Blood virosphere in febrile Tanzanian children

Samuel Cordey, Florian Laubscher, Mary-Anne Hartley, Thomas Junier, Kristina Keitel, Mylène Docquier, Nicolas Guex, Christian Iseli, Gael Vieille, Philippe Le Mercier, Anne Gleizes, Josephine Samaka, Tarsis Mlaganile, Frank Kagoro, John Masimba, Zamzam Said, Hosiana Temba, Gasser H Elbanna, Caroline Tapparel, Marie-Celine Zanella, Ioannis Xenarios, Jacques Fellay, Valérie D'Acremont, Laurent Kaiser, Samuel Cordey, Florian Laubscher, Mary-Anne Hartley, Thomas Junier, Kristina Keitel, Mylène Docquier, Nicolas Guex, Christian Iseli, Gael Vieille, Philippe Le Mercier, Anne Gleizes, Josephine Samaka, Tarsis Mlaganile, Frank Kagoro, John Masimba, Zamzam Said, Hosiana Temba, Gasser H Elbanna, Caroline Tapparel, Marie-Celine Zanella, Ioannis Xenarios, 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 in-depth 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.Trial registration: ClinicalTrials.gov identifier: NCT02225769.

Keywords: Blood virome; children; fever; metagenomic next-generation sequencing; virosphere.

Conflict of interest statement

No potential conflict of interest was reported by the author(s).

Figures

Figure 1.
Figure 1.
Flowchart of study selection.
Figure 1.
Figure 1.
Flowchart of study selection.
Figure 2.
Figure 2.
mNGS metrics for viruses of recognized clinical significance. (a) Distribution of the mapped reads for RNA viruses. Each dot represents a positive sample. (b) RNA virus genome coverages. Viral sequences detected by de novo only are represented by grey diamonds. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey corrugated symbols. (c) Distribution of the mapped reads for DNA viruses detected in DNA (left side) and RNA (right side) libraries. Each dot represents a positive sample. (d) DNA virus genome coverages in DNA (left side) and RNA (right side) libraries. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey corrugated symbols (except for herpesviruses that have too long genomes to figure in the panel). The horizontal lines in the box plots denote medians.
Figure 2.
Figure 2.
mNGS metrics for viruses of recognized clinical significance. (a) Distribution of the mapped reads for RNA viruses. Each dot represents a positive sample. (b) RNA virus genome coverages. Viral sequences detected by de novo only are represented by grey diamonds. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey corrugated symbols. (c) Distribution of the mapped reads for DNA viruses detected in DNA (left side) and RNA (right side) libraries. Each dot represents a positive sample. (d) DNA virus genome coverages in DNA (left side) and RNA (right side) libraries. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey corrugated symbols (except for herpesviruses that have too long genomes to figure in the panel). The horizontal lines in the box plots denote medians.
Figure 3.
Figure 3.
mNGS metrics for viruses of undetermined clinical significance. (a) Distribution of the mapped reads for RNA viruses. Each dot represents a positive sample. (b) RNA virus genome coverages. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey wave symbols. (c) Distribution of the mapped reads for DNA viruses detected in DNA (left side) and RNA (right side) libraries. Each dot represents a positive sample. (d) DNA virus genome coverages in DNA (left side) and RNA (right side) libraries. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey corrugated symbols. Viral sequences detected by de novo only are represented by grey diamonds. The horizontal lines in the box plots denote medians.
Figure 3.
Figure 3.
mNGS metrics for viruses of undetermined clinical significance. (a) Distribution of the mapped reads for RNA viruses. Each dot represents a positive sample. (b) RNA virus genome coverages. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey wave symbols. (c) Distribution of the mapped reads for DNA viruses detected in DNA (left side) and RNA (right side) libraries. Each dot represents a positive sample. (d) DNA virus genome coverages in DNA (left side) and RNA (right side) libraries. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey corrugated symbols. Viral sequences detected by de novo only are represented by grey diamonds. The horizontal lines in the box plots denote medians.
Figure 4.
Figure 4.
Representation of Anelloviridae co-detection. (a) Venn plot showing the distribution of Alpha-, Beta- and Gammatorquevirus genus among positive samples. (b) Phylogenetic diversity of primate anellovirus. Alpha-, Beta- and Gammatorquevirus genus are represented by three Maximum Likelihood trees based on complete ORF1 nucleotide sequences. Each branch is a representative sequence of a cluster, each cluster shows at least 20% nucleotide diversity with others. Clusters whose contain previously known complete ORF1 sequences are shaded grey, clusters with only sequences assembled in this study are shaded red. Scale is in number of substitutions per site. (c) Number of distinct anelloviruses of the same genus (i.e. Alpha-, Beta- and Gammatorquevirus) or in total co-detected in each positive sample. The horizontal lines in the box plots denote medians. Each dot represents one sample.
Figure 4.
Figure 4.
Representation of Anelloviridae co-detection. (a) Venn plot showing the distribution of Alpha-, Beta- and Gammatorquevirus genus among positive samples. (b) Phylogenetic diversity of primate anellovirus. Alpha-, Beta- and Gammatorquevirus genus are represented by three Maximum Likelihood trees based on complete ORF1 nucleotide sequences. Each branch is a representative sequence of a cluster, each cluster shows at least 20% nucleotide diversity with others. Clusters whose contain previously known complete ORF1 sequences are shaded grey, clusters with only sequences assembled in this study are shaded red. Scale is in number of substitutions per site. (c) Number of distinct anelloviruses of the same genus (i.e. Alpha-, Beta- and Gammatorquevirus) or in total co-detected in each positive sample. The horizontal lines in the box plots denote medians. Each dot represents one sample.
Figure 5.
Figure 5.
mNGS metrics for viruses of yet unknown significance. (a) Distribution of the mapped reads for RNA viruses. Each dot represents a positive sample. (b) RNA virus genome coverages. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey corrugated symbols (except for the segmented bunya-like virus 1–3). Viral sequences detected by de novo only are represented by grey diamonds. (c) Distribution of the mapped reads for DNA viruses detected in DNA (left side) and RNA (right side) libraries. Each dot represents a positive sample. (d) DNA virus genome coverages in DNA (left side) and RNA (right side) libraries. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey corrugated symbols. The horizontal lines in the box plots denote medians.
Figure 5.
Figure 5.
mNGS metrics for viruses of yet unknown significance. (a) Distribution of the mapped reads for RNA viruses. Each dot represents a positive sample. (b) RNA virus genome coverages. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey corrugated symbols (except for the segmented bunya-like virus 1–3). Viral sequences detected by de novo only are represented by grey diamonds. (c) Distribution of the mapped reads for DNA viruses detected in DNA (left side) and RNA (right side) libraries. Each dot represents a positive sample. (d) DNA virus genome coverages in DNA (left side) and RNA (right side) libraries. Each dot represents one sample. Viral full genome sizes (bp) are indicated by grey corrugated symbols. The horizontal lines in the box plots denote medians.

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