Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell
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 int...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-07-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60988-8 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849402011649310720 |
|---|---|
| author | Deshan Perera Evan Li Paul MK Gordon Frank van der Meer Tarah Lynch John Gill Deirdre L. Church A. P. Jason de Koning Christian D. Huber Guido van Marle Alexander Platt Quan Long |
| author_facet | Deshan Perera Evan Li Paul MK Gordon Frank van der Meer Tarah Lynch John Gill Deirdre L. Church A. P. Jason de Koning Christian D. Huber Guido van Marle Alexander Platt Quan Long |
| author_sort | Deshan Perera |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-b2c3f7d856644f219fabe48fe7a59986 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-b2c3f7d856644f219fabe48fe7a599862025-08-20T03:37:38ZengNature PortfolioNature Communications2041-17232025-07-0116111710.1038/s41467-025-60988-8Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cellDeshan Perera0Evan Li1Paul MK Gordon2Frank van der Meer3Tarah Lynch4John Gill5Deirdre L. Church6A. P. Jason de Koning7Christian D. Huber8Guido van Marle9Alexander Platt10Quan Long11Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of CalgaryDepartment of Biochemistry & Molecular Biology, Cumming School of Medicine, University of CalgaryAlberta Children’s Hospital Research Institute, University of CalgaryFaculty of Veterinary Medicine, University of CalgaryProvincial Public Health Laboratory SouthDepartment of Medicine, University of CalgaryDepartment of Medicine, University of CalgaryDepartment of Biochemistry & Molecular Biology, Cumming School of Medicine, University of CalgaryDepartment of Biology, The Pennsylvania State UniversityDepartment of Microbiology, Immunology and Infectious Diseases, University of CalgaryDepartment of Genetics, Perelman School of Medicine at the University of PennsylvaniaDepartment of Biochemistry & Molecular Biology, Cumming School of Medicine, University of CalgaryAbstract 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.https://doi.org/10.1038/s41467-025-60988-8 |
| spellingShingle | Deshan Perera Evan Li Paul MK Gordon Frank van der Meer Tarah Lynch John Gill Deirdre L. Church A. P. Jason de Koning Christian D. Huber Guido van Marle Alexander Platt Quan Long Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell Nature Communications |
| title | Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell |
| title_full | Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell |
| title_fullStr | Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell |
| title_full_unstemmed | Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell |
| title_short | Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell |
| title_sort | apollo a comprehensive gpu powered within host simulator for viral evolution and infection dynamics across population tissue and cell |
| url | https://doi.org/10.1038/s41467-025-60988-8 |
| work_keys_str_mv | AT deshanperera apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT evanli apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT paulmkgordon apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT frankvandermeer apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT tarahlynch apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT johngill apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT deirdrelchurch apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT apjasondekoning apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT christiandhuber apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT guidovanmarle apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT alexanderplatt apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell AT quanlong apolloacomprehensivegpupoweredwithinhostsimulatorforviralevolutionandinfectiondynamicsacrosspopulationtissueandcell |