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

Author

Listed:
  • 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
    Yangzhou University)

  • 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
    SingHealth Duke-NUS Global Health Institute)

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.

Suggested Citation

  • Supaporn Wacharapluesadee & Chee Wah Tan & Patarapol Maneeorn & Prateep Duengkae & Feng Zhu & Yutthana Joyjinda & Thongchai Kaewpom & Wan Ni Chia & Weenassarin Ampoot & Beng Lee Lim & Kanthita Woracho, 2021. "Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21240-1
    DOI: 10.1038/s41467-021-21240-1
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    Cited by:

    1. Xinyuan Cui & Kewei Fan & Xianghui Liang & Wenjie Gong & Wu Chen & Biao He & Xiaoyuan Chen & Hai Wang & Xiao Wang & Ping Zhang & Xingbang Lu & Rujian Chen & Kaixiong Lin & Jiameng Liu & Junqiong Zhai , 2023. "Virus diversity, wildlife-domestic animal circulation and potential zoonotic viruses of small mammals, pangolins and zoo animals," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Jun-Yu Si & Yuan-Mei Chen & Ye-Hui Sun & Meng-Xue Gu & Mei-Ling Huang & Lu-Lu Shi & Xiao Yu & Xiao Yang & Qing Xiong & Cheng-Bao Ma & Peng Liu & Zheng-Li Shi & Huan Yan, 2024. "Sarbecovirus RBD indels and specific residues dictating multi-species ACE2 adaptiveness," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Wenjuan Du & Oliver Debski-Antoniak & Dubravka Drabek & Rien Haperen & Melissa Dortmondt & Joline Lee & Ieva Drulyte & Frank J. M. Kuppeveld & Frank Grosveld & Daniel L. Hurdiss & Berend-Jan Bosch, 2024. "Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Cecilia A. Sánchez & Hongying Li & Kendra L. Phelps & Carlos Zambrana-Torrelio & Lin-Fa Wang & Peng Zhou & Zheng-Li Shi & Kevin J. Olival & Peter Daszak, 2022. "A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    5. Cedric C. S. Tan & Jahcub Trew & Thomas P. Peacock & Kai Yi Mok & Charlie Hart & Kelvin Lau & Dongchun Ni & C. David L. Orme & Emma Ransome & William D. Pearse & Christopher M. Coleman & Dalan Bailey , 2023. "Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Luo-Yuan Xia & Zhen-Fei Wang & Xiao-Ming Cui & Yuan-Guo Li & Run-Ze Ye & Dai-Yun Zhu & Fang-Xu Li & Jie Zhang & Wen-Hao Wang & Ming-Zhu Zhang & Wan-Ying Gao & Lian-Feng Li & Teng-Cheng Que & Tie-Cheng, 2024. "Isolation and characterization of a pangolin-borne HKU4-related coronavirus that potentially infects human-DPP4-transgenic mice," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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