 infection.
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Affiliation(s)
- Yuki Katayama
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Ryosei Murai
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Mikako Moriai
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Shinya Nirasawa
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Masachika Saeki
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Yuki Yakuwa
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Yuki Sato
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Koichi Asanuma
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Yoshihiro Fujiya
- Division of Infection Control, Sapporo Medical University Hospital, Sapporo, Japan,Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Koji Kuronuma
- Division of Infection Control, Sapporo Medical University Hospital, Sapporo, Japan,Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Satoshi Takahashi
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan,Division of Infection Control, Sapporo Medical University Hospital, Sapporo, Japan,Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan,Corresponding author. Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, South-1, West-16, Chuo-ku, Sapporo, 060-8543, Japan
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7
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Tallmadge RL, Laverack M, Cronk B, Venugopalan R, Martins M, Zhang X, Elvinger F, Plocharczyk E, Diel DG. Viral RNA Load and Infectivity of SARS-CoV-2 in Paired Respiratory and Oral Specimens from Symptomatic, Asymptomatic, or Postsymptomatic Individuals. Microbiol Spectr 2022; 10:e0226421. [PMID: 35575498 PMCID: PMC9241670 DOI: 10.1128/spectrum.02264-21] [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] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 04/17/2022] [Indexed: 11/30/2022] Open
Abstract
In the present study, we assessed the diagnostic sensitivity and determined the viral RNA load and infectivity of SARS-CoV-2 in paired respiratory (nasopharyngeal and anterior nares) and oral samples (saliva and sublingual swab). Samples were collected from 77 individuals of which 75 were diagnosed with COVID-19 and classified as symptomatic (n = 29), asymptomatic (n = 31), or postsymptomatic (n = 15). Specimens were collected at one time point from each individual, between day 1 and 23 after the initial COVID-19 diagnosis, and included self-collected saliva (S), or sublingual (SL) swab, and bilateral anterior nares (AN) swab, followed by health care provider collected nasopharyngeal (NP) swab. Sixty-three specimen sets were tested using five assay/platforms. The diagnostic sensitivity of each assay/platform and specimen type was determined. Of the 63 specimen sets, SARS-CoV-2 was detected in 62 NP specimens, 52 AN specimens, 59 saliva specimens, and 31 SL specimens by at least one platform. Infectious SARS-CoV-2 was isolated from 21 NP, 13 AN, 12 saliva, and one SL specimen out of 50 specimen sets. SARS-CoV-2 isolation was most successful up to 5 days after initial COVID-19 diagnosis using NP specimens from symptomatic patients (16 of 24 positives, 66.67%), followed by specimens from asymptomatic patients (5 of 17 positives, 29.41%), while it was not very successful with specimens from postsymptomatic patients. Benefits of self-collected saliva and AN specimens balance the loss of sensitivity relative to NP specimens. Therefore, saliva and AN specimens are acceptable alternatives for symptomatic SARS-CoV-2 diagnostic testing or surveillance with increased sampling frequency of asymptomatic individuals. IMPORTANCE The dynamics of infection with SARS-CoV-2 have a significant impact on virus infectivity and in the diagnostic sensitivity of molecular and classic virus detection tests. In the present study we determined the diagnostic sensitivity of paired respiratory (nasopharyngeal and anterior nares swabs) and oral secretions (saliva and sublingual swab) and assessed infectious virus shedding patterns by symptomatic, asymptomatic, or postsymptomatic individuals. Understanding the diagnostic performance of these specimens and the patterns of infectious virus shedding in these bodily secretions provides critical information to control COVID-19, and may help to refine guidelines on isolation and quarantine of positive individuals and their close contacts identified through epidemiological investigations.
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Affiliation(s)
- Rebecca L. Tallmadge
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Brittany Cronk
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Roopa Venugopalan
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - XiuLin Zhang
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - François Elvinger
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | | | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell COVID-19 Testing Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Fragkou PC, De Angelis G, Menchinelli G, Can F, Garcia F, Morfin-Sherpa F, Dimopoulou D, Mack E, de Salazar A, Grossi A, Lytras T, Skevaki C. ESCMID COVID-19 guidelines: diagnostic testing for SARS-CoV-2. Clin Microbiol Infect 2022; 28:812-822. [PMID: 35218978 PMCID: PMC8863949 DOI: 10.1016/j.cmi.2022.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/03/2022] [Accepted: 02/06/2022] [Indexed: 02/07/2023]
Abstract
SCOPE The objective of these guidelines is to identify the most appropriate diagnostic test and/or diagnostic approach for SARS-CoV-2. The recommendations are intended to provide guidance to clinicians, clinical microbiologists, other health care personnel, and decision makers. METHODS An ESCMID COVID-19 guidelines task force was established by the ESCMID Executive Committee. A small group was established, half appointed by the chair and the remaining selected with an open call. Each panel met virtually once a week. For all decisions, a simple majority vote was used. A list of clinical questions using the PICO (population, intervention, comparison, outcome) format was developed at the beginning of the process. For each PICO, two panel members performed a literature search focusing on systematic reviews, with a third panellist involved in case of inconsistent results. Quality of evidence assessment was based on the GRADE-ADOLOPMENT (Grading of Recommendations Assessment, Development and Evaluation - adoption, adaptation, and de novo development of recommendations) approach. RECOMMENDATIONS A total of 43 PICO questions were selected that involve the following types of populations: (a) patients with signs and symptoms of COVID-19; (b) travellers, healthcare workers, and other individuals at risk for exposure to SARS-CoV-2; (c) asymptomatic individuals, and (d) close contacts of patients infected with SARS-CoV-2. The type of diagnostic test (commercial rapid nucleic acid amplification tests and rapid antigen detection), biomaterial, time since onset of symptoms/contact with an infectious case, age, disease severity, and risk of developing severe disease are also taken into consideration.
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Affiliation(s)
- Paraskevi C Fragkou
- First Department of Critical Care Medicine & Pulmonary Services, Evangelismos General Hospital, National and Kapodistrian University of Athens, Athens, Greece; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses, Basel, Switzerland
| | - Giulia De Angelis
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy; Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulia Menchinelli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy; Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Fusun Can
- Department of Medical Microbiology, Koc University School of Medicine, Istanbul, Turkey; Koc University IsBank Research Center for Infectious Diseases (KUISCID), Istanbul, Turkey
| | - Federico Garcia
- Servicio de Microbiología Clínica, Hospital Universitario Clínico San Cecilio, Instituto de Investigación Biosanitaria, Granada, Spain; CIBER de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Florence Morfin-Sherpa
- Laboratory of Virology, Institut des Agents Infectieux, National Reference Centre for Respiratory Viruses, Hospices Civils de Lyon, Université Claude Bernard Lyon1, Lyon, France
| | - Dimitra Dimopoulou
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses, Basel, Switzerland; Second Department of Paediatrics, P. and A. Kyriakou Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Elisabeth Mack
- Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg Campus Marburg and Faculty of Medicine, Philipps University Marburg, Marburg, Germany
| | - Adolfo de Salazar
- Servicio de Microbiología Clínica, Hospital Universitario Clínico San Cecilio, Instituto de Investigación Biosanitaria, Granada, Spain; CIBER de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Adriano Grossi
- Sezione di Igiene, Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Theodore Lytras
- School of Medicine, European University Cyprus, Nicosia, Cyprus
| | - Chrysanthi Skevaki
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses, Basel, Switzerland; Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany.
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9
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Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites. Microbiol Spectr 2022; 10:e0079722. [PMID: 35546574 PMCID: PMC9241879 DOI: 10.1128/spectrum.00797-22] [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] [Indexed: 11/20/2022] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) continue to pose a public health threat which necessitates a real-time monitoring strategy to complement whole genome sequencing. Thus, we investigated the efficacy of competitive probe RT-qPCR assays for six mutation sites identified in SARS-CoV-2 VOCs and, after validating the assays with synthetic RNA, performed these assays on positive saliva samples. When compared with whole genome sequence results, the SΔ69-70 and ORF1aΔ3675-3677 assays demonstrated 93.60 and 68.00% accuracy, respectively. The SNP assays (K417T, E484K, E484Q, L452R) demonstrated 99.20, 96.40, 99.60, and 96.80% accuracies, respectively. Lastly, we screened 345 positive saliva samples from 7 to 22 December 2021 using Omicron-specific mutation assays and were able to quickly identify rapid spread of Omicron in Upstate South Carolina. Our workflow demonstrates a novel approach for low-cost, real-time population screening of VOCs. IMPORTANCE SARS-CoV-2 variants of concern and their many sublineages can be characterized by mutations present within their genetic sequences. These mutations can provide selective advantages such as increased transmissibility and antibody evasion, which influences public health recommendations such as mask mandates, quarantine requirements, and treatment regimens. Our RT-qPCR workflow allows for strain identification of SARS-CoV-2 positive saliva samples by targeting common mutation sites shared between variants of concern and detecting single nucleotides present at the targeted location. This differential diagnostic system can quickly and effectively identify a wide array of SARS-CoV-2 strains, which can provide more informed public health surveillance strategies in the future.
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10
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Kidd SP, Burns D, Armson B, Beggs AD, Howson ELA, Williams A, Snell G, Wise EL, Goring A, Vincent-Mistiaen Z, Grippon S, Sawyer J, Cassar C, Cross D, Lewis T, Reid SM, Rivers S, James J, Skinner P, Banyard A, Davies K, Ptasinska A, Whalley C, Ferguson J, Bryer C, Poxon C, Bosworth A, Kidd M, Richter A, Burton J, Love H, Fouch S, Tillyer C, Sowood A, Patrick H, Moore N, Andreou M, Morant N, Houghton R, Parker J, Slater-Jefferies J, Brown I, Gretton C, Deans Z, Porter D, Cortes NJ, Douglas A, Hill SL, Godfrey KM, Fowler VL. Reverse-Transcription Loop-Mediated Isothermal Amplification Has High Accuracy for Detecting Severe Acute Respiratory Syndrome Coronavirus 2 in Saliva and Nasopharyngeal/Oropharyngeal Swabs from Asymptomatic and Symptomatic Individuals. J Mol Diagn 2022; 24:320-336. [PMID: 35121140 PMCID: PMC8806713 DOI: 10.1016/j.jmoldx.2021.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/02/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Previous studies have described reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal/oropharyngeal swab and saliva samples. This multisite clinical evaluation describes the validation of an improved sample preparation method for extraction-free RT-LAMP and reports clinical performance of four RT-LAMP assay formats for SARS-CoV-2 detection. Direct RT-LAMP was performed on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva samples from asymptomatic and symptomatic individuals across health care and community settings. For direct RT-LAMP, overall diagnostic sensitivity (DSe) was 70.35% (95% CI, 63.48%-76.60%) on swabs and 84.62% (95% CI, 79.50%-88.88%) on saliva, with diagnostic specificity of 100% (95% CI, 98.98%-100.00%) on swabs and 100% (95% CI, 99.72%-100.00%) on saliva, compared with quantitative RT-PCR (RT-qPCR); analyzing samples with RT-qPCR ORF1ab CT values of ≤25 and ≤33, DSe values were 100% (95% CI, 96.34%-100%) and 77.78% (95% CI, 70.99%-83.62%) for swabs, and 99.01% (95% CI, 94.61%-99.97%) and 87.61% (95% CI, 82.69%-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and diagnostic specificity were 96.06% (95% CI, 92.88%-98.12%) and 99.99% (95% CI, 99.95%-100%) for swabs, and 80.65% (95% CI, 73.54%-86.54%) and 99.99% (95% CI, 99.95%-100%) for saliva, respectively. These findings demonstrate that RT-LAMP is applicable to a variety of use cases, including frequent, interval-based direct RT-LAMP of saliva from asymptomatic individuals who may otherwise be missed using symptomatic testing alone.
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Affiliation(s)
- Stephen P Kidd
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Daniel Burns
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; School of Electronics and Computer Science, University of Southampton, Southampton, United Kingdom
| | - Bryony Armson
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom; vHive, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Andrew D Beggs
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | | | - Anthony Williams
- University of Southampton and Division of Specialist Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Gemma Snell
- University of Southampton and Division of Specialist Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Emma L Wise
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Alice Goring
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | | | - Seden Grippon
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Jason Sawyer
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Claire Cassar
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - David Cross
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Thomas Lewis
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Scott M Reid
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Samantha Rivers
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Joe James
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Paul Skinner
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Ashley Banyard
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Kerrie Davies
- Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, United Kingdom
| | - Anetta Ptasinska
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Celina Whalley
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Jack Ferguson
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Claire Bryer
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Charlie Poxon
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Andrew Bosworth
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Michael Kidd
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom; Public Health West Midlands Laboratory, Birmingham, United Kingdom
| | - Alex Richter
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Jane Burton
- High Containment Microbiology, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - Hannah Love
- High Containment Microbiology, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - Sarah Fouch
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Claire Tillyer
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Amy Sowood
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Helen Patrick
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Nathan Moore
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, United Kingdom
| | - Rebecca Houghton
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Joe Parker
- National Biofilms Innovation Centre, University of Southampton, Southampton, United Kingdom
| | | | - Ian Brown
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Cosima Gretton
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Zandra Deans
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Deborah Porter
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Nicholas J Cortes
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; Gibraltar Health Authority, Gibraltar, United Kingdom
| | - Angela Douglas
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Sue L Hill
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Keith M Godfrey
- National Institute for Health Research Southampton Biomedical Research Centre, University of Southampton and University Hospital, Southampton, United Kingdom; MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, United Kingdom.
| | - Veronica L Fowler
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
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11
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Surveillance Web System and Mouthwash-Saliva qPCR for Labor Ambulatory SARS-CoV-2 Detection and Prevention. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031271. [PMID: 35162294 PMCID: PMC8835463 DOI: 10.3390/ijerph19031271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 12/12/2022]
Abstract
This study provides a safe and low-cost in-house protocol for RT-qPCR-based detection of SARS-CoV-2 using mouthwash-saliva self-collected specimens to achieve clinical and epidemiological surveillance in a real-time web environment applied to ambulatory populations. The in-house protocol comprises a mouthwash-saliva self-collected specimen, heat virus inactivation, and primers to target virus N-gene region and the human RPP30-gene. Aligning with 209 SARS-CoV-2 sequences confirmed specificity including the Alpha variant from the UK. Development, validation, and statistical comparison with official nasopharyngeal swabbing RT-qPCR test were conducted with 115 specimens of ambulatory volunteers. A web-mobile application platform was developed to integrate a real-time epidemiological and clinical core baseline database with mouthwash-saliva RT-qPCR testing. Nine built-in algorithms were generated for decision-making on testing, confining, monitoring, and self-reports to family, social, and work environments. Epidemiological and clinical follow-up and SARS-CoV-2 testing generated a database of 37,351 entries allowing individual decision-making for prevention. Mouthwash-saliva had higher sensitivity than nasopharyngeal swabbing in detecting asymptomatic and mild symptomatic cases with 720 viral copy number (VCN)/mL as the detection limit (Ct = 37.6). Cycling threshold and viral loading were marginally different (p = 0.057) between asymptomatic (35 Ct ± 2.8; 21,767.7 VCN/mL, range 720-77,278) and symptomatic (31.3 Ct ± 4.5; 747,294.3 VCN/mL, range 1433.6-3.08 × 106). We provided proof-of-concept evidence of effective surveillance to target asymptomatic and moderate symptomatic ambulatory individuals based on integrating a bio-safety level II laboratory, self-collected, low-risk, low-cost detection protocol, and a real-time digital monitoring system. Mouthwash-saliva was effective for SARS-CoV-2 sampling for the first time at the community level.
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12
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Ahmadzadeh M, Vahidi H, Mahboubi A, Hajifathaliha F, Nematollahi L, Mohit E. Different Respiratory Samples for COVID-19 Detection by Standard and Direct Quantitative RT-PCR: A Literature Review. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:285-299. [PMID: 34903989 PMCID: PMC8653661 DOI: 10.22037/ijpr.2021.115458.15383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The most common diagnostic method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is real-time quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR). Upper respiratory tract samples, including nasopharyngeal swab (NPS), oropharyngeal swab (OPS), saliva and lower respiratory tract samples such as sputum, are the most widely used specimens for diagnosis of SARS-CoV-2 using RT-qPCR. This study aimed to compare the diagnostic performance of different samples for Coronavirus disease 2019 (COVID-19) detection. It was found that NPS, the reference respiratory specimen for COVID-19 detection, is more sensitive than OPS. However, the application of NPS has many drawbacks, including challenging sampling process and increased risk of transmission to healthcare workers (HCWs). Saliva samples can be collected less invasively and quickly by HCWs with less contact or by own patients, and they can be considered as an alternative to NPS for COVID-19 detection by RT-qPCR. Additionally, sputum, which demonstrates higher viral load can be applied in patients with productive coughs and negative results from NPS. Commonly, after viral RNA purification from patient samples, which is time-consuming and costly, RT-qPCR is performed to diagnose SARS-CoV-2. Herein, different approaches including physical (heat inactivation) and chemical (proteinase K treatment) methods, used in RNA extraction free- direct RT-qPCR, were reviewed. The results of direct RT-qPCR assays were comparable to the results of standard RT-qPCR, while cost and time were saved. However, optimal protocol to decrease cost and processing time, proper transport medium and detection kit should be determined.
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Affiliation(s)
- Maryam Ahmadzadeh
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Vahidi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arash Mahboubi
- Department of Pharmaceutics, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fariba Hajifathaliha
- Department of Pharmaceutics, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Nematollahi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Elham Mohit
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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13
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Audigé A, Böni J, Schreiber PW, Scheier T, Buonomano R, Rudiger A, Braun DL, Eich G, Keller DI, Hasse B, Berger C, Günthard HF, Manrique A, Trkola A, Huber M. Reduced Relative Sensitivity of the Elecsys SARS-CoV-2 Antigen Assay in Saliva Compared to Nasopharyngeal Swabs. Microorganisms 2021; 9:1700. [PMID: 34442779 PMCID: PMC8401978 DOI: 10.3390/microorganisms9081700] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 12/23/2022] Open
Abstract
Early identification and isolation of SARS-CoV-2-infected individuals is central to contain the COVID-19 pandemic. Nasopharyngeal swabs (NPS) serve as a specimen for detection by RT-PCR and rapid antigen screening tests. Saliva has been confirmed as a reliable alternative specimen for RT-PCR and has been shown to be valuable for diagnosing children and in repetitive mass testing due to its non-invasive collection. Combining the advantages of saliva with those of antigen tests would be highly attractive to further increase test capacities. Here, we evaluated the performance of the Elecsys SARS-CoV-2 Antigen assay (Roche) in RT-PCR-positive paired NPS and saliva samples (N = 87) and unpaired NPS (N = 100) with confirmed SARS-CoV-2 infection (Roche cobas SARS-CoV-2 IVD test). We observed a high positive percent agreement (PPA) of the antigen assay with RT-PCR in NPS, reaching 87.2% across the entire cohort, whereas the overall PPA for saliva was insufficient (40.2%). At Ct values ≤ 28, PPA were 100% and 91.2% for NPS and saliva, respectively. At lower viral loads, the sensitivity loss of the antigen assay in saliva was striking. At Ct values ≤ 35, the PPA for NPS remained satisfactory (91.5%), whereas the PPA for saliva dropped to 46.6%. In conclusion, saliva cannot be recommended as a reliable alternative to NPS for testing with the Elecsys Anti-SARS-CoV-2 Antigen assay. As saliva is successfully used broadly in combination with RT-PCR testing, it is critical to create awareness that suitability for RT-PCR cannot be translated to implementation in antigen assays without thorough evaluation of each individual test system.
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Affiliation(s)
- Annette Audigé
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
| | - Peter W. Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; (P.W.S.); (T.S.); (D.L.B.); (B.H.)
| | - Thomas Scheier
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; (P.W.S.); (T.S.); (D.L.B.); (B.H.)
| | - Roberto Buonomano
- Division of Infectious Diseases and Hospital Hygiene, Spital Limmattal, 8952 Schlieren, Switzerland;
| | - Alain Rudiger
- Division of Medicine, Spital Limmattal, 8952 Schlieren, Switzerland;
| | - Dominique L. Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; (P.W.S.); (T.S.); (D.L.B.); (B.H.)
| | - Gerhard Eich
- Division of Infectious Diseases, Hospital Hygiene and Occupational Medicine, Stadtspital Triemli, 8063 Zurich, Switzerland;
| | - Dagmar I. Keller
- Emergency Department, University Hospital Zurich, 8091 Zurich, Switzerland;
| | - Barbara Hasse
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; (P.W.S.); (T.S.); (D.L.B.); (B.H.)
| | - Christoph Berger
- Division of Infectious Diseases and Hospital Epidemiology, University Children’s Hospital Zurich, 8032 Zurich, Switzerland;
| | - Huldrych F. Günthard
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; (P.W.S.); (T.S.); (D.L.B.); (B.H.)
| | - Amapola Manrique
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
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14
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Ibrahimi N, Delaunay-Moisan A, Hill C, Le Teuff G, Rupprecht JF, Thuret JY, Chaltiel D, Potier MC. Screening for SARS-CoV-2 by RT-PCR: Saliva or nasopharyngeal swab? Rapid review and meta-analysis. PLoS One 2021; 16:e0253007. [PMID: 34111196 PMCID: PMC8191978 DOI: 10.1371/journal.pone.0253007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Diagnosis of COVID-19 in symptomatic patients and screening of populations for SARS-CoV-2 infection require access to straightforward, low-cost and high-throughput testing. The recommended nasopharyngeal swab tests are limited by the need of trained professionals and specific consumables and this procedure is poorly accepted as a screening method In contrast, saliva sampling can be self-administered. METHODS In order to compare saliva and nasopharyngeal/oropharyngeal samples for the detection of SARS-CoV-2, we designed a meta-analysis searching in PubMed up to December 29th, 2020 with the key words "(SARS-CoV-2 OR COVID-19 OR COVID19) AND (salivary OR saliva OR oral fluid)) NOT (review[Publication Type]) NOT (PrePrint[Publication Type])" applying the following criteria: records published in peer reviewed scientific journals, in English, with at least 15 nasopharyngeal/orapharyngeal swabs and saliva paired samples tested by RT-PCR, studies with available raw data including numbers of positive and negative tests with the two sampling methods. For all studies, concordance and sensitivity were calculated and then pooled in a random-effects model. FINDINGS A total of 377 studies were retrieved, of which 50 were eligible, reporting on 16,473 pairs of nasopharyngeal/oropharyngeal and saliva samples. Meta-analysis showed high concordance, 92.5% (95%CI: 89.5-94.7), across studies and pooled sensitivities of 86.5% (95%CI: 83.4-89.1) and 92.0% (95%CI: 89.1-94.2) from saliva and nasopharyngeal/oropharyngeal swabs respectively. Heterogeneity across studies was 72.0% for saliva and 85.0% for nasopharyngeal/oropharyngeal swabs. INTERPRETATION Our meta-analysis strongly suggests that saliva could be used for frequent testing of COVID-19 patients and "en masse" screening of populations.
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Affiliation(s)
- Nusaïbah Ibrahimi
- Service de Biostatistique et d’Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Agnès Delaunay-Moisan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette Cedex, France
| | - Catherine Hill
- Service de Biostatistique et d’Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Gwénaël Le Teuff
- Service de Biostatistique et d’Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jean-François Rupprecht
- Aix Marseille Univ, Université de Toulon, CNRS, Centre de Physique Théorique, Turing Center for Living Systems, Marseille, France
| | - Jean-Yves Thuret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette Cedex, France
| | - Dan Chaltiel
- Service de Biostatistique et d’Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Marie-Claude Potier
- Institut du Cerveau (ICM), CNRS UMR 7225 – Inserm U1127, Sorbonne Université, Paris, France
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15
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Caixeta DC, Oliveira SW, Cardoso-Sousa L, Cunha TM, Goulart LR, Martins MM, Marin LM, Jardim ACG, Siqueira WL, Sabino-Silva R. One-Year Update on Salivary Diagnostic of COVID-19. Front Public Health 2021; 9:589564. [PMID: 34150692 PMCID: PMC8210583 DOI: 10.3389/fpubh.2021.589564] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/31/2021] [Indexed: 01/19/2023] Open
Abstract
Background: Coronavirus disease 2019 (COVID-19) is a global health problem, which is challenging healthcare worldwide. In this critical review, we discussed the advantages and limitations in the implementation of salivary diagnostic platforms of COVID-19. The diagnostic test of COVID-19 by invasive nasopharyngeal collection is uncomfortable for patients and requires specialized training of healthcare professionals in order to obtain an appropriate collection of samples. Additionally, these professionals are in close contact with infected patients or suspected cases of COVID-19, leading to an increased contamination risk for frontline healthcare workers. Although there is a colossal demand for novel diagnostic platforms with non-invasive and self-collection samples of COVID-19, the implementation of the salivary platforms has not been implemented for extensive scale testing. Up to date, several cross-section and clinical trial studies published in the last 12 months support the potential of detecting SARS-CoV-2 RNA in saliva as a biomarker for COVID-19, providing a self-collection, non-invasive, safe, and comfortable procedure. Therefore, the salivary diagnosis is suitable to protect healthcare professionals and other frontline workers and may encourage patients to get tested due to its advantages over the current invasive methods. The detection of SARS-CoV-2 in saliva was substantial also in patients with a negative nasopharyngeal swab, indicating the presence of false negative results. Furthermore, we expect that salivary diagnostic devices for COVID-19 will continue to be used with austerity without excluding traditional gold standard specimens to detect SARS-CoV-2.
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Affiliation(s)
- Douglas Carvalho Caixeta
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Brazil
| | - Stephanie Wutke Oliveira
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Brazil
- School of Dentistry, Federal University of Uberlandia, Uberlandia, Brazil
| | - Leia Cardoso-Sousa
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Brazil
| | | | - Luiz Ricardo Goulart
- Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, Brazil
| | - Mario Machado Martins
- Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, Brazil
| | - Lina Maria Marin
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ana Carolina Gomes Jardim
- Laboratory of Virology, Institute of Biomedical Science, Federal University of Uberlandia, Uberlandia, Brazil
- São Paulo State University, Institute of Biosciences, Humanities and Exact Sciences, São José Do Rio Preto, Brazil
| | | | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Brazil
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Herrera LA, Hidalgo-Miranda A, Reynoso-Noverón N, Meneses-García AA, Mendoza-Vargas A, Reyes-Grajeda JP, Vadillo-Ortega F, Cedro-Tanda A, Peñaloza F, Frías-Jimenez E, Arriaga-Canon C, Ruiz R, Angulo O, López-Villaseñor I, Amador-Bedolla C, Vilar-Compte D, Cornejo P, Cisneros-Villanueva M, Hurtado-Cordova E, Cendejas-Orozco M, Hernández-Morales JS, Moreno B, Hernández-Cruz IA, Herrera CA, García F, González-Woge MA, Munguía-Garza P, Luna-Maldonado F, Sánchez-Vizcarra A, Osnaya VG, Medina-Molotla N, Alfaro-Mora Y, Cáceres-Gutiérrez RE, Tolentino-García L, Rosas-Escobar P, Román-González SA, Escobar-Arrazola MA, Canseco-Méndez JC, Ortiz-Soriano DR, Domínguez-Ortiz J, González-Barrera AD, Aparicio-Bautista DI, Cruz-Rangel A, Alarcón-Zendejas AP, Contreras-Espinosa L, González R, Guerra-Calderas L, Meraz-Rodríguez MA, Montalvo-Casimiro M, Montiel-Manríquez R, Torres-Arciga K, Venegas D, Juárez-González V, Guajardo-Barreto X, Monroy-Martínez V, Guillén D, Fernández J, Herrera J, León-Rodriguez R, Canela-Pérez I, Ruíz-Ordaz BH, Valdez-Vazquez R, Bertin-Montoya J, Niembro-Ortega M, Villegas-Acosta L, López-Castillo D, Soriano-Ríos A, Gastelum-Ramos M, Zamora-Barandas T, Morales-Baez J, García-Rodríguez M, García-Martínez M, Nieto-Patlán E, Quirasco-Baruch M, López-Martínez I, Ramírez-Gonzalez E, Olivera-Díaz H, Escobar-Escamilla N. Saliva is a reliable and accessible source for the detection of SARS-CoV-2. Int J Infect Dis 2021; 105:83-90. [PMID: 33581365 PMCID: PMC7876483 DOI: 10.1016/j.ijid.2021.02.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES The aim of this study was to investigate the feasibility of saliva sampling as a non-invasive and safer tool to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to compare its reproducibility and sensitivity with nasopharyngeal swab samples (NPS). The use of sample pools was also investigated. METHODS A total of 2107 paired samples were collected from asymptomatic healthcare and office workers in Mexico City. Sixty of these samples were also analyzed in two other independent laboratories for concordance analysis. Sample processing and analysis of virus genetic material were performed according to standard protocols described elsewhere. A pooling analysis was performed by analyzing the saliva pool and the individual pool components. RESULTS The concordance between NPS and saliva results was 95.2% (kappa 0.727, p = 0.0001) and 97.9% without considering inconclusive results (kappa 0.852, p = 0.0001). Saliva had a lower number of inconclusive results than NPS (0.9% vs 1.9%). Furthermore, saliva showed a significantly higher concentration of both total RNA and viral copies than NPS. Comparison of our results with those of the other two laboratories showed 100% and 97% concordance. Saliva samples are stable without the use of any preservative, and a positive SARS-CoV-2 sample can be detected 5, 10, and 15 days after collection when the sample is stored at 4 °C. CONCLUSIONS The study results indicate that saliva is as effective as NPS for the identification of SARS-CoV-2-infected asymptomatic patients. Sample pooling facilitates the analysis of a larger number of samples, with the benefit of cost reduction.
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Affiliation(s)
- Luis A Herrera
- Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico; Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico.
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico.
| | - Nancy Reynoso-Noverón
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | | | - Alfredo Mendoza-Vargas
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | - Juan P Reyes-Grajeda
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | | | | | - Fernando Peñaloza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | | | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rosaura Ruiz
- Secretaria de Educación, Ciencia, Tecnología e Innovación, Mexico City, Mexico
| | - Ofelia Angulo
- Secretaria de Educación, Ciencia, Tecnología e Innovación, Mexico City, Mexico
| | - Imelda López-Villaseñor
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Amador-Bedolla
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Mireya Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | - Eduardo Hurtado-Cordova
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | - Mariana Cendejas-Orozco
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | | | - Bernardo Moreno
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Irwin A Hernández-Cruz
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - César A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Francisco García
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Miguel A González-Woge
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Paulina Munguía-Garza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Fernando Luna-Maldonado
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Antonia Sánchez-Vizcarra
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Vincent G Osnaya
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Nelly Medina-Molotla
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | - Yair Alfaro-Mora
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rodrigo E Cáceres-Gutiérrez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Laura Tolentino-García
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Patricia Rosas-Escobar
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | | | - Marco A Escobar-Arrazola
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Julio C Canseco-Méndez
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, INMEGEN, Mexico City, Mexico
| | | | - Julieta Domínguez-Ortiz
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | | | | | | | - Ana Paula Alarcón-Zendejas
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rodrigo González
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Lissania Guerra-Calderas
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Marco A Meraz-Rodríguez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Michel Montalvo-Casimiro
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rogelio Montiel-Manríquez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Karla Torres-Arciga
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Daniela Venegas
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Vasti Juárez-González
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Xiadani Guajardo-Barreto
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Verónica Monroy-Martínez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel Guillén
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jacquelina Fernández
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juliana Herrera
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Renato León-Rodriguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Israel Canela-Pérez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Blanca H Ruíz-Ordaz
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | | | | | - Erik Nieto-Patlán
- Unidad de Investigación Preclínica, Facultad de Química, Mexico City, Mexico
| | - Maricarmen Quirasco-Baruch
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Irma López-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos, InDRE, Mexico City, Mexico
| | | | - Hiram Olivera-Díaz
- Instituto de Diagnóstico y Referencia Epidemiológicos, InDRE, Mexico City, Mexico
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Bastos ML, Perlman-Arrow S, Menzies D, Campbell JR. The Sensitivity and Costs of Testing for SARS-CoV-2 Infection With Saliva Versus Nasopharyngeal Swabs : A Systematic Review and Meta-analysis. Ann Intern Med 2021; 174:501-510. [PMID: 33428446 PMCID: PMC7822569 DOI: 10.7326/m20-6569] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [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 Nasopharyngeal swabs are the primary sampling method used for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but they require a trained health care professional and extensive personal protective equipment. PURPOSE To determine the difference in sensitivity for SARS-CoV-2 detection between nasopharyngeal swabs and saliva and estimate the incremental cost per additional SARS-CoV-2 infection detected with nasopharyngeal swabs. DATA SOURCES Embase, Medline, medRxiv, and bioRxiv were searched from 1 January to 1 November 2020. Cost inputs were from nationally representative sources in Canada and were converted to 2020 U.S. dollars. STUDY SELECTION Studies including at least 5 paired nasopharyngeal swab and saliva samples and reporting diagnostic accuracy for SARS-CoV-2 detection. DATA EXTRACTION Data were independently extracted using standardized forms, and study quality was assessed using QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies 2). DATA SYNTHESIS Thirty-seven studies with 7332 paired samples were included. Against a reference standard of a positive result on either sample, the sensitivity of saliva was 3.4 percentage points lower (95% CI, 9.9 percentage points lower to 3.1 percentage points higher) than that of nasopharyngeal swabs. Among persons with previously confirmed SARS-CoV-2 infection, saliva's sensitivity was 1.5 percentage points higher (CI, 7.3 percentage points lower to 10.3 percentage points higher) than that of nasopharyngeal swabs. Among persons without a previous SARS-CoV-2 diagnosis, saliva was 7.9 percentage points less (CI, 14.7 percentage points less to 0.8 percentage point more) sensitive. In this subgroup, if testing 100 000 persons with a SARS-CoV-2 prevalence of 1%, nasopharyngeal swabs would detect 79 more (95% uncertainty interval, 5 fewer to 166 more) persons with SARS-CoV-2 than saliva, but with an incremental cost per additional infection detected of $8093. LIMITATION The reference standard was imperfect, and saliva collection procedures varied. CONCLUSION Saliva sampling seems to be a similarly sensitive and less costly alternative that could replace nasopharyngeal swabs for collection of clinical samples for SARS-CoV-2 testing. PRIMARY FUNDING SOURCE McGill Interdisciplinary Initiative in Infection and Immunity. (PROSPERO: CRD42020203415).
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Affiliation(s)
- Mayara Lisboa Bastos
- McGill University and McGill International TB Centre, Montreal, Quebec, Canada, and State University of Rio de Janeiro, Rio de Janeiro, Brazil (M.L.B.)
| | | | - Dick Menzies
- McGill University, McGill International TB Centre, and Montreal Chest Institute, Montreal, Quebec, Canada (D.M.)
| | - Jonathon R Campbell
- McGill University and McGill International TB Centre, Montreal, Quebec, Canada (J.R.C.)
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18
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RT-PCR Screening Tests for SARS-CoV-2 with Saliva Samples in Asymptomatic People: Strategy to Maintain Social and Economic Activities while Reducing the Risk of Spreading the Virus. Keio J Med 2021; 70:35-43. [PMID: 33746151 DOI: 10.2302/kjm.2021-0003-oa] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The year 2020 will be remembered for the coronavirus disease 2019 (COVID-19) pandemic, which continues to affect the whole world. Early and accurate identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is fundamental to combat the disease. Among the current diagnostic tests, real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) is the most reliable and frequently used method. Herein, we discuss the interpretation of RT-qPCR results relative to viral infectivity. Although nasopharyngeal swab samples are often used for RT-qPCR testing, they require collection by trained medical staff. Saliva samples are emerging as an inexpensive and efficient alternative for large-scale screening. Pooled-sample testing of saliva has been applied for mass screening of SARS-CoV-2 infection. Current policies recommend isolating people with borderline cycle threshold (Ct) values (35<Ct <40), despite these Ct values indicating minimal infection risk. We propose the new concept of a "social cut-off" Ct value and risk stratification based on the correlation of Ct with infectivity. We also describe the experience of RT-qPCR screening of saliva samples at our institution. It is important to implement a scientific approach to minimize viral transmission while allowing economic and social activities to continue.
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19
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Huber M, Schreiber PW, Scheier T, Audigé A, Buonomano R, Rudiger A, Braun DL, Eich G, Keller DI, Hasse B, Böni J, Berger C, Günthard HF, Manrique A, Trkola A. High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children. Microorganisms 2021; 9:microorganisms9030642. [PMID: 33808815 PMCID: PMC8003663 DOI: 10.3390/microorganisms9030642] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 01/10/2023] Open
Abstract
Rising demands for repetitive SARS-CoV-2 screens and mass testing necessitate additional test strategies. Saliva may serve as an alternative to nasopharyngeal swab (NPS) as its collection is simple, non-invasive and amenable for mass- and home testing, but its rigorous validation, particularly in children, is missing. We conducted a large-scale head-to-head comparison of SARS-CoV-2 detection by RT-PCR in saliva and NPS of 1270 adults and children reporting to outpatient test centers and an emergency unit. In total, 273 individuals were tested positive for SARS-CoV-2 in either NPS or saliva. SARS-CoV-2 RT-PCR results in the two specimens showed a high agreement (overall percent agreement = 97.8%). Despite lower viral loads in the saliva of both adults and children, detection of SARS-CoV-2 in saliva fared well compared to NPS (positive percent agreement = 92.5%). Importantly, in children, SARS-CoV-2 infections were more often detected in saliva than NPS (positive predictive value = 84.8%), underlining that NPS sampling in children can be challenging. The comprehensive parallel analysis reported here establishes saliva as a generally reliable specimen for the detection of SARS-CoV-2, with particular advantages for testing children, that is readily applicable to increase and facilitate repetitive and mass testing in adults and children.
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Affiliation(s)
- Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
- Correspondence: (M.H.); (A.T.); Tel.: +41-44-634-26-39 (M.H.); +41-44-634-26-53 (A.T.)
| | - Peter Werner Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; (P.W.S.); (T.S.); (D.L.B.); (B.H.)
| | - Thomas Scheier
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; (P.W.S.); (T.S.); (D.L.B.); (B.H.)
| | - Annette Audigé
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
| | - Roberto Buonomano
- Division of Infectious Diseases and Hospital Hygiene, Spital Limmattal, 8952 Schlieren, Switzerland;
| | - Alain Rudiger
- Division of Medicine, Spital Limmattal, 8952 Schlieren, Switzerland;
| | - Dominique L. Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; (P.W.S.); (T.S.); (D.L.B.); (B.H.)
| | - Gerhard Eich
- Division of Infectious Diseases, Hospital Hygiene and Occupational Medicine, Stadtspital Triemli, 8063 Zurich, Switzerland;
| | - Dagmar I. Keller
- Emergency Department, University Hospital Zurich, 8091 Zurich, Switzerland;
| | - Barbara Hasse
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; (P.W.S.); (T.S.); (D.L.B.); (B.H.)
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
| | - Christoph Berger
- Division of Infectious Diseases and Hospital Epidemiology, University Children’s Hospital Zurich, 8032 Zurich, Switzerland;
| | - Huldrych F. Günthard
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; (P.W.S.); (T.S.); (D.L.B.); (B.H.)
| | - Amapola Manrique
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (A.A.); (J.B.); (H.F.G.); (A.M.)
- Correspondence: (M.H.); (A.T.); Tel.: +41-44-634-26-39 (M.H.); +41-44-634-26-53 (A.T.)
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20
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Ronca SE, Sturdivant RX, Barr KL, Harris D. SARS-CoV-2 Viability on 16 Common Indoor Surface Finish Materials. HERD-HEALTH ENVIRONMENTS RESEARCH & DESIGN JOURNAL 2021; 14:49-64. [PMID: 33618545 DOI: 10.1177/1937586721991535] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AIM This study investigated the stability of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on 16 common environmental surface materials. BACKGROUND SARS-CoV-2 is the causative agent of severe coronavirus disease, a significant public health concern that quickly led to a pandemic. Contamination of environmental surface materials is of concern, with previous studies identifying long-term detection of infectious particles on surfaces. These contaminated surfaces create an increased risk for contact transmission. METHODS Surface materials were inoculated with 10,000 plaque forming units and samples were collected 4, 8, 12, 24, 30, 48, and 168 hours post infection (hpi). Viral titers were determined for each sample and time point using plaque assays. Nonparametric modeling utilized the Turnbull algorithm for interval-censored data. Maximum likelihood estimates for the survival curve were calculated. Parametric proportional hazards regression models for interval censored data were used to explore survival time across the surface materials. RESULTS There was a sharp decline in recoverable virus after 4 hpi for all tested surfaces. By 12 hpi, infectious SARS-CoV-2 was recoverable from only four surfaces; and by 30 hr, the virus was recoverable from only one surface. There were differences in survival curves based on the materials although some groups of materials are similar, both statistically and practically. CONCLUSIONS While very low amounts of infectious SARS-CoV-2 are recoverable over time, there remains a risk of viral transmission by surface contamination in indoor environments. Individuals and institutions must follow appropriate procedures to decontaminate indoor environment and increase diligence for hand hygiene and personal protective equipment.
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Affiliation(s)
- Shannon E Ronca
- Department of Pediatrics, National School of Tropical Medicine, 3989Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | | | - Kelli L Barr
- Department of Biology, 14643Baylor University, Waco, TX, USA
| | - Debra Harris
- Department of Human Sciences and Design, 14643Baylor University, Waco, TX, USA
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21
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Basso D, Aita A, Padoan A, Cosma C, Navaglia F, Moz S, Contran N, Zambon CF, Maria Cattelan A, Plebani M. Salivary SARS-CoV-2 antigen rapid detection: A prospective cohort study. Clin Chim Acta 2021; 517:54-59. [PMID: 33626369 PMCID: PMC7897404 DOI: 10.1016/j.cca.2021.02.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 01/19/2023]
Abstract
Background and aim SARS-CoV-2 quick testing is relevant for the containment of new pandemic waves. Antigen testing in self-collected saliva might be useful. We compared salivary and naso-pharyngeal swab (NPS) SARS-CoV-2 antigen detection by a rapid chemiluminescent assay (CLEIA) and two different point-of-care (POC) immunochromatographic assays, with results of molecular testing. Methods 234 patients were prospectively enrolled. Paired self-collected saliva (Salivette) and NPS were obtained to perform rRT-PCR, chemiluminescent (Lumipulse G) and POC (NPS: Fujirebio and Abbott; saliva: Fujirebio) for SARS-CoV-2 antigen detection. Results The overall agreement between NPS and saliva rRT-PCR was 78.7%, reaching 91.7% at the first week from symptoms. SARS-CoV-2 CLEIA antigen was highly accurate in distinguishing positive and negative NPS (ROC-AUC = 0.939, 95%CI:0.903–0.977), with 81.6% sensitivity and 93.8% specificity. This assay on saliva reached the optimal value within 7 days from symptoms onset (Sensitivity: 72%; Specificity: 97%). Saliva POC antigen was limited in sensitivity (13%), performing better in NPS (Sensitivity: 48% and 66%; Specificity: 100% and 99% for Espline and Abbott respectively), depending on viral loads. Conclusions Self-collected saliva is a valid alternative to NPS for SARS-CoV-2 detection by molecular, but also by CLEIA antigen testing, which is therefore potentially useful for large scale screening.
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Affiliation(s)
- Daniela Basso
- Department of Medicine - DIMED, Laboratory Medicine, University Hospital of Padova, Padova, Italy.
| | - Ada Aita
- Department of Medicine - DIMED, Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Andrea Padoan
- Department of Medicine - DIMED, Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Chiara Cosma
- Department of Medicine - DIMED, Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Filippo Navaglia
- Department of Medicine - DIMED, Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Stefania Moz
- Department of Medicine - DIMED, Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Nicole Contran
- Department of Medicine - DIMED, Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Carlo-Federico Zambon
- Department of Medicine - DIMED, Laboratory Medicine, University Hospital of Padova, Padova, Italy
| | - Anna Maria Cattelan
- Tropical and Infectious Diseases Unit, University Hospital of Padova, Padova, Italy
| | - Mario Plebani
- Department of Medicine - DIMED, Laboratory Medicine, University Hospital of Padova, Padova, Italy
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22
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Barat B, Das S, De Giorgi V, Henderson DK, Kopka S, Lau AF, Miller T, Moriarty T, Palmore TN, Sawney S, Spalding C, Tanjutco P, Wortmann G, Zelazny AM, Frank KM. Pooled Saliva Specimens for SARS-CoV-2 Testing. J Clin Microbiol 2021; 59:e02486-20. [PMID: 33262219 PMCID: PMC8106731 DOI: 10.1128/jcm.02486-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022] Open
Abstract
We evaluated saliva (SAL) specimens for SARS-CoV-2 reverse transcriptase PCR (RT-PCR) testing by comparison of 459 prospectively paired nasopharyngeal (NP) or midturbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (n = 380) and in the emergency department (ED) (n = 69). The percentages of positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% confidence interval [CI], 65.8% to 90.5%) and 99.8% (95% CI, 98.7% to 100%), respectively. The percent positive agreement increased to 90.0% (95% CI, 74.4% to 96.5%) when considering only samples with moderate to high viral load (cycle threshold [CT ] for the NP, ≤34). Pools of five saliva specimens were also evaluated on three platforms, bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion, and Roche Cobas 6800. The average loss of signal upon pooling was 2 to 3 CT values across the platforms. The sensitivities of detecting a positive specimen in a pool compared with testing individually were 94%, 90%, and 94% for the CDC 2019-nCoV real-time RT-PCR, Panther Fusion SARS-CoV-2 assay, and Cobas SARS-CoV-2 test, respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport medium for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.
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Affiliation(s)
- Bidisha Barat
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Sanchita Das
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valeria De Giorgi
- Department of Transfusion Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - David K Henderson
- Hospital Epidemiology Service, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Stacy Kopka
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Rockville, Maryland, USA
| | - Anna F Lau
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Tracey Miller
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Rockville, Maryland, USA
| | | | - Tara N Palmore
- Hospital Epidemiology Service, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Shari Sawney
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Chris Spalding
- Hospital Epidemiology Service, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | - Adrian M Zelazny
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Karen M Frank
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland, USA
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23
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Ana Laura GO, Abraham Josué NR, Briceida LM, Israel PO, Tania AF, Nancy MR, Lourdes JB, Daniela DLRZ, Fernando OR, Carlos Mauricio JE, Sergio René BP, Irineo RT, Horacio MG, Oscar MC, Héctor Q. Sensitivity of the Molecular Test in Saliva for Detection of COVID-19 in Pediatric Patients With Concurrent Conditions. Front Pediatr 2021; 9:642781. [PMID: 33912522 PMCID: PMC8071854 DOI: 10.3389/fped.2021.642781] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/17/2021] [Indexed: 01/27/2023] Open
Abstract
Background: The reference standard for the molecular diagnostic testing for COVID-19 is the use of nasopharyngeal or combined nasopharyngeal and oropharyngeal (NP/OP) swabs. Saliva has been proposed as a minimally invasive specimen whose collection reduces the risks for health care personnel. Objective: To assess the suitability of saliva for COVID-19 diagnosis as a replacement of the reference standard NP/OP swab in the setting of a tertiary care pediatric unit. Study design: A paired study based in the prospective cohort design in patients suspected of having COVID-19. Methods: RT-PCR was used to detect SARS-CoV-2 in paired samples of saliva and NP/OP swab collected from May through August 2020 from 156 pediatric participants, of whom 128 has at least one comorbidity and 91 showed clinical symptoms related to SARS-CoV-2 infection. Additionally, we studied a group of 326 members of the hospital staff, of whom 271 had symptoms related to SARS-CoV-2 infection. Results: In the group of pediatric participants the sensitivity of the diagnostic test in saliva was 82.3% (95% CI 56.6-96.2) and the specificity 95.6% (95% CI 90.8-98.4). The prevalence of COVID-19 was 10.9% (17/156). In 6 of the 23 participants who tested positive for SARS-CoV-2 in at least one specimen type, the virus was detected in saliva but not in NP/OP swab, while in 3 participants the NP/OP swab was positive and saliva negative. In the group of adults, the sensitivity of the test in saliva was 77.8% (95% CI 67.2-86.3) and prevalence 24.8% (81/326). Discordant results between the two types of specimens showed a significant association with low viral load in the pharynx of adults but not of pediatric participants. Interpretation: In the context of a pediatric tertiary care hospital, the sensibility of the test in saliva is not high enough to replace the use of NP/OP swab for COVID-19 diagnosis. Neither NP/OP swab nor saliva could detect all the participants infected with SARS-CoV-2.
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Affiliation(s)
- Guzmán-Ortiz Ana Laura
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Nevárez-Ramírez Abraham Josué
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Parra-Ortega Israel
- Laboratorio Clínico, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Martínez-Rodríguez Nancy
- Unidad de Investigación Epidemiológica en Endocrinología y Nutrición, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - De la Rosa-Zamboni Daniela
- Departamento de Epidemiología Hospitalaria, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | | | | | - Reyna-Trinidad Irineo
- Departamento de Enfermería, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Márquez-González Horacio
- Departamento de Investigación Clínica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Medina-Contreras Oscar
- Unidad de Investigación Epidemiológica en Endocrinología y Nutrición, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Quezada Héctor
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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24
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Medeiros da Silva RC, Nogueira Marinho LC, de Araújo Silva DN, Costa de Lima K, Pirih FQ, Luz de Aquino Martins AR. Saliva as a possible tool for the SARS-CoV-2 detection: A review. Travel Med Infect Dis 2020; 38:101920. [PMID: 33220456 PMCID: PMC7674016 DOI: 10.1016/j.tmaid.2020.101920] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Salivary tests for the new coronavirus (SARS-CoV-2) diagnosis have been suggested as alternative methods for the nasopharyngeal and oropharyngeal tests. METHOD Two reviewers independently performed a search in the following electronic databases: PubMed, Medline, Cochrane Library, Web of Science, Embase and Scopus to identify cross-sectional and cohort studies that used saliva samples for SARS-CoV-2 detection. The search strategy was: ("saliva") and ("SARS-CoV-2" or "coronavirus" or "COVID-1"). RESULTS A total of 363 studies were identified and 39 were selected for review. Salivary samples for SARS-CoV-2 detection was as consistent and sensitive as the nasopharyngeal swabs in most studies, having been effective in detecting asymptomatic infections previously tested negative in nasopharyngeal samples. Viral nucleic acids found in saliva obtained from the duct of the salivary gland may indicate infection in that gland. Live viruses could be detected in saliva by viral culture. CONCLUSIONS Salivary samples show great potential in SARS-CoV-2 detection and may be recommended as a simple and non-invasive alternative.
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Affiliation(s)
| | | | | | - Kenio Costa de Lima
- Dentistry Department, Rio Grande Do Norte Federal University, Natal, RN, Brazil.
| | - Flavia Queiroz Pirih
- Dentistry Department, Rio Grande Do Norte Federal University, Natal, RN, Brazil.
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25
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Barat B, Das S, De Giorgi V, Henderson DK, Kopka S, Lau AF, Miller T, Moriarty T, Palmore TN, Sawney S, Spalding C, Tanjutco P, Wortmann G, Zelazny AM, Frank KM. Pooled Saliva Specimens for SARS-CoV-2 Testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.10.02.20204859. [PMID: 33052363 PMCID: PMC7553188 DOI: 10.1101/2020.10.02.20204859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We evaluated saliva (SAL) specimens for SARS-CoV-2 RT-PCR testing by comparison of 459 prospectively paired nasopharyngeal (NP) or mid-turbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (N=380) and in the emergency department (ED) (N=69). The percent positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% CI: 65.8% - 90.5%) and 99.8% (95% CI: 98.7% - 100%), respectively. The sensitivity increased to 90.0% (95% CI: 74.4% - 96.5%) when considering only samples with moderate to high viral load (Cycle threshold (Ct) for the NP <=34). Pools of five saliva specimens were also evaluated on three platforms: bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion, and Roche COBAS 6800. The median loss of signal upon pooling was 2-4 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 100%, 93%, and 95% for CDC 2019-nCoV Real-Time RT-PCR, Panther Fusion® SARS-CoV-2 assay, and cobas® SARS-CoV-2 test respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport media for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.
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Affiliation(s)
- Bidisha Barat
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Sanchita Das
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Valeria De Giorgi
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - David K Henderson
- Hospital Epidemiology Service, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Stacy Kopka
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Rockville, MD, USA
| | - Anna F Lau
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Tracey Miller
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Rockville, MD, USA
| | | | - Tara N Palmore
- Hospital Epidemiology Service, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Shari Sawney
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Chris Spalding
- Hospital Epidemiology Service, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Adrian M Zelazny
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Karen M Frank
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
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