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Solito C, Hernández-García M, Arguedas Casamayor N, Pavón Ortiz A, Pino R, Alsina L, F de Sevilla M. COVID-19 admissions: Trying to define the real impact of infection in hospitalized patients. An Pediatr (Barc) 2024; 100:342-351. [PMID: 38580601 DOI: 10.1016/j.anpede.2024.03.049] [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: 10/24/2023] [Accepted: 02/08/2024] [Indexed: 04/07/2024] Open
Abstract
INTRODUCTION AND OBJECTIVE Several studies have suggested that the hospitalization rate for COVID-19 in children and adolescents may reflect the prevalence of the infection rather than the severity of the disease. The aim of this study was to describe the clinical features of hospitalised paediatric patients with SARS-CoV-2 infection in order to understand if the infection was the reason for admission. METHODS Retrospective cohort study including patients aged 0-18 years with SARS-CoV-2 infection or multisystem inflammatory syndrome in children (MIS-C) admitted to a tertiary care children's hospital in Spain between 01/01/2020 and 12/31/2021. RESULTS 228 patients were included, corresponding to 150 cases of COVID-related admission (SARS-CoV-2 infection as main cause of hospitalization) and 78 of non-COVID-related admission (SARS-CoV-2 infection unrelated to the hospitalization). In the group of COVID-related admissions, 58 patients had comorbidities. Forty-nine patients had acute respiratory disease (pneumonia, bronchospasm or bronchiolitis). Multisystem inflammatory syndrome in children was diagnosed in 27 and was significantly more frequent in the first year of the pandemic (wild type virus). Eighty percent of patients with acute respiratory disease needed respiratory support, mostly low-flow oxygen therapy. The severity of the disease was similar in all virus variants. Two patients (both with severe comorbidities) died from COVID-related conditions. CONCLUSIONS In our study, one third of the patients were admitted with SARS-CoV-2 infection but not because of it. Acute respiratory disease was less frequent and had a better prognosis compared to the adult population, while MIS-C was a major cause of morbidity and hospitalization. The fatality rate was extremely low.
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Affiliation(s)
- Claudia Solito
- Servicio de Pediatría, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - María Hernández-García
- Servicio de Pediatría, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain; Grupo de Estudio de Enfermedades Infecciosas y Microbioma, Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain.
| | | | - Alba Pavón Ortiz
- Servicio de Pediatría, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Rosa Pino
- Servicio de Pediatría, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Laia Alsina
- Grupo de Estudio de Enfermedades por Disfunción Inmune en Pediatría, Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain; Unidad de Inmunología Clínica e Inmunodeficiencias Primarias, Servicio de Alergia e Inmunología Clínica, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain; Facultad de Medicina y Ciencias de la Salud, Universitat de Barcelona, Barcelona, Spain; Programa de Inmunología Clínica, Hospital Sant Joan de Déu-Hospital Clínic Barcelona, Barcelona, Spain; Plataforma de Terapias Avanzadas, Hospital Sant Joan de Déu-Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Mariona F de Sevilla
- Servicio de Pediatría, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain; Grupo de Estudio de Enfermedades Infecciosas y Microbioma, Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain; Facultad de Medicina y Ciencias de la Salud, Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Instituto de Salud Carlos III, Madrid, Spain
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Al-Shaibari KSA, Mousa HAL, Alqumber MAA, Alqfail KA, Mohammed A, Bzeizi K. The Diagnostic Performance of Various Clinical Specimens for the Detection of COVID-19: A Meta-Analysis of RT-PCR Studies. Diagnostics (Basel) 2023; 13:3057. [PMID: 37835801 PMCID: PMC10572802 DOI: 10.3390/diagnostics13193057] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND The diagnostic performance of numerous clinical specimens to diagnose COVID-19 through RT-PCR techniques is very important, and the test result outcome is still unclear. This review aimed to analyze the diagnostic performance of clinical samples for COVID-19 detection by RT-PCR through a systematic literature review process. METHODOLOGY A compressive literature search was performed in PubMed/Medline, Scopus, Embase, and Cochrane Library from inception to November 2022. A snowball search on Google, Google Scholar, Research Gate, and MedRxiv, as well as bibliographic research, was performed to identify any other relevant articles. Observational studies that assessed the clinical usefulness of the RT-PCR technique in different human samples for the detection or screening of COVID-19 among patients or patient samples were considered for this review. The primary outcomes considered were sensitivity and specificity, while parameters such as positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient were considered secondary outcomes. RESULTS A total of 85 studies out of 10,213 non-duplicate records were included for the systematic review, of which 69 articles were considered for the meta-analysis. The meta-analysis indicated better pooled sensitivity with the nasopharyngeal swab (NPS) than saliva (91.06% vs. 76.70%) and was comparable with the combined NPS/oropharyngeal swab (OPS; 92%). Nevertheless, specificity was observed to be better with saliva (98.27%) than the combined NPS/OPS (98.08%) and NPS (95.57%). The other parameters were comparable among different samples. The respiratory samples and throat samples showed a promising result relative to other specimens. The sensitivity and specificity of samples such as nasopharyngeal swabs, saliva, combined nasopharyngeal/oropharyngeal, respiratory, sputum, broncho aspirate, throat swab, gargle, serum, and the mixed sample were found to be 91.06%, 76.70%, 92.00%, 99.44%, 86%, 96%, 94.4%, 95.3%, 73.63%, and above 98; and 95.57%, 98.27%, 98.08%, 100%, 37%, 100%, 100%, 97.6%, and above 97, respectively. CONCLUSIONS NPS was observed to have relatively better sensitivity, but not specificity when compared with other clinical specimens. Head-to-head comparisons between the different samples and the time of sample collection are warranted to strengthen this evidence.
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Affiliation(s)
| | | | | | | | | | - Khalid Bzeizi
- Department of Liver Transplantation, King Faisal Specialist Hospital and Research Center, Riyadh 13541, Saudi Arabia
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Jain RK, Perumal N, Chaurasia D, Shrivastava R, Ahirwar KK, Sharma A, Kapoor G, Lalwani J. Performance Evaluation of Different RT-PCR Kits for the Direct Detection of SARS-CoV-2 in Preheated Specimens. J Lab Physicians 2023; 15:383-391. [PMID: 37564223 PMCID: PMC10411152 DOI: 10.1055/s-0043-1760752] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created high demand for molecular kits and consumables for mass screening of suspected individuals. Direct real-time polymerase chain reaction (RT-PCR) assay without nucleic acid extraction has several advantages in saving testing time and cost and helps in the rapid reporting of SARS-CoV-2. The present study evaluated the analytical performance of four SARS-CoV-2 RT-PCR for direct RT-PCR testing using preheated specimens. Methods A total of 100 clinical specimens were selected and divided into three different groups: (1) group I: 20 SARS-CoV-2 positive specimens with high viral load, viz., low Ct values (< 30 Ct), (2) group II: 50 SARS-CoV-2 positive specimens with low viral load, viz., high Ct values (> 30 Ct), and (3) group III: 30 SARS-CoV-2 negative specimens. Specimens were heat-inactivated at 70°C for 10 minutes and cooled down at 4°C and were evaluated for standard and direct RT-PCR method by using ViralDtect-II Multiplex Real-Time PCR kit, TaqPath COVID-19 Combo kit, COVIDsure Pro Multiplex RT-PCR kit, and Hi-PCR Coronavirus (COVID-19) Multiplex Probe PCR kit. Results Results showed that except ViralDtect-II kit, the other three TaqPath COVID-19 Combo kit, COVIDsure Pro kit, and Hi-PCR Coronavirus (COVID-19) RT-PCR kit were able to amplify all the SARS-CoV-2 genes in the direct RT-PCR method using preheated specimens. In group I specimens, 100% sensitivity was observed in all three RT-PCR kits. In group II specimens, COVIDsure Pro kit was found to be superior among other kits. Conclusion Direct RT-PCR method during pandemic situation is valuable and cost effective for the detection of SARS-CoV-2. All three TaqPath COVID-19 Combo kit, COVIDsure Pro kit, and Hi-PCR Coronavirus (COVID-19) RT-PCR kit can be used for direct RT-PCR method and COVIDsure Pro kit performance was found to be superior among all.
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Affiliation(s)
- Rajeev Kumar Jain
- State Virology Laboratory, Gandhi Medical College, Bhopal, Madhya Pradesh, India
| | - Nagaraj Perumal
- State Virology Laboratory, Gandhi Medical College, Bhopal, Madhya Pradesh, India
| | - Deepti Chaurasia
- Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India
| | - Rakesh Shrivastava
- Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India
| | | | - Archa Sharma
- Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India
| | - Garima Kapoor
- Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India
| | - Jaya Lalwani
- Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India
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SARS-CoV-2 transmission in teenagers and young adults in Fútbol Club Barcelona's Multidisciplinary Sports Training Academy. Eur J Pediatr 2023; 182:2421-2432. [PMID: 36914778 PMCID: PMC10010953 DOI: 10.1007/s00431-023-04880-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 03/16/2023]
Abstract
Most studies, aimed at determining the incidence and transmission of SARS-CoV-2 in children and teenagers, have been developed in school settings. Our study conducted surveillance and inferred attack rates focusing on the practice of sports. Prospective and observational study of those attending the sports facilities of Fútbol Club Barcelona (FCB), in Barcelona, Spain, throughout the 2020-2021 season. Participants were young players (from five different sports) and adult workers, who belonged to stable teams (shared routines and were involved in same quarantine rules). Biweekly health questionnaires and SARS-CoV-2 screening were conducted. From the 234 participants included, 70 (30%) both lived and trained in the FCB facilities (Recruitment Pathway 1;RP1) and 164 (70%) lived at their own household and just came to the facilities to train (RP2). During the study, 38 positive cases were identified; none had severe symptoms or needed hospitalization. The overall weekly incidence in the cohorts did not differ compared to the one expected in the community, except for 2 weeks when an outbreak occurred. The attack rate (AR) was three times higher for the participants from RP1, in comparison to those from RP2 (p < 0.01). A Basketball team showed a significant higher AR. Conclusion: Physical activities in stable teams are not related to an increased risk of transmission of SARS-CoV-2, since there were the same observed cases than expected in the community. The risk is higher in indoor sports (Basketball vs. Football), and in closed cohort living settings (RP1 vs. RP2). The fulfilment of preventive measures is essential. What is Known: • Despite the low numerical impact caused in paediatric hospitalizations during COVID-19 pandemic, the social impact has been maximum. • The transmission potential in children and teenagers is limited, and it had been widely demonstrated in school settings. What is New: • Group physical activities in children and teenagers are not also related to an increased risk of transmission of SARS-CoV-2, when preventive measures, such as washing hands, and screening protocols are applied. • Routine and semi-professional sports activities seem safe environments to promote during this pandemic.
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Gadkar VJ, Goldfarb DM, Al-Rawahi GN, Srigley JA, Smailus DE, Coope RJN, Pleasance S, Watson N, Chen T, Lam S, Hoang L, Tilley PAG. Extraction-free clinical detection of SARS-CoV-2 virus from saline gargle samples using Hamilton STARlet liquid handler. Sci Rep 2023; 13:4241. [PMID: 36918604 PMCID: PMC10013237 DOI: 10.1038/s41598-023-30993-2] [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: 05/12/2022] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
As part of the COVID-19 pandemic, clinical laboratories have been faced with massive increases in testing, resulting in sample collection systems, reagent, and staff shortages. We utilized self-collected saline gargle samples to optimize high throughput SARS-CoV-2 multiplex polymerase chain reaction (PCR) testing in order to minimize cost and technologist time. This was achieved through elimination of nucleic acid extraction and automation of sample handling on a widely available robotic liquid handler, Hamilton STARlet. A customized barcode scanning script for reading the sample ID by the Hamilton STARlet's software system was developed to allow primary tube sampling. Use of pre-frozen SARS-CoV-2 assay reaction mixtures reduced assay setup time. In both validation and live testing, the assay produced no false positive or false negative results. Of the 1060 samples tested during validation, 3.6% (39/1060) of samples required retesting as they were either single gene positive, had internal control failure or liquid aspiration error. Although the overall turnaround time was only slightly faster in the automated workflow (185 min vs 200 min), there was a 76% reduction in hands-on time, potentially reducing staff fatigue and burnout. This described process from sample self-collection to automated direct PCR testing significantly reduces the total burden on healthcare systems in terms of human resources and reagent requirements.
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Affiliation(s)
- Vijay J Gadkar
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada.
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada.
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital, Room No 2K9, 4500 Oak St, Vancouver, V6H 3N1, Canada.
| | - David M Goldfarb
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Ghada N Al-Rawahi
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Jocelyn A Srigley
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Duane E Smailus
- Canada's Michael Smith Genome Science Centre at BC Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Robin J N Coope
- Canada's Michael Smith Genome Science Centre at BC Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Stephen Pleasance
- Canada's Michael Smith Genome Science Centre at BC Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Nicole Watson
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
| | - Tammy Chen
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
| | - Sunny Lam
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
| | - Linda Hoang
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, Canada
| | - Peter A G Tilley
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Virology and Infection Control, BC Children's and Women's Hospital + Sunny Health Center, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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Accelerating the Laboratory Testing Capacity through Saliva Pooling Prior to Direct RT-qPCR for SARS-CoV-2 Detection. Diagnostics (Basel) 2022; 12:diagnostics12123160. [PMID: 36553167 PMCID: PMC9777453 DOI: 10.3390/diagnostics12123160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
The testing capacity of the laboratory is paramount for better control of the pandemic caused by SARS-CoV-2. The pooling method is promising to increase testing capacity, and the use of direct NAAT-based detection of SARS-CoV-2 on a non-invasive specimen such as saliva will ultimately accelerate the testing capacity. This study aims to validate the pooling-of-four method to quadruple the testing capacity using RNA-extraction-free saliva specimens. In addition, we intend to investigate the preferable stage of pooling, including pre- or post-heating. The compatibility of this approach was also tested on five commercial kits. Saliva specimens stored at -80 °C for several months were proven viable and were used for various tests in this study. Our findings revealed that pooling-of-four specimens had an overall agreement rate of 98.18% with their individual testing. Moreover, we proved that the pooling procedure could be conducted either pre- or post-heating, with no discordance and no significant difference in Ct values generated. When compared to other commercial detection kits, it demonstrated an overall agreement greater than 85%, which exhibits broad compatibility and ensures easy adaptability in clinical settings. This method has been proven reliable and increases the testing capacity up to fourfold.
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Yu T, Liu F, Yin H, Yi N, Li M. Comment to the article by Pedro Brotons: Validation and implementation of a direct RT-qPCR method for rapid screening of SARS-CoV-2 infection by using non-invasive saliva samples, IJID 110 (2021) 363-370. Int J Infect Dis 2022; 123:131-132. [PMID: 35985568 PMCID: PMC9381421 DOI: 10.1016/j.ijid.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/07/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Tianfei Yu
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, 161006, China,Corresponding author: Ming Li, College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar 161006, China; College of Computer and Control Engineering, Qiqihar University, Qiqihar 161006, China
| | - Fangfang Liu
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Haichang Yin
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Nana Yi
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Ming Li
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, 161006, China,Corresponding author: Ming Li, College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar 161006, China; College of Computer and Control Engineering, Qiqihar University, Qiqihar 161006, China
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Tobik ER, Kitfield-Vernon LB, Thomas RJ, Steel SA, Tan SH, Allicock OM, Choate BL, Akbarzada S, Wyllie AL. Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe. Expert Rev Mol Diagn 2022; 22:519-535. [PMID: 35763281 DOI: 10.1080/14737159.2022.2094250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Symptomatic testing and asymptomatic screening for SARS-CoV-2 continue to be essential tools for mitigating virus transmission. Though COVID-19 diagnostics initially defaulted to oropharyngeal or nasopharyngeal sampling, the worldwide urgency to expand testing efforts spurred innovative approaches and increased diversity of detection methods. Strengthening innovation and facilitating widespread testing remains critical for global health, especially as additional variants emerge and other mitigation strategies are recalibrated. AREAS COVERED A growing body of evidence reflects the need to expand testing efforts and further investigate the efficiency, sensitivity, and acceptability of saliva samples for SARS-CoV-2 detection. Countries have made pandemic response decisions based on resources, costs, procedures, and regional acceptability - the adoption and integration of saliva-based testing among them. Saliva has demonstrated high sensitivity and specificity while being less invasive relative to nasopharyngeal swabs, securing saliva's position as a more acceptable sample type. EXPERT OPINION Despite the accessibility and utility of saliva sampling, global implementation remains low compared to swab-based approaches. In some cases, countries have validated saliva-based methods but face challenges with testing implementation or expansion. Here, we review the localities that have demonstrated success with saliva-based SARS-CoV-2 testing approaches and can serve as models for transforming concepts into globally-implemented best practices.
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Affiliation(s)
- Emily R Tobik
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Lily B Kitfield-Vernon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Russell J Thomas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sydney A Steel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Steph H Tan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.,Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, USA
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Brittany L Choate
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sumaira Akbarzada
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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Nguyen LT, Nguyen PM, Dinh DV, Pham HN, Bui LAT, Vo CV, Nguyen BH, Bui HD, Hoang CX, Ngo NMV, Dang TT, Do AN, Vu DD, Nguyen LT, Nguyen MN, Dinh THT, Ho SA, Hoang LV, Hoang SX, Do Q. Establishment of an in‐house real‐time RT‐PCR assay for the detection of severe acute respiratory syndrome coronavirus 2 using the first World Health Organization international standard in a resource‐limited country. J Clin Lab Anal 2022; 36:e24355. [PMID: 35312118 PMCID: PMC9102516 DOI: 10.1002/jcla.24355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/15/2022] [Accepted: 03/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background The COVID‐19 pandemic caused by SARS‐CoV‐2 remains public health burdens and many unresolved issues worldwide. Molecular assays based on real‐time RT‐PCR are critical for the detection of SARS‐CoV‐2 in clinical specimens from patients suspected of COVID‐19. Objective We aimed to establish and validate an in‐house real‐time RT‐PCR for the detection of SARS‐CoV‐2. Methodology Primers and probes sets in our in‐house real‐time RT‐PCR assay were designed in conserved regions of the N and E target genes. Optimized multiplex real‐time RT‐PCR assay was validated using the first WHO International Standard (NIBSC code: 20/146) and evaluated clinical performance. Results The limit of detection validated using the first WHO International Standard was 159 IU/ml for both E and N target genes. The evaluation of clinical performance on 170 clinical samples showed a positive percent agreement of 100% and the negative percent agreement of 99.08% for both target genes. The Kappa value of 0.99 was an excellent agreement, the strong correlation of Ct values observed between two tests with r2 = 0.84 for the E gene and 0.87 for the N gene. Notably, we assessed on 60 paired saliva and nasopharyngeal samples. The overall agreement was 91.66%, and Kappa value of 0.74 showed a high agreement between two types of samples. When using nasopharyngeal swabs as the reference standard, positive percent agreement, and negative percent agreement were 91.83% and 90.90%, respectively. Conclusion In the present study, we established and validated an in‐house real‐time RT‐PCR for molecular detection of SARS‐CoV‐2 in a resource‐limited country.
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Affiliation(s)
- Linh Tung Nguyen
- Department of Occupational Medicine Vietnam Military Medical University Hanoi Vietnam
| | - Phuong Minh Nguyen
- Department of Occupational Medicine Vietnam Military Medical University Hanoi Vietnam
| | - Duc Viet Dinh
- Department of Epidemiology Vietnam Military Medical University Hanoi Vietnam
| | - Hung Ngoc Pham
- Department of Epidemiology Vietnam Military Medical University Hanoi Vietnam
| | - Lan Anh Thi Bui
- Institute of Biomedicine Vietnam‐Russia Tropical Center Hanoi Vietnam
| | - Cuong Viet Vo
- Institute of Biomedicine Vietnam‐Russia Tropical Center Hanoi Vietnam
| | - Ben Huu Nguyen
- Department of Occupational Medicine Vietnam Military Medical University Hanoi Vietnam
| | - Hoan Duy Bui
- Department of Occupational Medicine Vietnam Military Medical University Hanoi Vietnam
| | - Cuong Xuan Hoang
- Department of Occupational Medicine Vietnam Military Medical University Hanoi Vietnam
| | - Nhat Minh Van Ngo
- Department of Human Anatomy Vietnam Military Medical University Hanoi Vietnam
| | - Truong Tien Dang
- Department of Human Anatomy Vietnam Military Medical University Hanoi Vietnam
| | - Anh Ngoc Do
- Department of Parasitology Vietnam Military Medical University Hanoi Vietnam
| | - Dung Dinh Vu
- Institute of Biomedicine and Pharmacy Vietnam Military Medical University Hanoi Vietnam
- Hanoi University of Science and Technology Hanoi Vietnam
| | - Linh Thuy Nguyen
- Institute of Biomedicine and Pharmacy Vietnam Military Medical University Hanoi Vietnam
- Faculty of Biology National University of Hanoi Hanoi Vietnam
| | - Mai Ngoc Nguyen
- Institute of Biomedicine and Pharmacy Vietnam Military Medical University Hanoi Vietnam
- Faculty of Biology National University of Hanoi Hanoi Vietnam
| | - Thu Hang Thi Dinh
- Institute of Biomedicine and Pharmacy Vietnam Military Medical University Hanoi Vietnam
| | - Son Anh Ho
- Institute of Biomedicine and Pharmacy Vietnam Military Medical University Hanoi Vietnam
| | - Luong Van Hoang
- Department of Human Anatomy Vietnam Military Medical University Hanoi Vietnam
- Institute of Biomedicine and Pharmacy Vietnam Military Medical University Hanoi Vietnam
| | - Su Xuan Hoang
- Institute of Biomedicine and Pharmacy Vietnam Military Medical University Hanoi Vietnam
| | - Quyet Do
- Military Hospital 103 Vietnam Military Medical University Hanoi Vietnam
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Ham RE, Smothers AR, King KL, Napolitano JM, Swann TJ, Pekarek LG, Blenner MA, Dean D. Efficient SARS-CoV-2 Quantitative Reverse Transcriptase PCR Saliva Diagnostic Strategy utilizing Open-Source Pipetting Robots. J Vis Exp 2022:10.3791/63395. [PMID: 35225290 PMCID: PMC9199378 DOI: 10.3791/63395] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
The emergence of the recent SARS-CoV-2 global health crisis introduced key challenges for epidemiological research and clinical testing. Characterized by a high rate of transmission and low mortality, the COVID-19 pandemic necessitated accurate and efficient diagnostic testing, particularly in closed populations such as residential universities. Initial availability of nucleic acid testing, like nasopharyngeal swabs, was limited due to supply chain pressure which also delayed reporting of test results. Saliva-based reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) testing has shown to be comparable in sensitivity and specificity to other testing methods, and saliva collection is less physically invasive to participants. Consequently, we developed a multiplex RT-qPCR diagnostic assay for population surveillance of Clemson University and the surrounding community. The assay utilized open-source liquid handling robots and thermocyclers instead of complex clinical automation systems to optimize workflow and system flexibility. Automation of saliva-based RT-qPCR enables rapid and accurate detection of a wide range of viral RNA concentrations for both large- and small-scale testing demands. The average turnaround for the automated system was < 9 h for 95% of samples and < 24 h for 99% of samples. The cost for a single test was $2.80 when all reagents were purchased in bulk quantities.
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Affiliation(s)
- Rachel E Ham
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University
| | - Austin R Smothers
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University; Department of Bioengineering, Clemson University
| | - Kylie L King
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University
| | - Justin M Napolitano
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University
| | | | | | - Mark A Blenner
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University; Department of Chemical & Biomolecular Engineering, Clemson University; Department of Chemical & Biomolecular Engineering, University of Delaware
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University; Department of Bioengineering, Clemson University;
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11
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Blanco I, Violán C, Suñer C, Garcia-Prieto J, Argerich MJ, Rodriguez-Illana M, Moreno N, Cardona PJ, Blanco A, Torán-Monserrat P, Clotet B, Bonet JM, Prat N. Comparison between mid-nasal swabs and buccal swabs for SARS-CoV-2 detection in mild COVID-19 patients. J Infect 2022; 84:e78-e79. [PMID: 35172195 PMCID: PMC8841008 DOI: 10.1016/j.jinf.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Ignacio Blanco
- Laboratori Clínic Metropolitana Nord, Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain.
| | - Concepción Violán
- Unitat de Suport a la Recerca Metropolitana Nord, Fundació Institut Universitari per a la recerca a l'Atenció Primària Jordi Gol i Gurina (IDIAP J Gol), Barcelona, Spain
| | - Clara Suñer
- Direcció d'Atenció Primària Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | | | | | | | - Nemesio Moreno
- Departament de Genètica i Microbiologia, UAB, Cerdanyola, Catalonia, Spain
| | - Pere-Joan Cardona
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Anna Blanco
- Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Bonaventura Clotet
- Universitat de Vic-Universitat Central de Catalunya (UVIC-UCC), Vic, Spain
| | - Josep M Bonet
- Direcció d'Atenció Primària Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - Nuria Prat
- Direcció d'Atenció Primària Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
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12
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Alemany A, Millat-Martinez P, Ouchi D, Corbacho-Monné M, Bordoy AE, Esteban C, Hernández Á, Casañ C, Gonzalez V, Costes G, Capdevila-Jáuregui M, Torrano-Soler P, San José A, Ara J, Prat N, Clotet B, Bassat Q, Gimenez M, Blanco I, Baro B, Mitjà O. Self-collected mid-nasal swabs and saliva specimens, compared with nasopharyngeal swabs, for SARS-CoV-2 detection in mild COVID-19 patients. J Infect 2021; 83:709-737. [PMID: 34537322 PMCID: PMC8444446 DOI: 10.1016/j.jinf.2021.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/23/2022]
Affiliation(s)
- Andrea Alemany
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain; Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | | | - Dan Ouchi
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain
| | | | - Antoni E Bordoy
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Cristina Esteban
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Águeda Hernández
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Cristina Casañ
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Victoria Gonzalez
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Gèlia Costes
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain
| | | | | | - Alba San José
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain
| | - Jordi Ara
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain; Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - Núria Prat
- Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - Bonaventura Clotet
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain; Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain; Universitat de Vic-Universitat Central de Catalunya (UVIC-UCC), Vic, Spain
| | - Quique Bassat
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain; Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Montserrat Gimenez
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Ignacio Blanco
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain; Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - Bàrbara Baro
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.
| | - Oriol Mitjà
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain; Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain; Lihir Medical Centre, International SOS Clinic, Lihir Island, Papua New Guinea
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13
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Brogna B, Bignardi E, Brogna C, Capasso C, Gagliardi G, Martino A, Musto LA. COVID-19 Pneumonia in Vaccinated Population: A Six Clinical and Radiological Case Series. MEDICINA-LITHUANIA 2021; 57:medicina57090891. [PMID: 34577814 PMCID: PMC8466241 DOI: 10.3390/medicina57090891] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 01/12/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and its related disease (COVID-19) continue to represent a challenge for humans. To date, vaccination programs have represented an opportunity to navigate the pandemic. However, the advent of new genetic COVID-19 variants has increased more attention representing a worrying threat not only for not vaccinated but also for vaccinated people as virus infections have been shown also in the last ones. Herein, we report different clinical cases and radiological findings of COVID-19 pneumonia in six fully vaccinated patients. Two patients had a history of Rituximab therapy for follicular lymphoma and with persistent positivity for SARS-CoV-2 on nasopharyngeal/oropharyngeal (NP/OP) swabs and with moderate pneumonia on the chest computed tomography (CT). One patient who resulted to be positive to delta variant 8 days after the second vaccination dose, died shortly after. Two patients were hospitalized due to the worsening of fever and dyspnea in presence of mild pneumonia on CT. In one patient mild pneumonia was found on the chest-CT performed after a lipothymic episode associated with chest pain and positive NP/OP swab tested for SARS-CoV-2. These data suggested that in fully vaccinated people, caution should be preserved, and the use of masks and social distancing should be continued in all closed environments. However, further clinical trials should be done to better understand how various factors can influence vaccine immunogenicity as the presence of virus mutations, age factors, and the presence of an immunocompromised state.
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Affiliation(s)
- Barbara Brogna
- Department of Radiology, San Giuseppe Moscati Hospital, Contrada Amoretta, 83100 Avellino, Italy; (G.G.); (L.A.M.)
- Correspondence:
| | - Elio Bignardi
- Radiology Unit, “Cotugno Hospital”, Naples, Via Quagliariello 54, 80131 Naples, Italy;
| | - Claudia Brogna
- Pediatric Neurology Unit, Fondazione Policlinico Universitario “A. Gemelli”, IRCSS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
- Neuropsychiatric Unit, ASL Avellino, Via Degli Imbimbo 10/12, 83100 Avellino, Italy
| | - Chiara Capasso
- Pharmacology Department, “Frangipane” Hospital, ASL Avellino, Via V. Emanuele, 83031 Ariano Irpino, Italy;
| | - Giuliano Gagliardi
- Department of Radiology, San Giuseppe Moscati Hospital, Contrada Amoretta, 83100 Avellino, Italy; (G.G.); (L.A.M.)
| | - Alberigo Martino
- Radiology Unit, “Frangipane” Hospital, ASL Avellino, Via V. Emanuele, 83031 Ariano Irpino, Italy;
| | - Lanfranco Aquilino Musto
- Department of Radiology, San Giuseppe Moscati Hospital, Contrada Amoretta, 83100 Avellino, Italy; (G.G.); (L.A.M.)
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