A novel SARS-CoV-2 related coronavirus in bats from Cambodia

Deborah Delaune (1, 2, 3) , Vibol Hul (4) , Erik A. Karlsson (4, 5) , Alexandre A. Hassanin (6) , Tey Putita Ou (4) , Artem Baidaliuk (1) , Fabiana Gámbaro (1, 7) , Matthieu Prot (1) , Vuong Tan Tu (6) , Sokha Chea (8) , Lucy Keatts (9, 10) , Jonna Mazet (10) , Christine K. Johnson (10) , Philippe Buchy (4) , Philippe Dussart (4) , Tracey Goldstein (10) , Etienne Simon-Loriere (1) , Veasna Duong (4)

1 Génomique évolutive des virus à ARN - Evolutionary genomics of RNA viruses
2 IRBA - Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge]
3 Université Paris-Saclay
4 Unité de Virologie / Virology Unit [Phnom Penh]
5 UVE - Unité des Virus Emergents
6 ISYEB - Institut de Systématique, Evolution, Biodiversité
7 UPCité - Université Paris Cité
8 Wildlife Conservation Society [Phnom Penh, Cambodia]
9 WCS - Wildlife Conservation Society
10 UC Davis - University of California [Davis]

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identifies nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a region of the spike, which is not compatible with human ACE2-mediated entry. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously reported, and suggests that Southeast Asia represents a key area to consider for future surveillance for coronaviruses.

Domains: Virology; Systematics, Phylogenetics and taxonomy

Deborah Delaune, Vibol Hul, Erik A. Karlsson, Alexandre A. Hassanin, Tey Putita Ou, et al.. A novel SARS-CoV-2 related coronavirus in bats from Cambodia. Nature Communications, 2021, 12 (1), pp.6563. ⟨10.1038/s41467-021-26809-4⟩. ⟨pasteur-03576361⟩