Nonlinear dynamics and intermittency in a long-term copepod time series

We consider the nonlinear dynamics of a long-term copepod (small crustaceans) time series sampled weekly in the Mediterranean sea from 1967 to 1992. Such population dynamics display a high variability that we consider here in an interdisciplinary study, using tools borrowed from the field of statistical physics. We analyse the extreme events of male and female abundances, and of the total population, and show that they both have heavy tailed probability density functions (pdf). We provide hyperbolic fits of the form p(x) ∼ 1/xμ+1, and estimate the value of μ using Hill’s estimator. We then study the ratio of male to female abundances, compared to the female abundances. Using conditional probability density functions and conditional averages, we show that this ratio is independent of the female density, when the latter is larger than a given threshold. This property is very useful for modelization. We also consider the product of male to female abundances, which can be ecologically related to the encounters. We show that this product is extremely intermittent, and link its pdf to the female pdf

Molecular diagnosis of COVID-19 in Burkina Faso: successful challenge

COVID-19 has worsened the health situation in Burkina Faso. In fact, the country has known a peak of the second wave, which began in November, and ended around January 2021. Biological diagnosis has played a key role in the management of COVID-19. The aim of this review paper is to address the practical aspects that laboratories have faced in order to meet the challenge of SARS-CoV-2 diagnosis in Burkina Faso. According to international requirements, Burkina Faso has used real-time Reverse Transcription Polymerase Chain Reaction (rRT-PCR) as the “gold standard” for the diagnosis of COVID-19. From March 9, 2020 to July 31, 2021, in Burkina Faso, laboratories involved in COVID-19 diagnosis analyzed 226,189 samples by molecular tests and 2, 352 samples by rapid antigenic tests, whose peak was in January 2021 with 35,984 samples analyzed. The daily average rate of samples analysis was 456.02 tests. The majority of the individuals requesting COVID-19 tests were travelers (62.00%), followed by contact cases (18.42%), suspected cases (7.95%), voluntary screening (7.57%), and 4.06% of other applicants consisting of health care personnel and at-risk patients. In terms of prevention, vaccines are being administered to the general population. However, some efforts must be made to provide automated sample analysis equipment and complete sequencing of SARS-CoV-2 remains among the challenges

Linkage between ACE2 Gene Polymorphisms and SARS-CoV-2 infection in Burkina Faso, sub-Saharan Africa

The ACE2 gene polymorphisms (rs143936283, rs146676783, and rs4646116) in infected and noninfected persons by SARS-CoV-2 in Burkina Faso. Our cross-sectional study population comprised 137 SARS-CoV-2 infected persons and 181 non-infected persons. Three ACE2 gene polymorphisms rs143936283, rs146676783, and rs4646116, were genotyped using the real-time PCR standard TaqMan allelic discrimination technique. The association between SARS-CoV-2 infection and the polymorphisms were evaluated by a binary logistic regression. There was no association between the polymorphisms rs143936283, rs4646116 haplotypes, and SARS-CoV-2 infection in our study population. However, in the female population, the heterozygous genotype CT of rs146676783 increased by two and half the risk (OR=2.58 95%CI (1.2-5.48), p= 0.014) of being infected by SARS-CoV-2. Additionally, carrying the homozygous minor allele (genotype TT) of rs146676783 increased by more than five and half the risk (OR=5.57 95%CI (1.64-18.78), p=0.006) of being infected by SARS-CoV-2 among females. This study showed that the ACE2 gene variant rs146676783 was associated with an increased risk of being infected by SARS-CoV-2 in females, suggesting a need for further investigation to contribute to a better understanding of the African COVID-19 enigma

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

Procréer en temps d'infection à VIH : offre de soins et expériences de femmes en milieu urbain (Burkina Faso)

Cette thèse porte sur la procréation dans le contexte de l'infection à VIH marqué de nos jours par les progrès thérapeutiques notables dans la prise en charge. Elle est construite autour de trois grandes parties qui présentent des éléments à la fois de portée générale et des éléments centrés sur les expériences de procréation de femmes séropositives du Burkina Faso. Dans les associations de lutte contre le VIH et dans les centres de santé, les individus reçoivent de plus en plus, des informations sur la possibilité d'avoir des enfants lorsqu'on est porteur du VIH sous réserve de conditions pour l'essentielles médicales, et parfois des offres d'accompagnement thérapeutique et nutritionnel soutenues par certaines agences. Ces informations et ces offres sont récupérées par les individus notamment les femmes, qui dès lors, organisent, orientent ou construisent non seulement leurs comportements et leurs choix de procréation mais aussi leurs parcours de soins. Ce traitement de la procréation dans le contexte du VIH au Burkina Faso met en lumière un processus de recomposition de la prise en charge du VIH dans les services de santé et dans les associations. Une recomposition caractérisée par une évolution des discours et des représentations, la naissance de nouvelles activités qui font appel à de nouvelles pratiques –pour les soignants–, un renforcement de l'immixtion du médical dans la vie sexuelle et reproductive des individus, et pour les femmes, l'émergence de nouvelles maternités qui, tout en s'inscrivant dans le rapport « maternité-féminité », fait plus de place à la figure du sujet dans les relations familiales et conjugales.This thesis is about the procreation in the context of HIV infection based on remarkable therapeutic progress nowadays in caring people. It's based on three big parts which show at the same time global ranges and elements based on HIV positive women's experience in Burkina Faso. In associations fighting against HIV and health centers, people receive more information on the possibility to have children when they are HIV positive but under the condition of essential medicines, furthermore the therapeutic and nutritional supply is sometimes supported by some agencies. These information and supply are got back by people namely women who once organize direct and build not only their behavior but also their choice of procreation and their distance of caring. This treatment of procreation in the context of HIV in Burkina Faso explains a process of recomposition and taking in charge HIV in health centers. A recomposition characterized by an evolution of speeches, representations and birth of new activities which requires new practices for care givers, a strengthening of interference of medicines in people's sexual and reproductive life. Besides for women, the emergency of new maternity which is written in the report in “maternity-femininity” make more place in the figure of the topic about the family and couple's relationship

Multi-scales fluctuations and extremes in a short and a long term biogeochemical time series recorded in the coastal waters

Cette thèse porte sur l’étude de séries temporelles biogéochimiques à moyen et long terme, de façon à caractériser leurs fluctuations à de multiples échelles, et en particulier leurs extrêmes. Les données a proviennent en grande partie des programmes MAREL et SOMLIT. Le programme MAREL a été mis en œuvre par l’Ifremer et basé sur des mesures à haute fréquence. Le programme SOMLIT est un service d’observation labellisé depuis 1997 par l’INSU. Ces mesures sont effectuées tous les 15 jours, par prélèvement, en un point fixe dans les eaux côtières en Manche. Pour l’analyse de ces séries temporelles, les méthodes utilisées sont empruntées aux domaines de l’analyse numérique et de la turbulence. Cette étude est effectuée en 3 parties. Dans la première partie, l’analyse du spectre de Fourier a permis de mesurer l’influence du forçage physique sur la distribution des paramètres à haute fréquence. Dans la seconde partie, la comparaison entre des données SOMLIT et MAREL recueillies en des endroits très proches à Boulogne-sur-mer a pu montrer une complémentarité mais tout en mettant en évidence le caractère plus informatif du système MAREL. La comparaison entre deux sites distincts en Manche (orientale et occidentale) a permis de déceler les similitudes et les différences dans les teneurs des ratios (N/P/Si ;COP/Chla). Dans la troisième partie, on a pu mettre en évidence l’influence des événements extrêmes du débit de la Seine sur la distribution de certains paramètres biogéochimiques mesurés à Honfleur. Nous avons également mis en évidence dans le cadre de la DCE, l’influence de l’échelle d’étude sur les estimations de certaines métriques nécessaires à la définition du bon état écologique à partir des données issues de la haute fréquence.This thesis focuses on the study of biogeochemical time series in order to characterize the dynamics of their fluctuations on a wide range of scales, and in particular their extremes. The databases analyzed here are mainly provided by the MAREL and SOMLIT programmes. The MAREL program is a network of automatic measuring devices monitoring coastal marine environments implemented by Ifremer. The SOMLIT is a French national program operated by INSU. The measurements are made once every two weeks on the fixed stations. In order to analyze these time series, methods have been borrowed from the fields of numerical analysis and turbulence. The study was conducted in three parts. In the first part, we consider the high frequency time series. The Fourier spectral analysis reveals the influence of physical forcing on the distribution of the parameters. The second part of the study compares SOMLIT and MAREL results recorded from sites near Boulogne-sur-mer. The comparison of the two measuring systems (manual and automatic) showed that while they are complementary, the automatic MAREL system is more informative. The probability density functions (pdfs) of some ratios reveal extreme values in their dynamics. These pdfs reveal in all cases a hyperbolic behavior in the tail probability of the ratios. In the third part, we consider the influence of extremes events of the Seine flow on the distribution of some biogeochemical parameters. This section is also concerned with the analysis of data at high frequency in order to estimate of water masses state in the English Channel within the context of the Water Framework Directive (WFD)