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Abstract Pathogen genomic analysis is central to tracking, understanding and containing outbreaks1,2,3,4,5,6,7,8,9,10,11,12,13, but the complexity and cost of state-of-the-art phylogenetic tools limit global access and impact. Here we introduce Delphy, an exact reformulation of Bayesian phylogenetics14,15,16,17 designed to transform its speed, scalability and accessibility while retaining Bayesian state-of-the-art accuracy.
Abstract Mpox is a re-emerging zoonotic disease caused by MPXV, which has led to outbreaks across multiple countries in recent years. Sierra Leone reported its first mpox case in 8 years in January 2025, rapidly becoming the epicenter of a continental outbreak with more than 5,000 confirmed cases by August, a surge with unknown origins, timings and drivers.
Epidemiological model Leveraging the anonymous contact networks generated by OO, we propose a method by which such data may be used to construct an epidemiological model that simulates the spread of pathogens and measures the impact of mitigation measures.
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