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

Nutritional properties of enriched local complementary flours

Abstract: This study aimed to identify the nutritional, functional, sensory and microbiological profile of experimental nutritional flours, produced with local products in Burkina Faso. The raw materials included maize (Zea mays), millet (Pennisetum glaucum) and rice (Oryza sativa). Local ingredients were pulps of Adansonia digitata and Parkia biglobosa and seeds of Cucurbita maxima and Moringa oleifera. Three formula were developed, the first (F1) with maize, the second (F2) with rice and the last (F3) with millet. Each of these cereals was mixed with predetermined portions of seeds and pulps in order to obtain enriched flour. Nutritional, microbiological and functional analysis and the acceptability criteria of these enriched flours were assessed and compared to Misola (F4), the existing local complementary flour. The fat content of experimental flours were respectively in the first (F1), second (F2) and third formula (F3) 15.91±0.01%, 11.82±0.02% and 17.02±0.02%. The carbohydrate range was 65.46±0.06%, 70.81±0.01% and 64.51±0.01% for F1, F2 and F3, while the energetic value is higher than recommended (453.07±0.05, 424.56±0.03 and 458.96±0.05 kcal respectively for F1, F2 and F3). Functional characteristics indicated the good viscosity (117, 119 and 121 mm/30 sec for F1, F2 and F3) least gelation (9, 6 and 7%) and water absorption capacity (2, 4 and 1 g/g). Trained sensory evaluation panellists gore the enriched flour porridge a score of acceptable. These enriched flours have great potential as a weaning food in resource-poor and technologically under-developed countries

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

Level and determinants of contraceptive uptake among women attending facilities with abortion-related complications in East and Southern Africa.

OBJECTIVE: To investigate the level and determinants of nonreceipt of contraception among women admitted to facilities with abortion-related complications in East and Southern Africa. METHODS: Cross-sectional data from Kenya, Malawi, Mozambique, and Uganda collected as part of the World Health Organization (WHO) Multi-Country Survey on Abortion-related morbidity. Medical record review and the audio computer-assisted self-interviewing system were used to collect information on women's demographic and clinical characteristics and their experience of care. The percentage of women who did not receive a contraceptive was estimated and the methods of choice for different types of contraceptives were identified. Potential determinants of nonreceipt of contraception were grouped into three categories: sociodemographic, clinical, and service-related characteristics. Generalized estimating equations were used to identify the determinants of nonreceipt of a contraceptive following a hierarchical approach. RESULTS: A total of 1190 women with abortion-related complications were included in the analysis, of which 33.9% (n = 403) did not receive a contraceptive. We found evidence that urban location of facility, no previous pregnancy, and not receiving contraceptive counselling were risk factors for nonreceipt of a contraceptive. Women from nonurban areas were less likely not to receive a contraceptive than those in urban areas (AOR 0.52; 95% CI, 0.30-0.91). Compared with women who had a previous pregnancy, women who had no previous pregnancy were 60% more likely to not receive a contraceptive (95% CI, 1.14-2.24). Women who did not receive contraceptive counselling were over four times more likely to not receive a contraceptive (AOR 4.01; 95% CI, 2.88-5.59). CONCLUSION: Many women leave postabortion care having not received contraceptive counselling and without a contraceptive method. There is a clear need to ensure all women receive high-quality contraceptive information and counselling at the facility to increase contraceptive acceptance and informed decision-making

Adolescents' satisfaction with care for abortion-related complications in 11 Sub-Saharan African countries: A cross-sectional facility-based study.

OBJECTIVE: To assess satisfaction with care for abortion-related complications experienced among adolescents compared to older women. METHODS: A secondary analysis of the WHO Multi-Country Survey on Abortion-related Morbidity and Mortality-a cross-sectional study conducted in health facilities in 11 Sub-Saharan African countries. Women with abortion-related complications who participated in an audio computer-assisted self-interview were included. Two composite measures of overall satisfaction were created based on five questions: (1) study participants who were either satisfied or very satisfied across all five questions; and (2) study participants who reported being very satisfied only across all five questions. Multivariable general estimating equation analyses were conducted to assess whether there was any evidence that age (adolescents 12-19 years and older women 20+) was associated with each composite measure of satisfaction, controlling for key confounders. RESULTS: The study sample consisted of 2817 women (15% adolescents). Over 75% of participants reported being satisfied or very satisfied for four out of five questions. Overall, 52.9% of study participants reported being satisfied/very satisfied across all five questions and 22.4% reported being consistently very satisfied. Multivariable analyses showed no evidence of an association between age group and being either satisfied or very satisfied (OR 1.07; 95% CI, 0.82-1.41, P = 0.60), but showed strong evidence that adolescents were 50% more likely to be consistently very satisfied with their overall care than older women (OR 1.49; 95% CI, 1.13-1.96, P = 0.005). CONCLUSION: Both adolescents and older women reported high levels of satisfaction with care when looking at different components of care individually, but the results of the composite measure for satisfaction showed that many study participants reported being less than satisfied with at least one element of their care. Further studies to explore the expectations, needs, and values of women's satisfaction with care for abortion-related complications are needed

The influence of C3 and C4 vegetation on soil organic matter dynamics in contrasting semi-natural tropical ecosystems

Variations in the carbon isotopic composition of soil organic matter (SOM) in bulk and fractionated samples were used to assess the influence of C3 and C4 vegetation on SOM dynamics in semi-natural tropical ecosystems sampled along a precipitation gradient in West Africa. Differential patterns in SOM dynamics in C3/C4 mixed ecosystems occurred at various spatial scales. Relative changes in C / N ratios between two contrasting SOM fractions were used to evaluate potential site-scale differences in SOM dynamics between C3- and C4-dominated locations. These differences were strongly controlled by soil texture across the precipitation gradient, with a function driven by bulk δ13C and sand content explaining 0.63 of the observed variability. The variation of δ13C with soil depth indicated a greater accumulation of C3-derived carbon with increasing precipitation, with this trend also being strongly dependant on soil characteristics. The influence of vegetation thickening on SOM dynamics was also assessed in two adjacent, but structurally contrasting, transitional ecosystems occurring on comparable soils to minimise the confounding effects posed by climatic and edaphic factors. Radiocarbon analyses of sand-size aggregates yielded relatively short mean residence times (τ) even in deep soil layers, while the most stable SOM fraction associated with silt and clay exhibited shorter τ in the savanna woodland than in the neighbouring forest stand. These results, together with the vertical variation observed in δ13C values, strongly suggest that both ecosystems are undergoing a rapid transition towards denser closed canopy formations. However, vegetation thickening varied in intensity at each site and exerted contrasting effects on SOM dynamics. This study shows that the interdependence between biotic and abiotic factors ultimately determine whether SOM dynamics of C3- and C4-derived vegetation are at variance in ecosystems where both vegetation types coexist. The results highlight the far-reaching implications that vegetation thickening may have for the stability of deep SOM. Â © Author(s) 2015

Advancing Access to Diagnostic Tools Essential for Universal Health Coverage and Antimicrobial Resistance Prevention: An Overview of Trials in Sub-Saharan Africa.

We introduce the Antimicrobial Resistance Diagnostic Use Accelerator program, and the articles in this Supplement, which cover the program in 3 sub-Saharan Africa countries

Nutritional status in young children prior to the malaria transmission season in Burkina Faso and Mali, and its impact on the incidence of clinical malaria.

BACKGROUND: Malaria and malnutrition remain major problems in Sahel countries, especially in young children. The direct effect of malnutrition on malaria remains poorly understood, and may have important implications for malaria control. In this study, nutritional status and the association between malnutrition and subsequent incidence of symptomatic malaria were examined in children in Burkina Faso and Mali who received either azithromycin or placebo, alongside seasonal malaria chemoprevention. METHODS: Mid-upper arm circumference (MUAC) was measured in all 20,185 children who attended a screening visit prior to the malaria transmission season in 2015. Prior to the 2016 malaria season, weight, height and MUAC were measured among 4149 randomly selected children. Height-for-age, weight-for-age, weight-for-height, and MUAC-for-age were calculated as indicators of nutritional status. Malaria incidence was measured during the following rainy seasons. Multivariable random effects Poisson models were created for each nutritional indicator to study the effect of malnutrition on clinical malaria incidence for each country. RESULTS: In both 2015 and 2016, nutritional status prior to the malaria season was poor. The most prevalent form of malnutrition in Burkina Faso was being underweight (30.5%; 95% CI 28.6-32.6), whereas in Mali stunting was most prevalent (27.5%; 95% CI 25.6-29.5). In 2016, clinical malaria incidence was 675 per 1000 person-years (95% CI 613-744) in Burkina Faso, and 1245 per 1000 person-years (95% CI 1152-1347) in Mali. There was some evidence that severe stunting was associated with lower incidence of malaria in Mali (RR 0.81; 95% CI 0.64-1.02; p = 0.08), but this association was not seen in Burkina Faso. Being moderately underweight tended to be associated with higher incidence of clinical malaria in Burkina Faso (RR 1.27; 95% CI 0.98-1.64; p = 0.07), while this was the case in Mali for moderate wasting (RR 1.27; 95% CI 0.98-1.64; p = 0.07). However, these associations were not observed in severely affected children, nor consistent between countries. MUAC-for-age was not associated with malaria risk. CONCLUSIONS: Both malnutrition and malaria were common in the study areas, high despite high coverage of seasonal malaria chemoprevention and long-lasting insecticidal nets. However, no strong or consistent evidence was found for an association between any of the nutritional indicators and the subsequent incidence of clinical malaria