Characterization and evolutionary history of novel SARS-CoV-2-related viruses in bats from Cambodia
Abstract Circulating bat coronaviruses present a significant pandemic threat, yet our understanding of their genetic diversity and evolutionary dynamics remains limited. Over 3 years, we sampled 1,462 bats in Cambodia’s Steung Treng province, identifying extensive and diverse coronaviruses co-circulation. Using metatranscriptomic and amplicon sequencing, we generated 33 complete sarbecovirus genomes, revealing novel lineages that cluster into four distinct groups, each associated with different Rhinolophus bat species. Our analysis highlights rapid migration and recombination of sarbecovirus lineages over short distances and timescales. Of note, the receptor-binding domains of two novel viral groups exhibit high similarity to SARS-CoV-2, and pseudovirus assays confirmed the ability of this spike protein to mediate entry into cells expressing human ACE2, suggesting a potential zoonotic risk. The observed genetic diversity underscores the urgent need for continuous surveillance to identify high-risk animal-to-human interfaces and inform pandemic preparedness.
Authors
- Sovann Ly
- Thavry Hoem (ORCID: https://orcid.org/0000-0003-2456-3273)
- Kei Sato (ORCID: https://orcid.org/0000-0003-4431-1380)
- Déborah Delaune (ORCID: https://orcid.org/0000-0003-4970-9566)
- Elise Bruder
- Gavin J. D. Smith (ORCID: https://orcid.org/0000-0001-5031-468X)
- Julia Guillebaud (ORCID: https://orcid.org/0000-0002-9722-9041)
- Veasna Duong (ORCID: https://orcid.org/0000-0003-0353-1678)
- Artem Baidaliuk (ORCID: https://orcid.org/0000-0002-8351-1142)
- Julien Cappelle (ORCID: https://orcid.org/0000-0001-7668-1971)
- Vibol Hul (ORCID: https://orcid.org/0000-0002-2095-7235)
- Etienne Simon‐Lorière (ORCID: https://orcid.org/0000-0001-8420-7743)
- Leakhena Pum
- Tey Putita Ou (ORCID: https://orcid.org/0000-0001-8179-1382)
- Erik A. Karlsson (ORCID: https://orcid.org/0000-0001-6004-5671)
- Heidi Auerswald (ORCID: https://orcid.org/0000-0002-4717-7618)
- V Chevalier
- Philippe Dussart (ORCID: https://orcid.org/0000-0002-1931-3037)
- Frédérick Arnaud (ORCID: https://orcid.org/0000-0001-6893-9848)
- Sothyra Tum (ORCID: https://orcid.org/0000-0002-6730-7264)
- Matthieu Prot (ORCID: https://orcid.org/0000-0003-2337-2491)
- Rafael Rahal Guaragna Machado (ORCID: https://orcid.org/0000-0001-6974-5092)
- Dany Chheang
Institutions
- Université Claude Bernard Lyon 1 (FR)
- Centre National de la Recherche Scientifique (FR)
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR)
- Institut Pasteur (FR)
- École Pratique des Hautes Études (FR)
- Ministry of Health (KH)
- Ministry of Agriculture Forestry and Fisheries (KH)
- Université de Montpellier (FR)
- Université Paris Cité (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Animal, Santé, Territoires, Risques et Ecosystèmes (FR)
- Evolutionary Genomics (United States) (US)
- Duke-NUS Medical School (SG)
- Montpellier Business School (FR)
- Institut Pasteur de Madagascar (MG)
- Institut Pasteur du Cambodge (KH)
- The University of Tokyo (JP)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-07-23
- DOI
- https://doi.org/10.1038/s41467-026-75954-1
- Citations
- 1
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00