Using next generation sequencing to identify yellow fever virus in Uganda

Area of Science:

• Virology
• Epidemiology
• Public Health

Background:

• Hospitals in northern Uganda reported patients with suspected hemorrhagic fevers in October-November 2010.
• Initial diagnostic tests for known hemorrhagic fever viruses (Ebola, Marburg, Rift Valley fever, Crimean-Congo hemorrhagic fever) were negative.

Purpose of the Study:

• To identify the etiological agent responsible for the unexplained hemorrhagic fever outbreak in Uganda.
• To demonstrate the utility of unbiased next-generation sequencing and metagenomic approaches in outbreak investigations.

Main Methods:

• Unbiased PCR amplification of total RNA extracted directly from patient sera.
• Next-generation sequencing (NGS) for unbiased pathogen detection.
• Metagenomic analysis to identify viral sequences.

Main Results:

• NGS successfully detected yellow fever virus (YFV) in patient samples.
• Approximately 98% of the YFV genome sequence was generated.
• The findings identified YFV as the causative agent of the outbreak.

Conclusions:

• Yellow fever virus was identified as the etiological agent of the 2010 hemorrhagic fever outbreak in northern Uganda.
• Next-generation sequencing and metagenomics are powerful tools for rapid identification of unknown pathogens during disease outbreaks.
• This approach can effectively guide public health responses to emerging infectious diseases.