Jean Iwaz’s research while affiliated with Hospices Civils de Lyon (Centre Hospitalier Universitaire de Lyon) and other places

Background Togo's National Malaria Control Programme has initiated an active home-based malaria management model for all age groups in rural areas of Bassar Health District. This report describes the model, reports its main results, and determines the factors associated with positive rapid diagnostic test results. Methods From 2014 to 2017, in three peripheral care units of Bassar Health District (Binaparba, Nangbani, and Baghan), community health workers visited residents' homes weekly to identify patients with malaria symptoms, perform rapid diagnostic tests in symptomatic patients, and give medication to positive cases. Univariate and multivariate logistic regression models were used to determine the factors associated with positive tests. Results The study covered 11,337 people (817 in 2014, 1804 in 2015, 2638 in 2016, and 6078 in 2017). The overall mean age was 18 years (95% CI 5–29; min–max: 0–112 years). The median age was 10 years (SD: 16.9). The proportions of people tested positive were 75.3% in Binaparba, 77.4% in Nangbani, and 56.6% in Baghan. The 5–10 age group was the most affected category (24.2% positive tests). Positive tests were more frequent during the rainy than during the dry season (62 vs. 38%) and the probability of positive test was 1.76 times higher during the rainy than during the dry season (adjusted OR = 1.74; 95% CI 1.60–1.90). A fever (37.5 °C or higher) increased significantly the probability of positive test (adjusted OR = 2.19; 95% CI 1.89–2.54). The risk of positive test was 1.89 times higher in passive than in active malaria detection (adjusted OR = 1.89; 95% CI 1.73–2.0). Conclusions This novel experimental community and home-based malaria management in Togo suggested that active detection of malaria cases is feasible within 24 h, which allows rapid treatments before progression to often-fatal complications. This PECADOM + program will help Togo's National Malaria Control Programme reduce malaria morbidity and mortality in remote and hard-to-reach communities.

Introduction: Ideally, evaluating NGS performance requires a gold standard; in its absence, concordance between replicates is often used as substitute standard. However, the appropriateness of the concordance-discordance criterion has been rarely evaluated. This study analyzes the relationship between the probability of discordance and the probability of error under different conditions. Methods: This study used a conditional probability approach under conditional dependence then conditional independence between two sequencing results and compares the probabilities of discordance and error in different theoretical conditions of sensitivity, specificity, and correlation between replicates, then on real results of sequencing genome NA12878. The study examines also covariate effects on discordance and error using generalized additive models with smooth functions. Results: With 99% sensitivity and 99.9% specificity under conditional independence, the probability of error for a positive concordant pair of calls is 0.1%. With additional hypotheses of 0.1% prevalence and 0.9 correlation between replicates, the probability of error for a positive concordant pair is 47.4%. With real data, the estimated sensitivity, specificity, and correlation between tests for variants are around 98.98%, 99.996%, and 93%, respectively, and the error rate for positive concordant calls approximates 2.5%. In covariate effect analyses, the effects' functional form are close between discordance and error models, though the parts of deviance explained by the covariates differ between discordance and error models. Conclusion: With conditional independence of two sequencing results, the concordance-discordance criterion seems acceptable as substitute standard. However, with high correlation, the criterion becomes questionable because a high percentage of false concordant results appears among concordant results.

The specialized literature abounds in recommendations about the most desirable technical ways of answering reviewers’ comments on a submitted manuscript. However, not all publications mention authors’ and / or reviewers’ feelings or reactions about what they may read or write in their respective reports, and even fewer publications tackle openly what may or may not be said in a set of answers to a reviewer’s comments. In answering reviewers’ comments, authors are often attentive to the technical or rational aspects of the task but might forget some of its relational aspects. In their answers, authors are expected to make every effort to abide by reviewers’ suggestions, including discussing major criticisms, editing the illustrations, or implementing minor corrections; abstain from questioning a reviewer’s competence or willingness to write a good review, including full and attentive reading and drafting useful comments; clearly separate their answers to each reviewer; avoid skipping, merging, or reordering reviewers’ comments; and, finally, specify the changes made. Authors are advised to call on facts, logic, and some diplomacy, but never on artifice, concealment, or flattery. Failing to do so erodes the trust between authors and reviewers, whereas integrity is expected and highly valued. The guiding principle should always be honesty.

Objectives In most African countries, confirmed COVID-19 case counts underestimate the number of new SARS-CoV-2 infection cases. We propose a multiplying factor to approximate the number of biologically probable new infections from the number of confirmed cases. Methods Each of the first thousand suspect (or alert) cases recorded in South Kivu (DRC) between 29 March and 29 November 2020 underwent a RT-PCR test and an IgM and IgG serology. A latent class model and a Bayesian inference method were used to estimate (i) the incidence proportion of SARS-CoV-2 infection using RT-PCR and IgM test results, (ii) the prevalence using RT-PCR, IgM and IgG test results; and, (iii) the multiplying factor (ratio of the incidence proportion on the proportion of confirmed –RT-PCR+– cases). Results Among 933 alert cases with complete data, 218 (23%) were RT-PCR+; 434 (47%) IgM+; 464 (~ 50%) RT-PCR+, IgM+, or both; and 647 (69%) either IgG + or IgM+. The incidence proportion of SARS-CoV-2 infection was estimated at 58% (95% credibility interval: 51.8–64), its prevalence at 72.83% (65.68–77.89), and the multiplying factor at 2.42 (1.95–3.01). Conclusions In monitoring the pandemic dynamics, the number of biologically probable cases is also useful. The multiplying factor helps approximating it.

Introduction: in Africa, the proportion of minors with AIDS is ever increasing and adherence to treatment protocols is still suboptimal. The study investigated the conditions of HIV status disclosure and adherence to treatment in patients < 19 in two West African cities. Methods: in 2016, thirteen health professionals and four parents filled out questionnaires to identify problems and solutions relative to disclosure of HIV status and adherence to treatment in 208 children and adolescents seen at University Hospitals in Abidjan (Ivory Coast) and Lomé (Togo). Results: medians (extrema) of patients´ ages at start and end of status disclosure process were 10 (8-13) and 15 (13-17.5) years. In 61% of cases, disclosure was made individually after preparation sessions. The main difficulties were: parents´ disapproval, skipped visits, and rarity of psychologists. The solutions proposed were: recruiting more full-time psychologists, improving personnel training, and promoting patients´ "clubs". One out of three respondents was not satisfied with patients´ adherence to treatments. The major reasons were: intake frequencies, frequent omissions, school constraints, adverse effects, and lack of perceived effect. Nevertheless, 94% of the respondents confirmed the existence of support groups, interviews with psychologists, and home visits. To improve adherence, the respondents proposed increasing the number of support groups, sustaining reminder phone calls and home visits, and supporting therapeutic mentoring. Conclusion: despite persisting disclosure and adherence problems, appropriate measures already put into practice still need to be taken further, especially through engaging psychologists, training counsellors, and promoting therapeutic support groups.

The specialized literature abounds in recommendations about the most desirable technical ways of answering reviewers’ comments on a submitted manuscript. However, not all publications mention authors’ and/or reviewers’ feelings or reactions about what they may read or write in their respective reports, and even fewer publications tackle openly what may or may not be said in a set of answers to a reviewer’s comments. In answering reviewers’ comments, authors are often attentive to the technical or rational aspects of the task but might forget some of its relational aspects. In their answers, authors are expected to make every effort to abide by reviewers’ suggestions (discuss major criticisms, edit the illustrations, or implement minor corrections); abstain from questioning a reviewer’s competence or willingness to write a good review (full and attentive reading, drafting useful comments); clearly separate their answers to each reviewer; avoid skipping, merging, or reordering reviewers’ comments; and, finally, specify the changes made. Authors are advised to call on facts, logic, and some diplomacy, but never on artifice, concealment, or flattery. Failing to do so erodes the trust between authors and reviewers, whereas integrity is expected and highly valued. The guiding principle should always be honesty.

Objectives: Quantify the effects of characteristics of nursing homes and their surroundings on the spread of COVID-19 outbreaks and assess the changes in resident protection between the first 2 waves (March 1 to July 31 and August 1 to December 31, 2020). Design: An observational study was carried out on data on COVID-19 outbreaks extracted from a database that monitored the spread of the virus in nursing homes. Setting and participants: The study concerned all 937 nursing homes with >10 beds in Auvergne-Rhône-Alpes region, France. Methods: The rate of nursing homes with at least 1 outbreak and the cumulative number of deaths were modeled for each wave. Results: During the second (vs the first wave), the proportion of nursing homes that reported at least 1 outbreak was higher (70% vs 56%) and the cumulative number of deaths more than twofold (3348 vs 1590). The outbreak rate was significantly lower in public hospital-associated nursing homes than in private for-profit ones. During the second wave, it was lower in public and private not-for-profit nursing homes than in private for-profit ones. During the first wave, the probability of outbreak and the mean number of deaths increased with the number of beds (P < .001). During the second wave, the probability of outbreak remained stable in >80-bed institutions and, under proportionality assumption, the mean number of deaths was less than expected in >100-bed institutions. The outbreak rate and the cumulative number of deaths increased significantly with the increase in the incidence of hospitalization for COVID-19 in the surrounding populations. Conclusions and implications: The outbreak in the nursing homes was stronger during the second than the first wave despite better preparedness and higher availabilities of tests and protective equipment. Solutions for insufficient staffing, inadequate rooming, and suboptimal functioning should be found before future epidemics.

To improve the performance of individual DNA sequencing results, researchers often use replicates from the same individual and various statistical clustering models to reconstruct a high-performance callset. Here, three technical replicates of genome NA12878 were considered and five model types were compared (consensus, latent class, Gaussian mixture, Kamila–adapted k-means, and random forest) regarding four performance indicators: sensitivity, precision, accuracy, and F1-score. In comparison with no use of a combination model, i) the consensus model improved precision by 0.1%; ii) the latent class model brought 1% precision improvement (97%–98%) without compromising sensitivity (= 98.9%); iii) the Gaussian mixture model and random forest provided callsets with higher precisions (both >99%) but lower sensitivities; iv) Kamila increased precision (>99%) and kept a high sensitivity (98.8%); it showed the best overall performance. According to precision and F1-score indicators, the compared non-supervised clustering models that combine multiple callsets are able to improve sequencing performance vs. previously used supervised models. Among the models compared, the Gaussian mixture model and Kamila offered non-negligible precision and F1-score improvements. These models may be thus recommended for callset reconstruction (from either biological or technical replicates) for diagnostic or precision medicine purposes.