Blood virosphere in febrile Tanzanian children
Samuel Cordey, Florian Laubscher, Mary‐Anne Hartley, Thomas Junier, Kristina Keitel, Mylène Docquier, Nicolas Guex, Christian Iseli, Gaël Vieille, Philippe Le Mercier, Anne Gleizes, Josephine Samaka, Tarsis Mlaganile, Frank Kagoro, John Masimba, Zamzam Said, Hosiana Temba, Gasser Elbanna, Caroline Tapparel, Marie-Céline Zanella, Ioannis Xénarios, Jacques Fellay, Valérie D’Acremont, Laurent Kaiser
Abstract
Viral infections are the leading cause of childhood acute febrile illnesses motivating consultation in sub-Saharan Africa. The majority of causal viruses are never identified in low-resource clinical settings as such testing is either not part of routine screening or available diagnostic tools have limited ability to detect new/unexpected viral variants. An indepth exploration of the blood virome is therefore necessary to clarify the potential viral origin of fever in children. Metagenomic next-generation sequencing is a powerful tool for such broad investigations, allowing the detection of RNA and DNA viral genomes. Here, we describe the blood virome of 816 febrile children (<5 years) presenting at outpatient departments in Dar es Salaam over one-year. We show that half of the patients (394/816) had at least one detected virus recognized as causes of human infection/disease (13.8% enteroviruses (enterovirus A, B, C, and rhinovirus A and C), 12% rotaviruses, 11% human herpesvirus type 6). Additionally, we report the detection of a large number of viruses (related to arthropod, vertebrate or mammalian viral species) not yet known to cause human infection/disease, highlighting those who should be on the radar, deserve specific attention in the febrile paediatric population and, more broadly, for surveillance of emerging pathogens.