Abstract
ABSTRACT Fever is the leading cause of paediatric outpatient consultations in Sub-Saharan Africa. Although most are suspected to be of viral origin, a putative causative pathogen is not identified in over a quarter of these febrile episodes. Using a de novo assembly sequencing approach, we report the detection (15.4%) of dicistroviruses (DicV) RNA in sera collected from 692 febrile Tanzanian children. In contrast, DicV RNA was only detected in 1/77 (1.3%) plasma samples from febrile Tanzanian adults, suggesting that children could represent the primary susceptible population. Estimated viral load by specific quantitative real-time RT–PCR assay ranged from < 1.32E3 to 1.44E7 viral RNA copies/mL serum. Three DicV full-length genomes were obtained, and a phylogenetic analyse on the capsid region showed the presence of two clusters representing tentative novel genus. Although DicV-positive cases were detected throughout the year, a significantly higher positivity rate was observed during the rainy season. This study reveals that novel DicV RNA is frequently detected in the blood of Tanzanian children, paving the way for further investigations to determine if DicV possibly represent a new agent in humans.
Highlights
Infectious febrile illnesses are leading causes of paediatric outpatient consultations in Sub-Saharan Africa
Using a de novo assembly sequencing approach, we report the detection (15.4%) of dicistroviruses (DicV) RNA in sera collected from 692 febrile Tanzanian children
80 sera found DicVnegative by High-throughput sequencing (HTS) analysis were randomly selected throughout the entire recruitment period of 2015 and assessed by the DicV-Capsid and DicV-ORF1/RNA-dependent RNA polymerase (RdRp) real-time RT–PCR assays; 5 were found positive (4 sera collected in February and 1 in July; viral load ranged from < 1.32E3 to 2.11E4 viral RNA copies/mL of sera) suggesting that the DicV prevalence of 15.4% observed by HTS represents a minimal estimate
Summary
Infectious febrile illnesses are leading causes of paediatric outpatient consultations in Sub-Saharan Africa. HTSbased screenings in both vertebrate and non-vertebrate biological specimens [1–3] have shown that the diversity of viruses circulating in the animal world is larger than anticipated (including potential human infections such as astroviruses, reoviruses, pseudorabies viruses, and bornaviruses [4–9]), and that many viral families are shared by the two kingdoms, raising the possibility of yet to be discovered viral infections in humans [10]. Using HTS and a de novo assembly approach, we screened sera collected from febrile Tanzanian children for the presence of unrecognized viral agents. These children were enrolled in a large cohort investigating the clinical impact of point-of-care patient management
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