A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.

ABSTRACT: Millions of SARS-CoV-2 genome sequences were collected during the COVID-19 pandemic, forming a dataset of unprecedented richness. Estimated genealogies are fundamental to understanding this ocean of data and form the primary input to many downstream analyses. A basic assumption of methods to infer genealogies from viral genetic data is that recombination is negligible and the genealogy is a tree. However, recombinant lineages have risen to global prevalence, and simple tree representations are therefore incomplete and potentially misleading. We present sc2ts, a method to infer reticulate genealogies as an Ancestral Recombination Graph (ARG) in real time at pandemic scale. We infer an ARG for 2.48 million SARS-CoV-2 genomes, which leverages the widely used tskit software ecosystem to suppor

SUBMITTER: Zhan SH 

PROVIDER: S-EPMC12642650 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature