A novel post-mortem pathogen discovery program detects an outbreak of Echovirus E7: Uganda, 2022-2023

Area of Science:

• Public Health Surveillance
• Infectious Disease Epidemiology
• Genomic Surveillance

Background:

• Routine post-mortem examination is an underutilized public health tool for monitoring infectious diseases.
• Pandemic preparedness requires innovative strategies for early detection of novel and re-emerging pathogens.
• Metagenomic next-generation sequencing (mNGS) offers unbiased pathogen detection in complex biological samples.

Purpose of the Study:

• To establish and evaluate a mortuary surveillance program in Uganda.
• To leverage mNGS for identifying a broad spectrum of pathogens in deceased individuals.
• To assess the utility of mortuary surveillance for public health and pandemic preparedness.

Main Methods:

• Collected specimens and metadata from 2,607 individuals across five mortuary sites in Kampala (October 2022 - December 2023).
• Performed RT-qPCR screening for hemorrhagic fever viruses.
• Conducted mNGS on a subset of RT-qPCR negative samples (n=134) for comprehensive pathogen detection.

Main Results:

• Detected a wide range of DNA and RNA viruses, including herpes, parvovirus, bufavirus, Saffold, Salivirus, and HAV.
• Identified bacterial infections such as Bartonella, Rickettsia, Enterobacter, and Klebsiella, alongside respiratory pathogens like Cryptococcus neoformans and Corynebacterium diphtheria.
• Discovered a localized outbreak of Enterovirus B (recombinant Echovirus E7) and determined most pathogens were transmitted via direct/indirect contact.

Conclusions:

• Mortuary surveillance integrated with mNGS is a powerful strategy for detecting unrecognized infectious disease outbreaks.
• This approach aids in monitoring the emergence and re-emergence of infectious diseases.
• The findings highlight the potential of mNGS-based mortuary surveillance for strengthening global public health security.