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Acevedo-Sánchez G, Mora-Aguilera G, Coria-Contreras JJ, Álvarez-Maya I. Were metabolic and other chronic diseases the driven onset epidemic forces of COVID-19 in Mexico? Front Public Health 2023; 11:995602. [PMID: 37608984 PMCID: PMC10441236 DOI: 10.3389/fpubh.2023.995602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 07/14/2023] [Indexed: 08/24/2023] Open
Abstract
The underline hypothesis of this study was that SARS-CoV-2 can infect individuals regardless of health condition, sex, and age in opposition to the classical epidemiological assumption of an identifiable susceptible subpopulation for epidemic development. To address this issue, a population cohort with 24.4 million metadata associated with 226,089 official RT-qPCR positive and 283,450 negative cases, including 27,769 deceased, linked putatively to B.1. and B.1.1. SARS-CoV-2 lineages were analyzed. The analysis baseline was to determine the infection and mortality structure of the diseased cohort at the onset-exponential phase of the first epidemic wave in Mexico under the assumption of limited herd immunity. Individuals with nonchronic diseases (NOCDs) were compared with those exhibiting at least one of 10 chronic diseases (CDs) adjusted by age and sex. Risk factors for infection and mortality were estimated with classification and regression tree (CART) and cluster analysis based on Spearman's matrix of rho-values in RStudio®, complemented with two proposed mortality indices. SARS-CoV-2 infection was independent of health condition (52.8% NOCD vs. 47.2% CDs; p = 0.001-0.009) but influenced by age >46 in one risk analysis scenario (p < 0.001). Sex contributed 9.7% to the overall risk. The independent effect was supported by the health structure of negative cases with a similar tendency but a higher proportion of NOCDs (61.4%, p = 0.007). The infection probability in individuals with one CD was determined by the disease type and age, which was higher in those older individuals (≥56 years) exhibiting diabetes (12.3%, cp = 0.0006), hypertension (10.1%, cp < 0.0001), and obesity (7.8%, cp = 0.001). In contrast, the mortality risk was heavily influenced by CD conditioned by sex and age, accounting for 72.3% of total deaths (p = 0.001-0.008). Significant mortality risk (48%) was comprised of women and men (w, m) aged ≥56 years with diabetes (19% w and 27.9% m, cp < 0.0004), hypertension (11.5% w, cp = 0.0001), and CKD (3.5% w and 5.3% m, cp = 0.0009). Older people with diabetes and hypertension comorbidity increased the risk to 60.5% (p = 0.001). Based on a mortality-weighted index, women were more vulnerable to preexisting metabolic or cardiovascular diseases. These findings support our hypothesis and justify the need for surveillance systems at a communitarian level. This is the first study addressing this fundamental epidemiological question.
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Affiliation(s)
- Gerardo Acevedo-Sánchez
- Laboratory of Epidemiological Risk Analysis (LANREF), Postgraduate College, Montecillo Campus, Texcoco, State of Mexico, Mexico
| | - Gustavo Mora-Aguilera
- Laboratory of Epidemiological Risk Analysis (LANREF), Postgraduate College, Montecillo Campus, Texcoco, State of Mexico, Mexico
| | - Juan J. Coria-Contreras
- Laboratory of Epidemiological Risk Analysis (LANREF), Postgraduate College, Montecillo Campus, Texcoco, State of Mexico, Mexico
| | - Ikuri Álvarez-Maya
- Center for Research and Applied Technology in Jalisco (CIATEJ), Guadalajara, Jalisco, Mexico
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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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KÖKBAŞ U. Korona Virüs Tanısı ve Biyosensörler. ARŞIV KAYNAK TARAMA DERGISI 2022. [DOI: 10.17827/aktd.1117871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hızla gelişen teknoloji dünyada dijitalleşme çağında laboratuvar tıbbının da bu gelişime ayak uydurarak sensör tabanlı ölçüm sistemlerinin kullanım alanları genişlemektedir. Biyosensörler kolay kullanımı, portatif olması, hızlı ve kesin sonuç vermesi gibi özelliklerinden dolayı salgın hastalık takibinde önemli rol oynayacaktır.
Çin'in Wuhan şehrinde 2019 yılında ortaya çıkan korona virüs hastalığı pandemi haline dönüşmüştür. Pandeminin takibi ve kontrolü için tanı testleri geliştirilmesi ve tanı testlerinde kullanılacak örnek seçimi büyük önem kazanmıştır.
Bu derlemede korona virüs hastalığının tanı ve takibinin günümüzde nasıl yapıldığı hakkında bilgi verip biyosensörlerin tanı ve takip amacıyla kullanılabilirliği hakkında bilgiler verilmektedir.
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Oh SM, Lee JS, Jo HJ, Kim D, Park D, Hwang YH, Choi Y, Lee CM, Lee S, Chang E, Lee E, Kim TS, Seong MW, Choe PG, Kim NJ. Clinical application of the Panbio™ COVID-19 Ag rapid test device and SSf-COVID19 kit for the detection of SARS-CoV-2 infection. BMC Res Notes 2022; 15:357. [PMID: 36471453 PMCID: PMC9720920 DOI: 10.1186/s13104-022-06226-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE We evaluated the sensitivity and specificity of the Panbio™ COVID-19 Ag rapid test device using nasal swabs and those of the SSf-COVID19 kit, one of RT-PCR tests, using saliva specimens. These tests were compared with RT-PCR tests using nasopharyngeal swabs for the diagnosis of SARS-CoV-2 infection. The three diagnostic tests were simultaneously conducted for patients aged ≥ 18 years, who were about to be hospitalized or had been admitted for COVID-19 confirmed by RT-PCR in two research hospitals from August 20 to October 29, 2021. Nasal swabs were tested using the Panbio™ COVID-19 Ag rapid test device. More than 1 mL of saliva was self-collected and tested using the SSf-COVID19 kit. RESULTS In total, 157 patients were investigated; 124 patients who were about to be hospitalized and 33 patients already admitted for COVID-19. The overall sensitivity and specificity of the Panbio™ COVID-19 Ag rapid test device with nasal swabs were 64.7% (95% confidence interval [CI] 47.9-78.5%) and 100.0% (95% CI 97.0-100.0%), respectively. The median time to confirm a positive result was 180 s (interquartile range 60-255 s). The overall sensitivity and specificity of the SSf-COVID19 kit with saliva specimens were 94.1% (95% CI 80.9-98.4%) and 100.0% (95% CI 97.0-100.0%), respectively.
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Affiliation(s)
- Sang-Min Oh
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea ,grid.411545.00000 0004 0470 4320Present Address: Department of Internal Medicine, Jeonbuk National University Medical School and Hospital, 20 Geonjiro, Deokjin-gu, 54907 Jeonju, Jeollabuk-do Republic of Korea
| | - Jee-Soo Lee
- grid.31501.360000 0004 0470 5905Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Hyeon Jae Jo
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Donghwan Kim
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Dohyeon Park
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Young Hoon Hwang
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Yunsang Choi
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Chan Mi Lee
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Seungjae Lee
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Euijin Chang
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Eunyoung Lee
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea ,grid.412479.dDivision of Infectious Diseases, Seoul Metropolitan Government – Seoul National University Boramae Medical Center, 20 Boramae-ro 5-gil, Dongjak-gu, 07061 Seoul, Republic of Korea
| | - Taek Soo Kim
- grid.31501.360000 0004 0470 5905Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Moon-Woo Seong
- grid.31501.360000 0004 0470 5905Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Pyoeng Gyun Choe
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
| | - Nam Joong Kim
- grid.31501.360000 0004 0470 5905Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, 03080 Seoul, Republic of Korea
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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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Okoturo E, Amure M. SARS-CoV-2 saliva testing using RT-PCR: a systematic review. Int J Infect Dis 2022; 121:166-171. [PMID: 35577250 PMCID: PMC9136484 DOI: 10.1016/j.ijid.2022.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/01/2022] Open
Abstract
OBJECTIVES There remain challenges in using SARS-CoV-2 RNA diagnostic assays in the respiratory tract in a pandemic. More so certain countries such as Hong Kong have already included saliva as part of their mass-testing protocol. The aim of this study was to conduct a systematic review on the alternate use of saliva as a SARS-CoV-2 RNA testing specimen in the context of mass screening with reverse transcription polymerase chain reaction. METHODS Our search methodology was modeled after the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) checklist, and the risk of bias of the selected studies was qualitatively assessed. The percentage individual positive and percentage agreement of both index (saliva) and reference (nasopharyngeal swab), in preference to specificity and sensitivity, were estimated using Kappa statistics. RESULTS A total of 44 studies met the inclusion criteria. The average percentage positive saliva cases was 72.7% (95% confidence interval), which was lower but not substantially different from the percentage positive NPS of 78.7% (95% confidence interval), and there was an average overall agreement of 89.7% (95% confidence interval). CONCLUSION Although the literature supports nasopharyngeal swab as a superior testing specimen, an alternative clinical specimen in saliva may offer potential benefits such that a potentially reduced accuracy may be tolerated, especially in low socioeconomic regions.
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Affiliation(s)
- Eyituoyo Okoturo
- Head & Neck Cancer Division, Oral & Maxillofacial Surgery Department, Lagos State University Teaching Hospital, Lagos, Nigeria; Molecular Oncology Program, Medical Research Centre, Lagos State University College of Medicine, Lagos, Nigeria.
| | - Mary Amure
- Oral & Maxillofacial Surgery Department, Lagos State University Teaching Hospital, Lagos, Nigeria
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Wang Y, Upadhyay A, Pillai S, Khayambashi P, Tran SD. Saliva as a diagnostic specimen for SARS-CoV-2 detection: a scoping review. Oral Dis 2022; 28 Suppl 2:2362-2390. [PMID: 35445491 PMCID: PMC9115496 DOI: 10.1111/odi.14216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 03/22/2022] [Accepted: 04/12/2022] [Indexed: 12/03/2022]
Abstract
Objectives This scoping review aims to summarize the diagnostic value of saliva assessed from current studies that (1) compare its performance in reverse transcriptase‐polymerase chain reaction testing to nasopharyngeal swabs, (2) evaluate its performance in rapid and point‐of‐care COVID‐19 diagnostic tests, and (3) explore its use as a specimen for detecting anti‐SARS‐CoV‐2 antibodies. Materials and Methods A systematic search was performed on the following databases: Medline and Embase (Ovid), World Health Organization, Centers for Disease Control and Prevention, and Global Health (Ovid) from January 2019 to September 2021. Of the 657 publications identified from the searches, n = 146 articles were included in the final scoping review. Results Our findings showcase that salivary samples exceed nasopharyngeal swabs in detecting SARS‐CoV‐2 using reverse transcriptase‐polymerase chain reaction testing in several studies. A select number of rapid antigen and point‐of‐care tests from the literature were also identified capable of high detection rates using saliva. Moreover, anti‐SARS‐CoV‐2 antibodies have been shown to be detectable in saliva through biochemical assays. Conclusion We highlight the potential of saliva as an all‐rounded specimen in detecting SARS‐CoV‐2. However, future large‐scale clinical studies will be needed to support its widespread use as a non‐invasive clinical specimen for COVID‐19 testing.
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Pierri B, Tafuro M, Cuomo MC, Concilio DD, Vassallo L, Pierri A, Ferro A, Rofrano G, Gallo A, Stasio AD, Mancusi A, Galdi L, Coppola A, Buonerba C, Atripaldi L, Cerino P. Assessment of Saliva Specimens' Reliability for COVID-19 Surveillance. Front Public Health 2022; 10:840996. [PMID: 35444987 PMCID: PMC9015071 DOI: 10.3389/fpubh.2022.840996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
The aim of the present study is to assess saliva as a reliable specimen for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by real-time reverse transcription-PCR (RT-PCR), especially in community mass screening programs. The performance analysis considered 1,221 total samples [nasopharyngeal (NP) swabs and corresponding saliva], tested by means of a reference diagnostic real-time RT-PCR assay. Conflicting results were further investigated with a second, more sensitive, reference assay. Analysis of agreement showed a good concordance (95.82%), with a k coefficient value of.74 (p < 0.001); moreover, a follow-up analysis revealed the presence of viral gene targets in saliva samples at the time point the corresponding NP swabs turned negative. Data obtained prove the reliability of this alternative biofluid for SARS-CoV-2 detection in real-time RT-PCR. Considering the role of saliva in the coronavirus disease 2019 (COVID-19) transmission and pathogenesis, and the advantages in the use of salivary diagnostics, the present validation supports the use of saliva as an optimal choice in large-scale population screening and monitoring of the SARS-CoV-2 virus.
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Affiliation(s)
- Biancamaria Pierri
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
- *Correspondence: Biancamaria Pierri
| | - Maria Tafuro
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Maria Concetta Cuomo
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Denise Di Concilio
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Lucia Vassallo
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Andrea Pierri
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Amedeo Ferro
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Giuseppe Rofrano
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Alfonso Gallo
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Antonio Di Stasio
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Andrea Mancusi
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Lydia Galdi
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Annachiara Coppola
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Carlo Buonerba
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Luigi Atripaldi
- Cotugno Hospital, Azienda Ospedaliera di Rilievo Nazionale Ospedali dei Colli, Naples, Italy
| | - Pellegrino Cerino
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
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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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10
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Suda Y, Tajima Y, Nishi JI, Kajiya T. Diagnostic Method for COVID-19 Using Sugar Chain-Immobilized Nanoparticles and Saliva Specimens. Methods Mol Biol 2022; 2452:63-74. [PMID: 35554901 DOI: 10.1007/978-1-0716-2111-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Identification of viruses that infects animals or plants, and determination of their quantity are essential for the diagnosis of infectious disease and for the determination of a strategy in the treatment of virus-derived diseases. However, the concentration of viruses existing in a living body (in bodily fluid), food, drinking water, river water, and so on. is not high enough to be detected using conventional diagnostic methods. For example, since the concentration of influenza virus released from an infected person is less than the detection limit of conventional simple examination kits (rapid kit) or even a PCR process at the initial stage of infection, it is difficult to detect the presence of influenza virus which will lead to influenza disease. Our technology allows for safe, efficient, and selective concentration of viruses without troublesome ultracentrifugation, using sugar chain-immobilized metal nanoparticles based on the binding interaction between viruses and sugar chains. For COVID-19, we have developed and commercialized two molecular diagnosis kits: SUDx SARS-CoV-2 detection kit, and SGNP nCoV/Flu PCR detection kit, for the Japanese market in 2020.
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Affiliation(s)
- Yasuo Suda
- Department of Chemistry and Biotechnology, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan.
| | - Yasuhisa Tajima
- Division of Infectious Disease, Hamamatsu Medical Center, Shizuoka, Japan
| | - Jun-Ichiro Nishi
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Takashi Kajiya
- Clinical Research Center, Tenyoukai Central Hospital, Kagoshima, Japan
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11
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Liu M, Roychowdhury P, Ito CJ. Role of the otolaryngologist in nasopharyngeal swab training: A case report and review of the literature. OTOLARYNGOLOGY CASE REPORTS 2021; 20:100316. [PMID: 34957363 PMCID: PMC8130604 DOI: 10.1016/j.xocr.2021.100316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Nasopharyngeal swabs are commonly done in the medical field for a multitude of reasons, and they recently have been an essential component of widespread testing to control the spread of COVID-19. Although rare, improper technique when performing nasopharyngeal swabs has the potential to lead to injury or misleading test results. We present a case of uncontrolled epistaxis requiring hospitalization following a routine nasopharyngeal swab in a healthy patient. Both the complexity and variability of the anatomy of the nasopharynx can contribute to poor swabbing technique. Otolaryngologists should be encouraged to educate and support other healthcare workers to improve the yield and reduce the risk of harm due to nasopharyngeal swabs. Increased comfort levels with performing nasopharyngeal swabs will also improve the sensitivity of screening tests for common respiratory viruses such as influenza, Epstein-Barr virus (EBV), or bacteria such as Staphylococcus aureus.
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Affiliation(s)
- Mark Liu
- University of Massachusetts Medical School, 55 N Lake Ave, Worcester, MA, 01655, United States
| | - Prithwijit Roychowdhury
- University of Massachusetts Medical School, 55 N Lake Ave, Worcester, MA, 01655, United States
| | - Christopher J Ito
- Department of Otolaryngology Head and Neck Surgery, UMass Memorial Medical Center, 55 N Lake Ave, Worcester, MA, 01655, United States
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12
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Klein RC, Fabres Klein MH, Barbosa LG, Gonzaga Knnup LV, Rodrigues Venâncio LP, Lima JB, Araújo-Santos T. Identifying Inconclusive Data in the SARS-CoV-2 Molecular Diagnostic Using Nucleocapsid Phosphoprotein Gene as Target. Arch Pathol Lab Med 2021; 146:272-277. [PMID: 34797908 DOI: 10.5858/arpa.2021-0423-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT The gold standard test to identify the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in coronavirus disease 2019 (COVID-19) patients is the real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR), but the inconclusive data and presence of false positive diagnosis remain the major problem of this approach. OBJECTIVE To compare the fitness of two primers sets to the SARS-CoV-2 nucleocapsid phosphoprotein (NP) gene in the molecular diagnosis of COVID-19, we verify the inconclusive data and confidence of high cycle threshold (Ct) values in the SARS-CoV-2 detection. DESIGN The 970 patient samples were tested using United States Centers for Disease Control and Prevention protocol. We compared the fitness of two primers sets to two different regions of NP gene. In addition, we check the consistency of positive samples with high Ct values by retesting extracted SARS-CoV-2 RNA or by second testing of patients. RESULTS The N1 and N2 displayed similar fitness during testing with no differences between Ct values. Then, we verified security range Cts related to positive diagnostic with Ct above 34 failing in 21/32 (65.6%) after retesting of samples. The samples patients with Ct above 34.89 that were doubly positive revealed a low sensitivity (52.4%) and specificity (63.6%) of the test in samples with Ct above 34. CONCLUSIONS It is secure to use one primer set to the NP gene to identify SARS-CoV-2 in samples. However, samples with high Ct values may be considered inconclusive and retested to avoid false positive diagnosis.
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Affiliation(s)
- Raphael Contelli Klein
- Infectious Agents and Vectors Research Group at the Center for Biological and Health Sciences, Federal University of Western Bahia, Barreiras, Bahia, Brazil
| | - Mary Hellen Fabres Klein
- Infectious Agents and Vectors Research Group at the Center for Biological and Health Sciences, Federal University of Western Bahia, Barreiras, Bahia, Brazil
| | - Larissa Gomes Barbosa
- Infectious Agents and Vectors Research Group at the Center for Biological and Health Sciences, Federal University of Western Bahia, Barreiras, Bahia, Brazil
| | - Lívia Vasconcelos Gonzaga Knnup
- Infectious Agents and Vectors Research Group at the Center for Biological and Health Sciences, Federal University of Western Bahia, Barreiras, Bahia, Brazil
| | - Larissa Paola Rodrigues Venâncio
- Infectious Agents and Vectors Research Group at the Center for Biological and Health Sciences, Federal University of Western Bahia, Barreiras, Bahia, Brazil
| | - Jonilson Berlink Lima
- Infectious Agents and Vectors Research Group at the Center for Biological and Health Sciences, Federal University of Western Bahia, Barreiras, Bahia, Brazil
| | - Théo Araújo-Santos
- Infectious Agents and Vectors Research Group at the Center for Biological and Health Sciences, Federal University of Western Bahia, Barreiras, Bahia, Brazil
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13
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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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14
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Atieh MA, Guirguis M, Alsabeeha NHM, Cannon RD. The diagnostic accuracy of saliva testing for SARS-CoV-2: A systematic review and meta-analysis. Oral Dis 2021; 28 Suppl 2:2347-2361. [PMID: 34080272 PMCID: PMC8242702 DOI: 10.1111/odi.13934] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/25/2021] [Accepted: 05/30/2021] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Early detection of coronavirus disease 2019 (COVID-19) is paramount for controlling the progression and spread of the disease. Currently, nasopharyngeal swabbing (NPS) is the standard method for collecting specimens. Saliva was recently proposed as an easy and safe option with many authorities adopting the methodology despite the limited evidence of efficacy. OBJECTIVES The aim of this review was to systematically evaluate the current literature on the use of saliva test for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and carry out a meta-analysis to determine its diagnostic accuracy. MATERIALS AND METHODS Prospective studies were searched for in electronic databases, complemented by hand-searching relevant journals. The risk of bias and applicability were assessed using the revised Quality Assessment of Studies of Diagnostic Accuracy Studies (QUADAS-2) tool. Meta-analyses and meta-regression modeling were performed to calculate the diagnostic accuracy and examine sources of heterogeneity. RESULTS A total of 16 studies were included with 2928 paired samples. The overall meta-analysis showed a high sensitivity and specificity for saliva test at 0.88 (95% CI 0.82-0.92) and 0.92 (95% CI 0.75-0.98), respectively. The diagnostic odds ratio was calculated at 87 (95% CI 19-395) and area under the curve was calculated as 0.92 (95% CI 0.90-0.94) suggesting very good performance of the saliva tests in detecting SARS-CoV-2. CONCLUSION Saliva testing has a very good discriminative and diagnostic ability to detect of SARS-CoV-2. Additional large and well-designed prospective studies are needed to further validate the diagnostic accuracy and determine a safe sample collection method prior to its recommendation for mass application. CLINICAL RELEVANCE Saliva demonstrated high sensitivity and specificity. The use of saliva will allow for self-collection of specimens and specimen collection in outpatient and community clinics.
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Affiliation(s)
- Momen A Atieh
- Mohammed Bin Rashid University of Medicine and Health Sciences, Hamdan Bin Mohammed College of Dental Medicine, Dubai Healthcare City, Dubai, United Arab Emirates.,Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - Marina Guirguis
- Mohammed Bin Rashid University of Medicine and Health Sciences, Hamdan Bin Mohammed College of Dental Medicine, Dubai Healthcare City, Dubai, United Arab Emirates
| | - Nabeel H M Alsabeeha
- Prosthetic Section, Ras Al-Khaimah Dental Center, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Richard D Cannon
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
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15
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Justo AFO, Bueno MS, Barbosa GR, Perosa AH, Carvalho JM, Bellei N. Comparison of viral load between saliva and nasopharyngeal swabs for SARS-CoV2: the role of days of symptoms onset on diagnosis. Mem Inst Oswaldo Cruz 2021; 116:e210018. [PMID: 33886872 PMCID: PMC8061341 DOI: 10.1590/0074-02760210018] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is highly infectious causing millions of deaths worldwide. Nasopharyngeal swabs are the primary sample of choice for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), thus, to decrease the exposure to potentially infected samples through the collection is a key point to reduce the risk of infection in healthcare workers. OBJECTIVES This study aimed to evaluate the sensitivity and viral load of saliva specimens by days of symptoms onset comparing to nasopharyngeal swabs in subjects with mild symptoms. METHODS Saliva and nasopharyngeal swabs samples were collected from São Paulo Hospital workers presenting mild symptoms, such as fever, cough, sore throat, rhinorrhea, myalgia, headaches, anosmia, ageusia, and fatigue. To understand the positivity and viral load, reverse transcription-polymerase chain reaction (RT-PCR) was performed. FINDINGS Saliva specimens presented a sensitivity of 98.6% compared to nasopharyngeal swabs. Overall, saliva showed lower viral load compared to nasopharyngeal swabs, regarding days of symptoms onset on diagnosis, the first four days had significant changes in viral load and no significant difference was reported in the days five to nine. MAIN CONCLUSIONS Although RT-PCR of saliva has presented a lower viral load compared to nasopharyngeal swabs, saliva specimens are a potential and reliable candidate for COVID-19 diagnosis through RT-PCR.
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Affiliation(s)
| | - Mariana Sardinha Bueno
- Universidade Federal de São Paulo, Departamento de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brasil
| | - Gabriela Rodrigues Barbosa
- Universidade Federal de São Paulo, Departamento de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brasil
| | | | - Joseane Ma Carvalho
- Universidade Federal de São Paulo, Departamento de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brasil
| | - Nancy Bellei
- Universidade Federal de São Paulo, Departamento de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brasil
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16
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Moreira VM, Mascarenhas P, Machado V, Botelho J, Mendes JJ, Taveira N, Almeida MG. Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis. Diagnostics (Basel) 2021; 11:diagnostics11020363. [PMID: 33670020 PMCID: PMC7926389 DOI: 10.3390/diagnostics11020363] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
The rapid and accurate testing of SARS-CoV-2 infection is still crucial to mitigate, and eventually halt, the spread of this disease. Currently, nasopharyngeal swab (NPS) and oropharyngeal swab (OPS) are the recommended standard sampling techniques, yet, these have some limitations such as the complexity of collection. Hence, several other types of specimens that are easier to obtain are being tested as alternatives to nasal/throat swabs in nucleic acid assays for SARS-CoV-2 detection. This study aims to critically appraise and compare the clinical performance of RT-PCR tests using oral saliva, deep-throat saliva/posterior oropharyngeal saliva (DTS/POS), sputum, urine, feces, and tears/conjunctival swab (CS) against standard specimens (NPS, OPS, or a combination of both). In this systematic review and meta-analysis, five databases (PubMed, Scopus, Web of Science, ClinicalTrial.gov and NIPH Clinical Trial) were searched up to the 30th of December, 2020. Case-control and cohort studies on the detection of SARS-CoV-2 were included. The methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2). We identified 1560 entries, 33 of which (1.1%) met all required criteria and were included for the quantitative data analysis. Saliva presented the higher accuracy, 92.1% (95% CI: 70.0-98.3), with an estimated sensitivity of 83.9% (95% CI: 77.4-88.8) and specificity of 96.4% (95% CI: 89.5-98.8). DTS/POS samples had an overall accuracy of 79.7% (95% CI: 43.3-95.3), with an estimated sensitivity of 90.1% (95% CI: 83.3-96.9) and specificity of 63.1% (95% CI: 36.8-89.3). The remaining index specimens could not be adequately assessed given the lack of studies available. Our meta-analysis shows that saliva samples from the oral region provide a high sensitivity and specificity; therefore, these appear to be the best candidates for alternative specimens to NPS/OPS in SARS-CoV-2 detection, with suitable protocols for swab-free sample collection to be determined and validated in the future. The distinction between oral and extra-oral salivary samples will be crucial, since DTS/POS samples may induce a higher rate of false positives. Urine, feces, tears/CS and sputum seem unreliable for diagnosis. Saliva testing may increase testing capacity, ultimately promoting the implementation of truly deployable COVID-19 tests, which could either work at the point-of-care (e.g. hospitals, clinics) or at outbreak control spots (e.g., schools, airports, and nursing homes).
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Affiliation(s)
- Vânia M. Moreira
- Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal;
| | - Paulo Mascarenhas
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal; (P.M.); (V.M.); (J.B.); (J.J.M.); (N.T.)
- Evidence-Based Hub, CiiEM, Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal
| | - Vanessa Machado
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal; (P.M.); (V.M.); (J.B.); (J.J.M.); (N.T.)
- Evidence-Based Hub, CiiEM, Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal
| | - João Botelho
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal; (P.M.); (V.M.); (J.B.); (J.J.M.); (N.T.)
- Evidence-Based Hub, CiiEM, Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal
| | - José João Mendes
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal; (P.M.); (V.M.); (J.B.); (J.J.M.); (N.T.)
- Evidence-Based Hub, CiiEM, Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal
| | - Nuno Taveira
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal; (P.M.); (V.M.); (J.B.); (J.J.M.); (N.T.)
- Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, 1649-003 Lisbon, Portugal
| | - M. Gabriela Almeida
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal; (P.M.); (V.M.); (J.B.); (J.J.M.); (N.T.)
- UCIBIO, REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Monte de Caparica, Portugal
- Correspondence: ; Tel.: +(351)-212-964-800
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17
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Hanson KE, Caliendo AM, Arias CA, Hayden MK, Englund JA, Lee MJ, Loeb M, Patel R, El Alayli A, Altayar O, Patel P, Falck-Ytter Y, Lavergne V, Morgan RL, Murad MH, Sultan S, Bhimraj A, Mustafa RA. The Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19: Molecular Diagnostic Testing. Clin Infect Dis 2021:ciab048. [PMID: 33480973 PMCID: PMC7929045 DOI: 10.1093/cid/ciab048] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19). Direct detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acids in respiratory tract specimens informs patient, healthcare institution and public health level decision-making. The numbers of available SARS-CoV-2 nucleic acid detection tests are rapidly increasing, as is the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) recognized a significant need for frequently updated systematic reviews of the literature to inform evidence-based best practice guidance. OBJECTIVE The IDSA's goal was to develop an evidence-based diagnostic guideline to assist clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss the nuance of test result interpretation in a variety of practice settings and highlight important unmet research needs in the COVID-19 diagnostic testing space. METHODS IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. RESULTS The panel agreed on 17 diagnostic recommendations. CONCLUSIONS Universal access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention and the public response to the COVID-19 pandemic. Information on the clinical performance of available tests is rapidly emerging, but the quality of evidence of the current literature is considered moderate to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is recommended for asymptomatic individuals with known or suspected contact with a COVID-19 case. Testing asymptomatic individuals without known exposure is suggested when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions, dictate eligibility for surgery, or inform solid organ or hematopoietic stem cell transplantation timing. Ultimately, prioritization of testing will depend on institutional-specific resources and the needs of different patient populations.
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Affiliation(s)
- Kimberly E Hanson
- Department of Internal Medicine and Pathology, University of Utah, Salt Lake City, Utah
| | - Angela M Caliendo
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Cesar A Arias
- Division of Infectious Diseases, Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health McGovern Medical School, Center for Infectious Diseases, University of Texas Health School of Public Health, Houston, TX
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, Illinois; Department of Pathology, Rush University Medical Center, Chicago, Illinois
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children’s Research Institute, Seattle, Washington
| | - Mark J Lee
- Department of Pathology and Clinical Microbiology Laboratory, Duke University School of Medicine, Durham, North Carolina
| | - Mark Loeb
- Divinsion of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario
| | - Robin Patel
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota
| | - Abdallah El Alayli
- Outcomes and Implementation Research Unit, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Osama Altayar
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Payal Patel
- Department of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Yngve Falck-Ytter
- VA Northeast Ohio Healthcare System, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Valery Lavergne
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Rebecca L Morgan
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario
| | - M Hassan Murad
- Division of Preventive Medicine, Mayo Clinic, Rochester, Minnesota
| | - Shahnaz Sultan
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis VA Healthcare System, Minneapolis, Minnesota
| | - Adarsh Bhimraj
- Department of Infectious Diseases, Cleveland Clinic, Cleveland, Ohio
| | - Reem A Mustafa
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
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18
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O'Leary TJ. Relative Sensitivity of Saliva and Upper Airway Swabs for Initial Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Ambulatory Patients: Rapid Review. J Mol Diagn 2021; 23:265-273. [PMID: 33395576 PMCID: PMC7775608 DOI: 10.1016/j.jmoldx.2020.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/08/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022] Open
Abstract
Saliva has been proposed as an alternative to upper airway swabs when testing for severe acute respiratory syndrome coronavirus 2. Although some studies have suggested higher viral loads and clinical sensitivity when testing saliva, studies have been relatively small and have given rise to contradictory results. To better understand the relative performance characteristics of saliva and upper airway samples, I performed a rapid systematic review (registered on PROSPERO as CRD42020205035), focusing on studies that included at least 20 subjects who provided diagnostic saliva and upper airway samples on the same day, which were tested by nucleic acid amplification methods and for which a confusion matrix could be constructed for based on a composite reference standard. Nineteen studies comprising 21 cohorts that met predetermined acceptance criteria were identified following a search of PubMed, medRxiv, and bioRxiv. Seven of these cohorts were incorporated into a meta-analysis using a random effects model, which suggests that nasopharyngeal swabs are somewhat more sensitive than saliva samples for the diagnosis of early disease in ambulatory patients, such as in drive-through centers or community health centers. Nevertheless, the difference is modest, and the reduced need for personal protective equipment for saliva sampling may justify the difference. Conclusions are limited by the significant heterogeneity of disease prevalence in the study populations and variation in the approaches to saliva sample collection.
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Affiliation(s)
- Timothy J O'Leary
- Office of Research and Development, Veterans Health Administration, Washington, District of Columbia; and the Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland.
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19
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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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