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Article ; Online: Comparative reconstruction of SARS-CoV-2 transmission in three African countries using a mathematical model integrating immunity data.

Naffeti, Bechir / BenAribi, Walid / Kebir, Amira / Diarra, Maryam / Schoenhals, Matthieu / Vigan-Womas, Inès / Dellagi, Koussay / BenMiled, Slimane

IJID regions

2023 Volume 10, Page(s) 100–107

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 ... ...

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.
Language	English
Publishing date	2023-11-23
Publishing country	England
Document type	Journal Article
ISSN	2772-7076
ISSN (online)	2772-7076
DOI	10.1016/j.ijregi.2023.11.011
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Article ; Online: High-dimensional supervised classification in a context of non-independence of observations to identify the determining SNPs in a phenotype.

Gaye, Aboubacry / Diongue, Abdou Ka / Komen, Lionel Nanguep / Diallo, Amadou / Sylla, Seydou Nourou / Diarra, Maryam / Talla, Cheikh / Loucoubar, Cheikh

Infectious Disease Modelling

2023 Volume 8, Issue 4, Page(s) 1079–1087

Abstract: This work addresses the problem of supervised classification for highly correlated high-dimensional data describing non-independent observations to identify SNPs related to a phenotype. We use a general penalized linear mixed model with a single random ... ...

Abstract	This work addresses the problem of supervised classification for highly correlated high-dimensional data describing non-independent observations to identify SNPs related to a phenotype. We use a general penalized linear mixed model with a single random effect that performs simultaneous SNP selection and population structure adjustment in high-dimensional prediction models. Specifically, the model simultaneously selects variables and estimates their effects, taking into account correlations between individuals. Single nucleotide polymorphisms (SNPs) are a type of genetic variation and each SNP represents a difference in a single DNA building block, namely a nucleotide. Previous research has shown that SNPs can be used to identify the correct source population of an individual and can act in isolation or simultaneously to impact a phenotype. In this regard, the study of the contribution of genetics in infectious disease phenotypes is of great importance. In this study, we used uncorrelated variables from the construction of blocks of correlated variables done in a previous work to describe the most related observations of the dataset. The model was trained with 90% of the observations and tested with the remaining 10%. The best model obtained with the generalized information criterion (GIC) identified the SNP named rs2493311 located on the first chromosome of the gene called PRDM16 ((PR/SET domain 16)) as the most decisive factor in malaria attacks.
Language	English
Publishing date	2023-09-09
Publishing country	China
Document type	Journal Article
ZDB-ID	3015225-2
ISSN	2468-0427 ; 2468-2152
ISSN (online)	2468-0427
ISSN	2468-2152
DOI	10.1016/j.idm.2023.09.002
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Article ; Online: Comparative Reconstruction of SARS-CoV-2 transmission in three African countries using a mathematical model integrating immunity data.

neffeti, bechir / kebir, amira / ben aribi, walid / Diarra, Maryam / schoenhals, matthieu / vigan-womas, ines / dellagi, koussay / ben miled, slimane

medRxiv

Abstract: Objectives: Africa has experienced fewer coronavirus disease 2019 (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. ... ...

Abstract	Objectives: Africa has experienced fewer coronavirus disease 2019 (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. Method: 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. Finding: 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 in Tunisia and Senegal on model parameters was evaluated. Interpretation: Loss of immunity and vaccination-induced immunity have played crucial role in controlling the African pandemic. Severe acute respiratory syndrome coronavirus 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.
Keywords	covid19
Language	English
Publishing date	2023-07-08
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.07.07.23292215
Database	COVID19

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Article ; Online: Seroprevalence of Crimean-Congo Hemorrhagic Fever Virus and Rift Valley Fever Virus in human population in Senegal from October to November 2020.

Sankhe, Safietou / Talla, Cheikh / Thiam, Mareme Seye / Faye, Martin / Barry, Mamadou Aliou / Diarra, Maryam / Dia, Moussa / Ndiaye, Oumar / Sembene, Pape Mbacke / Diop, Boly / Fall, Gamou / Faye, Oumar / Faye, Ousmane / Diagne, Moussa Moise / Loucoubar, Cheikh

IJID regions

2023 Volume 7, Page(s) 216–221

Abstract: Objectives: Rift Valley Fever and Crimean-Congo Hemorrhagic Fever are two infections classified among the emerging diseases to be monitored with highest priority. Studies undertaken in human and animals have shown endemicity of these two arboviruses in ... ...

Abstract	Objectives: Rift Valley Fever and Crimean-Congo Hemorrhagic Fever are two infections classified among the emerging diseases to be monitored with highest priority. Studies undertaken in human and animals have shown endemicity of these two arboviruses in several African countries. However, most of the investigations were carried out on domestic cattle and the studies conducted on human populations are either outdated or limited to a small number of well-known endemic areas. It is then critical to better evaluate the burden of these viruses in Senegal at a national scale. Methods: This work relies on a previous seroprevalence survey undertaken in all regions of Senegal at the end of 2020. The existing biobank was used to determine the immunoglobulin G [IgG] Rift Valley Fever and Crimean-Congo Hemorrhagic Fever seroprevalences by indirect enzyme-linked immunosorbent assay. Results: The crude seroprevalences of Rift Valley Fever and Crimean-Congo Hemorrhagic Fever were 3.94% and 0.7% respectively, with the northern and central part of the countries as the main exposed areas. However, acute infections reported in both high and low exposed regions suggest sporadic introductions. Conclusions: This study gives updated information and could be of interest to support the stakeholders in the management of these zoonoses.
Language	English
Publishing date	2023-03-31
Publishing country	England
Document type	Journal Article
ISSN	2772-7076
ISSN (online)	2772-7076
DOI	10.1016/j.ijregi.2023.03.016
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Article ; Online: Non-polio enteroviruses circulation in acute flaccid paralysis cases and sewage in Senegal from 2013 to 2021.

Ndiaye, Ndack / Kébé, Ousmane / Diarra, Maryam / Thiaw, Fatou Diène / Dia, Mohamed / Dia, NDongo / Sall, Amadou Alpha / Fall, Malick / Faye, Ousmane / Faye, Martin

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2023 Volume 138, Page(s) 54–62

Abstract: Objectives: Several factors can cause acute flaccid paralysis cases including non-polio enteroviruses. In Senegal, few studies on non-polio enteroviruses (NPEV) have been performed.: Methods: Our study assess the molecular epidemiology of non-polio ... ...

Abstract	Objectives: Several factors can cause acute flaccid paralysis cases including non-polio enteroviruses. In Senegal, few studies on non-polio enteroviruses (NPEV) have been performed. Methods: Our study assess the molecular epidemiology of non-polio enteroviruses in Senegal from 2013 to 2021 through the previously existing programs for surveillance of polioviruses. Results: A total of 3815 stool samples and 281 sewage samples were collected. After virus isolation by cell culture, non-polio enteroviruses-positive isolates were confirmed by reverse transcriptase-quantitative polymerase chain reaction. Following this detection, the positive samples were subjected to molecular characterization. Our data showed that 15.22% and 52.66% were positive in cell culture for non-polio enteroviruses in acute flaccid paralysis surveillance and environmental surveillance, respectively. These non-polio enteroviruses-positive isolates were detected all year round but tend to unequal peaks of circulation, and the age group 0-5 years was more vulnerable to infection (84.4%). Genetic characterization revealed the circulation of enteroviruses species infecting humans (Enterovirus A - Enterovirus D): Enterovirus A (29.2%) and Enterovirus B (63.1%) isolates from both the acute flaccid paralysis surveillance and environmental surveillance while Enterovirus C (5.3%) and Enterovirus D (2.4%) were only isolated from the acute flaccid paralysis surveillance. However, the highly prevalent Enterovirus B species from the acute flaccid paralysis surveillance included echovirus 7 and echovirus 13, whereas coxsackievirus A6 was the predominant species from the environmental surveillance. Conclusion: This first 8-year period study of NPEV in Senegal showed that NPEV represent important viral etiologies associated with acute flaccid paralysis cases and circulating in environmental surveillance in Senegal and highlighted the need to promote effective long-term strategies for monitoring of non-polio enteroviruses infections.
MeSH term(s)	Humans ; Infant, Newborn ; Infant ; Child, Preschool ; Sewage ; Senegal/epidemiology ; Paralysis/epidemiology ; Enterovirus/genetics ; Enterovirus Infections/epidemiology ; Enterovirus B, Human ; Antigens, Viral
Chemical Substances	Sewage ; Antigens, Viral
Language	English
Publishing date	2023-11-22
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2023.11.020
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Article ; Online: Shifting Patterns of Influenza Circulation during the COVID-19 Pandemic, Senegal.

Lampros, Alexandre / Talla, Cheikh / Diarra, Maryam / Tall, Billo / Sagne, Samba / Diallo, Mamadou Korka / Diop, Boly / Oumar, Ibrahim / Dia, Ndongo / Sall, Amadou Alpha / Barry, Mamadou Aliou / Loucoubar, Cheikh

Emerging infectious diseases

2023 Volume 29, Issue 9, Page(s) 1808–1817

Abstract: Historically low levels of seasonal influenza circulation were reported during the first years of the COVID-19 pandemic and were mainly attributed to implementation of nonpharmaceutical interventions. In tropical regions, influenza's seasonality differs ... ...

Abstract	Historically low levels of seasonal influenza circulation were reported during the first years of the COVID-19 pandemic and were mainly attributed to implementation of nonpharmaceutical interventions. In tropical regions, influenza's seasonality differs largely, and data on this topic are scarce. We analyzed data from Senegal's sentinel syndromic surveillance network before and after the start of the COVID-19 pandemic to assess changes in influenza circulation. We found that influenza shows year-round circulation in Senegal and has 2 distinct epidemic peaks: during January-March and during the rainy season in August-October. During 2021-2022, the expected January-March influenza peak completely disappeared, corresponding to periods of active SARS-CoV-2 circulation. We noted an unexpected influenza epidemic peak during May-July 2022. The observed reciprocal circulation of SARS-CoV-2 and influenza suggests that factors such as viral interference might be at play and should be further investigated in tropical settings.
MeSH term(s)	Humans ; COVID-19/epidemiology ; SARS-CoV-2 ; Senegal/epidemiology ; Influenza, Human/epidemiology ; Pandemics
Language	English
Publishing date	2023-08-22
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2909.230307
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Article ; Online: Reemergence of Sylvatic Dengue Virus Serotype 2 in Kedougou, Senegal, 2020.

Emerging infectious diseases

2024 Volume 30, Issue 4, Page(s) 770–774

Abstract: In 2020, a sylvatic dengue virus serotype 2 infection outbreak resulted in 59 confirmed dengue cases in Kedougou, Senegal, suggesting those strains might not require adaptation to reemerge into urban transmission cycles. Large-scale genomic surveillance ... ...

Abstract	In 2020, a sylvatic dengue virus serotype 2 infection outbreak resulted in 59 confirmed dengue cases in Kedougou, Senegal, suggesting those strains might not require adaptation to reemerge into urban transmission cycles. Large-scale genomic surveillance and updated molecular diagnostic tools are needed to effectively prevent dengue virus infections in Senegal.
MeSH term(s)	Humans ; Dengue Virus/genetics ; Senegal/epidemiology ; Serogroup ; Environment ; Dengue/epidemiology
Language	English
Publishing date	2024-03-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid3004.231301
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Article ; Online: Analysis of contact tracing data showed contribution of asymptomatic and non-severe infections to the maintenance of SARS-CoV-2 transmission in Senegal.

Diarra, Maryam / Ndiaye, Ramatoulaye / Barry, Aliou / Talla, Cheikh / Diagne, Moussa Moise / Dia, Ndongo / Faye, Joseph / Sarr, Fatoumata Diene / Gaye, Aboubacry / Diallo, Amadou / Cisse, Mamadou / Dieng, Idrissa / Fall, Gamou / Tall, Adama / Faye, Oumar / Faye, Ousmane / Sall, Amadou A / Loucoubar, Cheikh

Scientific reports

2023 Volume 13, Issue 1, Page(s) 9121

Abstract: During the COVID-19 pandemic in Senegal, contact tracing was done to identify transmission clusters, their analysis allowed to understand their dynamics and evolution. In this study, we used information from the surveillance data and phone interviews to ... ...

Abstract	During the COVID-19 pandemic in Senegal, contact tracing was done to identify transmission clusters, their analysis allowed to understand their dynamics and evolution. In this study, we used information from the surveillance data and phone interviews to construct, represent and analyze COVID-19 transmission clusters from March 2, 2020, to May 31, 2021. In total, 114,040 samples were tested and 2153 transmission clusters identified. A maximum of 7 generations of secondary infections were noted. Clusters had an average of 29.58 members and 7.63 infected among them; their average duration was 27.95 days. Most of the clusters (77.3%) are concentrated in Dakar, capital city of Senegal. The 29 cases identified as super-spreaders, i.e., the indexes that had the most positive contacts, showed few symptoms or were asymptomatic. Deepest transmission clusters are those with the highest percentage of asymptomatic members. The correlation between proportion of asymptomatic and degree of transmission clusters showed that asymptomatic strongly contributed to the continuity of transmission within clusters. During this pandemic, all the efforts towards epidemiological investigations, active case-contact detection, allowed to identify in a short delay growing clusters and help response teams to mitigate the spread of the disease.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/epidemiology ; Contact Tracing ; Pandemics ; Senegal/epidemiology
Language	English
Publishing date	2023-06-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-35622-6
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Article ; Online: Observed versus estimated actual trend of COVID-19 case numbers in Cameroon: A data-driven modelling.

Sandie, Arsène Brunelle / Tejiokem, Mathurin Cyrille / Faye, Cheikh Mbacké / Hamadou, Achta / Abah, Aristide Abah / Mbah, Serge Sadeuh / Tagnouokam-Ngoupo, Paul Alain / Njouom, Richard / Eyangoh, Sara / Abanda, Ngu Karl / Diarra, Maryam / Ben Miled, Slimane / Tchuente, Maurice / Tchatchueng-Mbougua, Jules Brice

Infectious Disease Modelling

2023 Volume 8, Issue 1, Page(s) 228–239

Abstract: Controlling the COVID-19 outbreak remains a challenge for Cameroon, as it is for many other countries worldwide. The number of confirmed cases reported by health authorities in Cameroon is based on observational data, which is not nationally ... ...

Abstract	Controlling the COVID-19 outbreak remains a challenge for Cameroon, as it is for many other countries worldwide. The number of confirmed cases reported by health authorities in Cameroon is based on observational data, which is not nationally representative. The actual extent of the outbreak from the time when the first case was reported in the country to now remains unclear. This study aimed to estimate and model the actual trend in the number of COVID -19 new infections in Cameroon from March 05, 2020 to May 31, 2021 based on an observed disaggregated dataset. We used a large disaggregated dataset, and multilevel regression and poststratification model was applied prospectively for COVID-19 cases trend estimation in Cameroon from March 05, 2020 to May 31, 2021. Subsequently, seasonal autoregressive integrated moving average (SARIMA) modeling was used for forecasting purposes. Based on the prospective MRP modeling findings, a total of about 7450935 (30%) of COVID-19 cases was estimated from March 05, 2020 to May 31, 2021 in Cameroon. Generally, the reported number of COVID-19 infection cases in Cameroon during this period underestimated the estimated actual number by about 94 times. The forecasting indicated a succession of two waves of the outbreak in the next two years following May 31, 2021. If no action is taken, there could be many waves of the outbreak in the future. To avoid such situations which could be a threat to global health, public health authorities should effectively monitor compliance with preventive measures in the population and implement strategies to increase vaccination coverage in the population.
Language	English
Publishing date	2023-02-08
Publishing country	China
Document type	Journal Article
ZDB-ID	3015225-2
ISSN	2468-0427 ; 2468-2152
ISSN (online)	2468-0427
ISSN	2468-2152
DOI	10.1016/j.idm.2023.02.001
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Article: Non-pharmaceutical interventions and COVID-19 vaccination strategies in Senegal: a modelling study.

Diarra, Maryam / Kebir, Amira / Talla, Cheikh / Barry, Aliou / Faye, Joseph / Louati, Dorra / Opatowski, Lulla / Diop, Mamadou / White, Lisa J / Loucoubar, Cheikh / Miled, Slimane Ben

BMJ global health

2022 Volume 7, Issue 2

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?: ... ...

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.
MeSH term(s)	Adolescent ; Adult ; Aged ; COVID-19 ; COVID-19 Vaccines ; Child ; Child, Preschool ; Humans ; Middle Aged ; Pandemics ; SARS-CoV-2 ; Senegal/epidemiology ; Vaccination ; Young Adult
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2022-02-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2059-7908
ISSN	2059-7908
DOI	10.1136/bmjgh-2021-007236
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