Characterization and evolutionary history of novel SARS-CoV-2-related viruses in bats from Cambodia
- Tey Putita Ou
- Julia Guillebaud
- Artem Baidaliuk
- Sothyra Tum
- Dany Chheang
- Deborah Delaune
- Matthieu Prot
- Elise Bruder
- Rafael Rahal Guaragna Machado
- Leakhena Pum
- Vibol Hul
- Thavry Hoem
- Sovann Ly
- Heidi Auerswald
- Frederick Arnaud
- Kei Sato
- Gavin JD Smith
- Philippe Dussart
- Erik A. Karlsson
- Véronique Chevalier
- Julien Cappelle
- Veasna Duong
- Etienne Simon-Lorière
2026-07-23
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 sequences, 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.