Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell

Deshan Perera, Evan Li, Paul MK Gordon, Frank Meer, Tarah Lynch, John Gill, Deirdre L. Church, A. P. Jason Koning, Christian D. Huber, Guido Marle (), Alexander Platt () and Quan Long ()
Additional contact information
Deshan Perera: University of Calgary
Evan Li: University of Calgary
Paul MK Gordon: University of Calgary
Frank Meer: University of Calgary
Tarah Lynch: Provincial Public Health Laboratory South
John Gill: University of Calgary
Deirdre L. Church: University of Calgary
A. P. Jason Koning: University of Calgary
Christian D. Huber: The Pennsylvania State University
Guido Marle: University of Calgary
Alexander Platt: Perelman School of Medicine at the University of Pennsylvania
Quan Long: University of Calgary

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Modern sequencing instruments bring unprecedented opportunity to study within-host viral evolution in conjunction with viral transmissions between hosts. However, no computational simulators are available to assist the characterization of within-host dynamics. This limits our ability to interpret epidemiological predictions incorporating within-host evolution and to validate computational inference tools. To fill this need we developed Apollo, a GPU-accelerated, out-of-core tool for within-host simulation of viral evolution and infection dynamics across population, tissue, and cellular levels. Apollo is scalable to hundreds of millions of viral genomes and can handle complex demographic and population genetic models. Apollo can replicate real within-host viral evolution; accurately recapturing observed viral sequences from HIV and SARS-CoV-2 cohorts derived from initial population-genetic configurations. For practical applications, using Apollo-simulated viral genomes and transmission networks, we validated and uncovered the limitations of a widely used viral transmission inference tool.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-60988-8 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60988-8

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-60988-8

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().