Institute of Research for Development

Several years of moored turbulence measurements from χpods at three sites in the equatorial cold tongues of Atlantic and Pacific Oceans yield new insights into proxy estimates of turbulence that specifically target the cold tongues. They also reveal previously unknown wind dependencies of diurnally-varying turbulence in the near-critical stratified shear layers beneath the mixed layer and above the core of the Equatorial Undercurrent that we have come to understand as deep cycle (DC) turbulence. Isolated by the mixed layer above, theDClayer is only indirectly linked to surface forcing. Yet it varies diurnally in concert with daily changes in heating/cooling. Diurnal composites computed from 10-minute averaged data at fixed χpod depths show that transitions from daytime to nighttime mixing regimes are increasingly delayed with weakening wind stress, τ. These transitions are also delayed with respect to depth such that they follow a descent rate of roughly 6 meters per hour, independent of τ. We hypothesize that this wind-dependent delay is a direct result of wind-dependent diurnal warm layer deepening, which acts as the trigger to DC layer instability by bringing shear from the surface downward but at rates much slower than 6 meters per hour. This delay in initiation of DC layer instability contributes to a reduction in daily averaged values of turbulence dissipation. Both the absence of descending turbulence in the sheared DC layer prior to arrival of the diurnal warm layer shear and the magnitude of the subsequent descent rate after arrival are roughly predicted by laboratory experiments on entrainment in stratified shear flows.

Plastics materials which are used in our daily life especially for packaging applications are derived from petrochemicals. Though these plastic materials satisfy the required properties of packaging materials in terms of strength, water resistance, and durability, they are not biodegradable and stay in landfills for plenty of years. This causes serious environmental threat and pollution. Owing to this, biodegradable plastics have been emerged as an alternative to conventional plastics. However, most of the biodegrade plastics are dependent on forest reserves even some may affect food supply. Nevertheless, agar and polyvinyl alcohol (PVA) neither causes deforestation nor affect the food stock. Though agar and PVA neither causes deforestation nor affect the food supply, they have high water absorption and a moderate tensile strength. This restricts the use of these polymers for applications. Researchers have used physicochemical modification methods to improve the properties of biodegradable polymers with due attention of agar and PVA. This review presents the basics of polymers, biodegradable polymers, chemistry of biodegradation, environmental impacts of biodegradable polymers, and the physicochemical modification of biodegradable polymers with a special focus of agar and PVA.

The lagging fertility transition in West Africa has important repercussions for global population growth but remains poorly understood. Inspired by Caldwell and colleagues' fertility transition framework, as well as by subsequent research, we examine diversity in women's holistic childbearing trajectories in Niakhar, Senegal, between the early 1960s and 2018 using a sequence analysis approach. We evaluate the prevalence of different trajectories, their contribution to overall fertility levels, and their association with women's socioeconomic and cultural characteristics. Four trajectories were observed: "high fertility," "delayed entry," "truncated," and "short." While the high fertility trajectory was most prevalent across cohorts, delayed entry grew in importance. The high fertility trajectory was more common among women born between 1960 and 1969 and was followed less often by divorced women and those from polygynous households. Women with primary education and those from higher status groups were more likely to experience delayed entry. The truncated trajectory was associated with lack of economic wealth, polygynous households, and caste membership. A short trajectory was related to lack of agropastoral wealth, divorce, and possibly secondary sterility. Our study advances knowledge on fertility transitions in Niakhar-and Sahelian West African contexts more generally-by showing the diversity of childbearing trajectories within high fertility regional contexts.

Introduction During the COVID-19 crisis, researchers had to collect data remotely. Telephone surveys and interviews can quickly gather data from a distance without heavy expense. Although interviewer-administered telephone surveys (IATS) can accommodate the needs of international public health research, the literature on their use during infectious disease outbreaks is scarce. This scoping review aimed to map the characteristics of IATS during infectious disease outbreaks. Methods IATS conducted principally during infectious disease outbreaks and answered by informants at least 18 years old were searched from PubMed and EBSCO. There was a manual addition of relevant documents identified during an initial search. Overall trends were reported using different groupings, including WHO regions, and study details were compared before and during the COVID-19 pandemic. Results 70 IATS published between 2003 and 2022 were identified. 57.1% were conducted during the COVID-19 pandemic. Among 30 IATS conducted before the COVID-19 pandemic in the world, only 3.3% were carried out in low-income and middle-income countries (LMICs). This percentage of studies in LMICs out of all the IATS rose to 32.5% during the pandemic. The share of qualitative studies grew from 6.7% before the COVID-19 outbreak to 32.5% during the outbreak. IATS performed during the COVID-19 pandemic focused on more diverse, specific population groups, such as patients and healthcare professionals. Mobile phones are increasingly used for IATS over time. Conclusion IATS are used globally with high frequency in the Western Pacific Region and high-income countries. Technical and financial challenges continue to exist, and assessments of inclusiveness and representativeness should be carefully conducted. A lack of details related to methods was observed, and this scoping review urges researchers using this data collection method in the future to specify how they executed IATS for better use and more efficient deployment.

Infectious diseases caused by parasites (malaria, leishmaniasis, trypanosomiasis, filariasis…), viruses (chikungunya, dengue, phlebovirus, etc [...]

Background We aimed to estimate the SARS-CoV-2 seroprevalence among the general population in Conakry, Guinea and Yaounde, Cameroon after the COVID-19 Omicron wave. Methods We conducted population-based age-stratified seroprevalence surveys in Conakry, Guinea and Yaounde, Cameroon (May and June 2022). We collected demographic, epidemiologic information and dried blood spot (DBS) samples that were tested for SARS-CoV-2 IgG antibodies using recombinant nucleocapsid (NC) and spike (SP) proteins with a Luminex technology. Results Samples were obtained from 1386 and 1425 participants in Guinea and Cameroon, respectively. The overall age-standardized SARS-CoV-2 IgG seroprevalence against SP and NC was 71.57% (95% CI: 67.48-75.33) in Guinea and 74.71% (95% CI: 71.99-77.25) in Cameroon. Seroprevalence increased significantly with age categories. Female participants were more likely to be seropositive than male. The seroprevalence in unvaccinated participants was 69.6% (95%CI; 65.5-73.41) in Guinea and 74.8% (95%CI; 72.04-77.38) in Cameroon). In multivariate analysis, only age, sex and education degree were independently associated with seropositivity. Conclusion These findings show a high community transmission after the different epidemiological waves including Omicron especially among people above 40 years old. In addition, our results suggest that the spread of SARS-CoV-2 has been underestimated as a significant proportion of the population has already contracted the virus and that vaccine strategies should focus on vulnerable populations.

The aim of the study was to assess the impact of composting on the release dynamics and partitioning of geogenic nickel (Ni), chromium (Cr) and anthropogenic copper (Cu) and zinc (Zn) in a mixture of sewage sludge and green waste in New Caledonia. In contrast to Cu and Zn, total concentrations of Ni and Cr were very high, tenfold the French regulation, due to their sourcing from Ni and Cr enriched ultramafic soils. The novel method used to assess the behavior of trace metals during composting involved combining EDTA kinetic extraction and BCR sequential extraction. BCR extraction revealed marked mobility of Cu and Zn: more than 30% of the total concentration of these trace metals was found in the mobile fractions (F1 + F2) whereas Ni and Cr were mainly found in the residual fraction (F4). Composting increased the proportion of the stable fractions (F3 + F4) of all four trace metals studied. Interestingly, only EDTA kinetic extraction was able to identify the increase in Cr mobility during composting, Cr mobility being driven by the more labile pool (Q1). However, the total mobilizable pool (Q1 + Q2) of Cr remained very low, < 1% of total Cr content. Among the four trace metals studied, only Ni showed significant mobility, the (Q1 + Q2) pool represented almost half the value given in the regulatory guidelines. This suggests possible environmental and ecological risks associated with spreading our type of compost that require further investigation. Beyond New Caledonia, our results also raise the question of the risks in other Ni-rich soils worldwide.

Microplastics (MPs) are increasingly being studied because they have become ubiquitous in aquatic and terrestrial environments. However, little is known about the negative effects of co-contamination by polypropylene microplastic (PP MPs) and heavy metal mixtures on terrestrial environment and biota. This study assessed the adverse effects of co-exposure to PP MPs and heavy metal mixture (Cu2+, Cr6+, and Zn2+) on soil quality and the earthworm Eisenia fetida. Soil samples were collected in the Dong Cao catchment, near Hanoi, Vietnam, and analyzed for changes in extracellular enzyme activity and carbon, nitrogen, and phosphorus availability in the soil. We determined the survival rate of earthworms Eisenia fetida that had ingested MPs and two doses of heavy metals (the environmental level — 1 × — and its double — 2 ×). Earthworm ingestion rates were not significantly impacted by the exposure conditions, but the mortality rate for the 2 × exposure conditions was 100%. Metal-associated PP MPs stimulated the activities of β-glucosidase, β-N-acetyl glucosaminidase, and phosphatase enzymes in soil. Principle component analysis showed that these enzymes were positively correlated with Cu2+ and Cr6+ concentrations, but negatively correlated with microbial activity. Zn2+ showed no correlation with soil extracellular enzyme activity or soil microbial activity. Our results showed that co-exposure of earthworms to MPs and heavy metals had no impact on soil nitrogen and phosphorus but caused a decrease in total soil carbon content, with a possible associated risk of increased CO2 emissions.

Background: The control of onchocerciasis currently relies on annual distribution of single dose ivermectin. Because ivermectin has minimal effects on the adult parasite, mass drug administration (MDA) campaigns against onchocerciasis require at least 15 years of annual uninterrupted ivermectin distribution. Mathematical models have predicted that short-term disruption of MDA (as was seen during COVID-19) could impacted the microfilaridermia prevalence depending on the pre-control endemicity and the histories of treatment, requiring corrective measures (such as biannual MDA) to mitigate the effect on onchocerciasis elimination. Field evidence supporting this prediction, however, has yet to be gathered. This study aimed to assess the impact of ~2 years disruption of MDA on onchocerciasis transmission indicators. Methodology: A cross-sectional survey was carried out in 2021 in seven villages of Bafia and Ndikinimeki, two health districts located in the Centre Region, Cameroon, where MDA has been ongoing for two decades, but interrupted in 2020 as a response to the COVID-19 pandemic. Volunteers aged 5 years and above were enrolled for clinical and parasitological examinations for onchocerciasis. Data were compared with pre-COVID-19 prevalence and intensity of infection from the same communities to measure changes over time. Principal findings: A total of 504 volunteers (50.3% males), aged 5-99 years (Median: 38; IQR: 15-54) was enrolled in the two health districts. The overall prevalence of microfilaridermia in 2021 was similar in Ndikinimeki health district (12.4%; 95% CI: 9.7-15.6) and Bafia health district (15.1%; 95% CI: 11.1-19.8) (p-value = 0.16). Microfilaridermia prevalence were either similar between 2018 and 2021 in the communities of Ndikinimeki health district (19.3% vs 12.8% (p = 0.057) for Kiboum 1; and 23.7% vs 21.4% (p = 0.814) for Kiboum 2), or higher in 2019 compared to 2021 in the communities of Bafia health district (33.3% vs 20.0% (p = 0.035) for Biatsota). The mean microfilarial densities in these communities dropped from 5.89 (95% CI: 4.77-7.28) mf/ss to 2.4 (95% CI: 1.68-3.45) mf/ss (p-value < 0.0001), and from 4.81 (95% CI: 2.77-8.31) mf/ss to 4.13 (95% CI: 2.49-6.86) mf/ss (p-value < 0.02) in Bafia and Ndikinimeki health districts, respectively. Community Microfilarial Load (CMFL) dropped from 1.08-1.33 mf/ss in 2019 to 0.052-0.288 mf/ss in 2021 in Bafia health district while remaining stable in the Ndikinimeki health district. Conclusion/significance: The continued decline in prevalence and CMFL observed ~2 years after MDA disruption is consistent with mathematical predictions (ONCHOSIM) and shows that additional efforts and resources are not needed to mitigate the effects of short-term MDA disruption in highly endemic settings prior to intervention with long treatment histories.

Rice yellow mottle virus (RYMV) is a major biotic constraint to rice cultivation in Africa. RYMV shows a high genetic diversity. Viral lineages were defined according to the coat protein (CP) phylogeny. Varietal selection is considered as the most efficient way to manage RYMV. Sources of high resistance were identified mostly in accessions of the African rice species, Oryza glaberrima. Emergence of resistance-breaking (RB) genotypes was observed in controlled conditions. The RB ability was highly contrasted, depending on the resistance sources and on the RYMV lineages. A molecular marker linked to the adaptation to susceptible and resistant O. glaberrima was identified in the viral protein genome-linked (VPg). By contrast, as no molecular method was available to identify the hypervirulent lineage able to overcome all known resistance sources, plant inoculation assays were still required. Here, we designed specific RT-PCR primers to infer the RB abilities of RYMV isolates without greenhouse experiments or sequencing steps. These primers were tested and validated on 52 isolates, representative of RYMV genetic diversity. The molecular tools described in this study will contribute to optimizing the deployment strategy of resistant lines, considering the RYMV lineages identified in fields and their potential adaptability.

Background: Soil Transmitted Helminths (STH) infect over 1.5 billion people globally and are associated with anemia and stunting, resulting in an annual toll of 1.9 million Disability-Adjusted Life Years (DALYs). School-based deworming (SBD), via mass drug administration (MDA) campaigns with albendazole or mebendazole, has been recommended by the World Health Organization to reduce levels of morbidity due to STH in endemic areas. DeWorm3 is a cluster-randomized trial, conducted in three study sites in Benin, India, and Malawi, designed to assess the feasibility of interrupting STH transmission with community-wide MDA as a potential strategy to replace SBD. This analysis examines data from the DeWorm3 trial to quantify discrepancies between school-level reporting of SBD and gold standard individual-level survey reporting of SBD. Methodology/principal findings: Population-weighted averages of school-level SBD calculated at the cluster level were compared to aggregated individual-level SBD estimates to produce a Mean Squared Error (MSE) estimate for each study site. In order to estimate individual-level SBD coverage, these MSE values were applied to SBD estimates from the control arm of the DeWorm3 trial, where only school-level reporting of SBD coverage had been collected. In each study site, SBD coverage in the school-level datasets was substantially higher than that obtained from individual-level datasets, indicating possible overestimation of school-level SBD coverage. When applying observed MSE to project expected coverages in the control arm, SBD coverage dropped from 89.1% to 70.5% (p-value < 0.001) in Benin, from 97.7% to 84.5% (p-value < 0.001) in India, and from 41.5% to 37.5% (p-value < 0.001) in Malawi. Conclusions/significance: These estimates indicate that school-level SBD reporting is likely to significantly overestimate program coverage. These findings suggest that current SBD coverage estimates derived from school-based program data may substantially overestimate true pediatric deworming coverage within targeted communities. Trial registration: NCT03014167.

This paper presents Peru’s unique experience in measuring governance through household surveys. Launched at the initiative of the authors in the early 2000s, and coordinated since then by one of them, this survey module is, to the best of our knowledge, the most ambitious (in terms of the length of series, statistical properties, ownership) ever carried out on a global scale by a national institute of statistics (INEI). The Peruvian experience has contributed to both demonstrating the validity of the approach chosen to measure governance, prior to the adoption of SDG 16 in 2015, and supporting the regular production of indicators on governance, primarily those of SDG 16. The first part provides a brief overview of the Peruvian context and demonstrates the importance of monitoring governance issues in general, and in this country in particular. In the second part, we describe the main methodological options and innovations adopted by INEI since the launch of the module. The third part illustrates the analytical potential of the approach based on a few empirical examples, while the fourth part presents various ways through which the data has been used so far and some institutional challenges faced in promoting the use of governance statistics. Finally, we conclude by drawing key lessons from this initiative and outlining prospects for the future.

Following the emergence of SARS-CoV-2, cases of pets infected with variants circulating among humans were reported. In order to evaluate the occurrence of SARS-CoV-2 circulation among pets in the Republic of the Congo, we conducted a ten-month study of dogs and cats living in COVID-19-positive households in Brazzaville and neighboring localities. Real-time PCR and the Luminex platform were used to detect SARS-CoV-2 RNA and antibodies to SARS-CoV-2 RBD and S proteins, respectively. Our results show for the first time the simultaneous circulation of several variants of SARS-CoV-2, including viruses from clades 20A and 20H and a putative recombinant variant between viruses from clades 20B and 20H. We found a high seroprevalence of 38.6%, with 14% of tested pets positive for SARS-CoV-2 RNA. Thirty-four percent of infected pets developed mild clinical signs, including respiratory and digestive signs, and shed the virus for about one day to two weeks. These results highlight the potential risk of SARS-CoV-2 interspecies transmission and the benefits of a “One Health” approach that includes SARS-CoV-2 diagnosis and surveillance of viral diversity in pets. This approach aims to prevent transmission to surrounding wildlife as well as spillback to humans.

Context Farmland on steep slopes is increasingly abandoned because it is unsuitable for most forms of modern agriculture. Succession back to forest is often slow or inexistent due to over-exploitation. Observations and measurements in Dong Cao catchment 47.9 ha Vietnam, started under farming and continued after abandonment: 20 years of uninterrupted monitoring of soil, water, land use and vegetation were integrated in this study. Objective Our aim is to identify the specific combination of soil features and agricultural practices that are responsible for fast, slow or blocked succession. We differentiate between the recovery of forest structure, relatively easy, and recovery of the original species composition, more difficult. Methods Multivariate analysis of vegetation data produced plant communities in a gradient of complexity. Using classic statistics, we sought relationships between environmental variables, land use and vegetation. Results Forest recovery failed the first 10 years, then part of the catchment developed forest. Land use explained best the distribution of plant communities over the catchment, slope and soil features were less related. Cassava cropping seriously slowed down the succession to closed forest. During abandonment soil carbon stocks (0–15 cm depth) increased with about 3% per year. Conclusion Starting from weedy thickets (2002) we distinguished two successional pathways: a positive pathway towards increased resemblance with the original Lowland forest via broken forest to closed deciduous to closed evergreen forest; a negative pathway away from the original forest species composition to degraded shrub land and low grass. Livestock was related to the negative pathway.

La expansión de la agricultura industrial en zonas rurales de Bogotá ha reducido la diversidad de plantas cultivadas por las familias campesinas, y ha transformado sus formas de vida y las relaciones bioculturales. Ello afecta los conocimientos ambientales de carácter local y las prácticas de uso y manejo de la agrobiodiversidad. Aunque se ha documentado en varios estudios la presencia de nichos agrobiodiversos, tales como huertas y jardines campesinos que persisten en medio de paisajes homogeneizados, es necesario ampliar la identificación y el análisis de las funciones culturales y agroecológicas que los caracterizan. En este artículo se detallan los conocimientos locales vinculados a huertas y jardines en términos de sus funciones y aportes a la conservación y recuperación de la agrobiodiversidad. Se realizaron entrevistas semiestructuradas a seis sabedores locales y en veinticinco hogares, además de observaciones etnográficas y recorridos etnobotánicos. Con la información obtenida, se caracterizaron las funciones de los nichos de agrobiodiversidad, según las experiencias cotidianas de sus cuidadores y cuidadoras. Se identificaron ocho funciones agroecológicas, 249 nombres comunes asociados al mismo número de especies vegetales, y varios saberes sobre usos y manejos. Se concluye explicando las posibles articulaciones entre los nichos y los paisajes circundantes, para entender su aporte potencial a la transformación territorial y a la conectividad de la estructura ecológica rural de Bogotá.

Human endogenous retroviruses (HERVs) are LTR retrotransposons that are present in the human genome. Among them, members of the HERV-K (HML-2) group are suspected to play a role in the development of different types of cancer, including lung, ovarian, and prostate cancer, as well as leukemia. Acute myeloid leukemia (AML) is an important disease that causes 1% of cancer deaths in the United States and has a survival rate of 28.7%. Here, we describe a method for assessing the statistical association between HERV-K (HML-2) transposable element insertion polymorphisms (or TIPs) and AML, using whole-genome sequencing and read mapping using TIP_finder software. Our results suggest that 101 polymorphisms involving HERV-K (HML-2) elements were correlated with AML, with a percentage between 44.4 to 56.6%, most of which (70) were located in the region from 8q24.13 to 8q24.21. Moreover, it was found that the TRIB1, LRATD2, POU5F1B, MYC, PCAT1, PVT1, and CCDC26 genes could be displaced or fragmented by TIPs. Furthermore, a general method was devised to facilitate analysis of the correlation between transposable element insertions and specific diseases. Finally, although the relationship between HERV-K (HML-2) TIPs and AML remains unclear, the data reported in this study indicate a statistical correlation, as supported by the χ² test with p-values < 0.05.

Sandy spits are quite frequent phenomena at river mouths but remain relatively rare for the largest rivers considering that their hydrodynamics generally prevent the creation of such sedimentary structures. In 2003 a trench was dug on this spit to relieve City of Saint-Louis from flooding, the river immediately used this depression as a new access to the Ocean, causing the disappearance of the major part of the sand-spit named the Langue de Barbarie. Since then the spit is rebuilding progressively and hence is a formidable laboratory for studying sedimentary dynamics. This study, carried out as part of the MEPELS project (Modeling and Evolution of Sandy Beaches and Coasts), makes it possible to review the methods for implementing the models and their validation because the geographical and temporal scales of the variations and the multiple processes involved in play seem too complex to be all included in a single model. The surface calculation method applied here will thus be able to know in the near future volume of sediment, thus allowing to obtain the variability of sedimentary fluxes at the scale of a satellite image, a region, a country or a continent. Shoreline data show that the recurrence of measurements has a strong impact on the perception of coastal dynamics. This relativizes the results based on comparisons of data acquired over short periods and poses a real problem of the conclusions about results of modeling that is often carried out on exceptional short-term processes.

Objective: In Canada and globally, the COVID-19 pandemic has increased social inequalities in health (SIH), furthering the vulnerability of certain groups and communities. Contact-tracing is a cornerstone intervention with COVID-19 prevention and control programs. The aim of this study was to describe whether and how SIH were considered during the design of the COVID-19 contact-tracing intervention in Montreal. Methods: This study is part of the multi-country research program HoSPiCOVID, looking at the resilience of public health systems during the COVID-19 pandemic. A descriptive qualitative study was carried out in Montreal, based on a "bricolage" conceptual framework describing the consideration for SIH in intervention and policy design. Qualitative data were collected using semi-structured interviews with 16 public health practitioners, recruited using both purposive and snowball sampling. Data were analyzed thematically, both inductively and deductively. Results: According to participants, SIH were not initially considered during the design of the contract-tracing intervention in Montreal. The participants were frustrated by the Minister of Health's initial resistance to integrating SIH into their public health response. However, adaptations were gradually made to better meet the needs of underserved populations. Conclusion: There is a need for a clear and common vision of SIH within the public health system. Decision-makers need to consider SIH prior to designing public health interventions in order for these not to further increase SIH in the future, especially in the face of a health crisis.