Identification of enteric viral pathogens in Tanzanian children under the age of five with diarrhea using nanopore-based metagenomic sequencing.

Authors

Mariana J Shayo, Davis Kuchaka, Melkiory Beti, Patrick Kimu, Boaz Wadugu, Emilie E B Jensen, Happiness Kumburu, Paul Kazyoba, Mohamed Ali, SeqTZ Consortium, Philip T L C Clausen, Florida Muro, Blandina T Mmbaga, Ireen Kiwelu, Michael Alifrangis, Frank M Aarestrup, Tolbert Sonda

Published in

Virology. Volume 623. Pages 111024. Jul 10, 2026. Epub Jul 10, 2026.

Abstract

Diarrhea continues to be a significant contributor to illness and death among children, especially in low-income settings. In Tanzania, diarrheal disease remains a public health concern with many minors under five seeking healthcare despite the wide coverage of rotavirus vaccine. The diagnosis of pediatric diarrhea in Tanzania primarily focuses on specific viral diseases, which may overlook the broad-spectrum of viral pathogens. In this study, Oxford Nanopore-based metagenomic sequencing was applied to characterize viral pathogens in 200 stool samples from children under the age of five presented with diarrhea. Samples were collected from April 2023 to April 2024 at health facilities in six regions across mainland Tanzania and Zanzibar. At least one known diarrhea linked virus was detected in 31% of the participants. Although no statistical difference could be observed across different age categories, a slightly higher detection was observed in children aged 6-23 months. Human adenovirus was the most frequently detected 16% (32/200) in this study. Rotavirus was the second most frequently detected virus 9.5% (19/200) despite participant vaccination status. Other enteric viruses detected was astrovirus, norovirus, human bocavirus and Aichi virus were detected in 2.5% (5/200), 2% (4/200), 0.5% (1/200) and 0.5% (1/200) of the study participants respectively. Rotavirus showed negative correlation with temperature and relative humidity while human adenovirus was positively correlated to relative humidity. Metagenomics also revealed the presence of non-enteric viral pathogens, including measles and HAdV-C and HAdV-B, within this cohort. This study identified a range of viral pathogens associated with pediatric diarrhea in this cohort, including agents not typically targeted by routine diagnostic assays by using untargeted metagenomic technique direct to the clinical samples. These findings contribute baseline data that could inform future, larger-scale surveillance efforts in Tanzania.

PMID:
42442081
Bibliographic data and abstract were imported from PubMed on 14 Jul 2026.

Read full publication at:
Please sign in to see all details.

Stats

1-terrible, 9-excellent. How would you rate this publication? Sign in in to submit your rating.

Post a comment

You need to be signed in to post comments. You can sign in here.

Comments

There are no comments yet.