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Articles by Patrick Varilly
Scalable near-real-time Bayesian phylogenetics for outbreaks with Delphy
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.
Genomic epidemiology of the 2025 mpox epidemic in Sierra Leone
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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.
By Allan Campbell, John Demby Sandi, Ifeanyi F. Omah, Martin Faye, Edyth Parker, Taylor M Brock-Fisher, Crystal M. Gigante, Mohamed Kamara, Anu Williams, Mouhamed Kane, Julian Campbell, Mignane Ndiaye, Ibrahim Umaru Fofanah, Al Ozonoff, Colby Wilkason, Danny Park Verified, Christopher Tomkins-Tinch, Christopher John Shin, Ian Baudi, Brendan Blumenstiel, Patrick Varilly, Ivan Specht, Ben Fry Verified, Paul Cronan, Harouna M Soumare, Alexandra Tuttle, Jonathan Greene, Aminata Shamit Koroma, Joseph Sam Kanu, Mamadou Aliou Barry, Aboubacry Gaye, Andy Diouf, Christine Hughes, Joshua I. Levy, Alhaji Umar N’jai, Moussa Moïse Diagne, George Ameh, John Klena, Monique A. Foster, Abebaw Kebede, Collins K. Tanui, Boubacar Diallo, Anise N Happi, Sofonias Kifle Tessema, Abdourahmane Sow, Yenew Kebede, James Squire, Doris R. Harding, Zikan Koroma, Mohamed Jalloh, Kristian G. Andersen, Andrew Rambaut, Mohamed Vandi, Ibrahima Fall, Pardis Sabeti, Christian T. Happi, Foday Sahr, Donald S. Grant, Vidalyn Folorunso, Kadiatu Salmata Sesay, Sia Mani, Choe Miller, Naomi Daniel Sesay, Francis Baimba, Roberta Lansana, Simon Ruhweza, Zein Souma, Amanda Kargbo, Komba Koninga, Alie Tia, Jone Ngobeh, Foday Thoronka, Alusine Fofanah, Marietou F. Paye, Karlie Zhao, Ellory Laning, Oludayo Oluwaseyi Ope-ewe, Ayotunde Elijah Sijuwola, Femi Saibu, Ebenezer Kehinde Ogundana, Ruth Oluwaseun Obaado, Jolly Amoche Adole, Imonikhe Kennedy Kio, Folefac Agnes Njeandoh, Walter O. Oguta, Dolo Nosamiefan, Isatta Wurie
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Nature
Verified
Delphy: scalable, near-real-time Bayesian phylogenetics for outbreaks
Abstract Pathogen genomic analysis is central to tracking, understanding, and containing outbreaks, but complexity and high costs of state-of-the-art (SOTA) phylogenetic tools limit global access and impact. We introduce Delphy, an exact reformulation of Bayesian phylogenetics designed to transform its speed, scalability and accessibility while retaining SOTA accuracy.
Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans
The authors have declared no competing interest.
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