Institute of Tropical Medicine Antwerp
The Institute of Tropical Medicine in Antwerp (Belgium) strives for the advancement of science and health for all, through innovative research, advanced education, professional medical services and capacity sharing with partner institutions in Africa, Asia and Latin America. The institute has a rich history of involvement in outbreak investigation, research, and response.
Researchers at the ITM developed a Nextflow pipeline to help analyze samples to help contain the 2022 global mpox outbreak.
While historically confined to remote forested regions in Central and West Africa, in 2022, a global MPXV outbreak occurred, affecting approximately 93,000 people, surpassing all preceding outbreaks. When the first suspected mpox patients presented at the HIV/STI Clinic from the Institute of Tropical Medicine (ITM), a multidisciplinary team of researchers was assembled to curb and better understand the ongoing outbreak, leveraging pre-existing knowledge stemming from long-standing partnerships with researchers in endemic countries.
ITM’s Unit of Clinical Virology and the Outbreak Research Team contributed by applying their viral sequencing protocols and pipelines to swiftly develop an MPXV whole-genome sequencing protocol using Nextflow, helping to understand the ongoing outbreak.
ITM went on to deliver evidence of asymptomatic infections among individuals who visited ITM’s HIV/STI Clinic and shared the associated MPXV genomes in the report Retrospective detection of asymptomatic monkeypox virus infections among male sexual health clinic attendees in Belgium.
“Nextflow was the ideal choice for pipeline development. The language is simple, has excellent parallel execution features, and has a rich library of existing modules that enable immediate productivity with a minimal learning curve.”
The team at ITM chose Nextflow to implement their pipeline because of its ease of implementation, parallel execution features, and the widespread ability of similar reference pipelines, which enabled them to speed up development.