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

Date Published: June 20, 2019

Publisher: Public Library of Science

Author(s): Akshaya Ramesh, Sara Nakielny, Jennifer Hsu, Mary Kyohere, Oswald Byaruhanga, Charles de Bourcy, Rebecca Egger, Boris Dimitrov, Yun-Fang Juan, Jonathan Sheu, James Wang, Katrina Kalantar, Charles Langelier, Theodore Ruel, Arthur Mpimbaza, Michael R. Wilson, Philip J. Rosenthal, Joseph L. DeRisi, Baochuan Lin.


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.

Partial Text

The evaluation of children with fever is challenging, particularly in Low and Middle income countries (LMIC). A febrile child in sub-Saharan Africa may have a mild self-resolving viral infection or may be suffering from bacterial sepsis or malaria—major causes of disability and death [1, 2]. Historically, febrile illness in much of Africa has been treated empirically as malaria due to the limited availability of diagnostics and the risk of untreated malaria progressing to life-threatening illness. This strategy changed in 2010 following revised guidelines from the World Health Organization (WHO), which recommended limiting malaria therapy to those with a confirmed diagnosis [3]. However, standard recommendations for management of febrile children who do not have malaria are lacking. Increased knowledge about the prevalence of non-malarial pathogens associated with fever is needed to inform management strategies for febrile children [2], especially in low resource settings.

A better understanding of the microbial agents causing fever in African children is needed to inform the development of better diagnostic algorithms, therapeutic guidelines and public health strategies. We performed an exploratory retrospective study with unbiased mNGS on various tissue types to determine whether this technology has potential to contribute to our understanding of the etiologies of fever in African children. In this limited sample set, mNGS identified a wide range of potential pathogens, including three novel viral species.

This study was approved by the Makerere University Research and Ethics Committee, the Uganda National Council of Science and Technology, and the University of California, San Francisco Committee on Human Research. Written informed consent was obtained from the parent or guardian on the child’s behalf for all child participants enrolled in this study.