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Ndiaye YD, Wong W, Thwing J, Schaffner SF, Brenneman KV, Tine A, Diallo MA, Deme AB, Sy M, Bei AK, Thiaw AB, Daniels R, Ndiaye T, Gaye A, Ndiaye IM, Toure M, Gadiaga N, Sene A, Sow D, Garba MN, Yade MS, Dieye B, Diongue K, Zoumarou D, Ndiaye A, Gomis JF, Fall FB, Ndiop M, Diallo I, Sene D, Macinnis B, Seck MC, Ndiaye M, Ngom B, Diedhiou Y, Mbaye AM, Ndiaye L, Sy N, Badiane AS, Hartl DL, Wirth DF, Volkman SK, Ndiaye D. Two decades of molecular surveillance in Senegal reveal rapid changes in known drug resistance mutations over time. Malar J 2024; 23:205. [PMID: 38982475 PMCID: PMC11234717 DOI: 10.1186/s12936-024-05024-8] [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: 04/17/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Drug resistance in Plasmodium falciparum is a major threat to malaria control efforts. Pathogen genomic surveillance could be invaluable for monitoring current and emerging parasite drug resistance. METHODS Data from two decades (2000-2020) of continuous molecular surveillance of P. falciparum parasites from Senegal were retrospectively examined to assess historical changes in malaria drug resistance mutations. Several known drug resistance markers and their surrounding haplotypes were profiled using a combination of single nucleotide polymorphism (SNP) molecular surveillance and whole genome sequence based population genomics. RESULTS This dataset was used to track temporal changes in drug resistance markers whose timing correspond to historically significant events such as the withdrawal of chloroquine (CQ) and the introduction of sulfadoxine-pyrimethamine (SP) in 2003. Changes in the mutation frequency at Pfcrt K76T and Pfdhps A437G coinciding with the 2014 introduction of seasonal malaria chemoprevention (SMC) in Senegal were observed. In 2014, the frequency of Pfcrt K76T increased while the frequency of Pfdhps A437G declined. Haplotype-based analyses of Pfcrt K76T showed that this rapid increase was due to a recent selective sweep that started after 2014. DISCUSSION (CONCLUSION) The rapid increase in Pfcrt K76T is troubling and could be a sign of emerging amodiaquine (AQ) resistance in Senegal. Emerging AQ resistance may threaten the future clinical efficacy of artesunate-amodiaquine (ASAQ) and AQ-dependent SMC chemoprevention. These results highlight the potential of molecular surveillance for detecting rapid changes in parasite populations and stress the need to monitor the effectiveness of AQ as a partner drug for artemisinin-based combination therapy (ACT) and for chemoprevention.
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Affiliation(s)
- Yaye D Ndiaye
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
| | - Julie Thwing
- Malaria Branch, Division of Parasitic Diseases and Malaria, Global Health Center, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen F Schaffner
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Katelyn Vendrely Brenneman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
| | - Abdoulaye Tine
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Mamadou A Diallo
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Awa B Deme
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Mouhamad Sy
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Amy K Bei
- Yale School of Public Health, 60 College St, New Haven, CT, 06510, USA
| | - Alphonse B Thiaw
- Department of Biochemistry and Functional Genomics, Sherbrooke University, 2500 Bd de L'Universite, Sherbrooke, QC, J1K 2R1, Canada
| | - Rachel Daniels
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Tolla Ndiaye
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Amy Gaye
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Ibrahima M Ndiaye
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Mariama Toure
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Nogaye Gadiaga
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Aita Sene
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Djiby Sow
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Mamane N Garba
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Mamadou S Yade
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Baba Dieye
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Khadim Diongue
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Daba Zoumarou
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Aliou Ndiaye
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Jules F Gomis
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Fatou B Fall
- National Malaria Control Programme (NMCP), 25270, Dakar, Senegal
| | - Medoune Ndiop
- National Malaria Control Programme (NMCP), 25270, Dakar, Senegal
| | - Ibrahima Diallo
- National Malaria Control Programme (NMCP), 25270, Dakar, Senegal
| | - Doudou Sene
- National Malaria Control Programme (NMCP), 25270, Dakar, Senegal
| | - Bronwyn Macinnis
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Mame C Seck
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Mouhamadou Ndiaye
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Bassirou Ngom
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Younouss Diedhiou
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Amadou M Mbaye
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Lamine Ndiaye
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Ngayo Sy
- Service de Lutte Antiparasitaire (SLAP), Thiès, Senegal
| | - Aida S Badiane
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
- Simmons University, 300 The Fenway, Boston, MA, 02115, USA.
| | - Daouda Ndiaye
- International Research Training Center On Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, 16477, Dakar, Senegal
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
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Ndiaye YD, Wong W, Thwing J, Schaffner SS, Tine A, Diallo MA, Deme A, Sy M, Bei AK, Thiaw AB, Daniels R, Ndiaye T, Gaye A, Ndiaye IM, Toure M, Gadiaga N, Sene A, Sow D, Garba MN, Yade MS, Dieye B, Diongue K, Zoumarou D, Ndiaye A, Gomis J, Fall FB, Ndiop M, Diallo I, Sene D, Macinnis B, Seck MC, Ndiaye M, Badiane AS, Hartl DL, Volkman SK, Wirth DF, Ndiaye D. Two decades of molecular surveillance in Senegal reveal changes in known drug resistance mutations associated with historical drug use and seasonal malaria chemoprevention. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.24.23288820. [PMID: 37163114 PMCID: PMC10168519 DOI: 10.1101/2023.04.24.23288820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Drug resistance in Plasmodium falciparum is a major threat to malaria control efforts. We analyzed data from two decades (2000-2020) of continuous molecular surveillance of P. falciparum parasite strains in Senegal to determine how historical changes in drug administration policy may have affected parasite evolution. We profiled several known drug resistance markers and their surrounding haplotypes using a combination of single nucleotide polymorphism (SNP) molecular surveillance and whole-genome sequence (WGS) based population genomics. We observed rapid changes in drug resistance markers associated with the withdrawal of chloroquine and introduction of sulfadoxine-pyrimethamine in 2003. We also observed a rapid increase in Pfcrt K76T and decline in Pfdhps A437G starting in 2014, which we hypothesize may reflect changes in resistance or fitness caused by seasonal malaria chemoprevention (SMC). Parasite populations evolve rapidly in response to drug use, and SMC preventive efficacy should be closely monitored.
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Affiliation(s)
- Yaye Die Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
| | - Julie Thwing
- Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA ,30329, USA
| | - Stephen S Schaffner
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Abdoulaye Tine
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mamadou Alpha Diallo
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Awa Deme
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mouhammad Sy
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Amy K Bei
- Yale School of Public Health, 60 College St, New Haven, CT 06510
| | - Alphonse B Thiaw
- Department of biochemistry and Functional Genomics, Sherbrooke University, 2500 Bd de l'Universite, Sherbrooke, QC J1K 2R1, Canada
| | - Rachel Daniels
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester MA 01605
| | - Tolla Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Amy Gaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Ibrahima Mbaye Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mariama Toure
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Nogaye Gadiaga
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Aita Sene
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Djiby Sow
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mamane N Garba
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mamadou Samba Yade
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Baba Dieye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Khadim Diongue
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Daba Zoumarou
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Aliou Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Jules Gomis
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Fatou Ba Fall
- Yale School of Public Health, 60 College St, New Haven, CT 06510
| | - Medoune Ndiop
- National Malaria Control Program (NMCP), Rue FN 20, Dakar 25270, Senegal
| | - Ibrahima Diallo
- National Malaria Control Program (NMCP), Rue FN 20, Dakar 25270, Senegal
| | - Doudou Sene
- National Malaria Control Program (NMCP), Rue FN 20, Dakar 25270, Senegal
| | - Bronwyn Macinnis
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Mame Cheikh Seck
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mouhamadou Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Aida S Badiane
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138 USA
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Simmons University, 300 The Fenway, Boston, MA, 02115, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Daouda Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
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Chechter M, Dutra da Silva GM, E Costa RAP, Miklos TG, Antonio da Silva N, Lorber G, Vasconcellos Mota NR, Dos Santos Cortada AP, de Nazare Lima da Cruz L, de Melo PMP, de Souza BC, Emmerich FG, de Andrade Zanotto PM, Aaron Scheinberg M. Evaluation of patients treated by telemedicine in the beginning of the COVID-19 pandemic in São Paulo, Brazil: A non-randomized clinical trial preliminary study. Heliyon 2023; 9:e15337. [PMID: 37073324 PMCID: PMC10089670 DOI: 10.1016/j.heliyon.2023.e15337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/30/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023] Open
Abstract
We performed a pilot open-label, non-randomized controlled clinical trial in a clinic in São Paulo, Brazil in the beginning of the COVID-19 pandemic. "This medical pilot project was carried out during the pandemic of a new and unknown agent. It was necessary to find a new and safe therapeutic approach for pathogens with high potential for severity and contamination. The repositioning of safe and accessible pre-existing and approved medications and the telemedicine approach improved treated covid patients' symptoms and reduced the risk of disease transmission. The emergency application of a new medical technology was the major limitation of the study. This innovative care model is a low-cost safe strategy, and we understand that applicability can be expanded to other regions in emergency situations." The 187 patients of the study (mean age of 37.6 ± 15,6 years) were divided into four groups: (1) asymptomatic, (2) mild symptoms, (3) moderate symptoms and (4) severe symptoms and were followed up for five days. A drug intervention was performed in group 3 and the patients of Group 4 were oriented to seek hospital care. Of all the patients, 23.0% were asymptomatic, 29.4% reported mild symptoms, 43.9% moderate symptoms and 3.7% severe symptoms. Three patients were hospitalized and discharged after recovery. Our results indicate that the use of telemedicine with diagnosis and drug treatment is a safe and effective strategy to reduce overload of health services and the exposure of healthcare providers and the population. The patients that initiated the treatment in the early stages of the disease presented satisfactory clinical response, reducing the need of face-to-face consultations and hospitalizations. The patients who followed the protocol treatment for COVID-19 with hydroxychloroquine and azithromycin for five days presented statistically significant improvement of clinical symptoms when compared to moderate patients who opted for not following the protocol (p < 0.05) and to all no treatment patients (p < 0.001).
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Affiliation(s)
| | | | | | - Thomas Gabriel Miklos
- Department of Obstetrics and Gynecology - Santa Casa of Sao Paulo Medical School, Sao Paulo (FCMSCSP), Brazil
| | | | | | | | | | | | | | | | | | - Paolo Marinho de Andrade Zanotto
- Laboratory of Molecular Evolution and Bioinformatics (LEMB), Department of Microbiology, Institute of Biomedical Sciences (ICB-II), University of Sao Paulo, Sao Paulo, Brazil
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Vigan-Womas I, Spadoni JL, Poiret T, Taïeb F, Randrianarisaona F, Faye R, Mbow AA, Gaye A, Dia N, Loucoubar C, Ny Mioramalala DJ, Ratovoson R, Randremanana RV, Sall AA, Seydi M, Noirel J, Moreau G, Simon A, Holenya P, Meyniel JP, Zagury JF, Schoenhals M. Linear epitope mapping of the humoral response against SARS-CoV-2 in two independent African cohorts. Sci Rep 2023; 13:782. [PMID: 36646780 PMCID: PMC9842613 DOI: 10.1038/s41598-023-27810-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Profiling of the antibody responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) proteins in African populations is scarce. Here, we performed a detailed IgM and IgG epitope mapping study against 487 peptides covering SARS-CoV-2 wild-type structural proteins. A panel of 41 pre-pandemic and 82 COVID-19 RT-PCR confirmed sera from Madagascar and Senegal were used. We found that the main 36 immunodominant linear epitopes identified were (i) similar in both countries, (ii) distributed mainly in the Spike and the Nucleocapsid proteins, (iii) located outside the RBD and NTD regions where most of the reported SARS-CoV-2 variant mutations occur, and (iv) identical to those reported in European, North American, and Asian studies. Within the severe group, antibody levels were inversely correlated with the viral load. This first antibody epitope mapping study performed in patients from two African countries may be helpful to guide rational peptide-based diagnostic assays or vaccine development.
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Affiliation(s)
- Inès Vigan-Womas
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal.
| | - Jean-Louis Spadoni
- Laboratoire Génomique, Bioinformatique, et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, Paris, France
| | - Thomas Poiret
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Fabien Taïeb
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Rokhaya Faye
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Adji Astou Mbow
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Aboubacry Gaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Rila Ratovoson
- Institut Pasteur de Madagascar, BP 1274, 101, Antananarivo, Madagascar
| | | | - Amadou Alpha Sall
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moussa Seydi
- Service des Maladies Infectieuses et Tropicales, Fann University Hospital Center, Dakar, Senegal
| | - Josselin Noirel
- Laboratoire Génomique, Bioinformatique, et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, Paris, France
| | - Gabriel Moreau
- Bioinformatics Team, Peptinov, Hôpital Cochin, 27 Rue du Fbg Saint-Jacques, 75014, Paris, France
| | - Arnaud Simon
- Laboratoire Génomique, Bioinformatique, et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, Paris, France
| | | | - Jean-Philippe Meyniel
- Bioinformatics Department, ISoft, Parc des Algorithmes, Bâtiment Euclide, Route de l'Orme, 91190, Saint-Aubin, France
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique, et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, Paris, France.
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Singh DD, Han I, Choi EH, Yadav DK. A Clinical Update on SARS-CoV-2: Pathology and Development of Potential Inhibitors. Curr Issues Mol Biol 2023; 45:400-433. [PMID: 36661514 PMCID: PMC9857284 DOI: 10.3390/cimb45010028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome) is highly infectious and causes severe acute respiratory distress syndrome (SARD), immune suppression, and multi-organ failure. For SARS-CoV-2, only supportive treatment options are available, such as oxygen supportive therapy, ventilator support, antibiotics for secondary infections, mineral and fluid treatment, and a significant subset of repurposed effective drugs. Viral targeted inhibitors are the most suitable molecules, such as ACE2 (angiotensin-converting enzyme-2) and RBD (receptor-binding domain) protein-based inhibitors, inhibitors of host proteases, inhibitors of viral proteases 3CLpro (3C-like proteinase) and PLpro (papain-like protease), inhibitors of replicative enzymes, inhibitors of viral attachment of SARS-CoV-2 to the ACE2 receptor and TMPRSS2 (transmembrane serine proteinase 2), inhibitors of HR1 (Heptad Repeat 1)-HR2 (Heptad Repeat 2) interaction at the S2 protein of the coronavirus, etc. Targeting the cathepsin L proteinase, peptide analogues, monoclonal antibodies, and protein chimaeras as RBD inhibitors interferes with the spike protein's ability to fuse to the membrane. Targeting the cathepsin L proteinase, peptide analogues, monoclonal antibodies, and protein chimaeras as RBD inhibitors interferes with the spike protein's ability to fuse to the membrane. Even with the tremendous progress made, creating effective drugs remains difficult. To develop COVID-19 treatment alternatives, clinical studies are examining a variety of therapy categories, including antibodies, antivirals, cell-based therapy, repurposed diagnostic medicines, and more. In this article, we discuss recent clinical updates on SARS-CoV-2 infection, clinical characteristics, diagnosis, immunopathology, the new emergence of variant, SARS-CoV-2, various approaches to drug development and treatment options. The development of therapies has been complicated by the global occurrence of many SARS-CoV-2 mutations. Discussion of this manuscript will provide new insight into drug pathophysiology and drug development.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
- Correspondence: (I.H.); (D.K.Y.); Tel.: +82-2-597-0365 (I.H. & D.K.Y.)
| | - Eun-Ha Choi
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Dharmendra Kumar Yadav
- Department of R&D Center, Arontier Co., Seoul 06735, Republic of Korea
- Correspondence: (I.H.); (D.K.Y.); Tel.: +82-2-597-0365 (I.H. & D.K.Y.)
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Bepouka B, Bandubuila Kaja P, Situakibanza H. Treatment and case fatality rate of COVID-19 in Africa. J Public Health Afr 2022; 13:1931. [DOI: 10.4081/jphia.2022.1931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 05/16/2022] [Indexed: 11/05/2022] Open
Abstract
In Africa, the treatment of COVID-19 depends on each country. Several protocols are observed with real results that we described in this study. The objective of this review was to describe the treatment of COVID-19 and the case fatality rate in African countries, by reviewing the literature on treatment and case fatality in African countries whose data was available through the internet during the writing period until February 7, 2021. The majority of African countries had a treatment based on hydroxychloroquine or chloroquine + azithromycin, used in varying doses depending on the country. The lethality in Africa remains low compared to European and American countries. The same treatment being used in some northern countries does not fully explain the low case fatality.
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Diarra M, Kebir A, Talla C, Barry A, Faye J, Louati D, Opatowski L, Diop M, White LJ, Loucoubar C, Miled SB. Non-pharmaceutical interventions and COVID-19 vaccination strategies in Senegal: a modelling study. BMJ Glob Health 2022; 7:bmjgh-2021-007236. [PMID: 35193893 PMCID: PMC8882665 DOI: 10.1136/bmjgh-2021-007236] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/04/2022] [Indexed: 11/18/2022] Open
Abstract
Background When vaccines against the novel COVID-19 were available in Senegal, many questions were raised. How long should non-pharmaceutical interventions (NPIs) be maintained during vaccination roll-out? What are the best vaccination strategies? Methods In this study, we used an age-structured dynamic mathematical model. This model uses parameters based on SARS-CoV-2 virus, information on different types of NPIs, epidemiological and demographic data, some parameters relating to hospitalisations and vaccination in Senegal. Results In all scenarios explored, the model predicts a larger third epidemic wave of COVID-19 in terms of new cases and deaths than the previous waves. In a context of limited vaccine supply, vaccination alone will not be sufficient to control the epidemic, and the continuation of NPIs is necessary to flatten the epidemic curve. Assuming 20% of the population have been vaccinated, the optimal period to relax NPIs would be a few days from the last peak. Regarding the prioritisation of age groups to be vaccinated, the model shows that it is better to vaccinate individuals aged 5–60 years and not just the elderly (over 60 years) and those in high-risk groups. This strategy could be more cost-effective for the government, as it would reduce the high costs associated with hospitalisation. In terms of vaccine distribution, the optimal strategy would be to allocate full dose to the elderly. If vaccine doses are limited, half dose followed by full dose would be sufficient for people under 40 years because whether they receive half or full dose, the reduction in hospitalisations would be similar and their death-to-case ratio is very low. Conclusions This study could be presented as a decision support tool to help devise strategies to control the COVID-19 pandemic and help the Ministry of Health to better manage and allocate the available vaccine doses.
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Affiliation(s)
- Maryam Diarra
- Epidemiology, Clinical Recherche and Data Science, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amira Kebir
- Bio-Informatics, Mathematics, Statistics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Cheikh Talla
- Epidemiology, Clinical Recherche and Data Science, Institut Pasteur de Dakar, Dakar, Senegal
| | - Aliou Barry
- Epidemiology, Clinical Recherche and Data Science, Institut Pasteur de Dakar, Dakar, Senegal
| | - Joseph Faye
- Epidemiology, Clinical Recherche and Data Science, Institut Pasteur de Dakar, Dakar, Senegal
| | - Dorra Louati
- Bio-Informatics, Mathematics, Statistics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Lulla Opatowski
- Epidemiology and Modelling of Antibiotic Evasion Unit, Institut Pasteur, Paris, France
| | - Mamadou Diop
- Epidemiology, Clinical Recherche and Data Science, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Lisa J White
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Cheikh Loucoubar
- Epidemiology, Clinical Recherche and Data Science, Institut Pasteur de Dakar, Dakar, Senegal
| | - Slimane Ben Miled
- Bio-Informatics, Mathematics, Statistics, Institut Pasteur de Tunis, Tunis, Tunisia
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