38: Bat ancestors, recombination, and rapid travel: origins of SARS-CoV and SARS-CoV-2

Pekar JE et al., Cell - Recombination-aware, whole-genome analyses of sarbecoviruses show that genomic fragments very closely related to SARS-CoV and SARS-CoV-2 circulated in horseshoe bats only years before human emergence. Phylogeography places recent ancestors in western China and northern Laos and indicates movement patterns inconsistent with bat-only dispersal, implicating intermediate hosts or wildlife trade. Key terms: sarbecovirus, recombination, phylogeography, horseshoe bats, zoonotic spillover. Study Highlights:The authors mapped recombination breakpoints and analyzed non-recombinant regions (NRRs) across sarbecovirus genomes to infer separate evolutionary histories for SARS-CoV-1-like and SARS-CoV-2-like viruses. Closest-inferred bat virus ancestors for both human SARS-CoVs often date just 1–6 years before human emergence in specific NRRs. Phylogeographic reconstructions place those recent ancestors in western China and northern Laos/Yunnan, and show viral diffusion rates approximating horseshoe bat movement. The geographic distances and required dispersal velocities make bat-only spread to emergence sites unlikely, supporting a role for intermediate hosts or wildlife trade. Conclusion:Non-recombinant genome segments reveal very recent bat ancestors of SARS-CoV and SARS-CoV-2 that likely could not have reached human emergence sites by bat movement alone, highlighting the importance of whole-genome surveillance in bats, targeted sampling in Southwest China and Northern Laos, and monitoring of wildlife trade pathways. Music:Enjoy the music based on this article at the end of the episode. Article title:The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 First author:Pekar JE Journal:Cell DOI:10.1016/j.cell.2025.03.035 Reference:Pekar JE, Lytras S, Ghafari M, et al. The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2. Cell. 2025;188:1–17. doi:10.1016/j.cell.2025.03.035 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/recency-geographical-origins-bat-viruses-sars-cov-sars-cov-2 QC:This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-06-07. QC Scope:- article metadata and core scientific claims from the narration- excludes analogies, intro/outro, and music- transcript coverage: Audited the transcript sections describing non-recombinant regions (NRRs), recombination-aware dating, the Prisoner of War (PoW) molecular clock, phylogeography, dispersal velocities, geographic origins of closest bat ancestors, and implications about wildlife trade as a bridge to emergence.- transcript topics: Recombination and non-recombinant regions (NRRs); NRR-based dating and closest-inferred bat ancestors; Prisoner of War (PoW) molecular clock and substitution saturation; Phylogeography and isolation by distance; Dispersal velocities and bat-host diffusion; Geographic origins of closest bat ancestors (SARS-CoV-1 in Western China; SARS-CoV-2 in Yunnan/Northern Laos) QC Summary:- factual score: 10/10- metadata score: 10/10- supported core claims: 8- claims flagged for review: 0- metadata checks passed: 4- metadata issues found: 0 Metadata Audited:- article_doi- article_title- article_...