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Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins

Author

Listed:
  • Kangpeng Xiao

    (College of Veterinary Medicine, South China Agricultural University
    Guangdong Laboratory for Lingnan Modern Agriculture)

  • Junqiong Zhai

    (Guangzhou Zoo & Guangzhou Wildlife Research Center)

  • Yaoyu Feng

    (College of Veterinary Medicine, South China Agricultural University
    Guangdong Laboratory for Lingnan Modern Agriculture)

  • Niu Zhou

    (Guangzhou Zoo & Guangzhou Wildlife Research Center)

  • Xu Zhang

    (College of Veterinary Medicine, South China Agricultural University
    Guangdong Laboratory for Lingnan Modern Agriculture)

  • Jie-Jian Zou

    (Guangdong Provincial Wildlife Rescue Center)

  • Na Li

    (College of Veterinary Medicine, South China Agricultural University
    Guangdong Laboratory for Lingnan Modern Agriculture)

  • Yaqiong Guo

    (College of Veterinary Medicine, South China Agricultural University
    Guangdong Laboratory for Lingnan Modern Agriculture)

  • Xiaobing Li

    (College of Veterinary Medicine, South China Agricultural University)

  • Xuejuan Shen

    (College of Veterinary Medicine, South China Agricultural University)

  • Zhipeng Zhang

    (College of Veterinary Medicine, South China Agricultural University)

  • Fanfan Shu

    (College of Veterinary Medicine, South China Agricultural University
    Guangdong Laboratory for Lingnan Modern Agriculture)

  • Wanyi Huang

    (College of Veterinary Medicine, South China Agricultural University
    Guangdong Laboratory for Lingnan Modern Agriculture)

  • Yu Li

    (China Agricultural University)

  • Ziding Zhang

    (China Agricultural University)

  • Rui-Ai Chen

    (College of Veterinary Medicine, South China Agricultural University
    Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology)

  • Ya-Jiang Wu

    (Guangzhou Zoo & Guangzhou Wildlife Research Center)

  • Shi-Ming Peng

    (Guangzhou Zoo & Guangzhou Wildlife Research Center)

  • Mian Huang

    (Guangzhou Zoo & Guangzhou Wildlife Research Center)

  • Wei-Jun Xie

    (Guangzhou Zoo & Guangzhou Wildlife Research Center)

  • Qin-Hui Cai

    (Guangzhou Zoo & Guangzhou Wildlife Research Center)

  • Fang-Hui Hou

    (Guangdong Provincial Wildlife Rescue Center)

  • Wu Chen

    (Guangzhou Zoo & Guangzhou Wildlife Research Center)

  • Lihua Xiao

    (College of Veterinary Medicine, South China Agricultural University
    Guangdong Laboratory for Lingnan Modern Agriculture)

  • Yongyi Shen

    (College of Veterinary Medicine, South China Agricultural University
    Guangdong Laboratory for Lingnan Modern Agriculture)

Abstract

The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health1. The new coronavirus responsible for this outbreak—severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG132. Although bats may be the reservoir host for a variety of coronaviruses3,4, it remains unknown whether SARS-CoV-2 has additional host species. Here we show that a coronavirus, which we name pangolin-CoV, isolated from a Malayan pangolin has 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S proteins, respectively. In particular, the receptor-binding domain of the S protein of pangolin-CoV is almost identical to that of SARS-CoV-2, with one difference in a noncritical amino acid. Our comparative genomic analysis suggests that SARS-CoV-2 may have originated in the recombination of a virus similar to pangolin-CoV with one similar to RaTG13. Pangolin-CoV was detected in 17 out of the 25 Malayan pangolins that we analysed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus from pangolins that is closely related to SARS-CoV-2 suggests that these animals have the potential to act as an intermediate host of SARS-CoV-2. This newly identified coronavirus from pangolins—the most-trafficked mammal in the illegal wildlife trade—could represent a future threat to public health if wildlife trade is not effectively controlled.

Suggested Citation

  • Kangpeng Xiao & Junqiong Zhai & Yaoyu Feng & Niu Zhou & Xu Zhang & Jie-Jian Zou & Na Li & Yaqiong Guo & Xiaobing Li & Xuejuan Shen & Zhipeng Zhang & Fanfan Shu & Wanyi Huang & Yu Li & Ziding Zhang & R, 2020. "Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins," Nature, Nature, vol. 583(7815), pages 286-289, July.
  • Handle: RePEc:nat:nature:v:583:y:2020:i:7815:d:10.1038_s41586-020-2313-x
    DOI: 10.1038/s41586-020-2313-x
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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. Zepeng Xu & Xinrui Kang & Pu Han & Pei Du & Linjie Li & Anqi Zheng & Chuxia Deng & Jianxun Qi & Xin Zhao & Qihui Wang & Kefang Liu & George Fu Gao, 2022. "Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    4. Fabian Zech & Daniel Schniertshauer & Christoph Jung & Alexandra Herrmann & Arne Cordsmeier & Qinya Xie & Rayhane Nchioua & Caterina Prelli Bozzo & Meta Volcic & Lennart Koepke & Janis A. Müller & Jan, 2021. "Spike residue 403 affects binding of coronavirus spikes to human ACE2," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    5. Run-Ze Ye & Xiao-Yang Wang & Yu-Yu Li & Bao-Yu Wang & Ke Song & Yi-Fei Wang & Jing Liu & Bai-Hui Wang & Shan-Shan Wang & Qing Xu & Ze-Hui Li & Yi-Di Du & Jin-Yue Liu & Jia-Jing Zheng & Li-Feng Du & We, 2023. "Systematic review and integrated data analysis reveal diverse pangolin-associated microbes with infection potential," Nature Communications, Nature, vol. 14(1), pages 1-10, 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.
    7. Liang Leng & Zhichao Xu & Bixia Hong & Binbin Zhao & Ya Tian & Can Wang & Lulu Yang & Zhongmei Zou & Lingyu Li & Ke Liu & Wanjun Peng & Jiangning Liu & Zhoujie An & Yalin Wang & Baozhong Duan & Zhigan, 2024. "Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    8. Dongsheng Chen & Jian Sun & Jiacheng Zhu & Xiangning Ding & Tianming Lan & Xiran Wang & Weiying Wu & Zhihua Ou & Linnan Zhu & Peiwen Ding & Haoyu Wang & Lihua Luo & Rong Xiang & Xiaoling Wang & Jiayin, 2021. "Single cell atlas for 11 non-model mammals, reptiles and birds," Nature Communications, Nature, vol. 12(1), pages 1-17, December.

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