The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Development of assisted road navigation by the drainage network

International audienc

Urban expansion of Korhogo City (Côte d’Ivoire) using gis and nocturnal remote sensing

Abstract Temporal data series of stable Artificial Lights At Night (ALAN) obtained from sources such as DMSP/OLS and VIIRS/DNB provide valuable insights into the dynamics of urban expansion. This study introduces a novel methodology for characterizing urban boundaries, which combines textural analysis utilizing the Co-occurrence matrix and urban surface delineation employing the Wombling contour detection algorithm. Applying this method to the city of Korhogo in northern Côte d'Ivoire, the findings reveal an irregular and gradual evolution of urban surfaces between 1992 and 2012, with a rate of change of 35 km2. However, starting from 2012, a rapid urbanization process is observed, continuing until 2020, characterized by an evolution rate of approximately 45 km2. Considering the significant urban expansion witnessed in the city of Korhogo, it is imperative to implement appropriate urban management strategies and measures for ecosystem protection

Spatial assessment of nighttime anthropization in the Comoé National Park in Côte d’Ivoira (West Africa)

Protected areas play a crucial role in preserving biological diversity, providing ecosystem services, and regulating hydroclimatic processes. However, the environmental balance of these areas is increasingly under threat due to rapid population growth, high demand for natural resources, and the effects of global warming. To address this, sustainable management of protected areas is essential. This study aims to develop a methodology for monitoring and assessing levels of nocturnal anthropogenic aggression in the Comoé National Park (CNP) in Côte d’Ivoire. By using geospatial data from the Day/Night Band of the Visible Infrared Imaging Radiometer Suite (VIIRS/DNB), the study characterizes the nocturnal anthropization of CNP through the use of several indices. First, light reflectance density is used to identify nighttime light emission foci. Second, the lighted area density index (LADI) is employed to understand the nature of nocturnal activities taking place within CNP, as indicated by artificial light at night (ALAN). Finally, the light intensity index (LII) is used to evaluate the degree of influence of nocturnal anthropogenic activities on biodiversity. The study also found important activities through LADI and observed a high level of light pollution in CNP. Ultimately, the findings of this study indicate that there is a significant level of nocturnal anthropization within CNP, highlighting the need for effective management and conservation efforts in the area

Observed Changes in Rainfall and Characteristics of Extreme Events in Côte d’Ivoire (West Africa)

International audienceThis study evaluates how the characteristics of daily rainfall and extreme events in Côte d’Ivoire changed during 1961–2015 using the rain gauge observation network of the National Meteorological Service (SODEXAM). The results indicate that the northern and southern parts of Cote d’Ivoire experienced a change from a wet to a dry period, with cut-offs in 1982 and 1983, respectively. In the northern part, this dry period was marked by a decrease in rainfall intensity, the length of wet spells, and the contribution of heavy and extreme rainfall, as well as an increase in the number of rainy days and a decrease in the length of dry spells. Over the southern part, this dry period was marked by an increase in the maximum length of dry spells associated with an increase in the maximum 1-day and 5-day precipitation events. The western part of Côte d’Ivoire experienced a late cut-off from the wet to dry period in 2000; the dry period was associated with a decrease in the number of rainy days, rainfall intensities, and maximum length of wet spells. Changes in the central part of Cote d’Ivoire presented high variability, and trends were less marked, even though a cut-off from a wet to dry period was detected in 1991. This study shows that Côte d’Ivoire, which is located in a subhumid and humid region and has an economy dependent on agriculture (especially cash crops, which comprise 60% of the GDP), is experiencing dry spells that are increasing in frequency and length. Combined with deforestation to increase production, this situation could lead to desertification and compromise the sustainable development goals of the country. The contribution of heavy rainfall was found to increase during the last 15 years, increasing the overall risk of floods, especially in urban areas where city authorities and populations are not prepared, thereby threatening infrastructure and human security

Effect of isoniazid preventive therapy on risk of death in west African, HIV-infected adults with high CD4 cell counts: long-term follow-up of the Temprano ANRS 12136 trial

International audienc

Effect of isoniazid preventive therapy on risk of death in west African, HIV-infected adults with high CD4 cell counts: long-term follow-up of the Temprano ANRS 12136 trial

Background: Temprano ANRS 12136 was a factorial 2 × 2 trial that assessed the benefits of early antiretroviral therapy (ART; ie, in patients who had not reached the CD4 cell count threshold used to recommend starting ART, as per the WHO guidelines that were the standard during the study period) and 6-month isoniazid preventive therapy (IPT) in HIV-infected adults in Côte d'Ivoire. Early ART and IPT were shown to independently reduce the risk of severe morbidity at 30 months. Here, we present the efficacy of IPT in reducing mortality from the long-term follow-up of Temprano. Methods: For Temprano, participants were randomly assigned to four groups (deferred ART, deferred ART plus IPT, early ART, or early ART plus IPT). Participants who completed the trial follow-up were invited to participate in a post-trial phase. The primary post-trial phase endpoint was death, as analysed by the intention-to-treat principle. We used Cox proportional models to compare all-cause mortality between the IPT and no IPT strategies from inclusion in Temprano to the end of the follow-up period. Findings: Between March 18, 2008, and Jan 5, 2015, 2056 patients (mean baseline CD4 count 477 cells per μL) were followed up for 9404 patient-years (Temprano 4757; post-trial phase 4647). The median follow-up time was 4·9 years (IQR 3·3–5·8). 86 deaths were recorded (Temprano 47 deaths; post-trial phase 39 deaths), of which 34 were in patients randomly assigned IPT (6-year probability 4·1%, 95% CI 2·9–5·7) and 52 were in those randomly assigned no IPT (6·9%, 5·1–9·2). The hazard ratio of death in patients who had IPT compared with those who did not have IPT was 0·63 (95% CI, 0·41 to 0·97) after adjusting for the ART strategy (early vs deferred), and 0·61 (0·39–0·94) after adjustment for the ART strategy, baseline CD4 cell count, and other key characteristics. There was no evidence for statistical interaction between IPT and ART (pinteraction=0·77) or between IPT and time (pinteraction=0·94) on mortality. Interpretation: In Côte d'Ivoire, where the incidence of tuberculosis was last reported as 159 per 100 000 people, 6 months of IPT has a durable protective effect in reducing mortality in HIV-infected people, even in people with high CD4 cell counts and who have started ART. Funding: National Research Agency on AIDS and Viral Hepatitis (ANRS)