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Min-Sheng Peng, Jian-Bo Li, Zheng-Fei Cai, Hang Liu, Xiaolu Tang, Ruochen Ying, Jia-Nan Zhang, Jia-Jun Tao, Ting-Ting Yin, Tao Zhang, Jing-Yang Hu, Ru-Nian Wu, Zhong-Yin Zhou, Zhi-Gang Zhang, Li Yu, Yong-Gang Yao, Zheng-Li Shi, Xue-Mei Lu, Jian Lu, Ya-Ping Zhang. The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks. Zoological Research, 2021, 42(6): 834-844. doi: 10.24272/j.issn.2095-8137.2021.334
Citation: Min-Sheng Peng, Jian-Bo Li, Zheng-Fei Cai, Hang Liu, Xiaolu Tang, Ruochen Ying, Jia-Nan Zhang, Jia-Jun Tao, Ting-Ting Yin, Tao Zhang, Jing-Yang Hu, Ru-Nian Wu, Zhong-Yin Zhou, Zhi-Gang Zhang, Li Yu, Yong-Gang Yao, Zheng-Li Shi, Xue-Mei Lu, Jian Lu, Ya-Ping Zhang. The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks. Zoological Research, 2021, 42(6): 834-844. doi: 10.24272/j.issn.2095-8137.2021.334

穿山甲新冠相关病毒高度多样性警示潜在的生态风险

doi: 10.24272/j.issn.2095-8137.2021.334

The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks

Funds: This work was supported by the National Key Research and Development Projects of the Ministry of Science and Technology of China, National Key Research and Development Program of China (2021YFC0863300), Ministry of Agriculture of China (2016ZX08009003-006), Key Program of Chinese Academy of Sciences (KJZD-SW-L11), and Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (the Large Research Infrastructure Funding)
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  • 摘要: 了解新冠病毒(SARS-CoV-2)的起源和进化历史将为COVID-19疫情的防控以及潜在的人兽共患病的预防提供重要见解。穿山甲携带新冠相关病毒,但其在病毒起源和进化中扮演的角色尚不清楚。我们对采集自4个穿山甲物种163只个体的172份组织样本进行新冠相关病毒筛选,在4只爪哇穿山甲(Manis javanica)和1只中华穿山甲(M. pentadactyla)的肌肉样本中检测到了病毒核酸阳性信号。对穿山甲线粒体DNA的系统地理分析表明这5份阳性穿山甲样本可能起源于东南亚。针对病毒核酸含量低且降解严重的特点,我们采用古代DNA研究中广泛使用的目标捕获测序技术,从中华穿山甲样本中获得了长为22895 nt的新冠相关病毒部分基因组序列(MP20)。系统发育分析显示MP20与广西查获的马来亚穿山甲携带的新冠相关病毒亲缘关系密切,聚类为一个支系。蝙蝠冠状病毒通过重组对这一支系的穿山甲新冠相关病毒具有遗传贡献。对原始测序数据的进一步分析显示穿山甲中新冠相关病毒的遗传多样性大大高于此前的预期。穿山甲中新冠相关病毒的潜在感染性和高度的遗传多样性提示了人兽共患的致病性冠状病毒进化和传播的生态风险。
    #Authors contributed equally to this work
  • Figure  1.  Genetic characterization of pangolin-CoVs in pangolin muscles

    A: The five samples that yielded positive RT-PCR signals of SC2r-CoVs. The nomenclature of mitochondrial DNA (mtDNA) clusters used for inferring the possible geographic origins of the samples is given in reference (Hu et al., 2020). B: Sequencing depth of clean reads remapped to MP20 using nucleotide extraction and enrichment technologies. The genome organization of the SARS-CoV-2 reference strain MN908947 is shown. C: Sliding window analysis of nucleotide sequence similarity between SARS-CoV-2 and SC2r-CoVs/SARSr-CoVs from bats and pangolins. D: Maximum likelihood tree based on the alignment of the 22 genomes with the substitution model GTR+I+G4. Bootstrap values calculated from 1000 replicates are shown.

    Figure  2.  The numbers of overlapping iHVs between pangolin viral sequencing libraries at the genome-wide level (A) and at the level of the S gene (B)

    Figure  3.  Recombination analysis of the pangolin-CoV-GXC sublineage

    A: Similarity plot comparing 21 viruses related to MP20 from successfully captured coding sequences (CDSs). *: Region for which a recombination signal was detected. SC2r-CoVs are displayed in warm colors, and SARSr-CoVs are displayed in cool colors. B: Similarity plot comparing 20 viruses related to the pangolin-CoV GXP5L. *: Region for which a recombination signal was detected. C, D: Neighboring-joining phylogenetic trees for regions with a recombination signal based on all positions (C) and based on only the third positions (D) in the codons. The bootstrap values calculated from 1000 replicates and branch scale bars are shown.

    Table  1.   The number of putative iHVs identified in the pangolin-CoV-GXC sublineage

    LibraryGXP1EGXP5LGXP5EGXP4LGXP2V Total
    iHVs
    (union)
    Median coverage
    (25%, 75%)
    420
    (56, 2558)
    341
    (37, 1547)
    829
    (130, 3662)
    247
    (126, 443)
    133
    (88, 254)

    Genome-wide
    Synonymous9361139151217
    Nonsynonymous162107181318336
    Frameshift1058510822114264
    Stop-gain310003
    Intergenic79232029
    Other322003
    Total37326543271143852
    S gene
    Synonymous318131036
    Nonsynonymous6320286073
    Frameshift23201661846
    Stop-gain100001
    Other211002
    Total12049581318158
    The SRA accession Nos. are as follows: SRR11093266 (GXP1E), SRR11093267 (GXP5L), SRR11093268 (GXP5E), SRR11093269 (GXP4L), and SRR11093271 (GXP2V). Sites with coverage of ≥150X and ≥10 reads covering the alternative alleles in each library.
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  • 收稿日期:  2021-09-22
  • 录用日期:  2021-11-09
  • 网络出版日期:  2021-11-10
  • 刊出日期:  2021-11-18

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