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Priyanka, Mohan B, Poonia E, Kumar S, Virender, Singh C, Xiong J, Liu X, Pombeiro AJL, Singh G. COVID-19 Virus Structural Details: Optical and Electrochemical Detection. J Fluoresc 2024; 34:479-500. [PMID: 37382834 DOI: 10.1007/s10895-023-03307-y] [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: 04/14/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
The increasing viral species have ruined people's health and the world's economy. Therefore, it is urgent to design bio-responsive materials to provide a vast platform for detecting a different family's passive or active virus. One can design a reactive functional unit for that moiety based on the particular bio-active moieties in viruses. Nanomaterials as optical and electrochemical biosensors have enabled better tools and devices to develop rapid virus detection. Various material science platforms are available for real-time monitoring and detecting COVID-19 and other viral loads. In this review, we discuss the recent advances of nanomaterials in developing the tools for optical and electrochemical sensing COVID-19. In addition, nanomaterials used to detect other human viruses have been studied, providing insights for developing COVID-19 sensing materials. The basic strategies for nanomaterials develop as virus sensors, fabrications, and detection performances are studied. Moreover, the new methods to enhance the virus sensing properties are discussed to provide a gateway for virus detection in variant forms. The study will provide systematic information and working of virus sensors. In addition, the deep discussion of structural properties and signal changes will offer a new gate for researchers to develop new virus sensors for clinical applications.
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Affiliation(s)
- Priyanka
- Department of Chemistry and Centre of Advanced Studies, Panjab University, Chandigarh, 160014, India
| | - Brij Mohan
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. RoviscoPais, 1049-001, Lisbon, Portugal.
| | - Ekta Poonia
- Department of Chemistry, Deenbandhu Chhotu Ram University of Science & Technology, Murthal, Sonepat, 131039, Haryana, India
| | - Sandeep Kumar
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China
| | - Virender
- Department of Chemistry, Kurukshetra University, Kurukshetra, 136119, Haryana, India
| | - Charan Singh
- Department of Pharmaceutical Sciences, School of Sciences, Hemvati Nandan Bahuguna Garhwal University (A Central University), Srinagar, Uttarakhand, 246174, India
| | - Jichuan Xiong
- Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, People's Republic of China
| | - Xuefeng Liu
- Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, People's Republic of China
| | - Armando J L Pombeiro
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. RoviscoPais, 1049-001, Lisbon, Portugal
| | - Gurjaspreet Singh
- Department of Chemistry and Centre of Advanced Studies, Panjab University, Chandigarh, 160014, India.
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Bakshi SS, Mangayarkarasi V, Dash D, Das S, Ramesh S, Jayam C, Kalidoss VK. Comparative study on Saliva and Nasopharyngeal swabs and the outcome of RT-PCR test in patients with mild symptoms of SARS-CoV-2. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2023; 74:315-319. [PMID: 36965822 DOI: 10.1016/j.otoeng.2023.03.004] [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: 08/06/2022] [Revised: 11/01/2022] [Accepted: 12/06/2022] [Indexed: 03/27/2023]
Abstract
AIM A simple and reliable method for diagnosing COVID 19 infections is the needed. The role of saliva in the transmission of the infection has already been established. METHOD Saliva and nasopharyngeal swabs from patients suspected to have COVID 19 infections were taken simultaneously, and the results of the RT-PCR were compared. RESULT Total 405 samples were collected, of which 250 males and 155 females. In the 391 samples included for analysis, 370 (94.63%) samples were found to have concordance results, and 21 (5.37%) samples had discordant results. CONCLUSION The use of saliva to diagnose COVID 19 infection is reliable, and its use can be recommended.
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Affiliation(s)
- Satvinder Singh Bakshi
- Department of ENT and Head & Neck Surgery, All India Institute of Medical Sciences Mangalagiri, Guntur, Andhra Pradesh, India.
| | - V Mangayarkarasi
- Department of Microbiology, AIIMS Mangalagiri, Guntur, Andhra Pradesh, India.
| | - Debabrata Dash
- Department of Microbiology, AIIMS Mangalagiri, Guntur, Andhra Pradesh, India.
| | - Soumyajit Das
- Department of ENT and Head & Neck Surgery, All India Institute of Medical Sciences Mangalagiri, Guntur, Andhra Pradesh, India.
| | - Seepana Ramesh
- Department of ENT and Head & Neck Surgery, All India Institute of Medical Sciences Mangalagiri, Guntur, Andhra Pradesh, India.
| | - Cheeranjeevi Jayam
- Department of Dentistry, AIIMS Mangalagiri, Guntur, Andhra Pradesh, India.
| | - Vinoth Kumar Kalidoss
- Department of Community and Family Medicine, AIIMS Mangalagiri, Guntur, Andhra Pradesh, India.
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3
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Millward GG, Popelka SM, Gutierrez AG, Kowallis WJ, von Tersch RL, Yerramilli SV. A novel strategy to avoid sensitivity loss in pooled testing for SARS-CoV-2 surveillance: validation using nasopharyngeal swab and saliva samples. Front Public Health 2023; 11:1190308. [PMID: 37637813 PMCID: PMC10450028 DOI: 10.3389/fpubh.2023.1190308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
At the peak of the COVID-19 pandemic, pooled surveillance strategies were employed to alleviate the overwhelming demand for clinical testing facilities. A major drawback of most pooled-testing methods is the dilution of positive samples, which leads to a loss of detection sensitivity and the potential for false negatives. We developed a novel pooling strategy that compensates for the initial dilution with an appropriate concentration during nucleic acid extraction and real-time PCR. We demonstrated the proof of principle using laboratory-created 10-sample pools with one positive and corresponding individual positive samples by spiking a known amount of heat-inactivated SARS-CoV-2 into viral transport medium (VTM) or pooled negative saliva. No Ct difference was observed between a 10-sample pool with one positive vs. the corresponding individually analyzed positive sample by this method, suggesting that there is no detectable loss of sensitivity. We further validated this approach by using nasopharyngeal swab (NPS) specimens and showed that there is no loss of sensitivity. Serial dilutions of the virus were spiked into VTM and pooled with negative saliva in simulated 10-sample pools containing one positive to determine the LOD and process efficiency of this pooling methodology. The LOD of this approach was 10 copies/PCR, and the process efficiencies are ~95%-103% for N1 and ~87%-98% for N2 with samples in different matrices and with two different master mixes tested. Relative to TaqPath 1-step master mix, the TaqMan Fast Virus 1-Step master mix showed better sensitivity for the N2 assay, while the N1 assay showed no Ct difference. Our pooled testing strategy can facilitate large-scale, cost-effective SARS-CoV-2 surveillance screening and maintain the same level of sensitivity when analyzed individually or in a pool. This approach is highly relevant for public health surveillance efforts aimed at mitigating SARS-CoV-2 spread.
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Affiliation(s)
| | | | | | | | | | - Subrahmanyam V. Yerramilli
- Emerging Biological Threats Branch, Molecular Biology Division, Laboratory Sciences, Defense Centers for Public Health - Aberdeen “Formerly the Army Public Health Center”, Aberdeen Proving Ground, Edgewood, MD, United States
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4
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Ochoa M, Peña B, Flores O, Gil AI, Ecker L, Cornejo R, Howard LM, Grijalva CG, Lanata CF. Pooling of six respiratory samples for the detection of SARS-CoV-2: A validation and cost study in a cohort in Lima, Peru. Heliyon 2023; 9:e18904. [PMID: 37600387 PMCID: PMC10432201 DOI: 10.1016/j.heliyon.2023.e18904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023] Open
Abstract
Background The continuous evolution of the SARS-CoV-2 pandemic has led to a high demand for diagnostic testing and major shortages in testing materials, especially in low- and middle-income countries. As an alternative to testing individual samples, pooling of respiratory samples has been suggested. Previous studies have assessed performance of pooling, mainly using nasopharyngeal samples for the detection of SARS-CoV-2, but few studies have examined the performance of pooling the more practical nasal swabs or saliva samples. Objective To evaluate the sensitivity, specificity, and potential cost reduction of pooling of nasal swab (NS) and saliva (SL) samples for detection of SARS-CoV-2 in a community-based cohort study in Lima, Peru. Study design A prospective cohort study was conducted in a community setting in San Juan de Lurigancho, Lima-Peru. NS and SL samples were collected from 132 participants twice-a-week for a 2-month period. Pools of 2 to 12 samples of the same type, from participants of the same household, were tested by RT-PCR. After pooled testing, all individual samples from positive pools and all individual samples from randomly chosen negative pools were evaluated. For assessment of diagnostic performance, pool testing results were compared with results from individual testing, which served as reference, and concordance in pooled and individual test detections was evaluated. Laboratory costs for both types of samples and testing were compared. Results A total of 2008 NS and 2002 SL samples were collected from 132 study participants. We tested 329 NS and 333 SL pools. The mean pool size for NS and SL pools was 6.22 (SD = 0.92) and 6.39 (SD = 1.71), respectively. Using individual testing as reference, NS pooling of 6 had a sensitivity and specificity of 94% and 100%, respectively, with kappa of 0.97 (CI 95%: 0.93-1.00). The corresponding values for SL pooling of 6 were 83%, 100%, and 0.90 (CI 95%: 0.83-0.97). Compared with individual testing, pooling resulted in a cost reduction of 74.8% for NS and 72.4% for SL samples. Conclusions Pooling easy-to-collect respiratory samples, especially NS, demonstrated very high diagnostic performance for detection of SARS-CoV-2 with substantial cost savings. This approach could be considered in large population screening programs, especially in LMIC.
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Affiliation(s)
- Mayra Ochoa
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | - Bia Peña
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | - Omar Flores
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | - Ana I. Gil
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | - Lucie Ecker
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | | | - Leigh M. Howard
- Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Carlos G. Grijalva
- Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Claudio F. Lanata
- Instituto de Investigación Nutricional, Lima 15024, Peru
- Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232, USA
- London School of Hygiene and Tropical Medicine, London WC1E, UK
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5
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Allicock OM, Yolda-Carr D, Todd JA, Wyllie AL. Pooled RNA-extraction-free testing of saliva for the detection of SARS-CoV-2. Sci Rep 2023; 13:7426. [PMID: 37156888 PMCID: PMC10165292 DOI: 10.1038/s41598-023-34662-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/05/2023] [Indexed: 05/10/2023] Open
Abstract
The key to limiting SARS-CoV-2 spread is to identify virus-infected individuals (both symptomatic and asymptomatic) and isolate them from the general population. Hence, routine weekly testing for SARS-CoV-2 in all asymptomatic (capturing both infected and non-infected) individuals is considered critical in situations where a large number of individuals co-congregate such as schools, prisons, aged care facilities and industrial workplaces. Such testing is hampered by operational issues such as cost, test availability, access to healthcare workers and throughput. We developed the SalivaDirect RT-qPCR assay to increase access to SARS-CoV-2 testing via a low-cost, streamlined protocol using self-collected saliva. To expand the single sample testing protocol, we explored multiple extraction-free pooled saliva testing workflows prior to testing with the SalivaDirect RT-qPCR assay. A pool size of five, with or without heat inactivation at 65 °C for 15 min prior to testing resulted in a positive agreement of 98% and 89%, respectively, and an increased Ct value shift of 1.37 and 1.99 as compared to individual testing of the positive clinical saliva specimens. Applying this shift in Ct value to 316 individual, sequentially collected, SARS-CoV-2 positive saliva specimen results reported from six clinical laboratories using the original SalivaDirect assay, 100% of the samples would have been detected (Ct value < 45) had they been tested in the 1:5 pool strategy. The availability of multiple pooled testing workflows for laboratories can increase test turnaround time, permitting results in a more actionable time frame while minimizing testing costs and changes to laboratory operational flow.
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Affiliation(s)
- Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Devyn Yolda-Carr
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - John A Todd
- SalivaDirect, Inc, New Haven, CT, 06510, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
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Bornes R, Montero J, Correia A, Marques T, Rosa N. Peri-implant diseases diagnosis, prognosis and dental implant monitoring: a narrative review of novel strategies and clinical impact. BMC Oral Health 2023; 23:183. [PMID: 36997949 PMCID: PMC10061972 DOI: 10.1186/s12903-023-02896-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/17/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND The diagnosis of peri-implantar and periodontal relies mainly on a set of clinical measures and the evaluation of radiographic images. However, these clinical settings alone are not sufficient to determine, much less predict, periimplant bone loss or future implant failure. Early diagnosis of periimplant diseases and its rate of progress may be possible through biomarkers assessment. Once identified, biomarkers of peri-implant and periodontal tissue destruction may alert the clinicians before clinical signs show up. Therefore, it is important to consider developing chair-side diagnostic tests with specificity for a particular biomarker, indicating the current activity of the disease. METHODS A search strategy was created at Pubmed and Web of Science to answer the question: "How the molecular point-of-care tests currently available can help in the early detection of peri-implant diseases and throws light on improvements in point of care diagnostics devices?" RESULTS The PerioSafe® PRO DRS (dentognostics GmbH, Jena) and ImplantSafe® DR (dentognostics GmbH, Jena ORALyzer® test kits, already used clinically, can be a helpful adjunct tool in enhancing the diagnosis and prognosis of periodontal/peri-implantar diseases. With the advances of sensor technology, the biosensors can perform daily monitoring of dental implants or periodontal diseases, making contributions to personal healthcare and improve the current status quo of health management and human health. CONCLUSIONS Based on the findings, more emphasis is given to the role of biomarkers in diagnosing and monitoring periodontal and peri-implant diseases. By combining these strategies with traditional protocols, professionals could increase the accuracy of early detection of peri-implant and periodontal diseases, predicting disease progression, and monitoring of treatment outcomes.
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Affiliation(s)
- Rita Bornes
- Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Universidade Católica Portuguesa, Viseu, Portugal.
| | - Javier Montero
- Department of Surgery, Faculty of Medicine, University of Salamanca, Salamanca, Spain
| | - André Correia
- Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Universidade Católica Portuguesa, Viseu, Portugal
| | - Tiago Marques
- Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Universidade Católica Portuguesa, Viseu, Portugal
| | - Nuno Rosa
- Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Universidade Católica Portuguesa, Viseu, Portugal
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Validation of SARS-CoV-2 pooled testing for surveillance using the Panther Fusion® system: Impact of pool size, automation, and assay chemistry. PLoS One 2022; 17:e0276729. [PMID: 36342921 PMCID: PMC9639840 DOI: 10.1371/journal.pone.0276729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022] Open
Abstract
Combining diagnostic specimens into pools has been considered as a strategy to augment throughput, decrease turnaround time, and leverage resources. This study utilized a multi-parametric approach to assess optimum pool size, impact of automation, and effect of nucleic acid amplification chemistries on the detection of SARS-CoV-2 RNA in pooled samples for surveillance testing on the Hologic Panther Fusion® System. Dorfman pooled testing was conducted with previously tested SARS-CoV-2 nasopharyngeal samples using Hologic’s Aptima® and Panther Fusion® SARS-CoV-2 Emergency Use Authorization assays. A manual workflow was used to generate pool sizes of 5:1 (five samples: one positive, four negative) and 10:1. An automated workflow was used to generate pool sizes of 3:1, 4:1, 5:1, 8:1 and 10:1. The impact of pool size, pooling method, and assay chemistry on sensitivity, specificity, and lower limit of detection (LLOD) was evaluated. Both the Hologic Aptima® and Panther Fusion® SARS-CoV-2 assays demonstrated >85% positive percent agreement between neat testing and pool sizes ≤5:1, satisfying FDA recommendation. Discordant results between neat and pooled testing were more frequent for positive samples with CT>35. Fusion® CT (cycle threshold) values for pooled samples increased as expected for pool sizes of 5:1 (CT increase of 1.92–2.41) and 10:1 (CT increase of 3.03–3.29). The Fusion® assay demonstrated lower LLOD than the Aptima® assay for pooled testing (956 vs 1503 cp/mL, pool size of 5:1). Lowering the cut-off threshold of the Aptima® assay from 560 kRLU (manufacturer’s setting) to 350 kRLU improved the assay sensitivity to that of the Fusion® assay for pooled testing. Both Hologic’s SARS-CoV-2 assays met the FDA recommended guidelines for percent positive agreement (>85%) for pool sizes ≤5:1. Automated pooling increased test throughput and enabled automated sample tracking while requiring less labor. The Fusion® SARS-CoV-2 assay, which demonstrated a lower LLOD, may be more appropriate for surveillance testing.
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Ávila LMS, Galvis MLD, Campos MAJ, Lozano-Parra A, Villamizar LAR, Arenas MO, Martínez-Vega RA, Cala LMV, Bautista LE. Validation of RT-qPCR test for SARS-CoV-2 in saliva specimens. J Infect Public Health 2022; 15:1403-1408. [PMID: 36371937 PMCID: PMC9628233 DOI: 10.1016/j.jiph.2022.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/19/2022] [Accepted: 10/30/2022] [Indexed: 11/05/2022] Open
Abstract
Background Saliva samples may be an easier, faster, safer, and cost-saving alternative to NPS samples, and can be self-collected by the patient. Whether SARS-CoV-2 RT-qPCR in saliva is more accurate than in nasopharyngeal swaps (NPS) is uncertain. We evaluated the accuracy of the RT-qPCR in both types of samples, assuming both approaches were imperfect. Methods We assessed the limit of detection (LoD) of RT-qPCR in each type of sample. We collected paired NPS and saliva samples and tested them using the Berlin Protocol to detect SARS-CoV-2 envelope protein (E). We used a Bayesian latent class analysis (BLCA) to estimate the sensitivity and specificity of each test, while accounting for their conditional dependence. Results The LoD were 10 copies/mL in saliva and 100 copies/mL in NPS. Paired samples of saliva and NPS were collected in 412 participants. Out of 68 infected cases, 14 were positive only in saliva. RT-qPCR sensitivity ranged from 82.7% (95% CrI: 54.8, 94.8) in NPS to 84.5% (50.9, 96.5) in saliva. Corresponding specificities were 99.1 (95% CrI: 95.3, 99.8) and 98.4 (95% CrI: 92.8, 99.7). Conclusions SARS-CoV-2 RT-qPCR test in saliva specimens has a similar or better accuracy than RT-qPCR test in NPS. Saliva specimens may be ideal for surveillance in general population, particularly in children, and in healthcare or other personnel in need of serial testing.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Leonelo E. Bautista
- University of Wisconsin-Madison, 610 Walnut Street, WARF 703, Madison, United States,Correspondence to: Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, 610 Walnut Street, WARF 703, Madison, WI 53711
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9
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Wu TY, Liao YC, Fuh CS, Weng PW, Wang JY, Chen CY, Huang YM, Chen CP, Chu YL, Chen CK, Yeh KL, Yu CH, Wu HK, Lin WP, Liou TH, Wu MS, Liaw CK. An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection. Front Public Health 2022; 10:994712. [PMID: 36339215 PMCID: PMC9627488 DOI: 10.3389/fpubh.2022.994712] [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: 07/15/2022] [Accepted: 09/20/2022] [Indexed: 01/26/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic can be effectively controlled by rapid and accurate identification of SARS-CoV-2-infected cases through large-scale screening. Hypercube pooling polymerase chain reaction (PCR) is frequently used as a pooling technique because of its high speed and efficiency. We attempted to implement the hypercube pooling strategy and found it had a large quantization effect. This raised two questions: is hypercube pooling with edge = 3 actually the optimal strategy? If not, what is the best edge and dimension? We used a C++ program to calculate the expected number of PCR tests per patient for different values of prevalence, edge, and dimension. The results showed that every edge had a best performance range. Then, using C++ again, we created a program to calculate the optimal edge and dimension required for pooling samples when entering prevalence into our program. Our program will be provided as freeware in the hope that it can help governments fight the SARS-CoV-2 pandemic.
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Affiliation(s)
- Tai-Yin Wu
- Department of Family Medicine, Zhongxing Branch, Taipei City Hospital, Taipei, Taiwan,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan,General Education Center, University of Taipei, Taipei, Taiwan
| | - Yu-Ciao Liao
- Institute of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Chiou-Shann Fuh
- Institute of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Pei-Wei Weng
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan,Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Research Center of Biomedical Device, Taipei Medical University, Taipei, Taiwan
| | - Jr-Yi Wang
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Chih-Yu Chen
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan,Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Research Center of Biomedical Device, Taipei Medical University, Taipei, Taiwan,International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan
| | - Yu-Min Huang
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Chung-Pei Chen
- Department of Orthopedics, Cathay General Hospital, Taipei, Taiwan
| | - Yo-Lun Chu
- Department of Orthopedics, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan,School of Medicine, College of Medicine, Fu Jen Catholic University, Taipei, Taiwan,Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
| | - Cheng-Kuang Chen
- Department of Orthopedics, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan,Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
| | - Kuei-Lin Yeh
- Institute of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan,Department of Orthopaedics, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan,Department of Long-Term Care and Management, WuFeng University, Chiayi, Taiwan
| | - Ching-Hsiao Yu
- Department of Orthopaedic Surgery, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan,Department of Orthopaedic Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Hung-Kang Wu
- Department of Orthopaedic Surgery, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan,Department of Orthopaedic Surgery, National Taiwan University Hospital, Taipei, Taiwan,Department of Nursing, Yuanpei University of Medical Technology, Hsinchu, Taiwan
| | - Wei-Peng Lin
- Department of Orthopaedic Surgery, National Taiwan University Hospital, Taipei, Taiwan,Department of Orthopedics, Postal Hospital, Taipei, Taiwan
| | - Tsan-Hon Liou
- Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Mai-Szu Wu
- Division of Nephrology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chen-Kun Liaw
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Orthopedics, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan,Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Research Center of Biomedical Device, Taipei Medical University, Taipei, Taiwan,TMU Biodesign Center, Taipei Medical University, Taipei, Taiwan,*Correspondence: Chen-Kun Liaw ;
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10
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COVID-19 Salivary Protein Profile: Unravelling Molecular Aspects of SARS-CoV-2 Infection. J Clin Med 2022; 11:jcm11195571. [PMID: 36233441 PMCID: PMC9570692 DOI: 10.3390/jcm11195571] [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: 09/03/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/18/2022] Open
Abstract
COVID-19 is the most impacting global pandemic of all time, with over 600 million infected and 6.5 million deaths worldwide, in addition to an unprecedented economic impact. Despite the many advances in scientific knowledge about the disease, much remains to be clarified about the molecular alterations induced by SARS-CoV-2 infection. In this work, we present a hybrid proteomics and in silico interactomics strategy to establish a COVID-19 salivary protein profile. Data are available via ProteomeXchange with identifier PXD036571. The differential proteome was narrowed down by the Partial Least-Squares Discriminant Analysis and enrichment analysis was performed with FunRich. In parallel, OralInt was used to determine interspecies Protein-Protein Interactions between humans and SARS-CoV-2. Five dysregulated biological processes were identified in the COVID-19 proteome profile: Apoptosis, Energy Pathways, Immune Response, Protein Metabolism and Transport. We identified 10 proteins (KLK 11, IMPA2, ANXA7, PLP2, IGLV2-11, IGHV3-43D, IGKV2-24, TMEM165, VSIG10 and PHB2) that had never been associated with SARS-CoV-2 infection, representing new evidence of the impact of COVID-19. Interactomics analysis showed viral influence on the host immune response, mainly through interaction with the degranulation of neutrophils. The virus alters the host’s energy metabolism and interferes with apoptosis mechanisms.
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Tobik ER, Kitfield-Vernon LB, Thomas RJ, Steel SA, Tan SH, Allicock OM, Choate BL, Akbarzada S, Wyllie AL. Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe. Expert Rev Mol Diagn 2022; 22:519-535. [PMID: 35763281 DOI: 10.1080/14737159.2022.2094250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Symptomatic testing and asymptomatic screening for SARS-CoV-2 continue to be essential tools for mitigating virus transmission. Though COVID-19 diagnostics initially defaulted to oropharyngeal or nasopharyngeal sampling, the worldwide urgency to expand testing efforts spurred innovative approaches and increased diversity of detection methods. Strengthening innovation and facilitating widespread testing remains critical for global health, especially as additional variants emerge and other mitigation strategies are recalibrated. AREAS COVERED A growing body of evidence reflects the need to expand testing efforts and further investigate the efficiency, sensitivity, and acceptability of saliva samples for SARS-CoV-2 detection. Countries have made pandemic response decisions based on resources, costs, procedures, and regional acceptability - the adoption and integration of saliva-based testing among them. Saliva has demonstrated high sensitivity and specificity while being less invasive relative to nasopharyngeal swabs, securing saliva's position as a more acceptable sample type. EXPERT OPINION Despite the accessibility and utility of saliva sampling, global implementation remains low compared to swab-based approaches. In some cases, countries have validated saliva-based methods but face challenges with testing implementation or expansion. Here, we review the localities that have demonstrated success with saliva-based SARS-CoV-2 testing approaches and can serve as models for transforming concepts into globally-implemented best practices.
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Affiliation(s)
- Emily R Tobik
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Lily B Kitfield-Vernon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Russell J Thomas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sydney A Steel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Steph H Tan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.,Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, USA
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Brittany L Choate
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sumaira Akbarzada
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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Nguyen-Kim H, Beckmann C, Redondo M, Ziliox J, Vallett V, Berger-Sturm K, Overbeck JV, Alberi Auber L. COVID Salivary diagnostics: a comparative technical study. J Med Virol 2022; 94:4277-4286. [PMID: 35614569 PMCID: PMC9347777 DOI: 10.1002/jmv.27883] [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: 03/25/2022] [Revised: 05/11/2022] [Accepted: 05/23/2022] [Indexed: 12/02/2022]
Abstract
Since the beginning of the coronavirus disease 2019 (COVID‐19) pandemic, molecular diagnostics of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) have taken center stage in the detection of infected individuals for isolation purposes but also in the mass surveillance as a preventive strategy to contain the virus spread. While nasopharyngeal swabs (NPS) have remained the golden standard substrate, salivary diagnostic for SARS‐CoV‐2 has been proposed as an alternative and noninvasive measure in vulnerable individuals. Nevertheless, there is a widespread assumption that salivary reverse‐transcription polymerase chain reaction (RT‐PCR) does not match the quality of testing using NPS and particular care should be taken in respect to food or beverage intake, when sampling saliva. Our study indicates that without any precaution in the selection of 190 patients, nor restriction over the time window of sampling, there is 99% match in the COVID‐19 positivity between NPS and saliva when using RT‐PCR, with a reported Delta in thermal cycles (Cts) values for the viral genes Envelope (E) and Open reading frame 1ab (Orf1ab) between 0 and 2, a 98.7% sensitivity and 100% specificity. This high accuracy is maintained in pooling configurations that can be used for mass‐testing purposes in professional and educational settings. The further advantage to using crude saliva as compared to NPS or mouthwash is that direct methods yield robust results. Overall, our study validates and promotes the use of salivary diagnostic for COVID‐19 eliminating the need of a medical practitioner for the sampling, resolving the unpleasantness of the NPS intervention and empowering the patient to do self‐testing in times of need.
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Affiliation(s)
- Hanh Nguyen-Kim
- Swiss Integrative Center for Human Health, Fribourg, Switzerland
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