Bats may be cause of SARS-CoV-2 related virus in Southeast Asia

Nov. 10, 2021

Horseshoe bats (genus Rhinolophus) are believed to be the main natural reservoir of SARS-related coronaviruses, also named Sarbecoviruses. A high diversity of coronavirus species have been found in Rhinolophus bats collected in several provinces of China, according to a new study in Nature Communications.

More than a year has passed since the emergence of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic. However, information on the origin, reservoir, diversity, and extent of circulation of ancestors to SARS-CoV-2 remains scarce.

To date, the closest relatives to SARS-CoV-2 were identified from horseshoe bats sampled in Yunan province in southern China. 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. Two viruses were also detected in Sunda pangolins (Manis javanica) seized in two provinces of southern China.

More distant and highly mosaic recombinant viruses were also sampled from bats in the Zhejiang province, in eastern China in 2015 and 2017. Southeast Asia is considered a hotspot for emerging diseases. More than 25% of the world’s bat diversity is found there, and a close relative of SARS-CoV-2 was identified in bats captured in a cave in Thailand in June 2020.

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.

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 Yunan 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.

Nature Communications press release

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