Comparative evaluation of automated KingFisher Flex Purification System 96 (ThermoFisher Scientific) and manual QIAamp Viral RNA Mini Kit (Qiagen) extraction methods for SARS-CoV-2

Background: The extraction step of the viral material of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) influences the quality of reverse transcriptase-polymerase chain reaction (RT-PCR) results in diagnosis of coronavirus disease 2019 (COVID-19). The purpose of this cross-sectional study was to evaluate the diagnostic performance of the automated extraction system "KingFisher Flex Purification System 96 (ThermoFisher)" compared to the manual method with the "QIAamp Viral RNA Mini Kit (Qiagen)". Methodology: From October to December 2020, comparative diagnostic evaluation of two methods of SARSCoV-2 RNA extraction methods was conducted on 159 fresh and 120 frozen nasopharyngeal and oropharyngeal specimens collected from travellers and suspected cases or contacts of COVID-19 patients in Burkina Faso. The FastPlexTM Triplex 1-Step COVID 19 Detection Kit (RT-PCR, RNA extraction free) (Precigenome LLC) was used to amplify on the same PCR plate, RNA extracts from manual QIAamp Viral RNA Mini Kit and automated KingFisher Flex Purification System 96 (ThermoFisher) using the QuantStudio5 thermal cycler (Applied Biosystems). Analysis of the diagnostic performance of the SARS-CoV-2 RT-PCR assay following RNA extraction by the two methods was done using an online OpenEpi software. Results: For fresh samples, the study found a slightly higher RT-PCR positivity rate following manual extraction (12.6%) than automated extraction (9.4%). For frozen samples, the positivity rate was far higher for manual (38.33%) than automated extraction method (20.83%). The results show that the performance of the automated extraction was inferior when compared to the manual extraction for both fresh samples (sensitivity 35%, specificity 94.2%) and frozen samples (sensitivity 43.5%, specificity 93.2%). However, using McNemar Chi-square with Yates correction, there was no significant difference in positivity rate of RT-PCR (x2=0.76, p=0.38) between the two extraction methods for the fresh samples, but there was a significant difference (x2=12.9, p= 0.0003) in the extraction of the frozen samples. Conclusion: The results of this study showed that KingFisher Flex Purification System 96 (ThermoFisher) automatic extraction method was less sensitive and specific than QIAamp Viral RNA Mini Kit (Qiagen) manual extraction method. This information can serve as guide to laboratories in the choice of RNA extraction methods to use for RT-PCR detection of SARS-CoV-2

Malaria mortality in Africa and Asia: evidence from INDEPTH health and demographic surveillance system sites.

BACKGROUND: Malaria continues to be a major cause of infectious disease mortality in tropical regions. However, deaths from malaria are most often not individually documented, and as a result overall understanding of malaria epidemiology is inadequate. INDEPTH Network members maintain population surveillance in Health and Demographic Surveillance System sites across Africa and Asia, in which individual deaths are followed up with verbal autopsies. OBJECTIVE: To present patterns of malaria mortality determined by verbal autopsy from INDEPTH sites across Africa and Asia, comparing these findings with other relevant information on malaria in the same regions. DESIGN: From a database covering 111,910 deaths over 12,204,043 person-years in 22 sites, in which verbal autopsy data were handled according to the WHO 2012 standard and processed using the InterVA-4 model, over 6,000 deaths were attributed to malaria. The overall period covered was 1992-2012, but two-thirds of the observations related to 2006-2012. These deaths were analysed by site, time period, age group and sex to investigate epidemiological differences in malaria mortality. RESULTS: Rates of malaria mortality varied by 1:10,000 across the sites, with generally low rates in Asia (one site recording no malaria deaths over 0.5 million person-years) and some of the highest rates in West Africa (Nouna, Burkina Faso: 2.47 per 1,000 person-years). Childhood malaria mortality rates were strongly correlated with Malaria Atlas Project estimates of Plasmodium falciparum parasite rates for the same locations. Adult malaria mortality rates, while lower than corresponding childhood rates, were strongly correlated with childhood rates at the site level. CONCLUSIONS: The wide variations observed in malaria mortality, which were nevertheless consistent with various other estimates, suggest that population-based registration of deaths using verbal autopsy is a useful approach to understanding the details of malaria epidemiology

Antioxidant properties and subchronic toxicity of the standardized extract of LAMIC, a phytomedicine prototype based on aqueous extracts from trunk bark of Lannea microcarpa Engl and K. Krause

Aims: This study investigated the antioxidant activity and the 90 days subchronic toxicity of the standardized LAMIC phytomedicine prototype based on aqueous extracts from Lannea microcarpa trunk bark. Methods: Three spectrophotometric methods were used to evaluated the antioxidant activity of LAMIC which were 2,2-Diphenyl-1-picrylhydrazyl (DPPH) free radical, 2,2’-azinobis(3-ethylbenzolin-6-sulphonate) (ABTS) radical scavenging assays and ferric reducing antioxidant power (FRAP) assays. For the standardized LAMIC subchronic toxicity study, male and female Wistar rats were used by daily oral administration at doses of 500, 1000 and 1500 mg/kg bw consecutively for 90 days. Results: The LAMIC extract exhibit better inhibitory activity against DPPH radical than ABTS radical with respective IC50 values of 45.38±3.21 µg/mL and 66.45±18.76 µg/mL, while FRAP assay exhibit antioxidant activity of 211.34±15.92 mmol EAA/g. Subchronic oral administration of LAMIC was well-tolerated at all tested doses. No behavioral and physiological changes and mortality were observed. The LAMIC extract did not present any impact on general hematological parameters and biochemical parameters. Moreover, no significant changes were raised in organ and body weight of treated groups compared to the Control group. Conclusion: These results support that LAMIC prototype was a valuable source of natural antioxidants and no toxicity was associated to its long terms oral consumption in rats indicating a potential application as a cardiovascular protective formulation. Keywords: LAMIC–Lannea microcarpa–Standardization–Antioxidant–Subchronic toxicity. &nbsp

Immune Reconstitution During the First Year of Antiretroviral Therapy of HIV-1-Infected Adults in Rural Burkina Faso

There are no data on the outcome of highly active antiretroviral therapy (HAART) in HIV-infected adults in rural Burkina Faso. We therefore assessed CD4+ T-cell counts and HIV-1 plasma viral load (VL), the proportion of naive T-cells (co-expressing CCR7 and CD45RA) and T-cell activation (expression of CD95 or CD38) in 61 previously untreated adult patients from Nouna, Burkina Faso, at baseline and 2 weeks, 1, 3, 6, 9 and 12 months after starting therapy. Median CD4+ T-cell counts increased from 174 (10th-90th percentile: 33-314) cells/µl at baseline to 300 (114- 505) cells/µl after 3 months and 360 (169-562) cells/µl after 12 months of HAART. Median VL decreased from 5.8 (4.6- 6.6) log10 copies/ml at baseline to 1.6 (1.6-2.3) log10 copies/ml after 12 months. Early CD4+ T-cell recovery was accompanied by a reduction of the expression levels of CD95 and CD38 on T-cells. Out of 42 patients with complete virological follow-up under HAART, 19 (45%) achieved concordant good immunological (gain of ≥100 CD4+ T-cells/µl above baseline) and virological (undetectable VL) responses after 12 months of treatment (intention-to-treat analysis). Neither a decreased expression of the T-cell activation markers CD38 and CD95, nor an increase in the percentage of naive T-cells reliably predicted good virological treatment responses in patients with good CD4+ T-cell reconstitution. Repeated measurement of CD4+ T-cell counts during HAART remains the most important parameter for immunologic monitoring. Substitution of repeated VL testing by determination of T-cell activation levels (e.g., CD38 expression on CD8+ T-cells) should be applied with caution

Fear and rumours regarding placental biopsies in a malaria-in-pregnancy trial in Benin.

BACKGROUND: A multi-country, community-based trial on scheduled screening and treatment for malaria in pregnancy was conducted in Benin, The Gambia and Burkina Faso. Despite standardized procedures and outcomes, the study became subject to rumours and accusations of placenta being sold for mystical and financial gain by trial staff, leading to drop-out rates of 30% and the consequent halting of placental biopsy sampling in Benin. This paper explores the role of socio-cultural beliefs related to placenta and identified additional factors contributing these rumours. METHODS: A qualitative comparative emergent-theory design was used to assess social factors related to trial implementation and uptake in the three countries. Data from participant observation, informal conversations, group discussions and interviews were triangulated and analysed with NVivo Qualitative Analysis software. RESULTS: Despite similar sociocultural beliefs about the sacred nature of the placenta in all three study countries, these beliefs did not affect participation rates in Burkina Faso and The Gambia and placenta-related rumours only emerged in Benin. Therefore, the presence of beliefs is not a sufficient condition to have generated placenta-selling fears. The rumours in Benin reflected the confluence of placenta-related beliefs and factors related to the implementation of the trial (including a catalysing adverse event and miscommunication during the informed consent procedure). Furthermore, distinct socio-political factors contributed to the emergence of rumours, including the historical distrust in governmental organizations and the tense relationship between some of the actors involved in the trial. CONCLUSION: Transdisciplinary social science research designs should accompany the implementation of the trial. The integration of multiple stakeholders' knowledge and involvement is required to define and solve upcoming barriers

Governance and Conservation Effectiveness in Protected Areas and Indigenous and Locally Managed Areas

Increased conservation action to protect more habitat and species is fueling a vigorous debate about the relative effectiveness of different sorts of protected areas. Here we review the literature that compares the effectiveness of protected areas managed by states and areas managed by Indigenous peoples and/or local communities. We argue that these can be hard comparisons to make. Robust comparative case studies are rare, and the epistemic communities producing them are fractured by language, discipline, and geography. Furthermore the distinction between these different forms of protection on the ground can be blurred. We also have to be careful about the value of this sort of comparison as the consequences of different forms of conservation for people and nonhuman nature are messy and diverse. Measures of effectiveness, moreover, focus on specific dimensions of conservation performance, which can omit other important dimensions. With these caveats, we report on findings observed by multiple study groups focusing on different regions and issues whose reports have been compiled into this article. There is a tendency in the data for community-based or co-managed governance arrangements to produce beneficial outcomes for people and nature. These arrangements are often accompanied by struggles between rural groups and powerful states. Findings are highly context specific and global generalizations have limited value

A Theoretical Analysis of the Geography of Schistosomiasis in Burkina Faso Highlights the Roles of Human Mobility and Water Resources Development in Disease Transmission

We study the geography of schistosomiasis across Burkina Faso by means of a spatially explicit model of water-based disease dynamics. The model quantitatively addresses the geographic stratification of disease burden in a novel framework by explicitly accounting for drivers and controls of the disease, including spatial information on the distributions of population and infrastructure, jointly with a general description of human mobility and climatic/ecological drivers. Spatial patterns of disease are analysed by the extraction and the mapping of suitable eigenvectors of the Jacobian matrix subsuming the stability of the disease-free equilibrium. The relevance of the work lies in the novel mapping of disease burden, a byproduct of the parametrization induced by regional upscaling, by model-guided field validations and in the predictive scenarios allowed by exploiting the range of possible parameters and processes. Human mobility is found to be a primary control at regional scales both for pathogen invasion success and the overall distribution of disease burden. The effects of water resources development highlighted by systematic reviews are accounted for by the average distances of human settlements from water bodies that are habitats for the parasite's intermediate host. Our results confirm the empirical findings about the role of water resources development on disease spread into regions previously nearly disease-free also by inspection of empirical prevalence patterns. We conclude that while the model still needs refinements based on field and epidemiological evidence, the proposed framework provides a powerful tool for large-scale public health planning and schistosomiasis management

Serologic Prevalence of Peste des Petits Ruminants in Soum Province, North of Burkina Faso

A serological survey on PPR was carried out on a sample of 2144 small ruminants sera collected from 42 herds in the nine departments of the Soum province located in the north of Burkina Faso. The overall serological PPR prevalence estimated by c-ELISA was 28.90%. The study showed that the prevalence varied between departments. It was higher in animals over three years of age than in younger ones (p = 0.042), in sheep (33.09%) than in goats (23.01%), and in females than in males (p = 0.000). The survey showed that the PPR virus was actually circulating in Soum province. Therefore control measures through vaccination should be undertaken against this disease

Investigating the remediation potential of iron oxide nanoparticles in Cu-polluted soil–plant systems: coupled geochemical, geophysical and biological approaches

International audienceAlthough the use of iron oxide nanoparticles (IONPs) has high potential in remediation and agriculture, a major hindrance to their use includes the risk of contamination of soil and water resources with underexplored effects of IONPs on biota. The fate, phytotoxicity and remediation potential of IONPs are investigated with soil column experiments using 7 nm-sized magnetite (Fe 3 O 4) nanoparticles (magnNPs) and sunflower (Helianthus annuus). Control soil, magnNP-containing soil (10 g magnNPs per kg soil), copper-polluted soil (500 mg Cu per kg soil) and copper-polluted soil containing magnNPs (10 g magnNPs per kg soil and 500 mg Cu per kg soil) support sunflower growth for 57 and 95 days. In magnNP-exposed plants, the occurrence of magnNPs does not affect the growth of the vegetative aerial parts and photosynthetic efficiency. Decreased lipid peroxidation indicates an enhanced antioxidant enzymatic response of magnNP-exposed plants. In plants grown in Cu-and magnNP-Cu-soils, the physiological and biochemical impacts of excess copper are clearly identified, resulting in growth retardation, decreased pigment contents and photosynthetic efficiency, and increased lipid peroxidation and peroxidase (POD) activities. Based on magnetic susceptibility, a higher amount of magnNPs is detected after 57 days in the roots of magnNP-exposed plants (1400 mg kg À1) than in the roots of magnNP-Cu-exposed plants (920 mg kg À1). In the latter, magnNP internalization is likely hampered because of the plants' physiological responses to Cu toxicity. At the working Cu and magnNP concentrations, magnNPs neither decrease Cu accumulation in the plant tissues nor alleviate the overall growth retardation of sunflowers and certain phytotoxic effects induced by excess Cu. However, this study highlights several positive environmental aspects relative to magnNP use, including the harmless effects of magnNPs on sunflowers (1% magnNPs in soil) and the ability of magnNPs to influence Cu mobility in the soil (which could be even more pronounced at lower Cu concentration)