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Loidl V, Klinc C, Fusiak J, Crispin A, Hoffmann VS, Nennstiel-Ratzel U, Mansmann U. [Results of PCR Pool Testing In Primary and Special Needs Schools In Bavaria For The School Year 2021/2022: Sentinel Surveillance In Face-To-Face Teaching During The Sars-CoV-2 Pandemic]. Gesundheitswesen 2024; 86:237-246. [PMID: 38316408 DOI: 10.1055/a-2216-0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
In the school years 2019/20 and 2020/21, children were physically, psychologically, and socially stressed by school closures caused by the SARS-CoV-2 pandemic. To ensure attendance with optimal infection protection, PCR pool testing was conducted during the 2021/22 school year at Bavarian elementary schools and schools for pupils with special needs for timely detection of SARS-CoV-2 infection. This study analyzes the results of PCR pool testing over time stratified by region, school type, and age of children. The data were obtained from classes in elementary and special needs schools, involving pupils aged 6 to 11 years, who participated in the Bavaria-wide PCR pool testing from 09/20/21 to 04/08/22. Samples were collected twice weekly, consisting of PCR pool samples and individual PCR samples, which were only evaluated in case of a positive pool test. A class was considered positive if at least one individual sample from that class was positive within a calendar week (CW). A school (class) was considered to be infection-prone if three or more classes in that school (students in that class) were positive within a CW. The data included 2,430 elementary schools (339 special needs schools) with 23,021 (2,711) classes and 456,478 (29,200) children. A total of 1,157,617 pools (of which 3.37% were positive) and 724,438 individual samples (6.76% positive) were analyzed. Larger schools exhibited higher PR compared to smaller schools. From January 2022, the Omicron variant led to a massive increase in PR across Bavaria. The incidence rates per 100,000 person-weeks within the individual school samples were significantly lower than the concurrently reported age-specific and general infection incidences in the overall Bavarian population. PCR pool testing revealed relatively few positive pools, with an average of four children per one hundred pools testing positive. Schools and classes were rarely considered infection-prone, even during periods of high incidences outside of schools. The combination of PCR pool testing and hygiene measures allowed for a largely safe in-person education for pupils in primary and special needs schools in the school year 2021/22.
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Affiliation(s)
- Verena Loidl
- Institut für Medizinische Informationsverarbeitung, Biometrie und Epidemiologie (IBE), Ludwig-Maximilians-Universität München, Medizinische Fakultät, München, Germany
- Pettenkofer School of Public Health, Ludwig-Maximilians-Universität München, Medizinische Fakultät, München, Germany
| | - Christina Klinc
- GP1, Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Oberschleißheim, Germany
| | - Jakub Fusiak
- Institut für Medizinische Informationsverarbeitung, Biometrie und Epidemiologie (IBE), Ludwig-Maximilians-Universität München, Medizinische Fakultät, München, Germany
| | - Alexander Crispin
- Institut für Medizinische Informationsverarbeitung, Biometrie und Epidemiologie (IBE), Ludwig-Maximilians-Universität München, Medizinische Fakultät, München, Germany
| | - Verena Sophia Hoffmann
- Institut für Medizinische Informationsverarbeitung, Biometrie und Epidemiologie (IBE), Ludwig-Maximilians-Universität München, Medizinische Fakultät, München, Germany
| | - Uta Nennstiel-Ratzel
- GP1, Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Oberschleißheim, Germany
| | - Ulrich Mansmann
- Institut für Medizinische Informationsverarbeitung, Biometrie und Epidemiologie (IBE), Ludwig-Maximilians-Universität München, Medizinische Fakultät, München, Germany
- Pettenkofer School of Public Health, Ludwig-Maximilians-Universität München, Medizinische Fakultät, München, Germany
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Liu Y, Yin Y, Ward MP, Li K, Chen Y, Duan M, Wong PPY, Hong J, Huang J, Shi J, Zhou X, Chen X, Xu J, Yuan R, Kong L, Zhang Z. Optimization of Screening Strategies for COVID-19: Scoping Review. JMIR Public Health Surveill 2024; 10:e44349. [PMID: 38412011 PMCID: PMC10933748 DOI: 10.2196/44349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 06/29/2023] [Accepted: 11/21/2023] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND COVID-19 screening is an effective nonpharmaceutical intervention for identifying infected individuals and interrupting viral transmission. However, questions have been raised regarding its effectiveness in controlling the spread of novel variants and its high socioeconomic costs. Therefore, the optimization of COVID-19 screening strategies has attracted great attention. OBJECTIVE This review aims to summarize the evidence and provide a reference basis for the optimization of screening strategies for the prevention and control of COVID-19. METHODS We applied a methodological framework for scoping reviews and the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) checklist. We conducted a scoping review of the present publications on the optimization of COVID-19 screening strategies. We searched the PubMed, Web of Science, and Elsevier ScienceDirect databases for publications up to December 31, 2022. English publications related to screening and testing strategies for COVID-19 were included. A data-charting form, jointly developed by 2 reviewers, was used for data extraction according to the optimization directions of the screening strategies. RESULTS A total of 2770 unique publications were retrieved from the database search, and 95 abstracts were retained for full-text review. There were 62 studies included in the final review. We summarized the results in 4 major aspects: the screening population (people at various risk conditions such as different regions and occupations; 12/62, 19%), the timing of screening (when the target population is tested before travel or during an outbreak; 12/62, 19%), the frequency of screening (appropriate frequencies for outbreak prevention, outbreak response, or community transmission control; 6/62, 10%), and the screening and detection procedure (the choice of individual or pooled detection and optimization of the pooling approach; 35/62, 56%). CONCLUSIONS This review reveals gaps in the optimization of COVID-19 screening strategies and suggests that a number of factors such as prevalence, screening accuracy, effective allocation of resources, and feasibility of strategies should be carefully considered in the development of future screening strategies.
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Affiliation(s)
- Yuanhua Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yun Yin
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Michael P Ward
- Sydney School of Veterinary Science, The University of Sydney, NSW, Australia
| | - Ke Li
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yue Chen
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Mengwei Duan
- Department of Mathematics and Physics, North China Electric Power University, Baoding, China
| | | | - Jie Hong
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jiaqi Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jin Shi
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xuan Zhou
- Department of Mathematics and Physics, North China Electric Power University, Baoding, China
| | - Xi Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jiayao Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Rui Yuan
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Lingcai Kong
- Department of Mathematics and Physics, North China Electric Power University, Baoding, China
| | - Zhijie Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
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Ali S, Cella E, Johnston C, Rojas AC, Brown AN, Deichen M, Azarian T. Environmental surface monitoring as a noninvasive method for SARS-CoV-2 surveillance in community settings: Lessons from a university campus study. Sci Total Environ 2024; 912:169456. [PMID: 38123097 DOI: 10.1016/j.scitotenv.2023.169456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/22/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Environmental testing of high-touch objects is a potential noninvasive approach for monitoring population-level trends of SARS-CoV-2 and other respiratory viruses within a defined setting. We aimed to determine the association between SARS-CoV-2 contamination on high-touch environmental surfaces, community level case incidence, and university student health data. Environmental swabs were collected from January 2022 to November 2022 from high-touch objects and surfaces from five locations on a large university campus in Florida, USA. RT-qPCR was used to detect and quantify viral RNA, and a subset of positive samples was analyzed by viral genome sequencing to identify circulating lineages. During the study period, we detected SARS-CoV-2 viral RNA on 90.7 % of 162 tested samples. Levels of environmental viral RNA correlated with trends in community-level activity and case reports from the student health center. A significant positive correlation was observed between the estimated viral gene copy number in environmental samples and the weekly confirmed cases at the university. Viral sequencing data from environmental samples identified lineages concurrently circulating in the local community and state based on genomic surveillance data. Further, we detected emerging variants in environmental samples prior to their identification by clinical genomic surveillance. Our results demonstrate the utility of viral monitoring on high-touch environmental surfaces for SARS-CoV-2 surveillance at a community level. In communities with delayed or limited testing facilities, immediate environmental surface testing may considerably inform epidemic dynamics.
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Affiliation(s)
- Sobur Ali
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Catherine Johnston
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Ana C Rojas
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Ashley N Brown
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Michael Deichen
- Student Health Services, University of Central Florida, Orlando, FL, USA
| | - Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA.
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Ratel J, Vigneau E, Mercier F, Lebreton S, Nguyen TLN, Courcoux P, Engel E. Implementation of sample pooling to strengthen the surveillance of food chemical safety: Case study of nDL-PCBs in pork meat. Food Chem 2024; 433:137111. [PMID: 37659292 DOI: 10.1016/j.foodchem.2023.137111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/04/2023]
Abstract
Current food chemical safety surveillance relies on highly sensitive but costly analyses, with low throughput. A promising option is a sample pooling-based approach: instead of analyzing samples one-by-one, high-sensitivity methods could be used to evaluate pools of n samples. A proof-of-concept was sought using the surveillance of nDL-PCBs in pork meat. The practical feasibility of producing large pools (up to 200 samples) was studied, and accuracy of results for the nDL-PCBs were validated for pool sizes up to 100. Numerical simulation of pooling strategies yielded optimal numbers of samples to be pooled to obtain best cost-effectiveness. Based on pooling strategy, simulations showed that for a realistic contamination prevalence of 0.1%, analyzing pools of 25 samples would allow the total number of tests to be reduced 19-fold compared with one-by-one analysis, while retaining the sensitivity and specificity.
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Affiliation(s)
- Jérémy Ratel
- INRAE, UR QuaPA, F-63122 Saint-Genès-Champanelle, France.
| | | | | | | | | | | | - Erwan Engel
- INRAE, UR QuaPA, F-63122 Saint-Genès-Champanelle, France.
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Rahmasari R, Raekiansyah M, Aliyah SH, Yodi P, Baihaqy F, Irhamsyah M, Sari KCDP, Suryadi H, Moi ML, Sauriasari R. Development and validation of cost-effective SYBR Green-based RT-qPCR and its evaluation in a sample pooling strategy for detecting SARS-CoV-2 infection in the Indonesian setting. Sci Rep 2024; 14:1817. [PMID: 38245603 PMCID: PMC10799953 DOI: 10.1038/s41598-024-52250-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
A low-cost SYBR Green-based RT-qPCR method to detect SARS-CoV-2 were developed and validated. Primers targeting a conserved and vital region of the N genes of SARS-CoV-2 were designed. In-silico study was performed to analyse the compatibility of the selected primer pair with Indonesian SARS-CoV-2 genome sequences available from the GISAID database. We determined the linearity of our new assay using serial dilution of SARS-CoV-2 RNA from clinical samples with known virus concentration. The assay was then evaluated using clinically relevant samples in comparison to a commercial TaqMan-based test kit. Finally, we applied the assay in sample pooling strategies for SARS-CoV-2 detection. The SYBR Green-based RT-qPCR method was successfully developed with sufficient sensitivity. There is a very low prevalence of genome variation in the selected N primer binding regions, indicating their high conservation. The validation of the assay using clinical samples demonstrated similar performance to the TaqMan method suggesting the SYBR methods is reliable. The pooling strategy by combining 5 RNA samples for SARS-CoV-2 detection using the SYBR RT-qPCR methods is feasible and provides a high diagnostic yield. However, when dealing with samples having a very low viral load, it may increase the risk of missing positive cases.
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Affiliation(s)
- Ratika Rahmasari
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia.
| | | | - Siti Hana Aliyah
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Priska Yodi
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Fathan Baihaqy
- Helix Laboratory & Clinic, Depok, West Java, Indonesia
- Department of Microbiology, School of Life Sciences & Technology, Institut Teknologi Bandung, Bandung, West Java, Indonesia
| | | | | | - Herman Suryadi
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Meng Ling Moi
- School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Rani Sauriasari
- Clinical Pharmacy and Social Pharmacy Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
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Heath B, Evans S, Robertson DS, Robotham JV, Villar SS, Presanis AM. Evaluating pooled testing for asymptomatic screening of healthcare workers in hospitals. BMC Infect Dis 2023; 23:900. [PMID: 38129789 PMCID: PMC10740241 DOI: 10.1186/s12879-023-08881-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND There is evidence that during the COVID pandemic, a number of patient and HCW infections were nosocomial. Various measures were put in place to try to reduce these infections including developing asymptomatic PCR (polymerase chain reaction) testing schemes for healthcare workers. Regularly testing all healthcare workers requires many tests while reducing this number by only testing some healthcare workers can result in undetected cases. An efficient way to test as many individuals as possible with a limited testing capacity is to consider pooling multiple samples to be analysed with a single test (known as pooled testing). METHODS Two different pooled testing schemes for the asymptomatic testing are evaluated using an individual-based model representing the transmission of SARS-CoV-2 in a 'typical' English hospital. We adapt the modelling to reflect two scenarios: a) a retrospective look at earlier SARS-CoV-2 variants under lockdown or social restrictions, and b) transitioning back to 'normal life' without lockdown and with the omicron variant. The two pooled testing schemes analysed differ in the population that is eligible for testing. In the 'ward' testing scheme only healthcare workers who work on a single ward are eligible and in the 'full' testing scheme all healthcare workers are eligible including those that move across wards. Both pooled schemes are compared against the baseline scheme which tests only symptomatic healthcare workers. RESULTS Including a pooled asymptomatic testing scheme is found to have a modest (albeit statistically significant) effect, reducing the total number of nosocomial healthcare worker infections by about 2[Formula: see text] in both the lockdown and non-lockdown setting. However, this reduction must be balanced with the increase in cost and healthcare worker isolations. Both ward and full testing reduce HCW infections similarly but the cost for ward testing is much less. We also consider the use of lateral flow devices (LFDs) for follow-up testing. Considering LFDs reduces cost and time but LFDs have a different error profile to PCR tests. CONCLUSIONS Whether a PCR-only or PCR and LFD ward testing scheme is chosen depends on the metrics of most interest to policy makers, the virus prevalence and whether there is a lockdown.
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Affiliation(s)
- Bethany Heath
- MRC Biostatistics Unit, Univeristy of Cambridge, Robinson Way, Cambridge, CB2 0SR, Cambridgeshire, United Kingdom.
| | - Stephanie Evans
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom
- Statistics, Modelling and Economics Division, UK Health Security Agency, London, United Kingdom
| | - David S Robertson
- MRC Biostatistics Unit, Univeristy of Cambridge, Robinson Way, Cambridge, CB2 0SR, Cambridgeshire, United Kingdom
| | - Julie V Robotham
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom
- Statistics, Modelling and Economics Division, UK Health Security Agency, London, United Kingdom
- NIHR Health Protection Research Unit in Modelling and Health Economics at Imperial College London in partnership with the UK Health Security Agency and London School of Hygiene and Tropical Medicine, London, United Kingdom
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with the UK Health Security Agency, Oxford, United Kingdom
| | - Sofía S Villar
- MRC Biostatistics Unit, Univeristy of Cambridge, Robinson Way, Cambridge, CB2 0SR, Cambridgeshire, United Kingdom
| | - Anne M Presanis
- MRC Biostatistics Unit, Univeristy of Cambridge, Robinson Way, Cambridge, CB2 0SR, Cambridgeshire, United Kingdom
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation at University of Bristol in partnership with the UK Health Security Agency and MRC Biostatistics Unit, University of Cambridge, Bristol, United Kingdom
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Tatsuoka C, Chen W, Lu X. Bayesian group testing with dilution effects. Biostatistics 2023; 24:885-900. [PMID: 35403204 PMCID: PMC10583721 DOI: 10.1093/biostatistics/kxac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/18/2022] [Accepted: 01/26/2022] [Indexed: 10/19/2023] Open
Abstract
A Bayesian framework for group testing under dilution effects has been developed, using lattice-based models. This work has particular relevance given the pressing public health need to enhance testing capacity for coronavirus disease 2019 and future pandemics, and the need for wide-scale and repeated testing for surveillance under constantly varying conditions. The proposed Bayesian approach allows for dilution effects in group testing and for general test response distributions beyond just binary outcomes. It is shown that even under strong dilution effects, an intuitive group testing selection rule that relies on the model order structure, referred to as the Bayesian halving algorithm, has attractive optimal convergence properties. Analogous look-ahead rules that can reduce the number of stages in classification by selecting several pooled tests at a time are proposed and evaluated as well. Group testing is demonstrated to provide great savings over individual testing in the number of tests needed, even for moderately high prevalence levels. However, there is a trade-off with higher number of testing stages, and increased variability. A web-based calculator is introduced to assist in weighing these factors and to guide decisions on when and how to pool under various conditions. High-performance distributed computing methods have also been implemented for considering larger pool sizes, when savings from group testing can be even more dramatic.
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Affiliation(s)
- Curtis Tatsuoka
- Department of Population and Quantitative Health Sciences, CaseWestern Reserve University, Cleveland, OH, 44106, USA
| | - Weicong Chen
- Department of Computer and Data Science, CaseWestern Reserve University, Cleveland, OH, USA
| | - Xiaoyi Lu
- Department of Computer Science and Engineering, University of California Merced, Merced, CA, 95343, USA
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Fernández-Huerta M, Salmerón P, Hernández-Hermida Y, Andrés C, Niubó J, Calatayud L, Domínguez MÁ, Pumarola T, Ardanuy C, Antón A, Càmara J. Multicenter clinical evaluation of a novel transcription-mediated amplification assay for SARS-CoV-2 molecular testing. Enferm Infecc Microbiol Clin (Engl Ed) 2023; 41:462-467. [PMID: 37076332 PMCID: PMC10107077 DOI: 10.1016/j.eimce.2022.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/28/2022] [Indexed: 04/21/2023]
Abstract
INTRODUCTION The onset and spread of COVID-19 pandemic has forced clinical laboratories to rapidly expand testing capacity for SARS-CoV-2. This study evaluates the clinical performance of the TMA Procleix SARS-CoV-2 assay in comparison to the RT-PCR assay Allplex™ SARS-CoV-2 for the qualitative detection of SARS-CoV-2 RNA. METHODS Between November 2020 and February 2021, 610 upper-respiratory specimens received for routine SARS-CoV-2 molecular testing were prospectively collected and selected at the Hospital Universitari Vall d'Hebron and the Hospital Universitari Bellvitge in Barcelona, Spain. All samples were processed in parallel with the TMA and the RT-PCR assays, and results were compared. Discrepancies were retested by an additional RT-PCR method and the clinical history of these patients was reviewed. RESULTS Overall, the level of concordance between both assays was 92.0% (κ, 0.772). Most discordant results (36/38, 94.7%) corresponded to samples testing positive with the TMA assay and negative with the RT-PCR method. Of these discrepant cases, most (28/36, 77.8%) were finally classified as confirmed or probable SARS-CoV-2 cases according to the discrepant analysis. CONCLUSION In conclusion, the TMA Procleix SARS-CoV-2 assay performed well for the qualitative detection of SARS-CoV-2 RNA in a multisite clinical setting. This novel TMA assay demonstrated a greater sensitivity in comparison to RT-PCR methods for the molecular detection of SARS-CoV-2. This higher sensitivity but also the qualitative feature of this detection of SARS-CoV-2 should be considered when making testing algorithm decisions.
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Affiliation(s)
- Miguel Fernández-Huerta
- Microbiology Department, Hospital Universitari Bellvitge, University of Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Paula Salmerón
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Yolanda Hernández-Hermida
- Microbiology Department, Hospital Universitari Bellvitge, University of Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Jordi Niubó
- Microbiology Department, Hospital Universitari Bellvitge, University of Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Laura Calatayud
- Microbiology Department, Hospital Universitari Bellvitge, University of Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain; CIBER de Enfermedades Respiratorias (CIBERER), ISCIII, Madrid, Spain
| | - M Ángeles Domínguez
- Microbiology Department, Hospital Universitari Bellvitge, University of Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain; Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain; Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
| | - Tomàs Pumarola
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari Bellvitge, University of Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain; CIBER de Enfermedades Respiratorias (CIBERER), ISCIII, Madrid, Spain; Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Jordi Càmara
- Microbiology Department, Hospital Universitari Bellvitge, University of Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain; CIBER de Enfermedades Respiratorias (CIBERER), ISCIII, Madrid, Spain.
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Cui X, Ngang S, Liu DD, Cheow LF. Rapid Single-Round Pool Testing of Infectious Disease Enabled by Multicolor Digital Melting PCR. Small 2023; 19:e2205636. [PMID: 37209020 DOI: 10.1002/smll.202205636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/27/2023] [Indexed: 05/21/2023]
Abstract
Pooled nucleic acid amplification test is a promising strategy to reduce cost and resources for screening large populations for infectious disease. However, the benefit of pooled testing is reversed when disease prevalence is high, because of the need to retest each sample to identify infected individual when a pool is positive. Split, Amplify, and Melt analysis of Pooled Assay (SAMPA) is presented, a multicolor digital melting PCR assay in nanoliter chambers that simultaneously identify infected individuals and quantify their viral loads in a single round of pooled testing. This is achieved by early sample tagging with unique barcodes and pooling, followed by single molecule barcode identification in a digital PCR platform using a highly multiplexed melt curve analysis strategy. The feasibility is demonstrated of SAMPA for quantitative unmixing and variant identification from pools of eight synthetic DNA and RNA samples corresponding to the N1 gene, as well as from heat-inactivated SARS-CoV-2 virus. Single round pooled testing of barcoded samples with SAMPA can be a valuable tool for rapid and scalable population testing of infectious disease.
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Affiliation(s)
- Xu Cui
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Shaun Ngang
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Dong Dong Liu
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
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Balakrishnan S, Palathingal S. An adaptive testing strategy for efficient utilization of healthcare resources during an epidemic. J Theor Biol 2023; 571:111555. [PMID: 37290500 PMCID: PMC10245284 DOI: 10.1016/j.jtbi.2023.111555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/29/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Lockdowns are found to be effective against rapidly spreading epidemics like COVID-19. Two downsides to strategies rooted in social distancing and lockdowns are that they adversely affect the economy and prolong the duration of the epidemic. The extended duration observed in these strategies is often due to the under-utilization of medical facilities. Even though an under-utilized health care system is preferred over an overwhelmed one, an alternate strategy could be to maintain medical facilities close to their capacity, with a factor of safety. We explore the practicality of this alternate mitigation strategy and show that it can be achieved by varying the testing rate. We present an algorithm to calculate the number of tests per day to maintain medical facilities close to their capacity. We illustrate the efficacy of our strategy by showing that it reduced the epidemic duration by 40% in comparison to lockdown-based strategies.
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Affiliation(s)
- Sreenath Balakrishnan
- School of Mechanical Sciences, Indian Institute of Technology Goa, Ponda, 403401, Goa, India; School of Interdisciplinary Life Sciences, Indian Institute of Technology Goa, Ponda, 403401, Goa, India.
| | - Safvan Palathingal
- Department of Mechanical and Aerospace Engineering, Indian Institute of Technology Hyderabad, Hyderabad, 502284, Telangana, India
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Li Q, Bai Y, Tang B. Modelling the pulse population-wide nucleic acid screening in mitigating and stopping COVID-19 outbreaks in China. BMC Infect Dis 2023; 23:280. [PMID: 37138230 PMCID: PMC10155657 DOI: 10.1186/s12879-023-08265-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND During 2021-2022, mainland China experienced multiple times of local COVID-19 outbreaks in several cities, including Yangzhou, Xi'an etc., and the Chinese government persistently adopted the zero-COVID policy in combating with the local outbreaks. METHODS We develop a mathematical model with pulse population-wide nucleic acid screening, part of the zero-COVID policy, to reveal its role in controlling the spread of COVID-19. We calibrate the model by fitting the COVID-19 epidemic data of the local outbreaks in Yangzhou and Xi'an, China. Sensitivity analysis is conducted to investigate the impact of population-wide nucleic acid screening on controlling the outbreak of COVID-19. RESULTS Without the screening, the cumulative number of confirmed cases increases by [Formula: see text] and [Formula: see text] in Yangzhou and Xi'an, respectively. Meanwhile, the screening program helps to shorten the lockdown period for more than one month when we aim at controlling the cases into zero. Considering its role in mitigating the epidemics, we observe a paradox phenomenon of the screening rate in avoiding the runs on medical resource. That is, the screening will aggravate the runs on medical resource when the screening rate is small, while it helps to relieve the runs on medical resource if the screening rate is high enough. We also conclude that the screening has limited effects on mitigating the epidemics if the outbreak is in a high epidemic level or there has already been runs on medical resources. Alternatively, a smaller screening population per time with a higher screening frequency may be a better program to avoid the runs on medical resources. CONCLUSIONS The population-wide nucleic acid screening strategy plays an important role in quickly controlling and stopping the local outbreaks under the zero-COVID policy. However, it has limited impacts and even increase the potential risk of the runs on medical resource for containing the large scale outbreaks.
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Affiliation(s)
- Qian Li
- Department of Applied Mathematics, Xi'an University of Technology, 710048, Xi'an, People's Republic of China
| | - Yao Bai
- Department of Infectious Disease Control and Prevention, Xi'an Center for Disease Prevention and Control, 710054, Xi'an, People's Republic of China
| | - Biao Tang
- School of Mathematics and Statistics, Xi'an Jiaotong University, 710049, Xi'an, People's Republic of China.
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Santos VS, Allgayer MF, Kontogianni K, Rocha JE, Pimentel BJ, Amorim MTP, Duarte MVSC, de Melo Ferreira P, Moura LCL, de Lima VPS, Guimarães LC, Dodd J, Creswell J, Cuevas LE. Pooling of sputum samples to increase tuberculosis diagnostic capacity in Brazil during the COVID-19 pandemic. Int J Infect Dis 2023; 129:10-14. [PMID: 36642209 PMCID: PMC9834119 DOI: 10.1016/j.ijid.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/17/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES We assessed whether combining (pooling) four individual's samples and testing with Xpert Ultra has the same accuracy as testing samples individually as a more efficient testing method. METHODS We conducted a cross-sectional study of individuals with presumptive tuberculosis attending primary health care or general hospital facilities in Alagoas, Brazil. The sputum samples of four consecutive individuals were pooled and the pool and individual samples were tested with Xpert Ultra. The agreement of the tests was compared using kappa statistics. We estimated the sensitivity and specificity of pooling using the individual test as the reference standard and potential cartridge savings. RESULTS A total of 396 participants were tested. A total of 95 (24.0%) individual samples were Mycobacterium tuberculosis (MTB)-positive, 300 (75.8%) "MTB not detected", including 20 "MTB trace", and one reported an error. A total of 99 pools of four samples were tested, of which 62 (62.6%) had MTB detected and 37 (37.4%) MTB not detected, including six (6.1%) with MTB trace. The agreement between individual and pooled testing was 96.0%. Pooling had a sensitivity of 95.0% (95% confidence interval 86.9-99%), specificity of 97.1% (95% confidence interval 85.1-99.9%), and kappa of 0.913. The method saved 12.4% of cartridge costs. CONCLUSION The pooled testing of specimens had a high level of agreement with individual testing. The pooling of samples for testing improves the efficiency of testing, potentially enabling the screening and testing of larger numbers of individuals more cost-effectively.
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Affiliation(s)
- Victor Santana Santos
- Department of Nursing. Centre for Epidemiology and Public Health. Federal University of Alagoas, Arapiraca, Brazil; Graduate Program in Health Sciences. Federal University of Alagoas, Maceió, Brazil; Graduate Program in Health Sciences. Federal University of Sergipe, Aracaju, Brazil
| | - Manuela Filter Allgayer
- Department of Nursing. Centre for Epidemiology and Public Health. Federal University of Alagoas, Arapiraca, Brazil
| | | | - José Erinaldo Rocha
- Laboratório de Diagnóstico, Pesquisa e Controle de Tuberculose, Maceió, Brazil
| | | | | | | | | | | | | | | | - James Dodd
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jacob Creswell
- Stop TB Partnership, Innovations and Grants, Geneva, Switzerland
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Bimba JS, Adekeye OA, Iem V, Eliya TT, Osagie I, Kontogianni K, Edwards T, Dodd J, Squire SB, Creswell J, Cuevas LE. Pooling sputum samples for Xpert® MTB/RIF and Xpert® Ultra testing for TB diagnosis. Public Health Action 2023; 13:12-16. [PMID: 37152212 PMCID: PMC10162368 DOI: 10.5588/pha.22.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/29/2022] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND The use of molecular amplification as-says for TB diagnosis is limited by their costs and cartridge stocks. Pooling multiple samples to test them together is reported to have similar accuracy to individual testing and to save costs. METHODS Two surveys of individuals with presumptive TB were conducted to assess the performance of pooled testing using Xpert® MTB/RIF (MTB/RIF) and Xpert® Ultra (Ultra). RESULTS A total of 500 individuals were tested using MTB/RIF, with 72 (14.4%) being MTB-positive. The samples were tested in 125 pools, with 50 pools having ⩾1 MTB-positive and 75 only MTB-negative samples: 46/50 (92%, 95% CI 80.8-97.8) MTB-positive pools tested MTB-positive and 71/75 (94.7%, 95% CI 86.9-98.5) MTB-negative pools tested MTB-negative in the pooled test (agreement: 93.6%, κ = 0.867). Five hundred additional samples were tested using Ultra, with 60 (12%) being MTB-positive. Samples were tested in 125 pools, with 42 having ⩾1 MTB-positive and 83 only MTB-negative samples: 35/42 (83.6%, 95% CI 68.6-93.0) MTB-positive pools tested MTB-positive and 82/83 (98.8%, 95% CI 93.5-100.0) MTB-negative pools tested MTB-negative in the pooled test (agreement: 93.6%, κ = 0.851; P > 0.1 between individual and pooled testing). Pooled testing saved 35% (MTB/RIF) and 46% (Ultra) of cartridges. CONCLUSIONS Pooled and individual testing has a high level of agreement and improves testing efficiency.
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Affiliation(s)
- J S Bimba
- Zankli Research Centre, Bingham University, Karu, Nigeria
| | - O A Adekeye
- Zankli Research Centre, Bingham University, Karu, Nigeria
| | - V Iem
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - T T Eliya
- Zankli Research Centre, Bingham University, Karu, Nigeria
| | - I Osagie
- Zankli Research Centre, Bingham University, Karu, Nigeria
| | - K Kontogianni
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - T Edwards
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - J Dodd
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - S B Squire
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - J Creswell
- Stop TB Partnership, Innovations and Grants, Geneva, Switzerland
| | - L E Cuevas
- Zankli Research Centre, Bingham University, Karu, Nigeria
- Liverpool School of Tropical Medicine, Liverpool, UK
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Jain V, Sherwani N, Monga N, Sahu A. Effectiveness of sample pooling strategies for diagnosis of SARS-CoV-2: Specimen pooling vs. RNA elutes pooling. Indian J Med Microbiol 2023; 42:34-38. [PMID: 36967213 PMCID: PMC9870240 DOI: 10.1016/j.ijmmb.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/13/2022] [Accepted: 12/31/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE The pandemic of SARS-CoV-2 or COVID-19 has hugely created an economic imbalance worldwide. With the exponential increase in the number of cases and to keep in check on the community transmission, there is high demand and acute shortage of diagnostic kits. The pooled-sample strategy turns out to be the promising strategy intended to determine the optimal testing for specimens with limited resources and without losing the test sensitivity and specificity. The study was performed with standard molecular biology graded lab equipment, FDA-approved COVID-19 RNA extraction, and SARS-CoV-2 tests kits. MATERIALS AND METHODS The study aims to comparatively analyze the pooling strategy of the naso-oropharyngeal specimen sample and RNA extracted from the same patient samples in the pool of 3,5, and 8 with no significant loss in test usability. Another primary focus of the study was detection of low or borderline SARS-CoV-2 positives in the pooling strategy. A total of 300 samples (240 positives and 60 negatives) were tested for 3, 5, and 8 pools of specimen samples and RNA elutes. RESULTS The comparative analysis determined the sensitivity for three and five pool strategy to be above 98% and eight pool strategy to be 100%. CONCLUSION The RNA elutes pooling strategy concordance rate is better than that of specimen pooling with 100% specificity. Thus, in the substantial crisis of resources with the global pandemic, pooling approaches for SARS-CoV-2 can be practical in a low prevalence rate of 5%.
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15
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Filiatreau LM, Zivich PN, Edwards JK, Mulholland GE, Max R, Westreich D. Optimizing SARS-CoV-2 Pooled Testing Strategies Through Differentiated Pooling for Distinct Groups. Am J Epidemiol 2023; 192:246-256. [PMID: 36222677 PMCID: PMC9620733 DOI: 10.1093/aje/kwac178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/02/2022] [Accepted: 10/06/2022] [Indexed: 02/07/2023] Open
Abstract
Pooled testing has been successfully used to expand SARS-CoV-2 testing, especially in settings requiring high volumes of screening of lower-risk individuals, but efficiency of pooling declines as prevalence rises. We propose a differentiated pooling strategy that independently optimizes pool sizes for distinct groups with different probabilities of infection to further improve the efficiency of pooled testing. We compared the efficiency (results obtained per test kit used) of the differentiated strategy with a traditional pooling strategy in which all samples are processed using uniform pool sizes under a range of scenarios. For most scenarios, differentiated pooling is more efficient than traditional pooling. In scenarios examined here, an improvement in efficiency of up to 3.94 results per test kit could be obtained through differentiated versus traditional pooling, with more likely scenarios resulting in 0.12 to 0.61 additional results per kit. Under circumstances similar to those observed in a university setting, implementation of our strategy could result in an improvement in efficiency between 0.03 to 3.21 results per test kit. Our results can help identify settings, such as universities and workplaces, where differentiated pooling can conserve critical testing resources.
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Affiliation(s)
- Lindsey M Filiatreau
- Correspondence Address: Department of Psychiatry, Washington University in St. Louis, 660 S. Euclid, St. Louis, MO 63110, E-mail:
| | - Paul N Zivich
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jessie K Edwards
- Gillings Center for Coronavirus Testing, Screening, and Surveillance, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Grace E Mulholland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ryan Max
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel Westreich
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Gillings Center for Coronavirus Testing, Screening, and Surveillance, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Chen Y, Ma Y, Han Y, Diao Z, Chang L, Li J, Zhang R. Evaluation of Four Strategies for SARS-CoV-2 Detection: Characteristics and Prospects. Microbiol Spectr 2022; 10:e0214322. [PMID: 36287010 PMCID: PMC9769534 DOI: 10.1128/spectrum.02143-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/27/2022] [Indexed: 01/06/2023] Open
Abstract
The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed an enormous burden on the global public health system and has had disastrous socioeconomic consequences. Currently, single sampling tests, 20-in-1 pooling tests, nucleic acid point-of-care tests (POCTs), and rapid antigen tests are implemented in different scenarios to detect SARS-CoV-2, but a comprehensive evaluation of them is scarce and remains to be explored. In this study, 3 SARS-CoV-2 inactivated cell culture supernatants were used to evaluate the analytical performance of these strategies. Additionally, 5 recombinant SARS-CoV-2 nucleocapsid (N) proteins were also used for rapid antigen tests. For the wild-type (WT), Delta, and Omicron strains, the lowest inactivated virus concentrations to achieve 100% detection rates of single sampling tests ranged between 1.28 × 102 to 1.02 × 103, 1.28 × 102 to 4.10 × 103, and 1.28 × 102 to 2.05 × 103 copies/mL. The 20-in-1 pooling tests ranged between 1.30 × 102 to 1.04 × 103, 5.19 × 102 to 2.07 × 103, and 2.59 × 102 to 1.04 × 103 copies/mL. The nucleic acid POCTs were all 1.42 × 103 copies/mL. The rapid antigen tests ranged between 2.84 × 105 to 7.14 × 106, 8.68 × 104 to 7.14 × 106, and 1.12 × 105 to 3.57 × 106 copies/mL. For the WT, Delta AY.2, Delta AY.1/AY.3, Omicron BA.1, and Omicron BA.2 recombinant N proteins, the lowest concentrations to achieve 100% detection rates of rapid antigen tests ranged between 3.47 to 142.86, 1.74 to 142.86, 3.47 to 142.86, 3.47 to 142.86, and 5.68-142.86 ng/mL, respectively. This study provided helpful insights into the scientific deployment of tests and recommended the full-scale consideration of the testing purpose, resource availability, cost performance, result rapidity, and accuracy to facilitate a profound pathway toward the long-term surveillance of coronavirus disease 2019 (COVID-19). IMPORTANCE In the study, we reported an evaluation of 4 detection strategies implemented in different scenarios for SARS-CoV-2 detection: single sampling tests, 20-in-1 pooling tests, nucleic acid point-of-care tests, and rapid antigen tests. 3 SARS-CoV-2-inactivated SARS-CoV-2 cell culture supernatants and 5 recombinant SARS-CoV-2 nucleocapsid proteins were used for evaluation. In this analysis, we found that for the WT, Delta, and Omicron supernatants, the lowest concentrations to achieve 100% detection rates of single sampling tests ranged between 1.28 × 102 to 1.02 × 103, 1.28 × 102 to 4.10 × 103, and 1.28 × 102 to 2.05 × 103 copies/mL. The 20-in-1 pooling tests ranged between 1.30 × 102 to 1.04 × 103, 5.19 × 102 to 2.07 × 103, and 2.59 × 102 to 1.04 × 103 copies/mL. The nucleic acid POCTs were all 1.42 × 103 copies/mL. The rapid antigen tests ranged between 2.84 × 105 to 7.14 × 106, 8.68 × 104 to 7.14 × 106, and 1.12 × 105 to 3.57 × 106 copies/mL. For the WT, Delta AY.2, Delta AY.1/AY.3, Omicron BA.1, and Omicron BA.2 recombinant N proteins, the lowest concentrations to achieve 100% detection rates of rapid antigen tests ranged between 3.47 to 142.86, 1.74 to 142.86, 3.47 to 142.86, 3.47 to 142.86, and 5.68 to 142.86 ng/mL, respectively.
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Affiliation(s)
- Yuqing Chen
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Yu Ma
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Zhenli Diao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Lu Chang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
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Chung HY, Jian MJ, Chang CK, Lin JC, Yeh KM, Chen CW, Yang YS, Hsieh SS, Chen ES, Yang MH, Tang SH, Perng CL, Yang JR, Liu MT, Chang FY, Shang HS. Multicenter study evaluating novel multi-specimen pooling assay for the detection of SARS-CoV-2: High sensitivity and high throughput testing. J Microbiol Immunol Infect 2022; 55:1069-1075. [PMID: 34538568 PMCID: PMC8411585 DOI: 10.1016/j.jmii.2021.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/30/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND/PURPOSE Mass screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is important to prevent the spread of coronavirus disease 2019 (COVID-19). Pooling samples can increase the number of tests processed. LabTurbo AIO 48 is an automated platform that allows ribonucleic acid extraction and sample analysis on the same instrument. We created a novel pooling assay on this platform for SARS-CoV-2 detection and demonstrated that the pooling strategy increases testing capacity without affecting accuracy and sensitivity. METHODS Comparative limit of detection (LoD) assessment was performed on the LabTurbo AIO 48 platform and the current standard detection system based on real-time reverse transcription polymerase chain reaction (rRT-PCR) using 55 clinically positive samples. An additional 330 primary clinical samples were assessed. RESULTS Six samples pooled into one reaction tube were detected in approximately 2.5 h using the World Health Organization rRT-PCR protocol. LabTurbo AIO 48 also demonstrated a higher throughput than our reference rRT-PCR assay, with an LoD of 1000 copies/mL. The overall percentage agreement between the methods for the 330 samples was 100%. CONCLUSION We created a novel multi-specimen pooling assay using LabTurbo AIO 48 for the robust detection of SARS-CoV-2, allowing high-throughput results; this assay will aid in better control and prevention of COVID-19. The diagnostic assay was cost-effective and time-efficient; thus, the pooling strategy is a practical and effective method for diagnosing large quantities of specimens without compromising precision.
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Affiliation(s)
- Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ya-Sung Yang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - En-Sung Chen
- Department of Clinical Pathology, Cathay General Hospital, Taipei, Taiwan
| | - Mei-Hsiu Yang
- Department of Clinical Pathology, Cathay General Hospital, Taipei, Taiwan
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | | | | | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC,Corresponding author. Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, No.325, Sec.2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan, ROC. Fax: +886 2 87927226
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Park R, Chandrasekaran P, Hernandez H, Lakhal-naouar I, Peachman KK, Hack HR, Coleman D, Ouellette J, Darden JM, M’hamdi O, Sugiharto VA, Chen H, Schilling MA, Simons MP, Collins ND, Johnson YS, Jagodzinski LL, Peel SA. Validation of SARS-CoV-2 pooled testing for surveillance using the Panther Fusion® system: Impact of pool size, automation, and assay chemistry. PLoS One 2022; 17:e0276729. [PMID: 36342921 PMCID: PMC9639840 DOI: 10.1371/journal.pone.0276729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022] Open
Abstract
Combining diagnostic specimens into pools has been considered as a strategy to augment throughput, decrease turnaround time, and leverage resources. This study utilized a multi-parametric approach to assess optimum pool size, impact of automation, and effect of nucleic acid amplification chemistries on the detection of SARS-CoV-2 RNA in pooled samples for surveillance testing on the Hologic Panther Fusion® System. Dorfman pooled testing was conducted with previously tested SARS-CoV-2 nasopharyngeal samples using Hologic’s Aptima® and Panther Fusion® SARS-CoV-2 Emergency Use Authorization assays. A manual workflow was used to generate pool sizes of 5:1 (five samples: one positive, four negative) and 10:1. An automated workflow was used to generate pool sizes of 3:1, 4:1, 5:1, 8:1 and 10:1. The impact of pool size, pooling method, and assay chemistry on sensitivity, specificity, and lower limit of detection (LLOD) was evaluated. Both the Hologic Aptima® and Panther Fusion® SARS-CoV-2 assays demonstrated >85% positive percent agreement between neat testing and pool sizes ≤5:1, satisfying FDA recommendation. Discordant results between neat and pooled testing were more frequent for positive samples with CT>35. Fusion® CT (cycle threshold) values for pooled samples increased as expected for pool sizes of 5:1 (CT increase of 1.92–2.41) and 10:1 (CT increase of 3.03–3.29). The Fusion® assay demonstrated lower LLOD than the Aptima® assay for pooled testing (956 vs 1503 cp/mL, pool size of 5:1). Lowering the cut-off threshold of the Aptima® assay from 560 kRLU (manufacturer’s setting) to 350 kRLU improved the assay sensitivity to that of the Fusion® assay for pooled testing. Both Hologic’s SARS-CoV-2 assays met the FDA recommended guidelines for percent positive agreement (>85%) for pool sizes ≤5:1. Automated pooling increased test throughput and enabled automated sample tracking while requiring less labor. The Fusion® SARS-CoV-2 assay, which demonstrated a lower LLOD, may be more appropriate for surveillance testing.
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Baldanti F, Ganguly NK, Wang G, Möckel M, O’Neill LA, Renz H, dos Santos Ferreira CE, Tateda K, Van Der Pol B. Choice of SARS-CoV-2 diagnostic test: challenges and key considerations for the future. Crit Rev Clin Lab Sci 2022; 59:445-459. [PMID: 35289222 PMCID: PMC8935452 DOI: 10.1080/10408363.2022.2045250] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A plethora of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests are available, each with different performance specifications, detection methods, and targets. This narrative review aims to summarize the diagnostic technologies available and how they are best selected to tackle SARS-CoV-2 infection as the pandemic evolves. Seven key settings have been identified where diagnostic tests are being deployed: symptomatic individuals presenting for diagnostic testing and/or treatment of COVID-19 symptoms; asymptomatic individuals accessing healthcare for planned non-COVID-19-related reasons; patients needing to access emergency care (symptom status unknown); patients being discharged from healthcare following hospitalization for COVID-19; healthy individuals in both single event settings (e.g. airports, restaurants, hotels, concerts, and sporting events) and repeat access settings (e.g. workplaces, schools, and universities); and vaccinated individuals. While molecular diagnostics remain central to SARS-CoV-2 testing strategies, we have offered some discussion on the considerations for when other tools and technologies may be useful, when centralized/point-of-care testing is appropriate, and how the various additional diagnostics can be deployed in differently resourced settings. As the pandemic evolves, molecular testing remains important for definitive diagnosis, but increasingly widespread point-of-care testing is essential to the re-opening of society.
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Affiliation(s)
- Fausto Baldanti
- Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | | | - Guiqiang Wang
- The Center for Liver Diseases, Peking University First Hospital, Beijing, China
| | - Martin Möckel
- Charité – Universitätsmedizin, Berlin, Germany,CONTACT Martin Möckel Departments of Emergency Medicine and Chest Pain Units CVK/CCM, Charité – Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany
| | - Luke A. O’Neill
- Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Harald Renz
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps University Marburg, University Hospital Giessen and Marburg GmbH, Giessen, Germany,Department of Clinical Immunology and Allergology, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Barbara Van Der Pol
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
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20
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Butler KS, Carson BD, Podlevsky JD, Mayes CM, Rowland JM, Campbell D, Ricken JB, Wudiri G, Timlin JA. Singleplex, multiplex and pooled sample real-time RT-PCR assays for detection of SARS-CoV-2 in an occupational medicine setting. Sci Rep 2022; 12:17733. [PMID: 36273023 PMCID: PMC9587995 DOI: 10.1038/s41598-022-22106-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/10/2022] [Indexed: 01/18/2023] Open
Abstract
For workplaces which cannot operate as telework or remotely, there is a critical need for routine occupational SARS-CoV-2 diagnostic testing. Although diagnostic tests including the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel (CDC Diagnostic Panel) (EUA200001) were made available early in the pandemic, resource scarcity and high demand for reagents and equipment necessitated priority of symptomatic patients. There is a clearly defined need for flexible testing methodologies and strategies with rapid turnaround of results for (1) symptomatic, (2) asymptomatic with high-risk exposures and (3) asymptomatic populations without preexisting conditions for routine screening to address the needs of an on-site work force. We developed a distinct SARS-CoV-2 diagnostic assay based on the original CDC Diagnostic Panel (EUA200001), yet, with minimum overlap for currently employed reagents to eliminate direct competition for limited resources. As the pandemic progressed with testing loads increasing, we modified the assay to include 5-sample pooling and amplicon target multiplexing. Analytical sensitivity of the pooled and multiplexed assays was rigorously tested with contrived positive samples in realistic patient backgrounds. Assay performance was determined with clinical samples previously assessed with an FDA authorized assay. Throughout the pandemic we successfully tested symptomatic, known contact and travelers within our occupational population with a ~ 24-48-h turnaround time to limit the spread of COVID-19 in the workplace. Our singleplex assay had a detection limit of 31.25 copies per reaction. The three-color multiplexed assay maintained similar sensitivity to the singleplex assay, while tripling the throughput. The pooling assay further increased the throughput to five-fold the singleplex assay, albeit with a subtle loss of sensitivity. We subsequently developed a hybrid 'multiplex-pooled' strategy to testing to address the need for both rapid analysis of samples from personnel at high risk of COVID infection and routine screening. Herein, our SARS-CoV-2 assays specifically address the needs of occupational healthcare for both rapid analysis of personnel at high-risk of infection and routine screening that is essential for controlling COVID-19 disease transmission. In addition to SARS-CoV-2 and COVID-19, this work demonstrates successful flexible assays developments and deployments with implications for emerging highly transmissible diseases and future pandemics.
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Affiliation(s)
- Kimberly S. Butler
- grid.474520.00000000121519272Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - Bryan D. Carson
- grid.474520.00000000121519272Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - Joshua D. Podlevsky
- grid.474520.00000000121519272Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - Cathryn M. Mayes
- grid.474520.00000000121519272WMD Threats and Aerosol Science, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - Jessica M. Rowland
- grid.474520.00000000121519272Global Chemical and Biological Security, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - DeAnna Campbell
- grid.474520.00000000121519272Biological and Chemical Sensors Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - J. Bryce Ricken
- grid.474520.00000000121519272Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - George Wudiri
- grid.474520.00000000121519272Cooperative Nuclear Counterproliferation, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | | | - Jerilyn A. Timlin
- grid.474520.00000000121519272Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM 87123 USA ,grid.474520.00000000121519272Computational Biology and Biophysics Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
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21
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Abstract
We analyze the group testing strategy that maximizes the efficiency of the SARS-CoV-2 screening test while ensuring its effectiveness, where the effectiveness of group testing guarantees that negative results from pooled samples can be considered presumptive negative. Two aspects of test efficiency are considered, one concerning the maximization of the welfare throughput and the other concerning the maximization of the identification rate (namely, identifying as many infected individuals as possible). We show that compared with individual testing, group testing leads to a higher probability of false negative results but a lower probability of false positive results. To ensure the test effectiveness, both the group size and the prevalence of SARS-CoV-2 must be below certain respective thresholds. To achieve test efficiency that concerns either the welfare throughput maximization or the identification rate maximization, the optimal group size is jointly determined by the test accuracy parameters, the infection prevalence rate, and the relative importance of identifying infected subjects. We also show that the optimal group size that maximizes the welfare throughput is weakly smaller than the one that maximizes the identification rate.
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Affiliation(s)
- Fengfeng Huang
- School of Management and Economics, University of Electronic Science and Technology of China, China
| | - Pengfei Guo
- College of Business, City University of Hong Kong, Kowloon, Hong Kong
| | - Yulan Wang
- Faculty of Business, The Hong Kong Polytechnic University, Kowloon, Hong Kong
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22
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Iem V, Xangsayarath P, Chittamany P, Suthepmany S, Siphanthong S, Paboriboune P, Somphavong S, Konstantina K, Khan JAM, Edwards T, Wingfield T, Creswell J, Dominguez J, Cuevas LE. Pooling samples to increase testing capacity with Xpert Xpress SARS-CoV-2 during the Covid-19 pandemic in Lao People’s Democratic Republic. PLoS One 2022; 17:e0275294. [PMID: 36173954 PMCID: PMC9522287 DOI: 10.1371/journal.pone.0275294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
The COVID-19 pandemic created the need for large-scale testing of populations. However, most laboratories do not have sufficient testing capacity for mass screening. We evaluated pooled testing of samples, as a strategy to increase testing capacity in Lao PDR. Samples of consecutive patients were tested in pools of four using the Xpert Xpress SARS CoV-2 assay. Positive pools were confirmed by individual testing, and we describe the performance of the test and savings achieved. We also diluted selected positive samples to describe its effect on the assays CT values. 1,568 patients were tested in 392 pools of four. 361 (92.1%) pools were negative and 31 (7.9%) positive. 29/31 (93.5% (95%CI 77–99%) positive pools were confirmed by individual testing of the samples but, in 2/31 (6.5%) the four individual samples were negative, suggesting contamination. Pools with only one positive sample had higher CT values (lower RNA concentrations) than the respective individual samples, indicating a dilution effect, which suggested an increased risk of false negative results with dilutions >1:10. However, this risk may be low if the prevalence of infection is high, when pools are more likely to contain more than one positive sample. Pooling saved 67% of cartridges and substantially increased testing capacity. Pooling samples increased SARS-CoV-2 testing capacity and resulted in considerable cartridge savings. Given the need for high-volume testing, countries may consider implementation of pooling for SARS-CoV-2 screening.
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23
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Gesto JSM, Cabanelas A, Farjun B, dos Santos MC, Fidalgo-Neto AA, Kuriyama SN, Souza TML. Implemented occupational health surveillance limits the spread of SARS-CoV-2 Omicron at the workplace. Front Med (Lausanne) 2022; 9:910176. [PMID: 36111122 PMCID: PMC9468326 DOI: 10.3389/fmed.2022.910176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/11/2022] [Indexed: 11/23/2022] Open
Abstract
The global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has put an enormous pressure on human societies, at both health and economic levels. Early diagnosis of SARS-CoV-2, the causative agent of 2019 coronavirus disease (COVID-19), has proved an efficient method to rapidly isolate positive individuals and reduce transmission rates, thus alleviating its negative impact on society’s well-being and economic growth. In this work, through a coordinated and centralized effort to monitor SARS-CoV-2 circulation in companies from the State of Rio de Janeiro, Brazil, we have detected and linked an early rise of infection rates in January 2022 to the introduction of the Omicron variant of concern (VoC) (BA.1). Interestingly, when the Omicron genomic isolates were compared to correlates from public datasets, it was revealed that introduction events were multiple, with possible migration routes mapping to: Mali; Oman and United States; and Italy, Latin America, and United States. In addition, we have built a haplotype network with our genomic dataset and found no strong evidence of transmission chains, between and within companies. Considering Omicron’s particularly high transmissibility, and that most of our samples (>87%) arose from 3 out of 10 companies, these findings suggest that workers from such environments were exposed to SARS-CoV-2 outside their company boundaries. Thus, using a mixed strategy in which quick molecular diagnosis finds support in comprehensive genomic analysis, we have shown that a successfully implemented occupational health program should contribute to document emerging VoC and to limit the spread of SARS-CoV-2 at the workplace.
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Affiliation(s)
- João Silveira Moledo Gesto
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Adriana Cabanelas
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
| | - Bruna Farjun
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
| | | | | | - Sergio N. Kuriyama
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
- SENAI Innovation Institute for Green Chemistry, Rio de Janeiro, Brazil
- *Correspondence: Sergio N. Kuriyama,
| | - Thiago Moreno L. Souza
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
- National Institute of Science and Technology for Innovation on Diseases of Neglected Populations (INCT/IDN), Rio de Janeiro, Brazil
- Thiago Moreno L. Souza,
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Pryce TM, Haygarth EJ, Bordessa J, Jeffery CT, Kay ID, Flexman JP, Boan PA. High-Throughput COVID-19 Testing of Naso-Oropharyngeal Swabs Using a Sensitive Extraction-Free Sample Preparation Method. Microbiol Spectr 2022;:e0135822. [PMID: 35950846 DOI: 10.1128/spectrum.01358-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-throughput diagnostic assays are required for large-scale population testing for severe acute respiratory coronavirus 2 (SARS-CoV-2). The gold standard technique for SARS-CoV-2 detection in nasopharyngeal swab specimens is nucleic acid extraction followed by real-time reverse transcription-PCR. Two high-throughput commercial extraction and detection systems are used routinely in our laboratory: the Roche cobas SARS-CoV-2 assay (cobas) and the Roche MagNA Pure 96 system combined with the SpeeDx PlexPCR SARS-CoV-2 assay (Plex). As an alternative to more costly instrumentation, or tedious sample pooling to increase throughput, we developed a high-throughput extraction-free sample preparation method for naso-oropharyngeal swabs using the PlexPCR SARS-CoV-2 assay (Direct). A collection of SARS-CoV-2-positive (n = 185) and -negative (n = 354) naso-oropharyngeal swabs in transport medium were tested in parallel to compare Plex to Direct. The overall agreement comparing the qualitative outcomes was 99.3%. The mean cycle of quantification (Cq) increase and corresponding mean reduction in viral load for Direct ORF1ab and RdRp compared to Plex was 3.11 Cq (-0.91 log10 IU/mL) and 4.78 Cq (-1.35 log10 IU/mL), respectively. We also compared Direct to a four-sample pool by combining each positive sample (n = 185) with three SARS-CoV-2-negative samples extracted with MagNA Pure 96 and tested with the PlexPCR SARS-CoV-2 assay (Pool). Although less sensitive than Plex or Pool, the Direct method is a sufficiently sensitive and viable approach to increase our throughput by 12,032 results per day. Combining cobas, Plex, and Direct, an overall throughput of 19,364 results can be achieved in a 24-h period. IMPORTANCE Laboratories have experienced extraordinary demand globally for reagents, consumables, and instrumentation, while facing unprecedented testing demand needed for the diagnosis of SARS-CoV-2 infection. A major bottleneck in testing throughput is the purification of viral RNA. Extraction-based methods provide the greatest yield and purity of RNA for downstream PCR. However, these techniques are expensive, time-consuming, and depend on commercial availability of consumables. Extraction-free methods offer an accessible and cost-effective alternative for sample preparation. However, extraction-free methods often lack sensitivity compared to extraction-based methods. We describe a sensitive extraction-free protocol based on a simple purification step using a chelating resin, combined with proteinase K and thermal treatment. We compare the sensitivity qualitatively and quantitatively to a well-known commercial extraction-based system, using a PCR assay calibrated to the 1st WHO international standard for SARS-CoV-2 RNA. This method entails high throughput and is suitable for all laboratories, particularly in jurisdictions where access to instrumentation and reagents is problematic.
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25
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Charles CM, Osman NB, Arijama D, Matingane B, Sitoé T, Kenga D, Lorenzoni C, Luís E, Pacagnella RDC, Sacarlal J. Clinical and epidemiological aspects of SARS-CoV-2 infection among pregnant and postpartum women in Mozambique: a prospective cohort study. Reprod Health 2022; 19:164. [PMID: 35854384 PMCID: PMC9297548 DOI: 10.1186/s12978-022-01469-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Background Although there is a significant increase of evidence regarding the prevalence and impact of COVID-19 on maternal and perinatal outcomes, data on the effects of the pandemic on the obstetric population in sub-Saharan African countries are still scarce. Therefore, the study aims were to assess the prevalence and impact of COVID-19 on maternal and neonatal outcomes in the obstetric population at Central Hospital of Maputo (HCM), Mozambique. Methods Prospective cohort study conducted at teaching and referral maternity, HCM, from 20 October 2020 to 22 July 2021. We collected maternal and perinatal outcomes up to 6 weeks postpartum of eligible women (pregnant and postpartum women—up to the 14th day postpartum) screened for COVID-19 (individual test for symptomatic participants and pool testing for asymptomatic). The primary outcome was maternal death, Severe Acute Respiratory Syndrome (SARS) and Intensive Care Unit (ICU) admission. We estimated the COVID-19 prevalence and the unadjusted RR (95% CI) for maternal and perinatal outcomes. We used the chi-square or Fisher's exact test to compare categorical variables (two-sided p-value < 0.05 for statistical significance). Results We included 239 participants. The overall prevalence of COVID-19 was 9.2% (22/239) and in the symptomatic group was 32.4% (11/34). About 50% of the participants with COVID-19 were symptomatic. Moreover, the most frequent symptoms were dyspnoea (33.3%), cough (28.6%), anosmia (23.8%), and fever (19%). Not having a partner, being pregnant, and alcohol consumption were vulnerability factors for SARS-CoV-2 infection. The risk of adverse maternal and neonatal outcomes (abortion, foetal death, preterm birth, Apgar, and NICU admission) was not significantly increased with COVID-19. Moreover, we did not observe a significant difference in the primary outcomes (SARS, ICU admission and maternal death) between COVID-19 positive and COVID-19 negative groups. Conclusion The prevalence of COVID-19 in the obstetric population is higher than in the general population, and fifty percent of pregnant and postpartum women with COVID-19 infection are asymptomatic. Not having a partner and alcohol consumption were factors of greatest vulnerability to SARS-COV-2 infection. Moreover, being pregnant versus postpartum was associated with increased vulnerability to COVID-19. Data suggest that pregnant women with COVID-19 may have a higher frequency of COVID-19 infection, reinforcing the need for universal testing, adequate follow-up for this population, and increasing COVID-19 therapy facilities in Mozambique. Moreover, provide counselling during Antenatal care for COVID-19 preventive measures. However, more prospective and robust studies are needed to assess these findings. The epidemiological pattern of the COVID-19 pandemic in Africa is heterogeneous, and many African countries are still struggling to establish efficient testing policy, guarantee sufficient laboratory supply and achieve or maintain adequate testing capacity. In addition, evidence suggests that sexual and reproductive health services were the most affected by the pandemic; this scenario might have devastating effects on maternal and perinatal health. Moreover, data from non-sub-Saharan countries the SARS-CoV-2 infection among pregnant and postpartum women is associated with an increased risk of adverse maternal and neonatal health (preterm birth, preeclampsia and maternal death). Although there is a significant increase of evidence regarding the prevalence and impact of COVID-19 on maternal and perinatal health, data on the effects of this condition on the obstetric population in low-income countries are scarce. Therefore, the study objective were to assess the prevalence and impact of COVID-19 on maternal and neonatal health at referral maternity in Maputo, Mozambique. Our findings suggest that the prevalence of COVID-19 in the obstetric population is higher than the general population, and most pregnant and postpartum women are asymptomatic. Being pregnant, not having a partner and alcohol consumption were factors of greatest vulnerability to SARS-COV-2 infection. Moreover, the risk of COVID-19 among pregnant was seven-fold higher than in postpartum women. Pregnant women with COVID-19 may have a higher frequency of adverse gestational outcomes (foetal death and abortion). Although the risk of adverse maternal outcomes (death, Severe Acute Respiratory Syndrome and Intensive Care Unit admission) did not differ significantly between the COVID-19 and COVID-19 negative groups, universal screening for COVID-19 should be implemented to ensure adequate management of pregnant women and newborns.
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Affiliation(s)
- Charles M'poca Charles
- Provincial Health Administration, DPS Manica, Chimoio, Manica Province, Mozambique. .,Department of Obstetrics and Gynecology, School of Medicine, University of Campinas, Campinas, São Paulo, Brazil.
| | - Nafissa Bique Osman
- Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique.,Department of Obstetrics and Gynecology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Domingos Arijama
- Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique
| | - Benjamim Matingane
- Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique.,Department of Obstetrics and Gynecology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Tomás Sitoé
- Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique
| | - Darlene Kenga
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Cesaltina Lorenzoni
- Pathology Department, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique.,Pathological Anatomy Service, Maputo Central Hospital, Maputo, Mozambique
| | - Elvira Luís
- Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique.,Department of Obstetrics and Gynecology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | | | - Jahit Sacarlal
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
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Li D, Zhou Z, Sun J, Mei X. Prospects of NIR fluorescent nanosensors for green detection of SARS-CoV-2. Sens Actuators B Chem 2022; 362:131764. [PMID: 35370362 PMCID: PMC8964475 DOI: 10.1016/j.snb.2022.131764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/22/2022] [Accepted: 03/21/2022] [Indexed: 05/02/2023]
Abstract
The pandemic of the novel coronavirus disease 2019 (COVID-19) is continuously causing hazards for the world. Effective detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can relieve the impact, but various toxic chemicals are also released into the environment. Fluorescence sensors offer a facile analytical strategy. During fluorescence sensing, biological samples such as tissues and body fluids have autofluorescence, giving false-positive/negative results because of the interferences. Fluorescence near-infrared (NIR) nanosensors can be designed from low-toxic materials with insignificant background signals. Although this research is still in its infancy, further developments in this field have the potential for sustainable detection of SARS-CoV-2. Herein, we summarize the reported NIR fluorescent nanosensors with the potential to detect SARS-CoV-2. The green synthesis of NIR fluorescent nanomaterials, environmentally compatible sensing strategies, and possible methods to reduce the testing frequencies are discussed. Further optimization strategies for developing NIR fluorescent nanosensors to facilitate greener diagnostics of SARS-CoV-2 for pandemic control are proposed.
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Key Words
- 5 G, the fifth generation technology standard for broadband cellular networks
- ACE2, Angiotensin-converting enzyme 2
- AIE, aggregation-induced emission
- AIE810NP, an aggregation-induced emission (AIE) nanoparticle (λem = 810 nm)
- AIEgens, AIE luminogens
- ASOs, antisense oligonucleotides
- AuNP, Gold nanoparticle
- CF647, a cyanine-based far-red fluorescent dye
- COVID-19, The pandemic of the novel coronavirus disease 2019
- CP-MNB, capture probe-conjugated magnetic bead particle
- CdS, core/shell lead sulfide/cadmium sulfide
- CoPhMoRe, corona phase molecular recognition
- Cy7Cl, a cationic cyanine dye
- DCNPs, Down-conversion nanoparticles
- DPV, Differential pulse voltammetry
- DSNP, down shifting nanoparticles
- DSNP@MY-1057-GPC-3, active targeting antibody glypican-3 (GPC-3) was conjugated with DSNP@MY-1057
- E, envelope
- EB-NS, prepared by the layered pigment CaCuSi4O10 (Egyptian Blue, EB) via ball milling and facile tip sonication into NIR fluorescent nanosheets
- ENMs, electrospun nanofibrous membranes
- Environmental-friendly
- FLU, an infectious disease caused by influenza viruses
- FRET, fluorescence resonance energy transfer
- Green synthesis
- HA1, hemagglutinin subunit.
- HA1., hemagglutinin subunit
- HAS, serum albumin
- HCC, hepatocellular carcinoma
- IONPs, iron oxide nanoparticles.
- IONPs., iron oxide nanoparticles
- IgG A, IgG aggregation
- IgG, immunoglobulin G
- IgM, immunoglobulin M
- LED, light emitting diode
- LICOR, IRDye-800CW
- Low-toxic
- M, membrane
- MCU, microcontroller unit
- MERS, Middle East respiratory syndrome coronavirus
- N protein, nucleocapsid protein
- N, nucleocapsid
- NIR
- NIR, Near-Infrared
- NIR775, an H2S-inert fluorophore
- Nanosensor
- P, FITC-labelled GzmB substrate peptides
- PBS, Phosphate-buffered saline
- PCR, Polymerase Chain Reaction
- PEG, branched by Polyethylene glycol
- PEG1000 PE, 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)− 1000]
- PEG2000 PE, (1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)− 2000);
- POC, point-of-care
- PS, polystyrene
- Pb-Ag2S ODs, lead doped Ag2S quantum dots
- QDs, quantum dots
- QY, quantum yield
- R, R represents a common recognition element for the target
- RCA, rolling circle amplification
- RNA, ribonucleic acid
- S RBD, SARS-CoV-2 spike receptor-binding domain
- S protein, spike protein
- S, spike
- SAM, self-assembled monolayer
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus
- SPNs, semiconducting polymer nanoparticles.
- SPNs., semiconducting polymer nanoparticles
- SWCNTs, single-walled carbon nanotubes
- Si-RP, silica-reporter probe
- VIS, visible
- VTM, viral transport medium
- pGOLD, plasmonic gold
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Affiliation(s)
- Dan Li
- Department of Basic Science, Jinzhou Medical University, 40 Songpo Road, Jinzhou 121001, China
| | - Zipeng Zhou
- Department of Key Laboratory of Medical Tissue Engineering of Liaoning, Jinzhou Medical University, 40 Songpo Road, Jinzhou 121001, China
| | - Jiachen Sun
- Department of Key Laboratory of Medical Tissue Engineering of Liaoning, Jinzhou Medical University, 40 Songpo Road, Jinzhou 121001, China
| | - Xifan Mei
- Department of Key Laboratory of Medical Tissue Engineering of Liaoning, Jinzhou Medical University, 40 Songpo Road, Jinzhou 121001, China
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Song Y, Wang X, Xiao Y, Wang H. A review of pooled‐sample strategy: Does complexity lead to better performance? VIEW 2022. [DOI: 10.1002/viw.20210005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Yu Song
- Department of Molecular Biology Shanghai Centre for Clinical Laboratory Shanghai China
| | - XueLiang Wang
- Department of Molecular Biology Shanghai Centre for Clinical Laboratory Shanghai China
| | - YanQun Xiao
- Department of Molecular Biology Shanghai Centre for Clinical Laboratory Shanghai China
| | - Hualiang Wang
- Department of Molecular Biology Shanghai Centre for Clinical Laboratory Shanghai China
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Mandhan P, Sharma M, Pandey S, Chandel N, Chourasia N, Moun A, Sharma D, Sukar R, Singh N, Mathur S, Kotnala A, Negi N, Gupta A, Kumar A, Suresh Kumar R, Kumar P, Singh S. A Regional Pooling Intervention in a High-Throughput COVID-19 Diagnostic Laboratory to Enhance Throughput, Save Resources and Time Over a Period of 6 Months. Front Microbiol 2022; 13:858555. [PMID: 35756046 PMCID: PMC9218601 DOI: 10.3389/fmicb.2022.858555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
An effective and rapid diagnosis has great importance in tackling the ongoing COVID-19 pandemic through isolation of the infected individuals to curb the transmission and initiation of specialized treatment for the disease. It has been proven that enhanced testing capacities contribute to efficiently curbing SARS-CoV-2 transmission during the initial phases of the outbreaks. RT-qPCR is considered a gold standard for the diagnosis of COVID-19. However, in resource-limited countries expenses for molecular diagnosis limits the diagnostic capacities. Here, we present interventions of two pooling strategies as 5 sample pooling (P-5) and 10 sample pooling (P-10) in a high-throughput COVID-19 diagnostic laboratory to enhance throughput and save resources and time over a period of 6 months. The diagnostic capacity was scaled-up 2.15-folds in P-5 and 1.8-fold in P-10, reagents (toward RNA extraction and RT-qPCR) were preserved at 75.24% in P-5 and 86.21% in P-10, and time saved was 6,290.93 h in P-5 and 3147.3 h in P-10.
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Affiliation(s)
- Prerna Mandhan
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Mansi Sharma
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Sushmita Pandey
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Neha Chandel
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Nidhi Chourasia
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Amit Moun
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Divyani Sharma
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Rubee Sukar
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Niyati Singh
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Shubhangi Mathur
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Aarti Kotnala
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Neetu Negi
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Ashish Gupta
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Anuj Kumar
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - R Suresh Kumar
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Pramod Kumar
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Shalini Singh
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
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Kretschmer AC, Junker L, Dewald F, Linne V, Hennen L, Horemheb-Rubio G, Kaiser R, Steger G, Joachim A, Schönenkorb J, Cosgun ZC, Mühlhans N, Heger E, Knops E, Leisse C, Kessel B, Heinsohn T, Rodiah I, Lange B, Ritter AL, Fries M, Kossow A, Nießen J, Dötsch J, Klein F, Rybniker J, Fätkenheuer G, Suárez I. Implementing the Lolli-Method and pooled RT-qPCR testing for SARS-CoV-2 surveillance in schools: a pilot project. Infection 2022. [PMID: 35759174 DOI: 10.1007/s15010-022-01865-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022]
Abstract
Purpose School closures have been used as part of lockdown strategies to contain the spread of SARS-CoV-2, adversely affecting children’s health and education. To ensure the accessibility of educational institutions without exposing society to the risk of increased transmissions, it is essential to establish SARS-CoV-2 testing strategies that are child-friendly, scalable and implementable in a daily school routine. Self-sampling using non-invasive saliva swabs combined with pooled RT-qPCR testing (Lolli-Method) has been proven to be a sensitive method for the detection of SARS-CoV-2. Methods We conducted a pilot project in Cologne, Germany, designed to determine the feasibility of a large-scale rollout of the Lolli-Method for testing without any additional on-site medical staff in schools. Over a period of three weeks, students from 22 schools were sampled using the Lolli-Method. At the end of the project, teachers were asked to evaluate the overall acceptance of the project. Results We analyzed a total of 757 pooled RT-qPCRs obtained from 8,287 individual swabs and detected 7 SARS-CoV-2 infected individuals. The Lolli-Method was shown to be a feasible and accepted testing strategy whose application is only slightly disruptive to the daily school routine. Conclusion Our observations suggest that the Lolli-Method in combination with pooled RT-qPCR can be implemented for SARS-CoV-2 surveillance in daily school routine, applicable on a large scale. Supplementary Information The online version contains supplementary material available at 10.1007/s15010-022-01865-0.
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Joly É, Mallein B. A tractable non-adaptative group testing method for non-binary measurements. ESAIM-PROBAB STAT 2022. [DOI: 10.1051/ps/2022007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The original problem of group testing consists in the identification of defective items in a collection, by applying tests on groups of items that detect the presence of at least one defective element in the group. The aim is then to identify all defective items of the collection with as few tests as possible. This problem is relevant in several fields, among which biology and computer sciences. In the present article we consider that the tests applied to groups of items returns a load, measuring how defective the most defective item of the group is. In this setting, we propose a simple non-adaptative algorithm allowing the detection of all defective items of the collection. Items are put on an n × n grid and pools are organised as lines, columns and diagonals of this grid. This method improves on classical group testing algorithms using only the binary response of the test. Group testing recently gained attraction as a potential tool to solve a shortage of COVID-19 test kits, in particular for RT-qPCR. These tests return the viral load of the sample and the viral load varies greatly among individuals. Therefore our model presents some of the key features of this problem. We aim at using the extra piece of information that represents the viral load to construct a one-stage pool testing algorithm on this idealized version. We show that under the right conditions, the total number of tests needed to detect contaminated samples can be drastically diminished.
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Salih DA, Ahmed JQ, Qader MK, Shukur MS, Zeebaree BKA, Sadeq MB, Mohammed SN, Masiha HN, Abdullah IM, Mohammed O, Taha LS, Al-Qadi R. SARS-CoV-2 and RT-PCR Testing in Travelers: Results of a Cross-sectional Study of Travelers at Iraq's International Borders. Disaster Med Public Health Prep 2022; 16:1-3. [PMID: 35671999 PMCID: PMC9304946 DOI: 10.1017/dmp.2022.140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 03/19/2022] [Accepted: 05/22/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND In late 2019, a novel coronavirus was detected in Wuhan, China, that caused a pandemic by September 2021, resulting in 224,180,411 cases and more than 4,600,000 deaths worldwide. In response to the pandemic, the Autonomous Kurdistan Regional Government of Iraq (KRG) imposed strict infection control measures at its borders for all travelers from neighboring countries, wherein each traveler was subjected to a mandatory reverse transcription polymerase chain reaction (RT-PCR) test on arrival to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected travelers. The aim of this study is to determine the rate of infection with SARS-CoV-2 among the travelers entering Kurdistan region through Ibrahim Al-Khalil crossing point with Turkey as a predictor for the upcoming infection waves. METHODS The data of RT-PCR tests to detect SARS-CoV-2 in all travelers arriving at the Ibrahim Al-Khalil Border Crossing between Iraq and the Republic of Turkey were reviewed from August 21, 2020 to August 21, 2021. RESULTS It was found that there were 9873 cases of SARS-CoV-2 infections among 1,082,074 travelers during the study period. CONCLUSIONS This study shows the importance of mass testing of travelers at border crossings to control the spread of SARS-CoV-2 infection.
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Affiliation(s)
- Doaa Abdulkhaleq Salih
- Ibrahim Al-Khalil Border Crossing Coronavirus Testing Center
- Directorate General of Health, Kurdistan Region of Iraq
| | - Jivan Qasim Ahmed
- Ibrahim Al-Khalil Border Crossing Coronavirus Testing Center
- Department of pathology and Microbiology, University of Duhok, Kurdistan Region, Iraq
| | - Marwan Khalil Qader
- Ibrahim Al-Khalil Border Crossing Coronavirus Testing Center
- College of Science, University of Duhok, Kurdistan Region, Iraq
| | - Mohammed S. Shukur
- Ibrahim Al-Khalil Border Crossing Coronavirus Testing Center
- Department of surgery and medicine, University of Duhok, Kurdistan Region, Iraq
| | - Bayar K. A. Zeebaree
- Ibrahim Al-Khalil Border Crossing Coronavirus Testing Center
- Department of surgery and medicine, University of Duhok, Kurdistan Region, Iraq
| | - Mateen Bahjat Sadeq
- Ibrahim Al-Khalil Border Crossing Coronavirus Testing Center
- Zanist Family Medicine Centre, Directorate General of Health, Kurdistan Region of Iraq
| | | | | | - Ibrahim Mohammed Abdullah
- Ibrahim Al-Khalil Border Crossing Coronavirus Testing Center
- Medical Lab Technology Department, College of Health and Medical Technology-Shekhan, Duhok Polytechnic University, Iraq
| | - Omar Mohammed
- Ibrahim Al-Khalil Border Crossing Coronavirus Testing Center
- Preventive Health Affairs Directorate, Directorate General of Health, Kurdistan Region of Iraq
| | - Luqman Saleh Taha
- Duhok Central Public Health Laboratory, Duhok, Kurdistan Region of Iraq
| | - Rawand Al-Qadi
- Ibrahim Al-Khalil Border Crossing Coronavirus Testing Center
- Duhok Central Public Health Laboratory, Duhok, Kurdistan Region of Iraq
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Phan T, Tran NYK, Gottlieb T, Siarakas S, McKew G. Evaluation of the influenza and respiratory syncytial virus (RSV) targets in the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay: sample pooling increases testing throughput. Pathology 2022; 54:466-471. [PMID: 35461715 PMCID: PMC9021007 DOI: 10.1016/j.pathol.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/09/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023]
Abstract
During the COVID-19 pandemic, sample pooling has proven an effective strategy to overcome the limitations of reagent shortages and expand laboratory testing capacity. The inclusion of influenza and respiratory syncytial virus (RSV) in a multiplex tandem PCR platform with SARS-CoV-2 provides useful diagnostic and infection control information. This study aimed to evaluate the performance of the influenza and RSV targets in the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay, including the effect of pooling samples on target detection. RSV target detection in clinical samples was compared to the Cepheid Xpert Xpress Flu/RSV assay as a reference standard. Samples were then tested in pools of four and detection rates were compared. Owing to the unavailability of clinical samples for influenza, only the effect of sample pooling on simulated samples was evaluated for these targets. RSV was detected in neat clinical samples with a positive percent agreement (PPA) of 100% and negative percent agreement (NPA) of 99.5% compared to the reference standard, demonstrating 99.7% agreement. This study demonstrates that sample pooling by four increases the average Ct value by 2.24, 2.29, 2.20 and 1.91 cycles for the target's influenza A, influenza A typing, influenza B and RSV, respectively. The commercial AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay was able to detect influenza and RSV at an intermediate concentration within the limit of detection of the assay. Further studies to explore the applicability of sample pooling at the lower limit of detection of the assay is needed. Nevertheless, sample pooling has shown to be a viable strategy to increase testing throughput and reduce reagent usage. In addition, the multiplexed platform targeting various respiratory viruses assists with public health and infection control responses, clinical care, and patient management.
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Affiliation(s)
- Thuy Phan
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia
| | - Ngoc Yen Kim Tran
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia,Address for correspondence: Dr Ngoc Yen Kim Tran, Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, Concord Road, Concord, NSW 2139, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia,Faculty of Medicine and Health, The University of Sydney, Concord, NSW, Australia
| | - Steven Siarakas
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia
| | - Genevieve McKew
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia,Faculty of Medicine and Health, The University of Sydney, Concord, NSW, Australia
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Cohen Y, Bamberger N, Mor O, Walfisch R, Fleishon S, Varkovitzky I, Younger A, Levi DO, Kohn Y, Steinberg DM, Zeevi D, Erster O, Mendelson E, Livneh Z. Effective bubble-based testing for SARS-CoV-2 using swab-pooling. Clin Microbiol Infect 2022; 28:859-864. [PMID: 35182758 PMCID: PMC8849906 DOI: 10.1016/j.cmi.2022.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Despite the success in developing COVID-19 vaccines, containment of the disease is obstructed worldwide by vaccine production bottlenecks, logistics hurdles, vaccine refusal, transmission through unvaccinated children, and the appearance of new viral variants. This underscores the need for effective strategies for identifying carriers/patients, which was the main aim of this study. METHODS We present a bubble-based PCR testing approach using swab-pooling into lysis buffer. A bubble is a cluster of people who can be periodically tested for SARS-CoV-2 by swab-pooling. A positive test of a pool mandates quarantining each of its members, who are then individually tested while in isolation to identify the carrier(s) for further epidemiological contact tracing. RESULTS We tested an overall sample of 25 831 individuals, divided into 1273 bubbles, with an average size of 20.3 ± 7.7 swabs/test tube, obtaining for all pools (≤37 swabs/pool) a specificity of 97.5% (lower bound 96.6%) and a sensitivity of 86.3% (lower bound 78.2%) and a post hoc analyzed sensitivity of 94.6% (lower bound 86.7%) and a specificity of 97.2% (lower bound 96.2%) in pools with ≤25 swabs, relative to individual testing. DISCUSSION This approach offers a significant scale-up in sampling and testing throughput and savings in testing cost, without reducing sensitivity or affecting the standard PCR testing laboratory routine. It can be used in school classes, airplanes, hospitals, military units, and workplaces, and may be applicable to future pandemics.
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Affiliation(s)
- Yuval Cohen
- Directorate of Defense Research & Development, Israeli Ministry of Defense, Tel Aviv, Israel
| | - Nadav Bamberger
- Directorate of Defense Research & Development, Israeli Ministry of Defense, Tel Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Ronen Walfisch
- Directorate of Defense Research & Development, Israeli Ministry of Defense, Tel Aviv, Israel
| | | | - Itay Varkovitzky
- Directorate of Defense Research & Development, Israeli Ministry of Defense, Tel Aviv, Israel
| | | | | | - Yishai Kohn
- Directorate of Defense Research & Development, Israeli Ministry of Defense, Tel Aviv, Israel
| | - David M Steinberg
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel
| | - Danny Zeevi
- Department of Biotechnology, Hadassah Academic College, Jerusalem, Israel
| | - Oran Erster
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zvi Livneh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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Chen Y, Liu F, Lee LP. Quantitative and ultrasensitive in situ immunoassay technology for SARS-CoV-2 detection in saliva. Sci Adv 2022; 8:eabn3481. [PMID: 35613342 PMCID: PMC9132547 DOI: 10.1126/sciadv.abn3481] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/11/2022] [Indexed: 05/26/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has become an immense global health crisis. However, the lack of efficient and sensitive on-site testing methods limits early detection for timely isolation and intervention. Here, we present a quantitative and ultrasensitive in situ immunoassay technology for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in saliva (QUIT SARS-CoV-2). Our nanoporous membrane resonator generates a rapid oscillating flow to purify and concentrate fully intact SARS-CoV-2 virus in saliva by 40-fold for in situ detection of viral antigens based on chemiluminescent immunoassay within 20 min. This method can not only achieve a detection sensitivity below 100 copies/ml of virus, comparable to the bench-top PCR equipment; it can also improve detection specificity via direct monitoring of viral loads. The integrated portable QUIT SARS-CoV-2 system, which enables rapid and accurate on-site viral screening with a high-throughput sample pooling strategy, can be performed in primary care settings and substantially improve the detection and prevention of COVID-19.
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Affiliation(s)
- Yuchao Chen
- WellSIM Biomedical Technologies Inc., 626 Bancroft Way, Suite A, Berkeley, CA, USA
| | - Fei Liu
- WellSIM Biomedical Technologies Inc., 626 Bancroft Way, Suite A, Berkeley, CA, USA
| | - Luke P. Lee
- Harvard Medical School, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Bioengineering and Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, USA
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
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35
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Lohse S, Sternjakob-Marthaler A, Lagemann P, Schöpe J, Rissland J, Seiwert N, Pfuhl T, Müllendorff A, Kiefer LS, Vogelgesang M, Vella L, Denk K, Vicari J, Zwick A, Lang I, Weber G, Geisel J, Rech J, Schnabel B, Hauptmann G, Holleczek B, Scheiblauer H, Wagenpfeil S, Smola S. German federal-state-wide seroprevalence study of 1 st SARS-CoV-2 pandemic wave shows importance of long-term antibody test performance. Commun Med (Lond) 2022; 2:52. [PMID: 35603305 PMCID: PMC9117207 DOI: 10.1038/s43856-022-00100-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 03/09/2022] [Indexed: 12/12/2022] Open
Abstract
Background Reliable data on the adult SARS-CoV-2 infection fatality rate in Germany are still scarce. We performed a federal state-wide cross-sectional seroprevalence study named SaarCoPS, that is representative for the adult population including elderly individuals and nursing home residents in the Saarland. Methods Serum was collected from 2940 adults via stationary or mobile teams during the 1st pandemic wave steady state period. We selected an antibody test system with maximal specificity, also excluding seroreversion effects due to a high longitudinal test performance. For the calculations of infection and fatality rates, we accounted for the delays of seroconversion and death after infection. Results Using a highly specific total antibody test detecting anti-SARS-CoV-2 responses over more than 180 days, we estimate an adult infection rate of 1.02% (95% CI: [0.64; 1.44]), an underreporting rate of 2.68-fold (95% CI: [1.68; 3.79]) and infection fatality rates of 2.09% (95% CI: (1.48; 3.32]) or 0.36% (95% CI: [0.25; 0.59]) in all adults including elderly individuals, or adults younger than 70 years, respectively. Conclusion The study highlights the importance of study design and test performance for seroprevalence studies, particularly when seroprevalences are low. Our results provide a valuable baseline for evaluation of future pandemic dynamics and impact of public health measures on virus spread and human health in comparison to neighbouring countries such as Luxembourg or France.
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Affiliation(s)
- Stefan Lohse
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | | | - Paul Lagemann
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Jakob Schöpe
- Institute for Medical Biometry, Epidemiology and Medical Informatics, Saarland University Medical Center, 66421 Homburg, Germany
| | - Jürgen Rissland
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Nastasja Seiwert
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Thorsten Pfuhl
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Alana Müllendorff
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Laurent S Kiefer
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Markus Vogelgesang
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Luca Vella
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Katharina Denk
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Julia Vicari
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Anabel Zwick
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Isabelle Lang
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Gero Weber
- Physical Geography and Environmental Research, Saarland University, 66125 Saarbrücken, Germany
| | - Jürgen Geisel
- Central Laboratory, Saarland University Hospital, 66421 Homburg, Germany
| | - Jörg Rech
- Ministry of Health, Social Affairs, Women and the Family, 66119 Saarbrücken, Germany
| | - Bernd Schnabel
- Ministry of Health, Social Affairs, Women and the Family, 66119 Saarbrücken, Germany
| | - Gunter Hauptmann
- Kassenärztliche Vereinigung Saarland, 66113 Saarbrücken, Germany
| | - Bernd Holleczek
- Ministry of Health, Social Affairs, Women and the Family, 66119 Saarbrücken, Germany.,Saarland Cancer Registry, 66117 Saarbrücken, Germany
| | | | - Stefan Wagenpfeil
- Institute for Medical Biometry, Epidemiology and Medical Informatics, Saarland University Medical Center, 66421 Homburg, Germany
| | - Sigrun Smola
- Institute of Virology, Saarland University Medical Center, 66421 Homburg, Germany.,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
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Miguita L, Martins-Chaves RR, Geddes VEV, Mendes SDR, Costa SFDS, Fonseca PLC, Menezes D, de Souza RM, Queiroz DC, Alves HJ, de Freitas RAB, Cruz AF, Moreira RG, Moreira FRR, Bemquerer LM, de Aguilar DR, de Souza e Silva ME, Sampaio AA, Jardilino FDM, de Souza LN, da Silva TA, Gomes CC, de Abreu MHNG, de Aguiar RS, de Souza RP, Gomez RS. Biosafety in Dental Health Care During the COVID-19 Pandemic: A Longitudinal Study. Front Oral Health 2022; 3:871107. [PMID: 35619688 PMCID: PMC9127188 DOI: 10.3389/froh.2022.871107] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic had quite an impact on dental health care. Concerns about the risk of SARS-CoV-2 transmission through contaminant fluids and droplet formation during several dental procedures highly impacted dental health care, drastically reducing the number of dental practices worldwide. To monitor SARS-CoV-2 contamination in dental clinics, a longitudinal study was carried out during the return of dental practice at university. Methods Dental health care professionals [(DHCPs); teachers, undergraduate dental students, and dental assistants] and patients were screened for SARS-CoV-2 RNA in a dental school clinic environment from 11th January to 12th March 2021 (9 weeks). Serological testing was performed on DHCPs in two-time points. Additionally, samples with low Ct values were sequenced to identify the circulating SARS-CoV-2 variant and possible transmission clusters. Results We found a low number of dental staff (5.8%), patients (0.9%), and environment sites (0.8%) positive for SARS-CoV-2. Most positive cases had asymptomatic to mild symptoms, and two asymptomatic DHCPs presented prolonged infection. In the first week after previous exposure to COVID-19, 16.2% of DHCPs had IgM or IgG antibodies against SARS-CoV-2, and 1/3 of them had undetected antibodies in the last weeks. The variant zeta (P.2) could be detected. No cross-infection was observed between participants. Conclusion Our study suggests that dental practice can be safely executed when adequate control measures and biosafety protocols are applied. DHCP and patient testing, patient telemonitoring, proper use of personal protection equipment, and sanitization of surfaces are essential to avoid SARS-CoV-2 cross-infection in dental practice.
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Affiliation(s)
- Lucyene Miguita
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Roberta Rayra Martins-Chaves
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Victor Emmanuel Viana Geddes
- Department of Genetics, Ecology and Evolution, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Suellen da Rocha Mendes
- Department of Community and Preventive Dentistry, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Sara Ferreira dos Santos Costa
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Paula Luize Camargos Fonseca
- Department of Genetics, Ecology and Evolution, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Diego Menezes
- Department of Genetics, Ecology and Evolution, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Rafael Marques de Souza
- Department of Genetics, Ecology and Evolution, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Daniel Costa Queiroz
- Department of Genetics, Ecology and Evolution, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Hugo José Alves
- Department of Genetics, Ecology and Evolution, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Aline Fernanda Cruz
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Rennan Garcias Moreira
- Multiusers Laboratories Center, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Filipe Romero Rebello Moreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Belo Horizonte, Brazil
| | - Larissa Marques Bemquerer
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Diego Rodrigues de Aguilar
- Department of Community and Preventive Dentistry, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Maria Elisa de Souza e Silva
- Department of Operative Dentistry, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Aline Araújo Sampaio
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Leandro Napier de Souza
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Tarcilia Aparecida da Silva
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Carolina Cavaliéri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Renato Santana de Aguiar
- Department of Genetics, Ecology and Evolution, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Renan Pedra de Souza
- Department of Genetics, Ecology and Evolution, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ricardo Santiago Gomez
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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Tavakoli F, Yavarian J, Shafiei Jandaghi NZ, Sadeghi K, Ghavami N, Salimi V, Mokhtari-Azad T. Evaluation of SARS-CoV-2 genome detection by real-time PCR assay using pooled specimens. Future Virol 2022. [PMID: 35586148 PMCID: PMC9090217 DOI: 10.2217/fvl-2021-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/12/2022] [Indexed: 01/08/2023]
Abstract
Objective: To evaluate SARS-CoV-2 genome detection using pooled samples by RT-qPCR assay, compared to individual samples. Method: At first all samples were tested individually using two commercial methods targeting ORF1ab, NP and E genes. Then, four experimental groups of samples were pooled and evaluated using the same detection methods. Findings: Compared to the individual sample testing, the sample pooling conserved the sensitivity of the detection in all groups of pooled samples when the Ct value in single test was lower than 33. Conclusion: Specimen pooling may fail to detect positive samples with high Ct values. However, in scarcity of reagents or in population surveys, it could be considered as an alternative method in low prevalence settings.
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Affiliation(s)
- Forough Tavakoli
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Jila Yavarian
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Kaveh Sadeghi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Nastaran Ghavami
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Salimi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-Azad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Tré-Hardy M, Piteüs S, Beukinga I, Blairon L. Clinical evaluation of the GSD NovaPrime® SARS-CoV-2 RTq-PCR assay. Diagn Microbiol Infect Dis 2022; 103:115718. [PMID: 35641362 PMCID: PMC9061580 DOI: 10.1016/j.diagmicrobio.2022.115718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/03/2022]
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Andreu-Perez J, Pérez-Espinosa H, Timonet E, Kiani M, Girón-Pérez MI, Benitez-Trinidad AB, Jarchi D, Rosales-Pérez A, Gatzoulis N, Reyes-Galaviz OF, Torres-García A, Reyes-García CA, Ali Z, Rivas F. A Generic Deep Learning Based Cough Analysis System From Clinically Validated Samples for Point-of-Need Covid-19 Test and Severity Levels. IEEE Trans Serv Comput 2022; 15:1220-1232. [PMID: 35936760 PMCID: PMC9328729 DOI: 10.1109/tsc.2021.3061402] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/27/2021] [Accepted: 02/17/2021] [Indexed: 06/01/2023]
Abstract
In an attempt to reduce the infection rate of the COrona VIrus Disease-19 (Covid-19) countries around the world have echoed the exigency for an economical, accessible, point-of-need diagnostic test to identify Covid-19 carriers so that they (individuals who test positive) can be advised to self isolate rather than the entire community. Availability of a quick turn-around time diagnostic test would essentially mean that life, in general, can return to normality-at-large. In this regards, studies concurrent in time with ours have investigated different respiratory sounds, including cough, to recognise potential Covid-19 carriers. However, these studies lack clinical control and rely on Internet users confirming their test results in a web questionnaire (crowdsourcing) thus rendering their analysis inadequate. We seek to evaluate the detection performance of a primary screening tool of Covid-19 solely based on the cough sound from 8,380 clinically validated samples with laboratory molecular-test (2,339 Covid-19 positive and 6,041 Covid-19 negative) under quantitative RT-PCR (qRT-PCR) from certified laboratories. All collected samples were clinically labelled, i.e., Covid-19 positive or negative, according to the results in addition to the disease severity based on the qRT-PCR threshold cycle (Ct) and lymphocytes count from the patients. Our proposed generic method is an algorithm based on Empirical Mode Decomposition (EMD) for cough sound detection with subsequent classification based on a tensor of audio sonographs and deep artificial neural network classifier with convolutional layers called 'DeepCough'. Two different versions of DeepCough based on the number of tensor dimensions, i.e., DeepCough2D and DeepCough3D, have been investigated. These methods have been deployed in a multi-platform prototype web-app 'CoughDetect'. Covid-19 recognition results rates achieved a promising AUC (Area Under Curve) of [Formula: see text] 98 . 80 % ± 0 . 83 % , sensitivity of [Formula: see text] 96 . 43 % ± 1 . 85 % , and specificity of [Formula: see text] 96 . 20 % ± 1 . 74 % and average AUC of [Formula: see text] 81 . 08 % ± 5 . 05 % for the recognition of three severity levels. Our proposed web tool as a point-of-need primary diagnostic test for Covid-19 facilitates the rapid detection of the infection. We believe it has the potential to significantly hamper the Covid-19 pandemic across the world.
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Affiliation(s)
- Javier Andreu-Perez
- School of Computer Science and Electronic Engineering, Faculty of Science and HealthUniversity of EssexColchesterCO4 3SQU.K.
- Department of Computer ScienceUniversity of Jaén16747JaénSpain
| | - Humberto Pérez-Espinosa
- School of Computer Science and Electronic Engineering, Faculty of Science and HealthUniversity of EssexColchesterCO4 3SQU.K.
- UT3 Centro de Investigacion Cientifica y de Educacion Superior de EnsenadaEnsenada22860Mexico
| | - Eva Timonet
- Agencia Sanitaria Costa del SolJunta de Andalucia Consejeria de Salud41020SevilleSpain
| | - Mehrin Kiani
- School of Computer Science and Electronic Engineering, Faculty of Science and HealthUniversity of EssexColchesterCO4 3SQU.K.
| | | | | | - Delaram Jarchi
- School of Computer Science and Electronic Engineering, Faculty of Science and HealthUniversity of EssexColchesterCO4 3SQU.K.
| | | | - Nick Gatzoulis
- School of Computer Science and Electronic Engineering, Faculty of Science and HealthUniversity of EssexColchesterCO4 3SQU.K.
| | | | | | | | - Zulfiqar Ali
- School of Computer Science and Electronic Engineering, Faculty of Science and HealthUniversity of EssexColchesterCO4 3SQU.K.
| | - Francisco Rivas
- Agencia Sanitaria Costa del SolJunta de Andalucia Consejeria de Salud41020SevilleSpain
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Feng Z, Zhang Y, Pan Y, Zhang D, Zhang L, Wang Q. Mass screening is a key component to fight against SARS-CoV-2 and return to normalcy. Med Rev (Berl) 2022; 2:197-212. [PMID: 35862506 PMCID: PMC9274759 DOI: 10.1515/mr-2021-0024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/19/2022] [Indexed: 06/01/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had highly transmissible and pathogenic, which caused serious economic loss and hazard to public health. Different countries have developed strategies to deal with the COVID-19 pandemic that fit their epidemiological situations, capacities, and values. Mass screening combined with control measures rapidly reduced the transmission of the SARS-CoV-2 infection. The COVID-19 pandemic has dramatically highlighted the essential role of diagnostics capacity in the control of communicable diseases. Mass screening has been increasingly used to detect suspected COVID-19 cases and their close contacts, asymptomatic case, patients attending fever clinics, high-risk populations, employees, even all population to identify infectious individuals. Mass screening is a key component to fight against SARS-CoV-2 and return to normalcy. Here we describe the history of mass screening, define the scope of mass screening, describe its application scenarios, and discuss the impact and challenges of using this approach to control COVID-19. We conclude that through a comprehension screening program and strong testing capabilities, mass screening could help us return to normalcy more quickly.
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Affiliation(s)
- Zhaomin Feng
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yi Zhang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yang Pan
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Daitao Zhang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Lei Zhang
- Queensland University of Technology, Brisbane, Australia
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
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Castellaro AM, Velez P, Giaj Merlera G, Rondan Dueñas J, Condat F, Gallardo J, Makhoul A, Cinalli C, Rosales Cavaglieri L, Di Cola G, Sicilia P, López L, Bocco JL, Barbás MG, Cardozo DH, Pisano MB, Ré V, Belaus A, Castro G. SARS-CoV-2 detection in multi-sample pools in a real pandemic scenario: A screening strategy of choice for active surveillance. PLoS One 2022; 17:e0266408. [PMID: 35363805 PMCID: PMC8975135 DOI: 10.1371/journal.pone.0266408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/18/2022] [Indexed: 11/18/2022] Open
Abstract
Background The current COVID-19 pandemic has overloaded the diagnostic capacity of laboratories by the gold standard method rRT-PCR. This disease has a high spread rate and almost a quarter of infected individuals never develop symptoms. In this scenario, active surveillance is crucial to stop the virus propagation. Methods Between July 2020 and April 2021, 11,580 oropharyngeal swab samples collected in closed and semi-closed institutions were processed for SARS-CoV-2 detection in pools, implementing this strategy for the first time in Córdoba, Argentina. Five-sample pools were constituted before nucleic acid extraction and amplification by rRT-PCR. Comparative analysis of cycle threshold (Ct) values from positive pools and individual samples along with a cost-benefit report of the whole performance of the results was performed. Results From 2,314 5-sample pools tested, 158 were classified as positive (6.8%), 2,024 as negative (87.5%), and 132 were categorized as indeterminate (5.7%). The Ct value shift due to sample dilution showed an increase in Ct of 2.6±1.53 cycles for N gene and 2.6±1.78 for ORF1ab gene. Overall, 290 pools were disassembled and 1,450 swabs were analyzed individually. This strategy allowed correctly identifying 99.8% of the samples as positive (7.6%) or negative (92.2%), avoiding the execution of 7,806 rRT-PCR reactions which represents a cost saving of 67.5%. Conclusion This study demonstrates the feasibility of pooling samples to increase the number of tests performed, helping to maximize molecular diagnostic resources and reducing the work overload of specialized personnel during active surveillance of the COVID-19 pandemic.
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Affiliation(s)
- Andrés Marcos Castellaro
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
- * E-mail:
| | - Pablo Velez
- Unidad de Biología Molecular, Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), Córdoba, Argentina
| | - Guillermo Giaj Merlera
- Unidad de Biología Molecular, Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), Córdoba, Argentina
| | - Juan Rondan Dueñas
- Unidad de Biología Molecular, Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), Córdoba, Argentina
| | - Felix Condat
- Unidad de Biología Molecular, Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), Córdoba, Argentina
| | - Jesica Gallardo
- Unidad de Biología Molecular, Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), Córdoba, Argentina
| | - Aylen Makhoul
- Unidad de Biología Molecular, Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), Córdoba, Argentina
| | - Camila Cinalli
- Unidad de Biología Molecular, Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), Córdoba, Argentina
| | - Lorenzo Rosales Cavaglieri
- Unidad de Biología Molecular, Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), Córdoba, Argentina
| | - Guadalupe Di Cola
- Instituto de Virología “Doctor José María Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Paola Sicilia
- Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Laura López
- Dirección de Epidemiología, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | | | - José Luis Bocco
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Gabriela Barbás
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Diego Hernán Cardozo
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - María Belén Pisano
- Instituto de Virología “Doctor José María Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Viviana Ré
- Instituto de Virología “Doctor José María Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Andrea Belaus
- Unidad de Biología Molecular, Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), Córdoba, Argentina
| | - Gonzalo Castro
- Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
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Hong D, Dey R, Lin X, Cleary B, Dobriban E. Group testing via hypergraph factorization applied to COVID-19. Nat Commun 2022; 13:1837. [PMID: 35383149 PMCID: PMC8983763 DOI: 10.1038/s41467-022-29389-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/14/2022] [Indexed: 11/09/2022] Open
Abstract
Large scale screening is a critical tool in the life sciences, but is often limited by reagents, samples, or cost. An important recent example is the challenge of achieving widespread COVID-19 testing in the face of substantial resource constraints. To tackle this challenge, screening methods must efficiently use testing resources. However, given the global nature of the pandemic, they must also be simple (to aid implementation) and flexible (to be tailored for each setting). Here we propose HYPER, a group testing method based on hypergraph factorization. We provide theoretical characterizations under a general statistical model, and carefully evaluate HYPER with alternatives proposed for COVID-19 under realistic simulations of epidemic spread and viral kinetics. We find that HYPER matches or outperforms the alternatives across a broad range of testing-constrained environments, while also being simpler and more flexible. We provide an online tool to aid lab implementation: http://hyper.covid19-analysis.org .
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Affiliation(s)
- David Hong
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Rounak Dey
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Statistics, Harvard University, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Brian Cleary
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Edgar Dobriban
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA.
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Zhou D, Zhou M. Mathematical Model and Optimization Methods of Wide-Scale Pooled Sample Testing for COVID-19. Mathematics 2022; 10:1183. [DOI: 10.3390/math10071183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, coronavirus disease 2019 (COVID-19) has become the most severe infectious disease affecting the world, which has spread around the world to more than 200 countries in 2020. Until the number of COVID-19 vaccines is insufficient, nucleic acid testing is considered as an effective way to screen virus carriers and control the spread of the virus. Considering that the medical resources and infection rates are different across various countries and regions, if all infected areas adopt the traditional individual nucleic acid testing method, the workload will be heavy and time-consuming. Therefore, this will not lead to the control of the pandemic. After Wuhan completed a citywide nucleic acid testing in May 2020, China basically controlled the spread of COVID-19 and entered the post-epidemic period. Since then, although some cities in China, such as Qingdao, Xinjiang, Beijing, and Dalian, have experienced a local epidemic resurgence, the pandemic was quickly suppressed through wide-scale pooled nucleic acid testing methods. Combined with the successful experience of mass nucleic acid testing in China, this study introduces two main pooled testing methods used in two cities with a population of more than ten million people, Wuhan’s “five-in-one” and Qingdao’s “ten-in-one” rapid pooled testing methods. This study proposes an improved method for optimising the second round of “ten-in-one” pooled testing, known as “the pentagram mini-pooled testing method”, which speeds up the testing process (as a result of reducing the numbers of testing by 40%) and significantly reduces the cost. Qingdao’s optimised “ten-in-one” pooled testing method quickly screens out the infections by running fewer testing samples. This study also mathematically examines the probabilistic principles and applicability conditions for pooled testing of COVID-19. Herein, the study theoretically determines the optimal number of samples that could successfully be combined into a pool under different infection rates. Then, it quantitatively discusses the applicability and principles for choosing the pooled testing instead of individual testing. Overall, this research offers a reference for other countries with different infection rates to help them in implementing the mass testing for COVID-19 to reduce the spread of coronavirus.
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Casper M, Reichert MC, Rissland J, Smola S, Lammert F, Krawczyk M. Pre-endoscopy SARS-CoV-2 testing strategy during COVID-19 pandemic: the care must go on. Eur J Med Res 2022; 27:41. [PMID: 35303954 PMCID: PMC8931568 DOI: 10.1186/s40001-022-00672-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 03/07/2022] [Indexed: 11/24/2022] Open
Abstract
Background In response to the COVID-19 pandemic, endoscopic societies initially recommended reduction of endoscopic procedures. In particular non-urgent endoscopies should be postponed. However, this might lead to unnecessary delay in diagnosing gastrointestinal conditions. Methods Retrospectively we analysed the gastrointestinal endoscopies performed at the Central Endoscopy Unit of Saarland University Medical Center during seven weeks from 23 March to 10 May 2020 and present our real-world single-centre experience with an individualized rtPCR-based pre-endoscopy SARS-CoV-2 testing strategy. We also present our experience with this strategy in 2021. Results Altogether 359 gastrointestinal endoscopies were performed in the initial period. The testing strategy enabled us to conservatively handle endoscopy programme reduction (44% reduction as compared 2019) during the first wave of the COVID-19 pandemic. The results of COVID-19 rtPCR from nasopharyngeal swabs were available in 89% of patients prior to endoscopies. Apart from six patients with known COVID-19, all other tested patients were negative. The frequencies of endoscopic therapies and clinically significant findings did not differ between patients with or without SARS-CoV-2 tests. In 2021 we were able to unrestrictedly perform all requested endoscopic procedures (> 5000 procedures) by applying the rtPCR-based pre-endoscopy SARS-CoV-2 testing strategy, regardless of next waves of COVID-19. Only two out-patients (1893 out-patient procedures) were tested positive in the year 2021. Conclusion A structured pre-endoscopy SARS-CoV-2 testing strategy is feasible in the clinical routine of an endoscopy unit. rtPCR-based pre-endoscopy SARS-CoV-2 testing safely allowed unrestricted continuation of endoscopic procedures even in the presence of high incidence rates of COVID-19. Given the low frequency of positive tests, the absolute effect of pre-endoscopy testing on viral transmission may be low when FFP-2 masks are regularly used.
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Affiliation(s)
- M Casper
- Department of Medicine II - Gastroenterology, Hepatology and Endocrinology, Saarland University Medical Center, Saarland University, Kirrberger Straße 100, 66421, Homburg, Germany.
| | - M C Reichert
- Department of Medicine II - Gastroenterology, Hepatology and Endocrinology, Saarland University Medical Center, Saarland University, Kirrberger Straße 100, 66421, Homburg, Germany
| | - J Rissland
- Institute of Virology, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - S Smola
- Institute of Virology, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - F Lammert
- Department of Medicine II - Gastroenterology, Hepatology and Endocrinology, Saarland University Medical Center, Saarland University, Kirrberger Straße 100, 66421, Homburg, Germany.,Hannover Medical School, Hannover Health Sciences Campus, Hannover, Germany
| | - M Krawczyk
- Department of Medicine II - Gastroenterology, Hepatology and Endocrinology, Saarland University Medical Center, Saarland University, Kirrberger Straße 100, 66421, Homburg, Germany.,Laboratory of Metabolic Liver Diseases, Department of General, Transplant and Liver Surgery, Center for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
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Barathidasan R, Sharmila FM, Raj RV, Dhanalakshmi G, Anitha G, Dhodapkar R. Pooled sample testing for COVID-19 diagnosis: Evaluation of bi-directional matrix pooling strategies. J Virol Methods 2022; 304:114524. [PMID: 35301022 PMCID: PMC8920575 DOI: 10.1016/j.jviromet.2022.114524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/09/2022] [Indexed: 11/27/2022]
Abstract
In the on-going COVID-19 pandemic, pooled testing of samples by RT-PCR has been recommended at certain scenarios to increase labs’ testing capacity and reduce cost of testing. This paper describes the evaluation of bi-directional matrix pooling strategies with clinical samples in a 5 × 5 and 10 × 10 matrix. Nasopharyngeal swab samples in viral transport medium (VTM) previously tested (positive or negative) by real time RT-PCR for SARS-CoV-2 were used for these experiments. Ten sets of 5 × 5 (250 samples) and ten sets of 10 × 10 (1000 samples) pooling of samples in both directions was done with known positive samples introduced at random positions. Extracted nucleic acid was tested for SARS-CoV-2 E-gene by RT-PCR. Sensitivity or concordance and feasibility of matrix pooling were assessed in comparison to direct RT-PCR testing. In comparison to direct testing, the overall concordance was 86.6% for 5 × 5 pooling, 73.3% for 10 × 10 with 200 µL extraction volume and 86.6% for 10 × 10 with 400 µL extraction volume. Bi-directional matrix pooling can be adopted with advantage over conventional direct or pool testing for COVID-19 by RT-PCR under the following conditions: i) sample positivity rate of ≤ 5%, ii) matrix pool size of 8–10 samples, iii) use of min. 40 µL VTM from each sample and iv) utilization of automated liquid handling equipment, if available, for sample addition to avoid human errors.
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Affiliation(s)
- Rajamani Barathidasan
- Regional Viral Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry 605006, India
| | - Ferdina Marie Sharmila
- Regional Viral Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry 605006, India
| | - Ratchagadasse Vimal Raj
- Regional Viral Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry 605006, India
| | - Gounassegarane Dhanalakshmi
- Regional Viral Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry 605006, India
| | - Gunalan Anitha
- Regional Viral Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry 605006, India
| | - Rahul Dhodapkar
- Regional Viral Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry 605006, India.
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Hueda-Zavaleta M, Copaja-Corzo C, Benites-Zapata VA, Cardenas-Rueda P, Maguiña JL, Rodríguez-Morales AJ. Diagnostic performance of RT-PCR-based sample pooling strategy for the detection of SARS-CoV-2. Ann Clin Microbiol Antimicrob 2022; 21:11. [PMID: 35287682 PMCID: PMC8919688 DOI: 10.1186/s12941-022-00501-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/01/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The rapid spread of SARS-CoV-2 has created a shortage of supplies of reagents for its detection throughout the world, especially in Latin America. The pooling of samples consists of combining individual patient samples in a block and analyzing the group as a particular sample. This strategy has been shown to reduce the burden of laboratory material and logistical resources by up to 80%. Therefore, we aimed to evaluate the diagnostic performance of the pool of samples analyzed by RT-PCR to detect SARS-CoV-2. METHODS A cross-sectional study of diagnostic tests was carried out. We individually evaluated 420 samples, and 42 clusters were formed, each one with ten samples. These clusters could contain 0, 1 or 2 positive samples to simulate a positivity of 0, 10 and 20%, respectively. RT-PCR analyzed the groups for the detection of SARS-CoV-2. The area under the ROC curve (AUC), the Youden index, the global and subgroup sensitivity and specificity were calculated according to their Ct values that were classified as high (H: ≤ 25), moderate (M: 26-30) and low (L: 31-35) concentration of viral RNA. RESULTS From a total of 42 pools, 41 (97.6%) obtained the same result as the samples they contained (positive or negative). The AUC for pooling, Youden index, sensitivity, and specificity were 0.98 (95% CI, 0.95-1); 0.97 (95% CI, 0.90-1.03); 96.67% (95% CI; 88.58-100%) and 100% (95% CI; 95.83-100%) respectively. In the stratified analysis of the pools containing samples with Ct ≤ 25, the sensitivity was 100% (95% CI; 90-100%), while with the pools containing samples with Ct ≥ 31, the sensitivity was 80% (95% CI, 34.94-100%). Finally, a higher median was observed in the Ct of the clusters, with respect to the individual samples (p < 0.001). CONCLUSIONS The strategy of pooling nasopharyngeal swab samples for analysis by SARS-CoV-2 RT-PCR showed high diagnostic performance.
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Affiliation(s)
- Miguel Hueda-Zavaleta
- Faculty of Health Sciences, Universidad Privada de Tacna, Tacna, 23003, Peru. .,Hospital III Daniel Alcides Carrión EsSalud, Tacna, 23000, Peru.
| | - Cesar Copaja-Corzo
- Faculty of Health Sciences, Universidad Privada de Tacna, Tacna, 23003, Peru
| | - Vicente A Benites-Zapata
- Unidad de Investigación para la Generación y Síntesis de Evidencias en Salud, Universidad San Ignacio de Loyola, Lima, 15024, Peru
| | | | - Jorge L Maguiña
- Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, 15024, Peru
| | - Alfonso J Rodríguez-Morales
- Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, 15024, Peru. .,Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Belmonte, 660003, Pereira, Risaralda, Colombia.
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Nyaruaba R, Mwaliko C, Dobnik D, Neužil P, Amoth P, Mwau M, Yu J, Yang H, Wei H. Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks. Clin Microbiol Rev 2022;:e0016821. [PMID: 35258315 DOI: 10.1128/cmr.00168-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.
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Paganini I, Sani C, Chilleri C, Baccini M, Antonelli A, Bisanzi S, Burroni E, Cellai F, Coppi M, Mealli F, Pompeo G, Viti J, Rossolini GM, Carozzi FM. Assessment of the feasibility of pool testing for SARS-CoV-2 infection screening. Infect Dis (Lond) 2022; 54:478-487. [PMID: 35239458 DOI: 10.1080/23744235.2022.2044512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND SARS-CoV-2 pandemic represented a huge challenge for national health systems worldwide. Pooling nasopharyngeal (NP) swabs seems to be a promising strategy, saving time and resources, but it could reduce the sensitivity of the RT-PCR and exacerbate samples management in terms of automation and tracing. In this study, taking advantage of the routine implementation of a screening plan on health workers, we evaluated the feasibility of pool testing for SARS-CoV-2 infection diagnosis in the presence of low viral load samples. METHOD Pools were prepared with an automated instrument, mixing 4, 6 or 20 NP specimens, including one, two or none positive samples. Ct values of positive samples were on average about 35 for the four genes analyzed. RESULTS The overall sensitivity of 4-samples and 6-samples pools was 93.1 and 90.0%, respectively. Focussing on pools including one sample with Ct value ≥35 for all analyzed genes, sensitivity decreased to 77.8 and 75.0% for 4- and 6-samples, respectively; pools including two positive samples, resulted positive in any size as well as pools including positive samples with Ct values <35. CONCLUSION Pool testing strategy should account the balance between cost-effectiveness, dilution effect and prevalence of the infection. Our study demonstrated the good performances in terms of sensitivity and saving resources of pool testing mixing 4 or 6 samples, even including low viral load specimens, in a real screening context possibly affected by prevalence fluctuation. In conclusion, pool testing strategy represents an efficient and resources saving surveillance and tracing tool, especially in specific context like schools, even for monitoring changes in prevalence associated to vaccination campaign.
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Affiliation(s)
- Irene Paganini
- Regional Laboratory of Cancer Prevention, ISPRO, Florence, Italy
| | - Cristina Sani
- Regional Laboratory of Cancer Prevention, ISPRO, Florence, Italy
| | - Chiara Chilleri
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Michela Baccini
- Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy
| | - Alberto Antonelli
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Elena Burroni
- Regional Laboratory of Cancer Prevention, ISPRO, Florence, Italy
| | - Filippo Cellai
- Regional Laboratory of Cancer Prevention, ISPRO, Florence, Italy
| | - Marco Coppi
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Fabrizia Mealli
- Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy
| | - Giampaolo Pompeo
- Regional Laboratory of Cancer Prevention, ISPRO, Florence, Italy
| | - Jessica Viti
- Regional Laboratory of Cancer Prevention, ISPRO, Florence, Italy
| | - Gian Maria Rossolini
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
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Lin YJ, Yu CH, Liu TH, Chang CS, Chen WT. Constructions and Comparisons of Pooling Matrices for Pooled Testing of COVID-19. IEEE Trans Netw Sci Eng 2022; 9:467-480. [PMID: 35582549 PMCID: PMC9014483 DOI: 10.1109/tnse.2021.3121709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 09/06/2021] [Accepted: 10/17/2021] [Indexed: 06/15/2023]
Abstract
In comparison with individual testing, group testing is more efficient in reducing the number of tests and potentially leading to tremendous cost reduction. There are two key elements in a group testing technique: (i) the pooling matrix that directs samples to be pooled into groups, and (ii) the decoding algorithm that uses the group test results to reconstruct the status of each sample. In this paper, we propose a new family of pooling matrices from packing the pencil of lines (PPoL) in a finite projective plane. We compare their performance with various pooling matrices proposed in the literature, including 2D-pooling, P-BEST, and Tapestry, using the two-stage definite defectives (DD) decoding algorithm. By conducting extensive simulations for a range of prevalence rates up to 5%, our numerical results show that there is no pooling matrix with the lowest relative cost in the whole range of the prevalence rates. To optimize the performance, one should choose the right pooling matrix, depending on the prevalence rate. The family of PPoL matrices can dynamically adjust their construction parameters according to the prevalence rates and could be a better alternative than using a fixed pooling matrix.
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Affiliation(s)
- Yi-Jheng Lin
- Institute of Communications EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Che-Hao Yu
- Institute of Communications EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Tzu-Hsuan Liu
- Institute of Communications EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Cheng-Shang Chang
- Institute of Communications EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Wen-Tsuen Chen
- Institute of Communications EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
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50
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Silva AVFG, Menezes D, Moreira FRR, Torres OA, Fonseca PLC, Moreira RG, Alves HJ, Alves VR, Amaral TMDR, Coelho AN, Saraiva Duarte JM, da Rocha AV, de Almeida LGP, de Araújo JLF, de Oliveira HS, de Oliveira NJC, Zolini C, de Sousa JH, de Souza EG, de Souza RM, Ferreira LDL, Lehmkuhl Gerber A, Guimarães APDC, Maia PHS, Marim FM, Miguita L, Monteiro CC, Neto TS, Pugêdo FSF, Queiroz DC, Queiroz DNAC, Resende-Moreira LC, Santos FM, Souza EFC, Voloch CM, Vasconcelos AT, de Aguiar RS, de Souza RP. Seroprevalence, Prevalence, and Genomic Surveillance: Monitoring the Initial Phases of the SARS-CoV-2 Pandemic in Betim, Brazil. Front Microbiol 2022; 13:799713. [PMID: 35197952 PMCID: PMC8859412 DOI: 10.3389/fmicb.2022.799713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/07/2022] [Indexed: 11/18/2022] Open
Abstract
The COVID-19 pandemic has created an unprecedented need for epidemiological monitoring using diverse strategies. We conducted a project combining prevalence, seroprevalence, and genomic surveillance approaches to describe the initial pandemic stages in Betim City, Brazil. We collected 3239 subjects in a population-based age-, sex- and neighborhood-stratified, household, prospective; cross-sectional study divided into three surveys 21 days apart sampling the same geographical area. In the first survey, overall prevalence (participants positive in serological or molecular tests) reached 0.46% (90% CI 0.12–0.80%), followed by 2.69% (90% CI 1.88–3.49%) in the second survey and 6.67% (90% CI 5.42–7.92%) in the third. The underreporting reached 11, 19.6, and 20.4 times in each survey. We observed increased odds to test positive in females compared to males (OR 1.88 95% CI 1.25–2.82), while the single best predictor for positivity was ageusia/anosmia (OR 8.12, 95% CI 4.72–13.98). Thirty-five SARS-CoV-2 genomes were sequenced, of which 18 were classified as lineage B.1.1.28, while 17 were B.1.1.33. Multiple independent viral introductions were observed. Integration of multiple epidemiological strategies was able to adequately describe COVID-19 dispersion in the city. Presented results have helped local government authorities to guide pandemic management.
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Affiliation(s)
| | - Diego Menezes
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Paula Luize Camargos Fonseca
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rennan Garcias Moreira
- Centro de Laboratórios Multiusuários, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hugo José Alves
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Júlia Maria Saraiva Duarte
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - João Locke Ferreira de Araújo
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Camila Zolini
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jôsy Hubner de Sousa
- Programa de Pós-graduação em Biologia Celular, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Rafael Marques de Souza
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luciana de Lima Ferreira
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Fernanda Martins Marim
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lucyene Miguita
- Departamento de Patologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Daniel Costa Queiroz
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luciana Cunha Resende-Moreira
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Franciele Martins Santos
- Programa de Pós-graduação em Biologia Celular, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Carolina Moreira Voloch
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Renato Santana de Aguiar
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Renan Pedra de Souza
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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