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Starshinova A, Osipov N, Dovgalyk I, Kulpina A, Belyaeva E, Kudlay D. COVID-19 and Tuberculosis: Mathematical Modeling of Infection Spread Taking into Account Reduced Screening. Diagnostics (Basel) 2024; 14:698. [PMID: 38611611 PMCID: PMC11011507 DOI: 10.3390/diagnostics14070698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/17/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
The COVID-19 pandemic resulted in the cessation of many tuberculosis (TB) support programs and reduced screening coverage for TB worldwide. We propose a model that demonstrates, among other things, how undetected cases of TB affect the number of future M. tuberculosis (M. tb) infections. The analysis of official statistics on the incidence of TB, preventive examination coverage of the population, and the number of patients with bacterial excretion of M. tb in the Russian Federation from 2008 to 2021 is carried out. The desired model can be obtained due to the fluctuation of these indicators in 2020, when the COVID-19 pandemic caused a dramatic reduction in TB interventions. Statistical analysis is carried out using R v.4.2.1. The resulting model describes the dependence of the detected incidence and prevalence of TB with bacterial excretion in the current year on the prevalence of TB with bacterial excretion in the previous year and on the coverage of preventive examinations in the current and previous years. The adjusted coefficient of model determination (adjusted R-squared) is 0.9969, indicating that the model contains almost no random component. It clearly shows that TB cases missed due to low screening coverage and left uncontrolled will lead to a significant increase in the number of new infections in the future. We may conclude that the obtained results clearly demonstrate the need for mass screening of the population in the context of the spread of TB infection, which makes it possible to timely identify patients with TB with bacterial excretion.
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Affiliation(s)
- Anna Starshinova
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia;
| | - Nikolay Osipov
- Department of Steklov Mathematical, Institute of Russian Academy of Sciences, 191023 St. Petersburg, Russia;
- Mathematical Department, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Irina Dovgalyk
- Research Institute of Phthisiopulmonology, 190961 St. Petersburg, Russia;
| | - Anastasia Kulpina
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia;
- Medical Department, State Pediatric Medical University, 194100 St. Petersburg, Russia
| | | | - Dmitry Kudlay
- Department of Pharmacology, I.M. Sechenov First Moscow State Medical University, 119435 Moscow, Russia;
- Immunology Department, Institute of Immunology FMBA, 115552 Moscow, Russia
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Martin DR, Mutombwera AT, Madiehe AM, Onani MO, Meyer M, Cloete R. Molecular modeling and simulation studies of SELEX-derived high-affinity DNA aptamers to the Ebola virus nucleoprotein. J Biomol Struct Dyn 2024:1-18. [PMID: 38217874 DOI: 10.1080/07391102.2024.2302922] [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: 04/19/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
Ebola viral disease (EVD) is a highly infectious and potentially fatal illness with a case fatality rate ranging from 25% to 90%. To effectively control its spread, there is a need for rapid, reliable and lowcost point-of-care (P OC) diagnostic tests. While various EVD diagnostic tests exist, few are P OC tests, and many are not cost-effective. The use of antibodies in these tests has limitations, prompting the exploration of aptamers as potential alternatives. Various proteins from the Ebola virus (EBOV) proteome, including EBOV nucleoprotein (NP), are considered viable targets for diagnostic assays. A previous study identified three aptamers (Apt1. Apt2 and Apt3) with high affinity for EBOV NP using systemic evolution of ligands by exponential enrichment (SELEX). This study aimed to employ in silico methods, such as Phyre2, RNAfold, RNAComposer, HADDOCK and GROMACS, to model the structures of EBOV NP and the aptamers, and to investigate their binding. The in silico analysis revealed successful binding of all the three aptamers to EBOV NP, with a suggested ranking of Apt1 > Apt2 > Apt3 based on binding affinity. Microscale thermophoresis (MST) analysis confirmed the binding, providing dissociation constants of 25 ± 2.84, 56 ± 2.76 and 140 ±3.69 nM for Apt1, Apt2 and Apt3, respectively. The study shows that the findings of the in silico analysis was in agreement with the MST analysis. Inclusion of these in silico approaches in diagnostic assay development can expedite the selection of candidate aptamers, potentially overcoming challenges associated with aptamer application in diagnostics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- D R Martin
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville, South Africa Cape Town, South Africa
| | - A T Mutombwera
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - A M Madiehe
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - M O Onani
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - M Meyer
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - R Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville, South Africa Cape Town, South Africa
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Seele PP, Dyan B, Skepu A, Maserumule C, Sibuyi NRS. Development of Gold-Nanoparticle-Based Lateral Flow Immunoassays for Rapid Detection of TB ESAT-6 and CFP-10. BIOSENSORS 2023; 13:354. [PMID: 36979566 PMCID: PMC10046134 DOI: 10.3390/bios13030354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
The current study reports on the development of a rapid and cost-effective TB-antigen diagnostic test for the detection of Mycobacterium biomarkers from non-sputum-based samples. Two gold nanoparticle (AuNP)-based rapid diagnostic tests (RDTs) in the form of lateral flow immunoassays (LFIAs) were developed for detection of immunodominant TB antigens, the 6 kDa early secreted antigen target EsxA (ESAT-6) and the 10 kDa culture filtrate protein EsxB (CFP-10). AuNPs were synthesized using the Turkevich method and characterized by UV-vis spectrophotometer and transmission electron microscope (TEM). The AuNP-detection probe conjugation conditions were determined by comparing the stability of 14 nm AuNPs at different pH conditions, following salt challenge. Thereafter, ESAT-6 and CFP-10 antibodies were conjugated to the AuNPs and used for the colorimetric detection of TB antigens. Selection of the best detection and capture antibody pairs was determined by Dot spotting. The limits of detection (LODs) for the LFIAs were evaluated by dry testing. TEM results showed that the 14 nm AuNPs were mostly spherical and well dispersed. The ESAT-6 LFIA prototype had an LOD of 0.0625 ng/mL versus the CFP-10 with an LOD of 7.69 ng/mL. Compared to other studies in the literature, the LOD was either similar or lower, outperforming them. Moreover, in some of the previous studies, an enrichment/extraction step was required to improve on the LOD. In this study, the LFIAs produced results within 15 min and could be suitable for use at PoCs either in clinics, mobile clinics, hospitals or at home by the end user. However, further studies need to be conducted to validate their use in clinical samples.
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Affiliation(s)
- Palesa Pamela Seele
- Nanotechnology Innovation Centre, Health Platform, Advanced Materials Division, Mintek, Private Bag X3015, Randburg, Johannesburg 2125, South Africa
| | - Busiswa Dyan
- Nanotechnology Innovation Centre, Health Platform, Advanced Materials Division, Mintek, Private Bag X3015, Randburg, Johannesburg 2125, South Africa
| | - Amanda Skepu
- Advanced Chemistry and Life Sciences Division, Next Generation Health Cluster, Council for Scientific and Industrial Research (CSIR), Pretoria 0001, South Africa
| | - Charlotte Maserumule
- Nanotechnology Innovation Centre, Health Platform, Advanced Materials Division, Mintek, Private Bag X3015, Randburg, Johannesburg 2125, South Africa
| | - Nicole Remaliah Samantha Sibuyi
- Nanotechnology Innovation Centre, Health Platform, Advanced Materials Division, Mintek, Private Bag X3015, Randburg, Johannesburg 2125, South Africa
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Dyan B, Seele PP, Skepu A, Mdluli PS, Mosebi S, Sibuyi NRS. A Review of the Nucleic Acid-Based Lateral Flow Assay for Detection of Breast Cancer from Circulating Biomarkers at a Point-of-Care in Low Income Countries. Diagnostics (Basel) 2022; 12:diagnostics12081973. [PMID: 36010323 PMCID: PMC9406634 DOI: 10.3390/diagnostics12081973] [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: 07/20/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
The current levels of breast cancer in African women have contributed to the high mortality rates among them. In South Africa, the incidence of breast cancer is also on the rise due to changes in behavioural and biological risk factors. Such low survival rates can be attributed to the late diagnosis of the disease due to a lack of access and the high costs of the current diagnostic tools. Breast cancer is asymptomatic at early stages, which is the best time to detect it and intervene to prevent high mortality rates. Proper risk assessment, campaigns, and access to adequate healthcare need to be prioritised among patients at an early stage. Early detection of breast cancer can significantly improve the survival rate of breast cancer patients, since therapeutic strategies are more effective at this stage. Early detection of breast cancer can be achieved by developing devices that are simple, sensitive, low-cost, and employed at point-of-care (POC), especially in low-income countries (LICs). Nucleic-acid-based lateral flow assays (NABLFAs) that combine molecular detection with the immunochemical visualisation principles, have recently emerged as tools for disease diagnosis, even for low biomarker concentrations. Detection of circulating genetic biomarkers in non-invasively collected biological fluids with NABLFAs presents an appealing and suitable method for POC testing in resource-limited regions and/or LICs. Diagnosis of breast cancer at an early stage will improve the survival rates of the patients. This review covers the analysis of the current state of NABLFA technologies used in developing countries to reduce the scourge of breast cancer.
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Affiliation(s)
- Busiswa Dyan
- Nanotechnology Innovation Centre, Health Platform, Mintek, 200 Malibongwe Drive, Randburg, Johannesburg 2194, South Africa
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Private Bag X6, Florida, Johannesburg 1710, South Africa
- Correspondence: (B.D.); (N.R.S.S.)
| | - Palesa Pamela Seele
- Nanotechnology Innovation Centre, Health Platform, Mintek, 200 Malibongwe Drive, Randburg, Johannesburg 2194, South Africa
| | - Amanda Skepu
- Nanotechnology Innovation Centre, Health Platform, Mintek, 200 Malibongwe Drive, Randburg, Johannesburg 2194, South Africa
| | - Phumlane Selby Mdluli
- Nanotechnology Innovation Centre, Health Platform, Mintek, 200 Malibongwe Drive, Randburg, Johannesburg 2194, South Africa
| | - Salerwe Mosebi
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Private Bag X6, Florida, Johannesburg 1710, South Africa
| | - Nicole Remaliah Samantha Sibuyi
- Nanotechnology Innovation Centre, Health Platform, Mintek, 200 Malibongwe Drive, Randburg, Johannesburg 2194, South Africa
- Correspondence: (B.D.); (N.R.S.S.)
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Garlant HN, Ellappan K, Hewitt M, Perumal P, Pekeleke S, Wand N, Southern J, Kumar SV, Belgode H, Abubakar I, Sinha S, Vasan S, Joseph NM, Kempsell KE. Evaluation of Host Protein Biomarkers by ELISA From Whole Lysed Peripheral Blood for Development of Diagnostic Tests for Active Tuberculosis. Front Immunol 2022; 13:854327. [PMID: 35720382 PMCID: PMC9205408 DOI: 10.3389/fimmu.2022.854327] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/28/2022] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis (TB) remains a significant global health crisis and the number one cause of death for an infectious disease. The health consequences in high-burden countries are significant. Barriers to TB control and eradication are in part caused by difficulties in diagnosis. Improvements in diagnosis are required for organisations like the World Health Organisation (WHO) to meet their ambitious target of reducing the incidence of TB by 50% by the year 2025, which has become hard to reach due to the COVID-19 pandemic. Development of new tests for TB are key priorities of the WHO, as defined in their 2014 report for target product profiles (TPPs). Rapid triage and biomarker-based confirmatory tests would greatly enhance the diagnostic capability for identifying and diagnosing TB-infected individuals. Protein-based test methods e.g. lateral flow devices (LFDs) have a significant advantage over other technologies with regard to assay turnaround time (minutes as opposed to hours) field-ability, ease of use by relatively untrained staff and without the need for supporting laboratory infrastructure. Here we evaluate the diagnostic performance of nine biomarkers from our previously published biomarker qPCR validation study; CALCOCO2, CD274, CD52, GBP1, IFIT3, IFITM3, SAMD9L, SNX10 and TMEM49, as protein targets assayed by ELISA. This preliminary evaluation study was conducted to quantify the level of biomarker protein expression across latent, extra-pulmonary or pulmonary TB groups and negative controls, collected across the UK and India, in whole lysed blood samples (WLB). We also investigated associative correlations between the biomarkers and assessed their suitability for ongoing diagnostic test development, using receiver operating characteristic/area under the curve (ROC) analyses, singly and in panel combinations. The top performing single biomarkers for pulmonary TB versus controls were CALCOCO2, SAMD9L, GBP1, IFITM3, IFIT3 and SNX10. TMEM49 was also significantly differentially expressed but downregulated in TB groups. CD52 expression was not highly differentially expressed across most of the groups but may provide additional patient stratification information and some limited use for incipient latent TB infection. These show therefore great potential for diagnostic test development either in minimal configuration panels for rapid triage or more complex formulations to capture the diversity of disease presentations.
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Affiliation(s)
- Harriet N. Garlant
- Science Group: Research and Evaluation, UK Health Security Agency, Salisbury, United Kingdom
| | - Kalaiarasan Ellappan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Matthew Hewitt
- Science Group: Research and Evaluation, UK Health Security Agency, Salisbury, United Kingdom
| | - Prem Perumal
- Science Group: Research and Evaluation, UK Health Security Agency, Salisbury, United Kingdom
| | - Simon Pekeleke
- Science Group: Research and Evaluation, UK Health Security Agency, Salisbury, United Kingdom
| | - Nadina Wand
- Science Group: Research and Evaluation, UK Health Security Agency, Salisbury, United Kingdom
| | - Jo Southern
- School of Life & Medical Sciences, Mortimer Market Centre, University College London, London, United Kingdom
| | - Saka Vinod Kumar
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Harish Belgode
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Ibrahim Abubakar
- School of Life & Medical Sciences, Mortimer Market Centre, University College London, London, United Kingdom
| | - Sanjeev Sinha
- Department of Medicine, All India Institute for Medical Sciences, New Delhi, India
| | - Seshadri Vasan
- Department of Health Sciences, University of York, York, United Kingdom
| | - Noyal Mariya Joseph
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Karen E. Kempsell
- Science Group: Research and Evaluation, UK Health Security Agency, Salisbury, United Kingdom
- *Correspondence: Karen E. Kempsell,
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