Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda

Abstract

Febrile illness is a major burden in African children, and non-malarial causes of fever are uncertain. In this retrospective exploratory study, we used metagenomic next-generation sequencing (mNGS) to evaluate serum, nasopharyngeal, and stool specimens from 94 children (aged 2-54 months) with febrile illness admitted to Tororo District Hospital, Uganda. The most common microbes identified were Plasmodium falciparum (51.1% of samples) and parvovirus B19 (4.4%) from serum; human rhinoviruses A and C (40%), respiratory syncytial virus (10%), and human herpesvirus 5 (10%) from nasopharyngeal swabs; and rotavirus A (50% of those with diarrhea) from stool. We also report the near complete genome of a highly divergent orthobunyavirus, tentatively named Nyangole virus, identified from the serum of a child diagnosed with malaria and pneumonia, a Bwamba orthobunyavirus in the nasopharynx of a child with rash and sepsis, and the genomes of two novel human rhinovirus C species. In this retrospective exploratory study, mNGS identified multiple potential pathogens, including 3 new viral species, associated with fever in Ugandan children.

Fig 1

(A) Microbial landscape found in serum samples in Ugandan children. Each column represents a febrile child. Results for GB virus C and torque teno virus, which are of uncertain clinical significance, are not included. (B) Microbial landscape found in nasopharyngeal (NP) swab samples in Ugandan children. Note that bacterial species were not considered in Fig 1B. Each column represents a febrile child, and the color bars represent the total reads per million (rpM) of a particular microbe present in the sample. Results for GB virus C and torque teno virus, which are of uncertain clinical significance, are not included.

Fig 2. Characterization of the novel orthobunyavirus identified in a febrile child.

(A) Schematic representation of the large (L) or RNA dependent RNA polymerase, medium (M) or polyprotein of Gn, NSm and Gc proteins and small (S) segment encoding the nucleocapsid (N) protein of Nyangole virus and percentage identity with the most closely related virus. Phylogenetic tree of all complete orthobunyavirus genome sequences along with Nyangole virus are represented in (B) for the RNA dependent RNA polymerase and (C) for the glycoprotein.

Fig 3. Phylogenetic tree of all complete HRV-C genomes from NCBI (with information on country of isolation) and HRV-C genomes assembled in this study.