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Silva M, Viana CM, Betco I, Nogueira P, Roquette R, Rocha J. Spatiotemporal dynamics of epidemiology diseases: mobility based risk and short-term prediction modeling of COVID-19. Front Public Health 2024; 12:1359167. [PMID: 39022425 PMCID: PMC11251998 DOI: 10.3389/fpubh.2024.1359167] [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: 12/20/2023] [Accepted: 06/17/2024] [Indexed: 07/20/2024] Open
Abstract
Nowadays, epidemiological modeling is applied to a wide range of diseases, communicable and non-communicable, namely AIDS, Ebola, influenza, Dengue, Malaria, Zika. More recently, in the context of the last pandemic declared by the World Health Organization (WHO), several studies applied these models to SARS-CoV-2. Despite the increasing number of researches using spatial analysis, some constraints persist that prevent more complex modeling such as capturing local epidemiological dynamics or capturing the real patterns and dynamics. For example, the unavailability of: (i) epidemiological information such as the frequency with which it is made available; (ii) sociodemographic and environmental factors (e.g., population density and population mobility) at a finer scale which influence the evolution patterns of infectious diseases; or (iii) the number of cases information that is also very dependent on the degree of testing performed, often with severe territorial disparities and influenced by context factors. Moreover, the delay in case reporting and the lack of quality control in epidemiological information is responsible for biases in the data that lead to many results obtained being subject to the ecological fallacy, making it difficult to identify causal relationships. Other important methodological limitations are the control of spatiotemporal dependence, management of non-linearity, ergodicy, among others, which can impute inconsistencies to the results. In addition to these issues, social contact, is still difficult to quantify in order to be incorporated into modeling processes. This study aims to explore a modeling framework that can overcome some of these modeling methodological limitations to allow more accurate modeling of epidemiological diseases. Based on Geographic Information Systems (GIS) and spatial analysis, our model is developed to identify group of municipalities where population density (vulnerability) has a stronger relationship with incidence (hazard) and commuting movements (exposure). Specifically, our framework shows how to operate a model over data with no clear trend or seasonal pattern which is suitable for a short-term predicting (i.e., forecasting) of cases based on few determinants. Our tested models provide a good alternative for when explanatory data is few and the time component is not available, once they have shown a good fit and good short-term forecast ability.
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Affiliation(s)
- Melissa Silva
- Associated Laboratory TERRA, Institute of Geography and Spatial Planning, University of Lisbon, Lisbon, Portugal
| | - Cláudia M. Viana
- Associated Laboratory TERRA, Institute of Geography and Spatial Planning, University of Lisbon, Lisbon, Portugal
| | - Iuria Betco
- Associated Laboratory TERRA, Institute of Geography and Spatial Planning, University of Lisbon, Lisbon, Portugal
| | - Paulo Nogueira
- Associated Laboratory TERRA, Nursing Research, Innovation and Development Centre of Lisbon (CIDNUR), Nursing School of Lisbon, Lisbon, Portugal
- Instituto de Saúde Ambiental (ISAMB), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Escola Nacional de Saúde Pública, ENSP, Centro de Investigação em Saúde Pública, CISP, Comprehensive Health Research Center, CHRC, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Rita Roquette
- NOVA IMS Information Management School, NOVA University of Lisbon, Lisbon, Portugal
| | - Jorge Rocha
- Associated Laboratory TERRA, Institute of Geography and Spatial Planning, University of Lisbon, Lisbon, Portugal
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Cahyono B, Amalina ND, Suzery M, Nur Wahyu Bima D. Exploring the Capability of Indonesia Natural Medicine Secondary Metabolite as Potential Inhibitors of SARS-CoV-2 Proteins to Prevent Virulence of COVID-19: In silico and Bioinformatic Approach. Open Access Maced J Med Sci 2021. [DOI: 10.3889/oamjms.2021.5945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: SARS-CoV-2 was causing COVID-19 disease resulting in many deaths and being a significant concern in the world today. There is an emergent need to search for possible medications for COVID-19 treatment. The key point to halt SARS-CoV-2 infection through inhibition of the virus-receptor interaction and stimulates the immune system. Utilization of the bioinformatic and in silico molecular docking a number of available medications might be proven to be effective in inhibiting SARS-CoV-2 main drug targets including the SARS-CoV2 spike glycoprotein, the 3CL protease SARS-CoV-2 active target, PD-ACE2, 2019-nCoV PLpro, and NF-kβ.
AIM: This present study was conducted to identify the potential target and molecular mechanism of the major compound on Alpinia galanga extract and Citrus sinensis (L.) extract in circumventing COVID-19 using a bioinformatics approach and in silico molecular docking.
RESULTS: Direct protein target of all secondary metabolite and the gene list from PubMed “Severe acute respiratory syndrome coronavirus 2” generated 2 genes (CCL2 and VEGFA) as potential therapeutics target genes (PTTG). The molecular docking was conducted by the Protein-Ligand Ant System (PLANTS) software. The results show that hesperidin, naringenin, and galangin have lower docking score for all five-protein target receptor compared with chloroquine and remdesivir. The lower docking score suggests a high affinity to bind the protein. Moreover, these compounds have a strong affinity in their inhibitory capacity for viral infection.
CONCLUSION: In general, this study’s findings show that the compound of Alpinia galanga extract dan Citrus sinensis (L.) extract exhibit the best potential as an inhibitor to the development of the SARS-CoV-2 and inhibited cytokine storm through inactivation NF-kβ _pathway.
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Akhtar S, Das JK, Ismail T, Wahid M, Saeed W, Bhutta ZA. Nutritional perspectives for the prevention and mitigation of COVID-19. Nutr Rev 2021. [PMID: 33570583 DOI: 10.1093/nutrit/nuaa063018-1355-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
Worldwide, there is an array of clinical trials under way to evaluate treatment options against coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2. Concurrently, several nutritional therapies and alternative supportive treatments are also being used and tested to reduce the mortality associated with acute respiratory distress in patients with COVID-19. In the context of COVID-19, improved nutrition that includes micronutrient supplementation to augment the immune system has been recognized as a viable approach to both prevent and alleviate the severity of the infection. The potential role of micronutrients as immune-boosting agents is particularly relevant for low- and middle-income countries, which already have an existing high burden of undernutrition and micronutrient deficiencies. A systematic literature review was performed to identify nutritional interventions that might prevent or aid in the recovery from COVID-19. The PubMed, ScienceDirect, Cochrane, Scopus, Web of Science, and Google Scholar databases were searched electronically from February to April 2020. All abstracts and full-text articles were examined for their relevance to this review. The information gathered was collated under various categories. Deficiencies of micronutrients, especially vitamins A, B complex, C, and D, zinc, iron, and selenium, are common among vulnerable populations in general and among COVID-19 patients in particular and could plausibly increase the risk of mortality. Judicious use of need-based micronutrient supplementation, alongside existing micronutrient fortification programs, is warranted in the current global pandemic, especially in low- and middle-income economies.
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Affiliation(s)
- Saeed Akhtar
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Pakistan
| | - Jai K Das
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tariq Ismail
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Pakistan
| | - Muqeet Wahid
- Division of Woman and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Wisha Saeed
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Pakistan
| | - Zulfiqar A Bhutta
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi, Pakistan
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Akhtar S, Das JK, Ismail T, Wahid M, Saeed W, Bhutta ZA. Nutritional perspectives for the prevention and mitigation of COVID-19. Nutr Rev 2021; 79:289-300. [PMID: 33570583 PMCID: PMC7454773 DOI: 10.1093/nutrit/nuaa063] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/15/2020] [Indexed: 02/06/2023] Open
Abstract
Worldwide, there is an array of clinical trials under way to evaluate treatment options against coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2. Concurrently, several nutritional therapies and alternative supportive treatments are also being used and tested to reduce the mortality associated with acute respiratory distress in patients with COVID-19. In the context of COVID-19, improved nutrition that includes micronutrient supplementation to augment the immune system has been recognized as a viable approach to both prevent and alleviate the severity of the infection. The potential role of micronutrients as immune-boosting agents is particularly relevant for low- and middle-income countries, which already have an existing high burden of undernutrition and micronutrient deficiencies. A systematic literature review was performed to identify nutritional interventions that might prevent or aid in the recovery from COVID-19. The PubMed, ScienceDirect, Cochrane, Scopus, Web of Science, and Google Scholar databases were searched electronically from February to April 2020. All abstracts and full-text articles were examined for their relevance to this review. The information gathered was collated under various categories. Deficiencies of micronutrients, especially vitamins A, B complex, C, and D, zinc, iron, and selenium, are common among vulnerable populations in general and among COVID-19 patients in particular and could plausibly increase the risk of mortality. Judicious use of need-based micronutrient supplementation, alongside existing micronutrient fortification programs, is warranted in the current global pandemic, especially in low- and middle-income economies.
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Affiliation(s)
- Saeed Akhtar
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Pakistan
| | - Jai K Das
- Division of Woman and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Tariq Ismail
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Pakistan
| | - Muqeet Wahid
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Wisha Saeed
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Pakistan
| | - Zulfiqar A Bhutta
- Centre of Excellence in Women and Child Health, Aga Khan University, Karachi, Pakistan, and the Centre for Global Child Health, The Hospital for Sick Children, Toronto, Ontario, Canada
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Tayarani N MH. Applications of artificial intelligence in battling against covid-19: A literature review. CHAOS, SOLITONS, AND FRACTALS 2021; 142:110338. [PMID: 33041533 PMCID: PMC7532790 DOI: 10.1016/j.chaos.2020.110338] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/01/2020] [Indexed: 05/14/2023]
Abstract
Colloquially known as coronavirus, the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), that causes CoronaVirus Disease 2019 (COVID-19), has become a matter of grave concern for every country around the world. The rapid growth of the pandemic has wreaked havoc and prompted the need for immediate reactions to curb the effects. To manage the problems, many research in a variety of area of science have started studying the issue. Artificial Intelligence is among the area of science that has found great applications in tackling the problem in many aspects. Here, we perform an overview on the applications of AI in a variety of fields including diagnosis of the disease via different types of tests and symptoms, monitoring patients, identifying severity of a patient, processing covid-19 related imaging tests, epidemiology, pharmaceutical studies, etc. The aim of this paper is to perform a comprehensive survey on the applications of AI in battling against the difficulties the outbreak has caused. Thus we cover every way that AI approaches have been employed and to cover all the research until the writing of this paper. We try organize the works in a way that overall picture is comprehensible. Such a picture, although full of details, is very helpful in understand where AI sits in current pandemonium. We also tried to conclude the paper with ideas on how the problems can be tackled in a better way and provide some suggestions for future works.
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Affiliation(s)
- Mohammad-H Tayarani N
- Biocomputation Group, School of Computer Science, University of Hertfordshire, Hatfield, AL10 9AB, United Kingdom
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Yamamoto M, Kiso M, Sakai-Tagawa Y, Iwatsuki-Horimoto K, Imai M, Takeda M, Kinoshita N, Ohmagari N, Gohda J, Semba K, Matsuda Z, Kawaguchi Y, Kawaoka Y, Inoue JI. The Anticoagulant Nafamostat Potently Inhibits SARS-CoV-2 S Protein-Mediated Fusion in a Cell Fusion Assay System and Viral Infection In Vitro in a Cell-Type-Dependent Manner. Viruses 2020; 12:E629. [PMID: 32532094 PMCID: PMC7354595 DOI: 10.3390/v12060629] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/29/2022] Open
Abstract
Although infection by SARS-CoV-2, the causative agent of coronavirus pneumonia disease (COVID-19), is spreading rapidly worldwide, no drug has been shown to be sufficiently effective for treating COVID-19. We previously found that nafamostat mesylate, an existing drug used for disseminated intravascular coagulation (DIC), effectively blocked Middle East respiratory syndrome coronavirus (MERS-CoV) S protein-mediated cell fusion by targeting transmembrane serine protease 2 (TMPRSS2), and inhibited MERS-CoV infection of human lung epithelium-derived Calu-3 cells. Here we established a quantitative fusion assay dependent on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S protein, angiotensin I converting enzyme 2 (ACE2) and TMPRSS2, and found that nafamostat mesylate potently inhibited the fusion while camostat mesylate was about 10-fold less active. Furthermore, nafamostat mesylate blocked SARS-CoV-2 infection of Calu-3 cells with an effective concentration (EC)50 around 10 nM, which is below its average blood concentration after intravenous administration through continuous infusion. On the other hand, a significantly higher dose (EC50 around 30 mM) was required for VeroE6/TMPRSS2 cells, where the TMPRSS2-independent but cathepsin-dependent endosomal infection pathway likely predominates. Together, our study shows that nafamostat mesylate potently inhibits SARS-CoV-2 S protein-mediated fusion in a cell fusion assay system and also inhibits SARS-CoV-2 infection in vitro in a cell-type-dependent manner. These findings, together with accumulated clinical data regarding nafamostat's safety, make it a likely candidate drug to treat COVID-19.
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Affiliation(s)
- Mizuki Yamamoto
- Research Center for Asian Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; (M.Y.); (J.G.); (Z.M.); (Y.K.)
| | - Maki Kiso
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; (M.K.); (Y.S.-T.); (K.I.-H.); (M.I.); (Y.K.)
| | - Yuko Sakai-Tagawa
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; (M.K.); (Y.S.-T.); (K.I.-H.); (M.I.); (Y.K.)
| | - Kiyoko Iwatsuki-Horimoto
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; (M.K.); (Y.S.-T.); (K.I.-H.); (M.I.); (Y.K.)
| | - Masaki Imai
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; (M.K.); (Y.S.-T.); (K.I.-H.); (M.I.); (Y.K.)
| | - Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan;
| | - Noriko Kinoshita
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; (N.K.); (N.O.)
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; (N.K.); (N.O.)
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; (M.Y.); (J.G.); (Z.M.); (Y.K.)
| | - Kentaro Semba
- Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan;
| | - Zene Matsuda
- Research Center for Asian Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; (M.Y.); (J.G.); (Z.M.); (Y.K.)
| | - Yasushi Kawaguchi
- Research Center for Asian Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; (M.Y.); (J.G.); (Z.M.); (Y.K.)
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; (M.K.); (Y.S.-T.); (K.I.-H.); (M.I.); (Y.K.)
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
- Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Jun-ichiro Inoue
- Research Center for Asian Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; (M.Y.); (J.G.); (Z.M.); (Y.K.)
- Senior Professor Office, University of Tokyo, Tokyo 113-0033, Japan
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