Badione A

Dengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is known about the genetic diversity of dengue virus (DENV) in Senegal. Here we report complete viral genomes from 17 previously undetected DENV cases from the city of Thiès. In total we identified 19 cases of DENV in a cohort of 198 individuals with fever collected in October and November 2018. We detected 3 co-circulating serotypes; DENV 3 was the most frequent accounting for 11/17 sequences (65%), 4 (23%) were DENV2 and 2 (12%) were DENV1. Sequences were most similar to recent sequences from West Africa, suggesting ongoing local circulation of viral populations; however, detailed inference is limited by the scarcity of available genomic data. We did not find clear associations with reported clinical signs or symptoms, highlighting the importance of testing for diagnosing febrile diseases. Overall, these findings expand the known range of DENV in Senegal, and underscore the need for better genomic characterization of DENV in West Africa.

Multiple-strain (polygenomic) infections are a ubiquitous feature of Plasmodium falciparum parasite population genetics. Under simple assumptions of superinfection, polygenomic infections are hypothesized to be the result of multiple infectious bites. As a result, polygenomic infections have been used as evidence of repeat exposure and used to derive genetic metrics associated with high transmission intensity. However, not all polygenomic infections are the result of multiple infectious bites. Some result from the transmission of multiple, genetically related strains during a single infectious bite (cotransmission). Superinfection and cotransmission represent two distinct transmission processes, and distinguishing between the two could improve inferences regarding parasite transmission intensity. Here, we describe a new metric, R H, that utilizes the correlation in allelic state (heterozygosity) within polygenomic infections to estimate the likelihood that the observed complexity resulted from either superinfection or cotransmission. R H is flexible and can be applied to any type of genetic data. As a proof of concept, we used R H to quantify polygenomic relatedness and estimate cotransmission and superinfection rates from a set of 1,758 malaria infections genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode. Contrary to expectation, we found that cotransmission was responsible for a significant fraction of 43% to 53% of the polygenomic infections collected in three distinct epidemiological regions in Senegal. The prediction that polygenomic infections frequently result from cotransmission stresses the need to incorporate estimates of relatedness within polygenomic infections to ensure the accuracy of genomic epidemiology surveillance data for informing public health activities.

Vitamin A supplementation (VAS) in 6-59-month-old children is recommended but its sustainability is currently questioned. In Senegal, available data suggest that VAS should be maintained, but geographic and age-related specificities need to be addressed to better implement and target VAS programming. The objective of this comparative cross-sectional study, conducted in urban settings of Dakar, was to compare the vitamin A liver stores (VALS) assessed using the modified-relative dose response (MRDR) test between supplemented and non-supplemented 9-23 month-old children and to study their relationship with VAS. The supplemented group (n = 119) received VAS (either 100 000 UI or 200 000 UI) 2 to 6 months before evaluation while the non-supplemented group (n = 110) had not received VAS during the past 6 months. In addition to MRDR, serum retinol concentrations (SR), and biomarkers of subclinical inflammation were measured. Children's health-related data and feeding patterns were collected. Mean MRDR values (VAS: 0.030 ± 0.017, non-VAS: 0.028 ± 0.016, P = 0.389) and inflammation-adjusted SR (VAS: 1.34 ± 0.37, non-VAS: 1.3 ± 0.35, P = 0.515) of children were adequate. Low prevalence of VALS (VAS: 5.2%, non-VAS: 5.4%) and inflammation-adjusted VAD (VAS: 2.6%, non-VAS: 0.9%) were detected despite high presence of infections and inflammation. Children were mostly still being breastfed (VAS: 85.7%, non-VAS: 77.3%) and complementary feeding indicators were similar in both groups. Only breastfeeding was associated with VALS and was found to reduce by 76% at least, the odds of VAD (adjusted OR = 0.24, 95% CI: 0.07-0.8, P = 0.020). Based on MRDR values, VAS was not related to improved VALS and SR as well as VAD reduction among these children with adequate VALS. Reinforcing breastfeeding advocacy and morbidity prevention/control are essential in this setting. Scaling-back VAS in this subpopulation should be examined regarding the risk of hypervitaminosis A after an evaluation of dietary vitamin A intake sufficiency and a more quantitative assessment of VALS.