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

Deborah Delaune,Artem Baidaliuk,Vibol Hul,Sokha Chea,Christine K Johnson,Philippe Dussart,Lucy Keatts,Tey Putita Ou,Fabiana Gámbaro,Philippe Buchy,Erik A Karlsson,Vuong Tan Tu,Tracey Goldstein,Veasna Duong,Etienne Simon-Lorière,Jonna Mazet,Alexandre Hassanin,Matthieu Prot

doi:10.1038/s41467-021-26809-4

Abstract

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.

Highlights

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID19 pandemic is still fragmentary
Over a year has passed since the emergence of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2)[1], responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic
RaTG13 was sequenced from a Rhinolophus affinis bat in 2013, RmYN02 from a Rhinolophus malayanus bat in 2019, and RpYN06 from a Rhinolophus pusillus in 2020

Summary

Introduction

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID19 pandemic is still fragmentary. The closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. 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. The closest relatives to SARS-CoV-2 were identified from horseshoe bats sampled in the Yunnan province, southern China[1,4,5]. In this work we report the identification and characterization of two coronaviruses closely related to SARS-CoV-2 in bats sampled in Cambodia in 2010, indicating that this viral lineage circulates in a much wider geographic area than previous reported

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Conclusion