1
|
Naffeti B, BenAribi W, Kebir A, Diarra M, Schoenhals M, Vigan-Womas I, Dellagi K, BenMiled S. Comparative reconstruction of SARS-CoV-2 transmission in three African countries using a mathematical model integrating immunity data. IJID REGIONS 2024; 10:100-107. [PMID: 38204927 PMCID: PMC10776948 DOI: 10.1016/j.ijregi.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 01/12/2024]
Abstract
Objectives Africa has experienced fewer COVID-19 cases and deaths than other regions, with a contrasting epidemiological situation between countries, raising questions regarding the determinants of disease spread in Africa. Methods We built a susceptible-exposed-infected-recovered model including COVID-19 mortality data where recovery class is structured by specific immunization and modeled by a partial differential equation considering the opposed effects of immunity decline and immunization. This model was applied to Tunisia, Senegal, and Madagascar. Results Senegal and Tunisia experienced two epidemic phases. Initially, infections emerged in naive individuals and were limited by social distancing. Variants of concern (VOCs) were also introduced. The second phase was characterized by successive epidemic waves driven by new VOCs that escaped host immunity. Meanwhile, Madagascar demonstrated a different profile, characterized by longer intervals between epidemic waves, increasing the pool of susceptible individuals who had lost their protective immunity. The impact of vaccination on model parameters in Tunisia and Senegal was evaluated. Conclusions Loss of immunity and vaccination-induced immunity have played crucial role in controlling the African pandemic. SARS-CoV-2 has become endemic now and will continue to circulate in African populations. However, previous infections provide significant protection against severe diseases, thus providing a basis for future vaccination strategies.
Collapse
Affiliation(s)
- Bechir Naffeti
- University of Tunis el Manar, Institut Pasteur de Tunis, Bio-(Informatic, Mathematics and Statistic) BIMS-Lab LR09-IPT16, Tunis, Tunisia
| | - Walid BenAribi
- University of Tunis el Manar, Institut Pasteur de Tunis, Bio-(Informatic, Mathematics and Statistic) BIMS-Lab LR09-IPT16, Tunis, Tunisia
| | - Amira Kebir
- University of Tunis el Manar, Institut Pasteur de Tunis, Bio-(Informatic, Mathematics and Statistic) BIMS-Lab LR09-IPT16, Tunis, Tunisia
- University of Tunis, Institut préparatoire aux études d'ingénieurs de Tunis, Tunis, Tunisia
| | - Maryam Diarra
- Institut Pasteur de Dakar, Epidemiology, Clinical Research and Data Sciences Department, Dakar, Senegal
| | - Matthieu Schoenhals
- Institut Pasteur de Madagascar, Immunology of Infectious Diseases Unit, Antananarivo, Madagascar
| | - Inès Vigan-Womas
- Institut Pasteur de Dakar, Immuno-physiopathology and Infectious Diseases Department, Dakar, Senegal
| | | | - Slimane BenMiled
- University of Tunis el Manar, Institut Pasteur de Tunis, Bio-(Informatic, Mathematics and Statistic) BIMS-Lab LR09-IPT16, Tunis, Tunisia
| |
Collapse
|
2
|
Faye M, Faye MN, Ndiaye B, Diagne MM, Sankhe S, Top NM, Diallo A, Loucoubar C, Dia N, Sall AA, Faye O. Detection of a cluster of Omicron's BA.4 sublineage in Northern Senegal and identification of the first XAS recombinant variant in Senegal. Virus Res 2024; 339:199259. [PMID: 37926155 PMCID: PMC10652113 DOI: 10.1016/j.virusres.2023.199259] [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: 06/14/2023] [Revised: 10/18/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
In Senegal, since its first detection in early March 2020, genomic surveillance of SARS-CoV-2 isolates has led to the identification of the emergence of the Omicron BA.4 and BA.5 sublineages from early June 2022. To investigate the origin of a cluster of cases in Northern Senegal on July 2022, isolates were analysed using Next-generation sequencing and phylogeny. Our data provided evidence of the origin of the cluster of BA.4 cases from a XAS recombinant, that is to date, the first reported sequence of this variant from Senegal. Continuous genomic surveillance of positive SARS-CoV-2 samples is a crucial need.
Collapse
Affiliation(s)
- Martin Faye
- Virology Department, Institut Pasteur de Dakar, 36, avenue Pasteur, Dakar BP220, Senegal.
| | - Modeste Name Faye
- Virology Department, Institut Pasteur de Dakar, 36, avenue Pasteur, Dakar BP220, Senegal
| | - Babacar Ndiaye
- Biomedical Laboratory, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Moussa Moïse Diagne
- Virology Department, Institut Pasteur de Dakar, 36, avenue Pasteur, Dakar BP220, Senegal
| | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, 36, avenue Pasteur, Dakar BP220, Senegal
| | - Ndeye Marième Top
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, 36, avenue Pasteur, Dakar BP220, Senegal
| | - Amadou Alpha Sall
- Virology Department, Institut Pasteur de Dakar, 36, avenue Pasteur, Dakar BP220, Senegal
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, 36, avenue Pasteur, Dakar BP220, Senegal
| |
Collapse
|
3
|
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.
Collapse
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.
| | | |
Collapse
|