Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia

Supaporn Wacharapluesadee, Chee Wah Tan, Patarapol Maneeorn, Prateep Duengkae, Feng Zhu, Yutthana Joyjinda, Thongchai Kaewpom, Wan Ni Chia, Weenassarin Ampoot, Beng Lee Lim, Kanthita Worachotsueptrakun, Vivian Chih-Wei Chen, Nutthinee Sirichan, Chanida Ruchisrisarod, Apaporn Rodpan, Kirana Noradechanon, Thanawadee Phaichana, Niran Jantarat, Boonchu Thongnumchaima, Changchun Tu, Gary Crameri, Martha M. Stokes, Thiravat Hemachudha () and Lin-Fa Wang ()
Additional contact information
Supaporn Wacharapluesadee: Chulalongkorn University
Chee Wah Tan: Duke-NUS Medical School
Patarapol Maneeorn: Ministry of Natural Resources and Environment
Prateep Duengkae: Kasetsart University
Feng Zhu: Duke-NUS Medical School
Yutthana Joyjinda: Chulalongkorn University
Thongchai Kaewpom: Chulalongkorn University
Wan Ni Chia: Duke-NUS Medical School
Weenassarin Ampoot: Chulalongkorn University
Beng Lee Lim: Duke-NUS Medical School
Kanthita Worachotsueptrakun: Chulalongkorn University
Vivian Chih-Wei Chen: Duke-NUS Medical School
Nutthinee Sirichan: Kasetsart University
Chanida Ruchisrisarod: Chulalongkorn University
Apaporn Rodpan: Chulalongkorn University
Kirana Noradechanon: Ministry of Natural Resources and Environment
Thanawadee Phaichana: Ministry of Natural Resources and Environment
Niran Jantarat: Ministry of Natural Resources and Environment
Boonchu Thongnumchaima: Ministry of Natural Resources and Environment
Changchun Tu: Chinese Academy of Agricultural Sciences
Gary Crameri: CSIRO Australian Animal Health Laboratory
Martha M. Stokes: Defense Threat Reduction Agency
Thiravat Hemachudha: Chulalongkorn University
Lin-Fa Wang: Duke-NUS Medical School

Nature Communications, 2021, vol. 12, issue 1, 1-9

Abstract: Abstract Among the many questions unanswered for the COVID-19 pandemic are the origin of SARS-CoV-2 and the potential role of intermediate animal host(s) in the early animal-to-human transmission. The discovery of RaTG13 bat coronavirus in China suggested a high probability of a bat origin. Here we report molecular and serological evidence of SARS-CoV-2 related coronaviruses (SC2r-CoVs) actively circulating in bats in Southeast Asia. Whole genome sequences were obtained from five independent bats (Rhinolophus acuminatus) in a Thai cave yielding a single isolate (named RacCS203) which is most related to the RmYN02 isolate found in Rhinolophus malayanus in Yunnan, China. SARS-CoV-2 neutralizing antibodies were also detected in bats of the same colony and in a pangolin at a wildlife checkpoint in Southern Thailand. Antisera raised against the receptor binding domain (RBD) of RmYN02 was able to cross-neutralize SARS-CoV-2 despite the fact that the RBD of RacCS203 or RmYN02 failed to bind ACE2. Although the origin of the virus remains unresolved, our study extended the geographic distribution of genetically diverse SC2r-CoVs from Japan and China to Thailand over a 4800-km range. Cross-border surveillance is urgently needed to find the immediate progenitor virus of SARS-CoV-2.

Date: 2021
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DOI: 10.1038/s41467-021-21240-1

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