ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Ancient DNA and Forensic Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1557576
A novel post-mortem pathogen discovery program detects an outbreak of Echovirus E7: Uganda, 2022-2023
Provisionally accepted
Sonja L Weiss1
Nicholas Bbosa2
Gregory S. Orf1
Michael G Berg1*Deogratius Ssemwanga2Sam Kalungi3
STEPHEN BALINANDI2
Maximillian Mata1
Henry Kyobe Bosa4Stella E Nabirye2Joshua Buule2
Tom Lutalo2
Angela Havron1Robert Downing2
Mary Rodgers1
Francisco Averhoff1
Gavin Cloherty1
Pontiano Kaleebu2- 1Abbott (United States), Chicago, United States
- 2Uganda Virus Research Institute (UVRI), Entebbe, Uganda
- 3Mulago Hospital, Kampala, Uganda
- 4Ministry of Health (Uganda), Kampala, Uganda
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Objectives: Utilizing post-mortem examination for routine monitoring of infectious diseases and pandemic preparedness is a common-sense, yet uncommon, public health measure. Here, we established a novel mortuary surveillance program in Uganda that leverages the unbiased nature of metagenomic nextgeneration sequencing (mNGS) to detect pathogens in recently deceased individuals.Methods: Between October 2022 and December 2023, specimens and patient metadata were collected from 2,607 individuals across five mortuary sites around Kampala. Specimens were pre-screened for hemorrhagic fever viruses by RT-qPCR and a subset (n=134) of RT-qPCR negatives were sequenced by mNGS.Results: A variety of DNA (herpes, parvovirus, bufavirus) and RNA (Saffold, Salivirus, HAV) viruses, vectored (Bartonella, Rickettsia) and nosocomial (Enterobacter, Klebsiella) bacterial infections, and potentially lethal respiratory pathogens (e.g., Cryptococcus neoformans, Corynebacterium diphtheria) were detected. A localized outbreak of Enterovirus B (EV-B), specifically a recombinant Echovirus E7, was observed in Kampala. An epidemiologic assessment indicated that most identified pathogens were acquired via direct and/or indirect contact (e.g., fecal-oral, fomites) and that other modes of transmission (e.g., foodborne, insect-vectored) played a less significant role.Conclusions: Integration of mortuary surveillance, coupled with mNGS, into public health systems represents a powerful strategy for identifying unrecognized outbreaks and monitoring the (re-) emergence of infectious diseases.
Keywords: mortuary surveillance, Metagenomics, Echovirus, Uganda, Enterovirus
Received: 09 Jan 2025; Accepted: 10 Jun 2025.
Copyright: © 2025 Weiss, Bbosa, Orf, Berg, Ssemwanga, Kalungi, BALINANDI, Mata, Kyobe Bosa, Nabirye, Buule, Lutalo, Havron, Downing, Rodgers, Averhoff, Cloherty and Kaleebu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Michael G Berg, Abbott (United States), Chicago, United States
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