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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] [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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Vuchas C, Teyim P, Dang BF, Neh A, Keugni L, Che M, Che PN, Beloko H, Fondoh V, Ndi NN, Wandji IAG, Fundoh M, Manga H, Mbuli C, Creswell J, Bisso A, Donkeng V, Sander M. Implementation of large-scale pooled testing to increase rapid molecular diagnostic test coverage for tuberculosis: a retrospective evaluation. Sci Rep 2023; 13:15358. [PMID: 37717043 PMCID: PMC10505184 DOI: 10.1038/s41598-023-41904-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/01/2023] [Indexed: 09/18/2023] Open
Abstract
In 2021, only 6.4 million of the 10.6 million people with tuberculosis (TB) were diagnosed and treated for the disease. Although the World Health Organization recommends initial diagnostic testing using a rapid sensitive molecular assay, only 38% of people diagnosed with TB benefited from these, due to barriers including the high cost of available assays. Pooled testing has been used as an approach to increase testing efficiency in many resource-constrained situations, such as the COVID-19 pandemic, but it has not yet been widely adopted for TB diagnostic testing. Here we report a retrospective analysis of routine pooled testing of 10,117 sputum specimens using the Xpert MTB/RIF and Xpert MTB/RIF Ultra assays that was performed from July 2020 to February 2022. Pooled testing saved 48% of assays and enabled rapid molecular testing for 4156 additional people as compared to individual testing, with 6.6% of specimens positive for TB. From an in silico analysis, the positive percent agreement of pooled testing in pools of 3 as compared with individual testing for the Xpert MTB/RIF Ultra assay was estimated as 99.4% (95% CI, 96.6% to 100%). These results support the scale-up of pooled testing for efficient TB diagnosis.
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Affiliation(s)
- Comfort Vuchas
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon.
| | - Pride Teyim
- Tuberculosis Reference Laboratory Douala, Douala, Littoral, Cameroon
| | | | - Angela Neh
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | - Liliane Keugni
- Tuberculosis Reference Laboratory Douala, Douala, Littoral, Cameroon
| | - Mercy Che
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | - Pantalius Nji Che
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | - Hamada Beloko
- Tuberculosis Reference Laboratory Douala, Douala, Littoral, Cameroon
| | - Victor Fondoh
- Bamenda Regional Hospital, Bamenda, Northwest, Cameroon
| | - Norah Nyah Ndi
- Baptist Convention Health Services and Baptist Institute of Health Sciences, Bamenda, Northwest, Cameroon
| | | | - Mercy Fundoh
- National TB Program- Northwest Region, Bamenda, Northwest, Cameroon
| | - Henri Manga
- National TB Program, Yaoundé, Center, Cameroon
| | - Cyrille Mbuli
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | | | - Annie Bisso
- National TB Program, Yaoundé, Center, Cameroon
| | | | - Melissa Sander
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon.
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3
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Wang Z, Wu P, Wang L, Li B, Liu Y, Ge Y, Wang R, Wang L, Tan H, Wu CH, Laine M, Salje H, Song H. Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study. PLoS Comput Biol 2023; 19:e1011492. [PMID: 37721947 PMCID: PMC10538769 DOI: 10.1371/journal.pcbi.1011492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/28/2023] [Accepted: 09/05/2023] [Indexed: 09/20/2023] Open
Abstract
China had conducted some of the most stringent public health measures to control the spread of successive SARS-CoV-2 variants. However, the effectiveness of these measures and their impacts on the associated disease burden have rarely been quantitatively assessed at the national level. To address this gap, we developed a stochastic age-stratified metapopulation model that incorporates testing, contact tracing and isolation, based on 419 million travel movements among 366 Chinese cities. The study period for this model began from September 2022. The COVID-19 disease burden was evaluated, considering 8 types of underlying health conditions in the Chinese population. We identified the marginal effects between the testing speed and reduction in the epidemic duration. The findings suggest that assuming a vaccine coverage of 89%, the Omicron-like wave could be suppressed by 3-day interval population-level testing (PLT), while it would become endemic with 4-day interval PLT, and without testing, it would result in an epidemic. PLT conducted every 3 days would not only eliminate infections but also keep hospital bed occupancy at less than 29.46% (95% CI, 22.73-38.68%) of capacity for respiratory illness and ICU bed occupancy at less than 58.94% (95% CI, 45.70-76.90%) during an outbreak. Furthermore, the underlying health conditions would lead to an extra 2.35 (95% CI, 1.89-2.92) million hospital admissions and 0.16 (95% CI, 0.13-0.2) million ICU admissions. Our study provides insights into health preparedness to balance the disease burden and sustainability for a country with a population of billions.
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Affiliation(s)
- Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Peiyi Wu
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Lin Wang
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Yonghong Liu
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yuxi Ge
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Ruixue Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Ligui Wang
- Center of Disease Control and Prevention, PLA, Beijing, China
| | - Hua Tan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, United Kingdom
| | - Marko Laine
- Finnish Meteorological Institute, Meteorological Research Unit, Helsinki, Finland
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Hongbin Song
- Center of Disease Control and Prevention, PLA, Beijing, China
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4
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Zhang J, Heath LS. Adaptive group testing strategy for infectious diseases using social contact graph partitions. Sci Rep 2023; 13:12102. [PMID: 37495642 PMCID: PMC10372051 DOI: 10.1038/s41598-023-39326-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023] Open
Abstract
Mass testing is essential for identifying infected individuals during an epidemic and allowing healthy individuals to return to normal social activities. However, testing capacity is often insufficient to meet global health needs, especially during newly emerging epidemics. Dorfman's method, a classic group testing technique, helps reduce the number of tests required by pooling the samples of multiple individuals into a single sample for analysis. Dorfman's method does not consider the time dynamics or limits on testing capacity involved in infection detection, and it assumes that individuals are infected independently, ignoring community correlations. To address these limitations, we present an adaptive group testing (AGT) strategy based on graph partitioning, which divides a physical contact network into subgraphs (groups of individuals) and assigns testing priorities based on the social contact characteristics of each subgraph. Our AGT aims to maximize the number of infected individuals detected and minimize the number of tests required. After each testing round (perhaps on a daily basis), the testing priority is increased for each neighboring group of known infected individuals. We also present an enhanced infectious disease transmission model that simulates the dynamic spread of a pathogen and evaluate our AGT strategy using the simulation results. When applied to 13 social contact networks, AGT demonstrates significant performance improvements compared to Dorfman's method and its variations. Our AGT strategy requires fewer tests overall, reduces disease spread, and retains robustness under changes in group size, testing capacity, and other parameters. Testing plays a crucial role in containing and mitigating pandemics by identifying infected individuals and helping to prevent further transmission in families and communities. By identifying infected individuals and helping to prevent further transmission in families and communities, our AGT strategy can have significant implications for public health, providing guidance for policymakers trying to balance economic activity with the need to manage the spread of infection.
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Affiliation(s)
- Jingyi Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24060, USA.
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24060, USA
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5
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Dupree TB, Assen AD, Janusson E, Wise AR, Swider JM, Roggen M. Simulations of Test Reduction Using Pooled Heavy Metals Analysis in Cannabis. J AOAC Int 2023; 106:484-489. [PMID: 36331387 DOI: 10.1093/jaoacint/qsac140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Cannabis species have a propensity to bioaccumulate toxic heavy metals from their growth media. Increased testing for these metals is required to improve the safety of the legal medical and recreational cannabis industries. However, the current methods used for mandated heavy metals tests are not efficient for a large framework. As a result, there is limited testing capacity, high testing costs, and long wait times for results across North America. OBJECTIVE This study aimed to demonstrate that pooling strategies can be used to increase the throughput in cannabis testing labs and reduce some of the strain on the industry. METHODS This paper presents an algorithm to simulate different pooling strategies. The algorithm was applied to real world data sets collected from Washington and California state testing labs. RESULTS Using a single pooling method, a pool size of three samples on average resulted in a 23.8% reduction in tests required for 100 samples for the Washington lab. For the California lab, pooling four samples on average resulted in a 54.1% reduction in tests required for 100 samples. CONCLUSION The algorithms generated from the Washington and California lab data demonstrated that pooled testing strategies can be developed on a case-by-case method to reduce the time, effort, and costs associated with heavy metals tests. HIGHLIGHTS The benefits of pooled testing will vary depending on the region and rate of contamination seen in each testing lab. Overall, our results demonstrate pooled testing has the potential to reduce the fiscal costs of testing through increased efficiency, allowing increased testing, leading to greater safety.
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Affiliation(s)
- Tom B Dupree
- Delic Labs, 3800 Wesbrook Mall, Vancouver, BC V6S2L9, Canada
| | - Amanda D Assen
- Delic Labs, 3800 Wesbrook Mall, Vancouver, BC V6S2L9, Canada
| | - Eric Janusson
- Delic Labs, 3800 Wesbrook Mall, Vancouver, BC V6S2L9, Canada
| | - Amber R Wise
- Medicine Creek Analytics, 3700 Pacific Hwy E #400, Fife, WA 98424, USA
| | - Josh M Swider
- Infinite Chemical Analysis Labs, 8312 Miramar Mall, San Diego, CA 92121, USA
| | - Markus Roggen
- Delic Labs, 3800 Wesbrook Mall, Vancouver, BC V6S2L9, Canada
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6
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Wang Z, Wang R, Wu P, Li B, Li Y, Liu Y, Wang X, Yang P, Tian H, Tian H. Optimization of Population-Level Testing, Contact Tracing, and Isolation in Emerging COVID-19 Outbreaks: a Mathematical Modeling Study - Tonghua City and Beijing Municipality, China, 2021-2022. China CDC Wkly 2023; 5:82-89. [PMID: 36777897 PMCID: PMC9902757 DOI: 10.46234/ccdcw2023.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/07/2022] [Indexed: 01/28/2023] Open
Abstract
Introduction The transmissibility of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant poses challenges for the existing measures containing the virus in China. In response, this study investigates the effectiveness of population-level testing (PLT) and contact tracing (CT) to help curb coronavirus disease 2019 (COVID-19) resurgences in China. Methods Two transmission dynamic models (i.e. with and without age structure) were developed to evaluate the effectiveness of PLT and CT. Extensive simulations were conducted to optimize PLT and CT strategies for COVID-19 control and surveillance. Results Urban Omicron resurgences can be controlled by multiple rounds of PLT, supplemented by CT - as long as testing is frequent. This study also evaluated the time needed to detect COVID-19 cases for surveillance under different routine testing rates. The results show that there is a 90% probability of detecting COVID-19 cases within 3 days through daily testing. Otherwise, it takes around 7 days to detect COVID-19 cases at a 90% probability level if biweekly testing is used. Routine testing applied to the age group 21-60 for COVID-19 surveillance would achieve similar performance to that applied to all populations. Discussion Our analysis evaluates potential PLT and CT strategies for COVID-19 control and surveillance.
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Affiliation(s)
- Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Ruixue Wang
- School of National Safety and Emergency Management, Beijing Normal University, Beijing, China
| | - Peiyi Wu
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Yidan Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Yonghong Liu
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Xiaoli Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Peng Yang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China,Huaiyu Tian,
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7
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Wan J, Cazer CL, Clarkberg ME, Henderson SG, Lee SE, Meredith GR, Osman M, Shmoys DB, Frazier PI. Booster vaccination protection against SARS-CoV-2 infections in young adults during an Omicron BA.1-predominant period: A retrospective cohort study. PLoS Med 2023; 20:e1004153. [PMID: 36626376 PMCID: PMC9876273 DOI: 10.1371/journal.pmed.1004153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 01/25/2023] [Accepted: 12/09/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND While booster vaccinations clearly reduce the risk of severe Coronavirus Disease 2019 (COVID-19) and death, the impact of boosters on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections has not been fully characterized: Doing so requires understanding their impact on asymptomatic and mildly symptomatic infections that often go unreported but nevertheless play an important role in spreading SARS-CoV-2. We sought to estimate the impact of COVID-19 booster doses on SARS-CoV-2 infections in a vaccinated population of young adults during an Omicron BA.1-predominant period. METHODS AND FINDINGS We implemented a cohort study of young adults in a college environment (Cornell University's Ithaca campus) from a period when Omicron BA.1 was the predominant SARS-CoV-2 variant on campus (December 5 to December 31, 2021). Participants included 15,800 university students who completed initial vaccination series with vaccines approved by the World Health Organization for emergency use, were enrolled in mandatory at-least-weekly surveillance polymerase chain reaction (PCR) testing, and had no positive SARS-CoV-2 PCR test within 90 days before the start of the study period. Robust multivariable Poisson regression with the main outcome of a positive SARS-CoV-2 PCR test was performed to compare those who completed their initial vaccination series and a booster dose to those without a booster dose. A total of 1,926 unique SARS-CoV-2 infections were identified in the study population. Controlling for sex, student group membership, date of completion of initial vaccination series, initial vaccine type, and temporal effect during the study period, our analysis estimates that receiving a booster dose further reduces the rate of having a PCR-detected SARS-CoV-2 infection relative to an initial vaccination series by 56% (95% confidence interval [42%, 67%], P < 0.001). While most individuals had recent booster administration before or during the study period (a limitation of our study), this result is robust to the assumed delay over which a booster dose becomes effective (varied from 1 day to 14 days). The mandatory active surveillance approach used in this study, under which 86% of the person-days in the study occurred, reduces the likelihood of outcome misclassification. Key limitations of our methodology are that we did not have an a priori protocol or statistical analysis plan because the analysis was initially done for institutional research purposes, and some analysis choices were made after observing the data. CONCLUSIONS We observed that boosters are effective, relative to completion of initial vaccination series, in further reducing the rate of SARS-CoV-2 infections in a college student population during a period when Omicron BA.1 was predominant; booster vaccinations for this age group may play an important role in reducing incidence of COVID-19.
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Affiliation(s)
- Jiayue Wan
- School of Operations Research and Information Engineering, Cornell University College of Engineering, Ithaca, New York, United States of America
| | - Casey L. Cazer
- Department of Public and Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America
| | - Marin E. Clarkberg
- Institutional Research and Planning, Cornell University, Ithaca, New York, United States of America
| | - Shane G. Henderson
- School of Operations Research and Information Engineering, Cornell University College of Engineering, Ithaca, New York, United States of America
| | - Scarlett E. Lee
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America
| | - Genevive R. Meredith
- Department of Public and Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America
- Master of Public Health Program, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Marwan Osman
- Department of Public and Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, New York, United States of America
| | - David B. Shmoys
- School of Operations Research and Information Engineering, Cornell University College of Engineering, Ithaca, New York, United States of America
| | - Peter I. Frazier
- School of Operations Research and Information Engineering, Cornell University College of Engineering, Ithaca, New York, United States of America
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Kang J, Jang H, Kim TH, Cho U, Bang H, Jang J, Lee W, Joo H, Noh J, Lee GY, Shin DH, Kang CK, Choe PG, Kim NJ, Oh MD, Song M, Kwon S, Veas F, Park WB. Accurate Diagnosis of COVID-19 from Self-Collectable Biospecimens Using Synthetic Apolipoprotein H Peptide-Coated Nanoparticle Assay. Anal Chem 2022; 94:17186-17194. [PMID: 36399654 PMCID: PMC9718094 DOI: 10.1021/acs.analchem.2c03813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A high-throughput, accurate screening is crucial for the prevention and control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Current methods, which involve sampling from the nasopharyngeal (NP) area by medical staffs, constitute a fundamental bottleneck in expanding the testing capacity. To meet the scales required for population-level surveillance, self-collectable specimens can be used; however, its low viral load has hindered its clinical adoption. Here, we describe a magnetic nanoparticle functionalized with synthetic apolipoprotein H (ApoH) peptides to capture, concentrate, and purify viruses. The ApoH assay demonstrates a viral enrichment efficiency of >90% for both SARS-CoV-2 and its variants, leading to an order of magnitude improvement in analytical sensitivity. For validation, we apply the assay to a total of 84 clinical specimens including nasal, oral, and mouth gargles obtained from COVID-19 patients. As a result, a 100% positivity rate is achieved from the patient-collected nasal and gargle samples, which exceeds that of the traditional NP swab method. The simple 12 min pre-enrichment assay enabling the use of self-collectable samples will be a practical solution to overcome the overwhelming diagnostic capacity. Furthermore, the methodology can easily be built on various clinical protocols, allowing its broad applicability to various disease diagnoses.
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Affiliation(s)
- Junwon Kang
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul08826, Korea
- Integrated Major in Innovative Medical Science, Seoul National University, Seoul03080, Korea
| | - Haewook Jang
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul08826, Korea
| | - Tae Hyun Kim
- Bio-MAX Institute, Seoul National University, Seoul08826, Korea
- Department of Electrical and Computer Engineering, Seoul National University, Seoul08826, Korea
| | - Untack Cho
- QuantaMatrix Inc., Seoul08506, Korea
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul03080, Korea
| | | | | | - Wooseok Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul08826, Korea
| | - Hyelyn Joo
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul08826, Korea
| | - Jinsung Noh
- Bio-MAX Institute, Seoul National University, Seoul08826, Korea
- Department of Electrical and Computer Engineering, Seoul National University, Seoul08826, Korea
| | - Gi Yoon Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul08826, Korea
| | - Dong Hoon Shin
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
| | - Manki Song
- International Vaccine Institute, Seoul08826, Korea
| | - Sunghoon Kwon
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul08826, Korea
- Bio-MAX Institute, Seoul National University, Seoul08826, Korea
- Department of Electrical and Computer Engineering, Seoul National University, Seoul08826, Korea
- QuantaMatrix Inc., Seoul08506, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul03080, Korea
| | - Francisco Veas
- Copernicus Integrated Solutions for Biosafety Risks (CISBR), Mauguio34130, France
- ApoH-Technologies, 94 Allée des Fauvettes, La Grande Motte34280, France
- UMR5151/French Research Institute for Development (IRD), University of Montpellier (UM), Montpellier 34093, France
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
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9
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Heckel S, Pacini A, Paredes F, Petreli MV, Perez M, Adriani N, Ibarra G, Menzella H, Colaneri A, Sesma J. Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR. PLoS One 2022; 17:e0271860. [PMID: 36331920 PMCID: PMC9635689 DOI: 10.1371/journal.pone.0271860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
Detection of SARS-CoV-2 has created an enormous workload for laboratories worldwide resulting in a restriction at the time of massive testing. Pool testing is a strategy that reduces time and costs. However, beyond the detection of infectious diseases in blood banks, this approach is rarely implemented in routine laboratories. Therefore, what was learned from the SARS-CoV-2 pool testing should represent an opportunity to increase diagnostic capabilities. The present work, carried out in the context of a diagnostic laboratory of a public hospital during the COVID-19 pandemic, represents a contribution to this end. The main limitation of pool testing is the risk of false negatives that could have been identified by individual tests. These limitations are the dilution of samples with a low virus load during pooling and that the integrity of the sample may be affected by the quality of the sample collection. Fortunately, both limitations coincide with the main strengths of droplet digital PCR (ddPCR). ddPCR is a third-generation PCR that splits the amplification into thousands of droplets that work in parallel, increasing sensitivity and resistance to inhibitors. Therefore, ddPCR is particularly useful for pool testing. Here we show how to factor between test sensitivity and savings in test time and resources. We have identified and optimized critical parameters for pool testing. The present study, which analyzed 1000 nasopharyngeal samples, showed that the pool testing could detect even a single positive sample with a CT value of up to 30 in pools of 34 samples. This test was performed using three different standard extraction methods, the simplest being heating only, which resulted in substantial savings of extraction reagents in addition to PCR reagents. Moreover, we show that pooling can be extended to use saliva, which is less invasive and allows self-collection, reducing the risk for health personnel.
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Affiliation(s)
- Sofía Heckel
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Antonella Pacini
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET), Rosario, Santa Fe, Argentina
| | - Franco Paredes
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Ma. Victoria Petreli
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Marilina Perez
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
| | - Natalia Adriani
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
| | - Guadalupe Ibarra
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Hugo Menzella
- Instituto de Procesos Biotecnológicos y Químicos Rosario (IPROByQ), Rosario, Santa Fe, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alejandro Colaneri
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juliana Sesma
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Médicas (FCM-UNR), Rosario, Santa Fe, Argentina
- * E-mail:
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10
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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] [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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11
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Sender R, Bar-On Y, Woo Park S, Noor E, Dushoff J, Milo R. The unmitigated profile of COVID-19 infectiousness. eLife 2022; 11:79134. [PMID: 35913120 PMCID: PMC9391043 DOI: 10.7554/elife.79134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
Quantifying the temporal dynamics of infectiousness of individuals infected with SARS-CoV-2 is crucial for understanding the spread of COVID-19 and for evaluating the effectiveness of mitigation strategies. Many studies have estimated the infectiousness profile using observed serial intervals. However, statistical and epidemiological biases could lead to underestimation of the duration of infectiousness. We correct for these biases by curating data from the initial outbreak of the pandemic in China (when mitigation was minimal), and find that the infectiousness profile of the original strain is longer than previously thought. Sensitivity analysis shows our results are robust to model structure, assumed growth rate and potential observational biases. Although unmitigated transmission data is lacking for variants of concern (VOCs), previous analyses suggest that the alpha and delta variants have faster within-host kinetics, which we extrapolate to crude estimates of variant-specific unmitigated generation intervals. Knowing the unmitigated infectiousness profile of infected individuals can inform estimates of the effectiveness of isolation and quarantine measures. The framework presented here can help design better quarantine policies in early stages of future epidemics.
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Affiliation(s)
- Ron Sender
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yinon Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sang Woo Park
- Department of Ecology and Evolutionary, Princeton University, Princeton, United States
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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12
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Heterogeneous adaptive behavioral responses may increase epidemic burden. Sci Rep 2022; 12:11276. [PMID: 35788663 PMCID: PMC9252562 DOI: 10.1038/s41598-022-15444-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/23/2022] [Indexed: 12/15/2022] Open
Abstract
Non-pharmaceutical interventions (NPIs) constitute the front-line responses against epidemics. Yet, the interdependence of control measures and individual microeconomics, beliefs, perceptions and health incentives, is not well understood. Epidemics constitute complex adaptive systems where individual behavioral decisions drive and are driven by, among other things, the risk of infection. To study the impact of heterogeneous behavioral responses on the epidemic burden, we formulate a two risk-groups mathematical model that incorporates individual behavioral decisions driven by risk perceptions. Our results show a trade-off between the efforts to avoid infection by the risk-evader population, and the proportion of risk-taker individuals with relaxed infection risk perceptions. We show that, in a structured population, privately computed optimal behavioral responses may lead to an increase in the final size of the epidemic, when compared to the homogeneous behavior scenario. Moreover, we find that uncertain information on the individuals’ true health state may lead to worse epidemic outcomes, ultimately depending on the population’s risk-group composition. Finally, we find there is a set of specific optimal planning horizons minimizing the final epidemic size, which depend on the population structure.
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13
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Liu Y, Kumblathan T, Feng W, Pang B, Tao J, Xu J, Xiao H, Joyce MA, Tyrrell DL, Zhang H, Li XF, Le XC. On-Site Viral Inactivation and RNA Preservation of Gargle and Saliva Samples Combined with Direct Analysis of SARS-CoV-2 RNA on Magnetic Beads. ACS MEASUREMENT SCIENCE AU 2022; 2:224-232. [PMID: 36785867 PMCID: PMC8848515 DOI: 10.1021/acsmeasuresciau.1c00057] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Samples of nasopharyngeal swabs (NPS) are commonly used for the detection of SARS-CoV-2 and diagnosis of COVID-19. As an alternative, self-collection of saliva and gargle samples minimizes transmission to healthcare workers and relieves the pressure of resources and healthcare personnel during the pandemic. This study aimed to develop an enhanced method enabling simultaneous viral inactivation and RNA preservation during on-site self-collection of saliva and gargle samples. Our method involves the addition of saliva or gargle samples to a newly formulated viral inactivation and RNA preservation (VIP) buffer, concentration of the viral RNA on magnetic beads, and detection of SARS-CoV-2 using reverse transcription quantitative polymerase chain reaction directly from the magnetic beads. This method has a limit of detection of 25 RNA copies per 200 μL of gargle or saliva sample and 9-111 times higher sensitivity than the viral RNA preparation kit recommended by the United States Centers for Disease Control and Prevention. The integrated method was successfully used to analyze more than 200 gargle and saliva samples, including the detection of SARS-CoV-2 in 123 gargle and saliva samples collected daily from two NPS-confirmed positive SARS-CoV-2 patients throughout the course of their infection and recovery. The VIP buffer is stable at room temperature for at least 6 months. SARS-CoV-2 RNA (65 copies/200 μL sample) is stable in the VIP buffer at room temperature for at least 3 weeks. The on-site inactivation of SARS-CoV-2 and preservation of the viral RNA enables self-collection of samples, reduces risks associated with SARS-CoV-2 transmission, and maintains the stability of the target analyte.
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Affiliation(s)
- Yanming Liu
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Teresa Kumblathan
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Wei Feng
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Bo Pang
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Jeffrey Tao
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Jingyang Xu
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Huyan Xiao
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Michael A. Joyce
- Li
Ka Shing Institute of Virology, Department of Medical Microbiology
and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2E1
| | - D. Lorne Tyrrell
- Li
Ka Shing Institute of Virology, Department of Medical Microbiology
and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2E1
| | - Hongquan Zhang
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Xing-Fang Li
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - X. Chris Le
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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14
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Carey TR, Kozminsky M, Hall J, Vargas-Zapata V, Geiger K, Coscoy L, Sohn LL. Detecting Intact Virus Using Exogenous Oligonucleotide Labels. Anal Chem 2022; 94:7619-7627. [PMID: 35584293 DOI: 10.1021/acs.analchem.2c00835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The COVID-19 pandemic has revealed how an emerging pathogen can cause a sudden and dramatic increase in demand for viral testing. Testing pooled samples could meet this demand; however, the sensitivity of reverse transcription quantitative polymerase chain reaction (RT-qPCR), the gold standard, significantly decreases with an increasing number of samples pooled. Here, we introduce detection of intact virus by exogenous-nucleotide reaction (DIVER), a method that quantifies intact virus and is robust to sample dilution. As demonstrated using two models of severe acute respiratory syndrome coronavirus 2, DIVER first tags membraned particles with exogenous oligonucleotides, then captures the tagged particles on beads functionalized with a virus-specific capture agent (in this instance, angiotensin-converting enzyme 2), and finally quantifies the oligonucleotide tags using qPCR. Using spike-presenting liposomes and spike-pseudotyped lentivirus, we show that DIVER can detect 1 × 105 liposomes and 100 plaque-forming units of lentivirus and can successfully identify positive samples in pooling experiments. Overall, DIVER is well positioned for efficient sample pooling and clinical validation.
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Affiliation(s)
- Thomas R Carey
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, California 94720, United States
| | - Molly Kozminsky
- California Institute for Quantitative Biosciences, University of California, Berkeley, 174 Stanley Hall, Berkeley, California 94720, United States
| | - Jennifer Hall
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Valerie Vargas-Zapata
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Kristina Geiger
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Laurent Coscoy
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Lydia L Sohn
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, California 94720, United States.,Department of Mechanical Engineering, University of California, Berkeley, 5118 Etcheverry Hall, Berkeley, California 94720, United States
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15
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Verwilt J, Hellemans J, Sante T, Mestdagh P, Vandesompele J. Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for SARS-CoV-2 RT-qPCR screening purposes. Sci Rep 2022; 12:6603. [PMID: 35459775 PMCID: PMC9033859 DOI: 10.1038/s41598-022-10581-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/06/2022] [Indexed: 11/22/2022] Open
Abstract
To increase the throughput, lower the cost, and save scarce test reagents, laboratories can pool patient samples before SARS-CoV-2 RT-qPCR testing. While different sample pooling methods have been proposed and effectively implemented in some laboratories, no systematic and large-scale evaluations exist using real-life quantitative data gathered throughout the different epidemiological stages. Here, we use anonymous data from 9673 positive cases to model, simulate and compare 1D and 2D pooling strategies. We show that the optimal choice of pooling method and pool size is an intricate decision with a testing population-dependent efficiency-sensitivity trade-off and present an online tool to provide the reader with custom real-time 1D pooling strategy recommendations.
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Affiliation(s)
- Jasper Verwilt
- OncoRNALab, Cancer Research Institute Ghent, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Jan Hellemans
- Biogazelle, Technologiepark 82, 9052, Zwijnaarde, Belgium
| | - Tom Sante
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Cancer Research Institute Ghent, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Biogazelle, Technologiepark 82, 9052, Zwijnaarde, Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Biogazelle, Technologiepark 82, 9052, Zwijnaarde, Belgium.
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16
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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] [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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17
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Liang X, Sun Y, Xiao L, Ren Y, Tang X. The Positive Rate of Nucleic Acid Testing and the Epidemiological Characteristics of COVID-19 in Chongqing. Front Med (Lausanne) 2022; 8:802708. [PMID: 35096891 PMCID: PMC8795618 DOI: 10.3389/fmed.2021.802708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022] Open
Abstract
Objective The purpose of this study is to analyze the positive rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid testing (NAT), cases of and deaths due to SARS-CoV-2, and the epidemiological characteristics of SARS-CoV-2 to identify high-risk populations. Methods A retrospective study in Jiulongpo district of Chongqing was conducted by performing continuous observations of the frequency of SARS-CoV-2 NAT, analyzing the data of close contacts of patients and asymptomatic carriers, and collecting epidemiological data. Data were collected from January 20, 2020, when the first case of SARS-CoV-2 infection was reported, to March 26, 2020. Descriptive statistical analysis and Cochrane–Mantel–Haenszel analysis were used to compare the positive detection rates and positive diagnostic rates of different exposure groups. Results A total of 7,118 people received 10,377 SARS-CoV-2 nucleic acid tests in one district, and the SARS-CoV-2 positive rates were 0.40% (18/4446) and 0.15% (4/2672) in people receiving one and ≥ two nucleic acid tests (p = 0.06), respectively. Those with suspected cases (12.35%) and close contacts (8%) had higher positive rates than people tested at fever clinics (0.39%) (p < 0.001). The median latency (range) of cases was 5 (2, 9) days, and the median time from diagnosis to recovery was 22 (14, 25) days. One recovered patient received a positive test result at 28 days after recovery when she attempted to donate blood. Six clustered cases, including one patient who died, indicated persistent human-to-human transmission. One patient who was diagnosed after death was found to have infected 13 close contacts. People working in catering and other public service departments (36.36%) and people who are unemployed and retirees (45.45%) have an increased risk of infection compared with technical staff (9.09%) and farmers (9.09%). Conclusion The total positive rate was low in the tested population, and more effective detection ranges should be defined to improve precise and differentiated epidemic control strategies. Moreover, in asymptomatic carriers, SARS-CoV-2 tests were positive after recovery, and patients with suspected SARS-CoV-2 infection who die may pose serious potential transmission threats.
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Affiliation(s)
- Xiaohua Liang
- Department of Clinical Epidemiology and Biostatistics, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
| | - Yajun Sun
- Center for Disease Control and Prevention of Jiulongpo District, Chongqing, China
| | - Lun Xiao
- Center for Disease Control and Prevention of Jiulongpo District, Chongqing, China
| | - YanLing Ren
- Department of Clinical Epidemiology and Biostatistics, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
| | - Xian Tang
- Department of Clinical Epidemiology and Biostatistics, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
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18
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Wunsch M, Aschemeier D, Heger E, Ehrentraut D, Krüger J, Hufbauer M, Syed AS, Horemheb-Rubio G, Dewald F, Fish I, Schlotz M, Gruell H, Augustin M, Lehmann C, Kaiser R, Knops E, Silling S, Klein F. Safe and effective pool testing for SARS-CoV-2 detection. J Clin Virol 2021; 145:105018. [PMID: 34775143 PMCID: PMC8552800 DOI: 10.1016/j.jcv.2021.105018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/01/2021] [Accepted: 10/19/2021] [Indexed: 12/30/2022]
Abstract
Objectives The global spread of SARS-CoV-2 is a serious public health issue. Large-scale surveillance screenings are crucial but can exceed test capacities. We (A) optimized test conditions and (B) implemented pool testing of respiratory swabs into SARS-CoV-2 diagnostics. Study design (A) We determined the optimal pooling strategy and pool size. In addition, we measured the impact of vortexing prior to sample processing, compared a pipette-pooling method (by combining transport medium of several specimens) and a swab-pooling method (by combining several swabs into a test tube filled with PBS) as well as determined the sensitivities of three PCR assays. (B) Finally, we applied high-throughput pool testing for diagnostics. Results (A) In a low prevalence setting, we defined a preferable pool size of ten in a two-stage hierarchical pool testing strategy. Vortexing of swabs (n = 33) increased cellular yield by a factor of 2.34. By comparing Ct-values of 16 pools generated with two different pooling strategies, pipette-pooling was more efficient compared to swab-pooling. Measuring dilution series of 20 SARS-CoV-2 positive samples in three PCR assays simultaneously revealed detection rates of 85% (assay I), 50% (assay II), and 95% (assay III) at a 1:100 dilution. (B) We systematically pooled 55,690 samples in a period of 44 weeks resulting in a reduction of 47,369 PCR reactions. Conclusions For implementing pooling strategies into high-throughput diagnostics, we recommend utilizing a pipette-pooling method, performing sensitivity validation of the PCR assays used, and vortexing swabs prior to analyses. Pool testing for SARS-CoV-2 detection is feasible and effective in a low prevalence setting.
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Affiliation(s)
- Marie Wunsch
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany; University of Cologne, Center for Molecular Medicine Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany
| | - Dominik Aschemeier
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Eva Heger
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Denise Ehrentraut
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Straße 26, 50931 Cologne, Germany
| | - Jan Krüger
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Straße 26, 50931 Cologne, Germany
| | - Martin Hufbauer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Adnan S Syed
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Gibran Horemheb-Rubio
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany; Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, 14080, Mexico
| | - Felix Dewald
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany; University of Cologne, Center for Molecular Medicine Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany
| | - Irina Fish
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Maike Schlotz
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany; University of Cologne, Center for Molecular Medicine Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany
| | - Henning Gruell
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany; University of Cologne, Center for Molecular Medicine Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany
| | - Max Augustin
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Kerpener Str. 62, 50937 Cologne, Germany
| | - Clara Lehmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Kerpener Str. 62, 50937 Cologne, Germany
| | - Rolf Kaiser
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Elena Knops
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Steffi Silling
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Florian Klein
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Virology, Fürst-Pückler-Straße 56, 50935 Cologne, Germany; University of Cologne, Center for Molecular Medicine Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany.
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19
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Yu J, Huang Y, Shen ZJ. Optimizing and evaluating PCR-based pooled screening during COVID-19 pandemics. Sci Rep 2021; 11:21460. [PMID: 34728759 PMCID: PMC8564549 DOI: 10.1038/s41598-021-01065-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Population screening played a substantial role in safely reopening the economy and avoiding new outbreaks of COVID-19. PCR-based pooled screening makes it possible to test the population with limited resources by pooling multiple individual samples. Our study compared different population-wide screening methods as transmission-mitigating interventions, including pooled PCR, individual PCR, and antigen screening. Incorporating testing-isolation process and individual-level viral load trajectories into an epidemic model, we further studied the impacts of testing-isolation on test sensitivities. Results show that the testing-isolation process could maintain a stable test sensitivity during the outbreak by removing most infected individuals, especially during the epidemic decline. Moreover, we compared the efficiency, accuracy, and cost of different screening methods during the pandemic. Our results show that PCR-based pooled screening is cost-effective in reversing the pandemic at low prevalence. When the prevalence is high, PCR-based pooled screening may not stop the outbreak. In contrast, antigen screening with sufficient frequency could reverse the epidemic, despite the high cost and the large numbers of false positives in the screening process.
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Affiliation(s)
- Jiali Yu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, China
| | - Yiduo Huang
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Zuo-Jun Shen
- College of Engineering, University of California Berkeley, Berkeley, CA, USA.
- Faculty of Engineering and Faculty of Business and Economics, University of Hong Kong, Hong Kong, China.
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20
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Kong D, Wang X, Gu C, Guo M, Wang Y, Ai Z, Zhang S, Chen Y, Liu W, Wu Y, Dai C, Guo Q, Qu D, Zhu Z, Xie Y, Liu Y, Wei D. Direct SARS-CoV-2 Nucleic Acid Detection by Y-Shaped DNA Dual-Probe Transistor Assay. J Am Chem Soc 2021; 143:17004-17014. [PMID: 34623792 PMCID: PMC8524959 DOI: 10.1021/jacs.1c06325] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 12/18/2022]
Abstract
Rapid screening of infected individuals from a large population is an effective means in epidemiology, especially to contain outbreaks such as COVID-19. The gold standard assays for COVID-19 diagnostics are mainly based on the reverse transcription polymerase chain reaction, which mismatches the requirements for wide-population screening due to time-consuming nucleic acid extraction and amplification procedures. Here, we report a direct nucleic acid assay by using a graphene field-effect transistor (g-FET) with Y-shaped DNA dual probes (Y-dual probes). The assay relies on Y-dual probes modified on g-FET simultaneously targeting ORF1ab and N genes of SARS-CoV-2 nucleic acid, enabling high a recognition ratio and a limit of detection (0.03 copy μL-1) 1-2 orders of magnitude lower than existing nucleic acid assays. The assay realizes the fastest nucleic acid testing (∼1 min) and achieves direct 5-in-1 pooled testing for the first time. Owing to its rapid, ultrasensitive, easily operated features as well as capability in pooled testing, it holds great promise as a comprehensive tool for population-wide screening of COVID-19 and other epidemics.
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Affiliation(s)
- Derong Kong
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
| | - Xuejun Wang
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
| | - Chenjian Gu
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department
of Medical Microbiology and Parasitology, School of Basic Medical
Sciences, Shanghai Medical College, Fudan
University, Shanghai 200433, China
| | - Mingquan Guo
- Department
of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yao Wang
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department
of Medical Microbiology and Parasitology, School of Basic Medical
Sciences, Shanghai Medical College, Fudan
University, Shanghai 200433, China
| | - Zhaolin Ai
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
| | - Shen Zhang
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
| | - Yiheng Chen
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
| | - Wentao Liu
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
| | - Yungen Wu
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
| | - Changhao Dai
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
| | - Qianying Guo
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
| | - Di Qu
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department
of Medical Microbiology and Parasitology, School of Basic Medical
Sciences, Shanghai Medical College, Fudan
University, Shanghai 200433, China
| | - Zhaoqin Zhu
- Department
of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Youhua Xie
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department
of Medical Microbiology and Parasitology, School of Basic Medical
Sciences, Shanghai Medical College, Fudan
University, Shanghai 200433, China
| | - Yunqi Liu
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
- Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Dacheng Wei
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute
of Molecular Materials and Devices, Fudan
University, Shanghai 200433, China
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21
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Diagnostic Techniques for COVID-19: A Mini-review of Early Diagnostic Methods. JOURNAL OF ANALYSIS AND TESTING 2021; 5:314-326. [PMID: 34631199 PMCID: PMC8488931 DOI: 10.1007/s41664-021-00198-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/25/2021] [Indexed: 12/26/2022]
Abstract
The outbreak of severe pneumonia at the end of 2019 was proved to be caused by the SARS-CoV-2 virus spreading out the world. And COVID-19 spread rapidly through a terrible transmission way by human-to-human, which led to many suspected cases waiting to be diagnosed and huge daily samples needed to be tested by an effective and rapid detection method. With an increasing number of COVID-19 infections, medical pressure is severe. Therefore, more efficient and accurate diagnosis methods were keen urgently established. In this review, we summarized several methods that can rapidly and sensitively identify COVID-19; some of them are widely used as the diagnostic techniques for SARS-CoV-2 in various countries, some diagnostic technologies refer to SARS (Severe Acute Respiratory Syndrome) or/and MERS (Middle East Respiratory Syndrome) detection, which may provide potential diagnosis ideas.
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22
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Handous I, Hannachi N, Marzouk M, Hazgui O, Bouafif Ep Ben Alaya N, Boukadida J. Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR. Biol Proced Online 2021; 23:19. [PMID: 34592917 PMCID: PMC8483732 DOI: 10.1186/s12575-021-00156-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 09/10/2021] [Indexed: 01/15/2023] Open
Abstract
Background The detection of SARS-CoV-2 using qRT-PCR with the pooling of samples can reduce workload and costs especially when the prevalence rate of COVID-19 in a population is low. To analyse the effect of pooling samples on the sensitivity of RT-qPCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection, we compared the cycle threshold (Ct) values of pools of 5 and 10 that tested positive with Ct values of individual samples that tested positive in that pool. Twenty positive nasopharyngeal (NP) specimens with low to high viral load were selected and pooled individually with four and nine negative NP. Results In NP specimens, the sensitivity of pools of 5 and 10 were 90 and 85%, compared to individual sample testing, respectively. The RT-qPCR sensitivity of pools of 5 and 10 against individual testing were not significantly different (p > 0.05). Detection of positive samples with low Ct values (< 36) was consistently achieved in pools of 5 and 10. However, there were higher false negatives when samples with high ct values (> 36) were pooled and tested. The mean Ct values obtained with the 5-sample pooled testing exceeded individual sample testing by 1.85 ± 1.09 cycles, while Ct values obtained with the 10-sample pooling exceeded individual sample testing by 3.4 ± 1.65 cycles. Conclusions In a low prevalence setting, testing capacity can be increased by pooling 5 or 10 samples, but the risk of additional false negatives needs to be considered.
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Affiliation(s)
- Imene Handous
- Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de Sousse, Sousse, 4000, Tunisie. .,Université de Sfax, Ecole Nationale d'Ingénieurs de Sfax, Sfax, 3038, Tunisie.
| | - Naila Hannachi
- Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de Sousse, Sousse, 4000, Tunisie
| | - Manel Marzouk
- Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de Sousse, Sousse, 4000, Tunisie
| | - Olfa Hazgui
- Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de Sousse, Sousse, 4000, Tunisie
| | | | - Jalel Boukadida
- Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de Sousse, Sousse, 4000, Tunisie
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23
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Sweeney-Reed CM, Wolff D, Hörnschemeyer S, Faßhauer H, Haase A, Schomburg D, Niggel J, Kabesch M, Apfelbacher C. Feasibility of a surveillance programme based on gargle samples and pool testing to prevent SARS-CoV-2 outbreaks in schools. Sci Rep 2021; 11:19521. [PMID: 34593887 PMCID: PMC8484445 DOI: 10.1038/s41598-021-98849-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/15/2021] [Indexed: 01/12/2023] Open
Abstract
School closures have a negative impact on physical and mental well-being, and education, of children and adolescents. A surveillance programme to detect asymptomatic SARS-CoV-2 infection could allow schools to remain open, while protecting the vulnerable. We assessed the feasibility of a programme employing gargle samples and pool testing of individually extracted RNA using rRT-qPCR in a primary and a secondary school in Germany, based on programme logistics and acceptance. Twice a week, five participants per class were selected to provide samples, using an algorithm weighted by a risk-based priority score to increase likelihood of case detection. The positive response rate was 54.8% (550 of 1003 pupils). Logistics evaluation revealed the rate-limiting steps: completing the regular pre-test questionnaire and handing in the samples. Acceptance questionnaire responses indicated strong support for research into developing a surveillance programme and a positive evaluation of gargle tests. Participation was voluntary. As not all pupils participated, individual reminders could lead to participant identification. School-wide implementation of the programme for infection monitoring purposes would enable reminders to be given to all school pupils to address these steps, without compromising participant anonymity. Such a programme would provide a feasible means to monitor asymptomatic respiratory tract infection in schools.
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Affiliation(s)
- Catherine M Sweeney-Reed
- Neurocybernetics and Rehabilitation, Dept. of Neurology, Medical Faculty, Otto von Guericke University Magdeburg, Leipziger Str. 44, Magdeburg, Germany.
- Center for Behavioral Brain Sciences, Otto von Guericke University Magdeburg, Magdeburg, Germany.
| | - Doreen Wolff
- Institute of Social Medicine and Health System Research, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Sarah Hörnschemeyer
- Institute of Social Medicine and Health System Research, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Henriette Faßhauer
- Institute of Social Medicine and Health System Research, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Antonia Haase
- Institute of Social Medicine and Health System Research, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Dirk Schomburg
- Institute of Biometry und Medical Informatics (IBMI), Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Jakob Niggel
- University of Regensburg, Regensburg, Germany
- MaganaMed GmbH, Regensburg, Germany
| | - Michael Kabesch
- University Children's Hospital Regensburg (KUNO), Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
- Research and Development Campus Regensburg (WECARE), Hospital St. Hedwig of the Order of St. John and University of Regensburg, Regensburg, Germany
| | - Christian Apfelbacher
- Institute of Social Medicine and Health System Research, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Research and Development Campus Regensburg (WECARE), Hospital St. Hedwig of the Order of St. John and University of Regensburg, Regensburg, Germany
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24
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Joachim A, Dewald F, Suárez I, Zemlin M, Lang I, Stutz R, Marthaler A, Bosse HM, Lübke N, Münch J, Bernard MA, Jeltsch K, Tönshoff B, Weidner N, Kräusslich HG, Birzele L, Hübner J, Schmied P, Meyer-Bühn M, Horemheb-Rubio G, Cornely OA, Haverkamp H, Wiesmüller G, Fätkenheuer G, Hero B, Kaiser R, Dötsch J, Rybniker J. Pooled RT-qPCR testing for SARS-CoV-2 surveillance in schools - a cluster randomised trial. EClinicalMedicine 2021; 39:101082. [PMID: 34458708 PMCID: PMC8384501 DOI: 10.1016/j.eclinm.2021.101082] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The extent to which children and adolescents contribute to SARS-CoV-2 transmission remains not fully understood. Novel high-capacity testing methods may provide real-time epidemiological data in educational settings helping to establish a rational approach to prevent and minimize SARS-CoV-2 transmission. We investigated whether pooling of samples for SARS-CoV-2 detection by RT-qPCR is a sensitive and feasible high-capacity diagnostic strategy for surveillance of SARS-CoV-2 infections in schools. METHODS In this study, students and school staff of 14 educational facilities in Germany were tested sequentially between November 9 and December 23, 2020, two or three times per week for at least three consecutive weeks. Participants were randomized for evaluation of two different age adjusted swab sampling methods (oropharyngeal swabs or buccal swabs compared to saliva swabs using a 'lolli method'). Swabs were collected and pooled for SARS-CoV-2 RT-qPCR. Individuals of positive pooled tests were retested by RT-qPCR the same or the following day. Positive individuals were quarantined while the SARS-CoV-2 negative individuals remained in class with continued pooled RT-qPCR surveillance. The study is registered with the German Clinical Trials register (registration number: DRKS00023911). FINDINGS 5,537 individuals were eligible and 3970 participants were enroled and included in the analysis. In students, a total of 21,978 swabs were taken and combined in 2218 pooled RT-qPCR tests. We detected 41 positive pooled tests (1·8%) leading to 36 SARS-CoV-2 cases among students which could be identified by individual re-testing. The cumulative 3-week incidence for primary schools was 564/100,000 (6/1064, additionally 1 infection detected in week 4) and 1249/100,000 (29/2322) for secondary schools. In secondary schools, there was no difference in the number of SARS-CoV-2 positive students identified from pooled oropharyngeal swabs compared to those identified from pooled saliva samples (lolli method) (14 vs. 15 cases; 1·3% vs. 1·3%; OR 1.1; 95%-CI 0·5-2·5). A single secondary school accounted for 17 of 36 cases (47%) indicating a high burden of asymptomatic prevalent SARS-CoV-2 cases in the respective school and community. INTERPRETATION In educational settings, SARS-CoV-2 screening by RT-qPCR-based pooled testing with easily obtainable saliva samples is a feasible method to detect incident cases and observe transmission dynamics. FUNDING Federal Ministry of education and research (BMBF; Project B-FAST in "NaFoUniMedCovid19"; registration number: 01KX2021).
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Affiliation(s)
- Alexander Joachim
- Department of Pediatrics, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Felix Dewald
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Isabelle Suárez
- Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Michael Zemlin
- Department of General Pediatrics and Neonatology, Saarland University Homburg, Homburg, Germany
| | - Isabelle Lang
- Department of General Pediatrics and Neonatology, Saarland University Homburg, Homburg, Germany
| | - Regine Stutz
- Department of General Pediatrics and Neonatology, Saarland University Homburg, Homburg, Germany
| | - Anna Marthaler
- Institute of Virology, Saarland University Homburg, Homburg, Germany
| | - Hans Martin Bosse
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children´s Hospital, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Germany
| | - Nadine Lübke
- Institute of Virology, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Germany
| | - Juliane Münch
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children´s Hospital, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Germany
| | - Marie-Annett Bernard
- Institute of Virology, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Germany
| | - Kathrin Jeltsch
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Burkhard Tönshoff
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Niklas Weidner
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Lena Birzele
- Division of Pediatric Infectious Disease, Dr. v. Hauner Children's Hospital, University of Munich (LMU), Munich, Germany
| | - Johannes Hübner
- Division of Pediatric Infectious Disease, Dr. v. Hauner Children's Hospital, University of Munich (LMU), Munich, Germany
| | - Patricia Schmied
- Division of Pediatric Infectious Disease, Dr. v. Hauner Children's Hospital, University of Munich (LMU), Munich, Germany
| | - Melanie Meyer-Bühn
- Division of Pediatric Infectious Disease, Dr. v. Hauner Children's Hospital, University of Munich (LMU), Munich, Germany
| | - Gibran Horemheb-Rubio
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Oliver A Cornely
- Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Heinz Haverkamp
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Gerhard Wiesmüller
- Public Health Department Cologne, Cologne, Germany
- Institute for Occupational, Social and Environmental Medicine, Uniclinic RWTH Aachen University, Aachen, Germany
| | - Gerd Fätkenheuer
- Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatrics, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Rolf Kaiser
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Jörg Dötsch
- Department of Pediatrics, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
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25
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He Y, Tong Y. A theoretical simulation of SARS-CoV-2 pooled testing: Pooled sample collection outperforms pooled RNA extraction. Clin Chim Acta 2021; 521:155-157. [PMID: 34274344 PMCID: PMC8282448 DOI: 10.1016/j.cca.2021.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Yugan He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China.
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26
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Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho DD, Grubaugh ND, Grad YH. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies. PLoS Biol 2021; 19:e3001333. [PMID: 34252080 PMCID: PMC8297933 DOI: 10.1371/journal.pbio.3001333] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/22/2021] [Accepted: 06/21/2021] [Indexed: 02/04/2023] Open
Abstract
SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening. We used prospective longitudinal quantitative reverse transcription PCR testing to measure the viral RNA trajectories for 68 individuals during the resumption of the 2019-2020 National Basketball Association season. For 46 individuals with acute infections, we inferred the peak viral concentration and the duration of the viral proliferation and clearance phases. According to our mathematical model, we found that viral RNA concentrations peaked an average of 3.3 days (95% credible interval [CI] 2.5, 4.2) after first possible detectability at a cycle threshold value of 22.3 (95% CI 20.5, 23.9). The viral clearance phase lasted longer for symptomatic individuals (10.9 days [95% CI 7.9, 14.4]) than for asymptomatic individuals (7.8 days [95% CI 6.1, 9.7]). A second test within 2 days after an initial positive PCR test substantially improves certainty about a patient's infection stage. The effective sensitivity of a test intended to identify infectious individuals declines substantially with test turnaround time. These findings indicate that SARS-CoV-2 viral concentrations peak rapidly regardless of symptoms. Sequential tests can help reveal a patient's progress through infection stages. Frequent, rapid-turnaround testing is needed to effectively screen individuals before they become infectious.
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Affiliation(s)
- Stephen M. Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Christina Mack
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Scott W. Olesen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Caroline Tai
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
| | - Kristin Y. Shiue
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Sarah Jednak
- Department of Health Management and Policy, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Jay Wohlgemuth
- Quest Diagnostics, San Juan Capistrano, California, United States of America
| | - James Weisberger
- Bioreference Laboratories, Elmwood Park, New Jersey, United States of America
| | - John DiFiori
- Hospital for Special Surgery, New York, New York, United States of America
- National Basketball Association, New York, New York, United States of America
| | - Deverick J. Anderson
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, United States of America
| | - Jimmie Mancell
- Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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27
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Yoo HM, Kim IH, Kim S. Nucleic Acid Testing of SARS-CoV-2. Int J Mol Sci 2021; 22:6150. [PMID: 34200331 PMCID: PMC8201071 DOI: 10.3390/ijms22116150] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 12/13/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) has caused a large global outbreak. It is accordingly important to develop accurate and rapid diagnostic methods. The polymerase chain reaction (PCR)-based method including reverse transcription-polymerase chain reaction (RT-PCR) is the most widely used assay for the detection of SARS-CoV-2 RNA. Along with the RT-PCR method, digital PCR has emerged as a powerful tool to quantify nucleic acid of the virus with high accuracy and sensitivity. Non-PCR based techniques such as reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) are considered to be rapid and simple nucleic acid detection methods and were reviewed in this paper. Non-conventional molecular diagnostic methods including next-generation sequencing (NGS), CRISPR-based assays and nanotechnology are improving the accuracy and sensitivity of COVID-19 diagnosis. In this review, we also focus on standardization of SARS-CoV-2 nucleic acid testing and the activity of the National Metrology Institutes (NMIs) and highlight resources such as reference materials (RM) that provide the values of specified properties. Finally, we summarize the useful resources for convenient COVID-19 molecular diagnostics.
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Affiliation(s)
- Hee Min Yoo
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (H.M.Y.); (I.-H.K.)
- Department of Bio-Analytical Science, University of Science & Technology (UST), Daejeon 34113, Korea
| | - Il-Hwan Kim
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (H.M.Y.); (I.-H.K.)
| | - Seil Kim
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (H.M.Y.); (I.-H.K.)
- Department of Bio-Analytical Science, University of Science & Technology (UST), Daejeon 34113, Korea
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
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28
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Richard-Greenblatt M, Ziegler MJ, Bromberg V, Huang E, Abdallah H, Tolomeo P, Lautenbach E, Glaser L, Kelly BJ. Quantifying the Impact of Nasopharyngeal Specimen Quality on Severe Acute Respiratory Syndrome Coronavirus 2 Test Performance. Open Forum Infect Dis 2021; 8:ofab235. [PMID: 34095340 PMCID: PMC8136075 DOI: 10.1093/ofid/ofab235] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/05/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse-transcription polymerase chain reaction (RT-PCR) cycle threshold (Ct) has been used to estimate quantitative viral load, with the goal of targeting isolation precautions for individuals with coronavirus disease 2019 (COVID-19) and guiding public health interventions. However, variability in specimen quality can alter the Ct values obtained from SARS-CoV-2 clinical assays. We sought to define how variable nasopharyngeal (NP) swab quality impacts clinical SARS-CoV-2 test sensitivity. METHODS We performed amplification of a human gene target (β-actin) in parallel with a clinical RT-PCR targeting the SARS-CoV-2 ORF1ab gene for 1282 NP specimens collected from patients with clinical concern for COVID-19. We evaluated the relationship between NP specimen quality, characterized by late Ct values for the human gene target β-actin Ct, and the probability of SARS-CoV-2 detection via logistic regression, as well as the linear relationship between SARS-CoV-2 and β-actin Ct. RESULTS Low-quality NP swabs are less likely to detect SARS-CoV-2 (odds ratio, 0.607 [95% credible interval {CrI}, .487-.753]). We observed a positive linear relationship between SARS-CoV-2 and β-actin Ct values (slope, 0.181 [95% CrI, .097-.264]), consistent with a reduction in detection of 0.181 cycles for each additional cycle of the β-actin target. COVID-19 disease severity was not associated with β-actin Ct values. CONCLUSIONS Variability in NP specimen quality significantly impacts the performance of clinical SARS-CoV-2 assays, and caution should be taken when interpreting quantitative SARS-CoV-2 Ct results. If unrecognized, low-quality NP specimens, which are characterized by a low level of amplifiable human DNA target, may limit the successful application of SARS-CoV-2 Ct values to direct infection control and public health interventions.
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Affiliation(s)
- Melissa Richard-Greenblatt
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew J Ziegler
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Valerie Bromberg
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth Huang
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hatem Abdallah
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pam Tolomeo
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ebbing Lautenbach
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Laurel Glaser
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J Kelly
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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29
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Mina MJ, Peto TE, García-Fiñana M, Semple MG, Buchan IE. Clarifying the evidence on SARS-CoV-2 antigen rapid tests in public health responses to COVID-19. Lancet 2021; 397:1425-1427. [PMID: 33609444 PMCID: PMC8049601 DOI: 10.1016/s0140-6736(21)00425-6] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 12/23/2022]
Affiliation(s)
- Michael J Mina
- Center for Communicable Disease Dynamics, Department of Epidemiology and Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health and Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tim E Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marta García-Fiñana
- Institute of Population Health, University of Liverpool, Liverpool L36 3GF, UK
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Iain E Buchan
- Institute of Population Health, University of Liverpool, Liverpool L36 3GF, UK.
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30
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Barak N, Ben-Ami R, Sido T, Perri A, Shtoyer A, Rivkin M, Licht T, Peretz A, Magenheim J, Fogel I, Livneh A, Daitch Y, Oiknine-Djian E, Benedek G, Dor Y, Wolf DG, Yassour M. Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests. Sci Transl Med 2021; 13:eabf2823. [PMID: 33619081 PMCID: PMC8099176 DOI: 10.1126/scitranslmed.abf2823] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/28/2020] [Accepted: 02/16/2021] [Indexed: 12/28/2022]
Abstract
Pooling multiple swab samples before RNA extraction and real-time reverse transcription polymerase chain reaction (RT-PCR) analysis has been proposed as a strategy to reduce costs and increase throughput of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tests. However, reports on practical large-scale group testing for SARS-CoV-2 have been scant. Key open questions concern reduced sensitivity due to sample dilution, the rate of false positives, the actual efficiency (number of tests saved by pooling), and the impact of infection rate in the population on assay performance. Here, we report an analysis of 133,816 samples collected between April and September 2020 and tested by Dorfman pooling for the presence of SARS-CoV-2. We spared 76% of RNA extraction and RT-PCR tests, despite the frequently changing prevalence (0.5 to 6%). We observed pooling efficiency and sensitivity that exceeded theoretical predictions, which resulted from the nonrandom distribution of positive samples in pools. Overall, our findings support the use of pooling for efficient large-scale SARS-CoV-2 testing.
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Affiliation(s)
- Netta Barak
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Roni Ben-Ami
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Tal Sido
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
- Department of Mathematics, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Amir Perri
- Computing Department of Laboratories and Institutes, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Aviad Shtoyer
- Computing Department of Laboratories and Institutes, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Mila Rivkin
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Tamar Licht
- Department of Medical Neurobiology, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Ayelet Peretz
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Irit Fogel
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Ayalah Livneh
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Yutti Daitch
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Esther Oiknine-Djian
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Gil Benedek
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
- Tissue Typing and Immunogenetics Unit, Hadassah Hebrew University Medical Center, Jerusalem 91121, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel.
| | - Dana G Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel.
- The Lautenberg Centre for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Moran Yassour
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
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31
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Carey TR, Kozminsky M, Hall J, Vargas-Zapata V, Geiger K, Coscoy L, Sohn LL. Toward Community Surveillance: Detecting Intact SARS-CoV-2 Using Exogeneous Oligonucleotide Labels. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.23.21254201. [PMID: 33791715 PMCID: PMC8010747 DOI: 10.1101/2021.03.23.21254201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The persistence of the COVID-19 pandemic demands a dramatic increase in testing efficiency. Testing pooled samples for SARS-CoV-2 could meet this need; however, the sensitivity of RT-qPCR, the gold standard, significantly decreases with an increasing number of samples pooled. Here, we introduce DIVER, a method that quantifies intact virus and is robust to sample dilution. DIVER first tags viral particles with exogeneous oligonucleotides, then captures the tagged particles on ACE2-functionalized beads, and finally quantifies the oligonucleotide tags using qPCR. Using spike-presenting liposomes and Spike-pseudotyped lentivirus as SARS-CoV-2 models, we show that DIVER can detect 1×10 5 liposomes and 100 pfu lentivirus and can successfully identify positive samples in pooling experiments. Overall, DIVER is well-positioned for efficient sample pooling and expanded community surveillance.
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32
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Perfect as the enemy of good: tracing transmissions with low-sensitivity tests to mitigate SARS-CoV-2 outbreaks. LANCET MICROBE 2021; 2:e219-e224. [PMID: 33748803 PMCID: PMC7954468 DOI: 10.1016/s2666-5247(21)00004-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Throughout the COVID-19 pandemic, governments and individuals have attempted a wide variety of strategies to limit the damage of the pandemic on human lives, population health, and economies. Contact tracing has been a commonly used strategy, and various approaches have been proposed and attempted. We summarise some methods of contact tracing and testing, considering the resources demanded by each and how features of SARS-CoV-2 transmission affect their effectiveness. We also propose an approach focusing on tracing transmission events, which can be particularly effective when superspreading events play a large role in transmission. Accounting for the best available evidence on a pathogen and for the availability of resources can make control strategies more effective, even if they are not perfect.
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33
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Brault V, Mallein B, Rupprecht JF. Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance. PLoS Comput Biol 2021; 17:e1008726. [PMID: 33661887 PMCID: PMC7932094 DOI: 10.1371/journal.pcbi.1008726] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/20/2021] [Indexed: 12/31/2022] Open
Abstract
We propose an analysis and applications of sample pooling to the epidemiologic monitoring of COVID-19. We first introduce a model of the RT-qPCR process used to test for the presence of virus in a sample and construct a statistical model for the viral load in a typical infected individual inspired by large-scale clinical datasets. We present an application of group testing for the prevention of epidemic outbreak in closed connected communities. We then propose a method for the measure of the prevalence in a population taking into account the increased number of false negatives associated with the group testing method.
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Affiliation(s)
- Vincent Brault
- Université Grenoble Alpes, CNRS, Grenoble INP, LJK, Grenoble, France
| | - Bastien Mallein
- Université Sorbonne Paris Nord, LAGA, UMR 7539, Villetaneuse, France
| | - Jean-François Rupprecht
- Aix Marseille Univ, CNRS, Centre de Physique Théorique, Turing Center for Living Systems, Marseille, France
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34
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Kheiroddin P, Schöberl P, Althammer M, Cibali E, Würfel T, Wein H, Kulawik B, Buntrock-Döpke H, Weigl E, Gran S, Gründl M, Langguth J, Lampl B, Judex G, Niggel J, Pagel P, Schratzenstaller T, Schneider-Brachert W, Gastiger S, Bodenschatz M, Konrad M, Levchuk A, Roth C, Schöner D, Schneebauer F, Rohrmanstorfer R, Dekens MP, Brandstetter S, Zuber J, Wallerstorfer D, Burkovski A, Ambrosch A, Wagner T, Kabesch M. Results of WICOVIR Gargle Pool PCR Testing in German Schools Based on the First 100,000 Tests. Front Pediatr 2021; 9:721518. [PMID: 34778127 PMCID: PMC8581236 DOI: 10.3389/fped.2021.721518] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/27/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Opening schools and keeping children safe from SARS-CoV-2 infections at the same time is urgently needed to protect children from direct and indirect consequences of the COVID-19 pandemic. To achieve this goal, a safe, efficient, and cost-effective SARS-CoV-2 testing system for schools in addition to standard hygiene measures is necessary. Methods: We implemented the screening WICOVIR concept for schools in the southeast of Germany, which is based on gargling at home, pooling of samples in schools, and assessment of SARS-CoV-2 by pool rRT-PCR, performed decentralized in numerous participating laboratories. Depooling was performed if pools were positive, and results were transmitted with software specifically developed for the project within a day. Here, we report the results after the first 13 weeks in the project. Findings: We developed and implemented the proof-of-concept test system within a pilot phase of 7 weeks based on almost 17,000 participants. After 6 weeks in the main phase of the project, we performed >100,000 tests in total, analyzed in 7,896 pools, identifying 19 cases in >100 participating schools. On average, positive children showed an individual CT value of 31 when identified in the pools. Up to 30 samples were pooled (mean 13) in general, based on school classes and attached school staff. All three participating laboratories detected positive samples reliably with their previously established rRT-PCR standard protocols. When self-administered antigen tests were performed concomitantly in positive cases, only one of these eight tests was positive, and when antigen tests performed after positive pool rRT-PCR results were already known were included, 3 out of 11 truly positive tests were also identified by antigen testing. After 3 weeks of repetitive WICOVIR testing twice weekly, the detection rate of positive children in that cohort decreased significantly from 0.042 to 0.012 (p = 0.008). Interpretation: Repeated gargle pool rRT-PCR testing can be implemented quickly in schools. It is an effective, valid, and well-received test system for schools, superior to antigen tests in sensitivity, acceptance, and costs.
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Affiliation(s)
- Parastoo Kheiroddin
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany
| | - Patricia Schöberl
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany.,Science and Innovation Campus Regensburg (WECARE) at the Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
| | - Michael Althammer
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany
| | - Ezgi Cibali
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany.,Institute of Laboratory Medicine, Microbiology and Hygiene, Hospital of the Order of St. John, Regensburg, Germany
| | - Thea Würfel
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany
| | - Hannah Wein
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany
| | - Birgit Kulawik
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany.,Science and Innovation Campus Regensburg (WECARE) at the Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
| | - Heike Buntrock-Döpke
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany.,Science and Innovation Campus Regensburg (WECARE) at the Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
| | - Eva Weigl
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany.,Science and Innovation Campus Regensburg (WECARE) at the Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
| | - Silvia Gran
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany.,Science and Innovation Campus Regensburg (WECARE) at the Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
| | | | - Jana Langguth
- Public Health Department Regensburg, Regensburg, Germany
| | - Benedikt Lampl
- Public Health Department Regensburg, Regensburg, Germany
| | | | | | | | - Thomas Schratzenstaller
- Medical Device Lab, Ostbayerische Technische Hochschule Regensburg, Regensburg, Germany.,Regensburg Center for Biomedical Engineering, University and OTH Regensburg, Regensburg, Germany
| | - Wulf Schneider-Brachert
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - Susanne Gastiger
- Microbiology Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Mona Bodenschatz
- Microbiology Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Maike Konrad
- Microbiology Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Artem Levchuk
- Microbiology Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Cornelius Roth
- Microbiology Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany.,DATEV eG, Nürnberg, Germany
| | | | | | | | - Marcus P Dekens
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Susanne Brandstetter
- Science and Innovation Campus Regensburg (WECARE) at the Hospital St. Hedwig of the Order of St. John, Regensburg, Germany.,University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.,Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | | | - Andreas Burkovski
- Microbiology Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Andreas Ambrosch
- Institute of Laboratory Medicine, Microbiology and Hygiene, Hospital of the Order of St. John, Regensburg, Germany
| | | | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University of Regensburg, Regensburg, Germany.,Science and Innovation Campus Regensburg (WECARE) at the Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
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