Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor

  1. Hua Guo
  2. Ben Hu
  3. Hao-rui Si
  4. Yan Zhu
  5. Wei Zhang
  6. Bei Li
  7. Ang Li
  8. Rong Geng
  9. Hao-Feng Lin
  10. Xing-Lou Yang
  11. Peng Zhou
  12. Zheng-Li Shi

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Abstract

Severe respiratory disease coronavirus-2 (SARS-CoV-2) causes the most devastating disease, COVID-19, of the recent century. One of the unsolved scientific questions around SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbor the highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). Here, we report the identification of a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities to SARS-CoV-2 in the conserved ORF1b region, but only show less than 77.6% to all known SARSr-CoVs in genome level, thus forms a distinct lineage in the Sarbecovirus phylogenetic tree. We then found that RaTG15 receptor binding domain (RBD) can bind to and use Rhinolophus affinis bat ACE2 (RaACE2) but not human ACE2 as entry receptor, although which contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we show that none of the known viruses in bat SARSr-CoV-2 lineage or the novel lineage discovered so far use human ACE2 efficiently compared to SARSr-CoV-2 from pangolin or some of the SARSr-CoV-1 lineage viruses. Collectively, we suggest more systematic and longitudinal work in bats to prevent future spillover events caused by SARSr-CoVs or to better understand the origin of SARS-CoV-2.

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  1. ScreenIT

    SciScore for 10.1101/2021.05.21.445091: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsField Sample Permit: Bat Sampling and Coronavirus Detection: Sampling of bat was conducted in Mojiang county, Yunnan province at May 2015.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationAuthentication: Bat species identification was based on the partial sequence of cytochrome c oxidase subunit I (COI) gene.

    Table 2: Resources

    Antibodies
    SentencesResources
    Cells were subsequently washed five times and supplied with fresh DMEM + 10% FBS medium + anti-VSV-G antibody (Kerafast).
    anti-VSV-G
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    The RBD and ACE2 proteins used for the BLI binding assay were produced in HEK 293T/17 cells.
    HEK 293T/17
    suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
    Software and Algorithms
    SentencesResources
    NGS reads were first processed by Cutadapt (v.1.18) to eliminate the possible contamination.
    Cutadapt
    suggested: (cutadapt, RRID:SCR_011841)
    Then the clean reads were assembled into genomes using Geneious (v11.0.3) and MEGAHIT (v1.2.9).
    Geneious
    suggested: (Geneious, RRID:SCR_010519)
    Sequence alignments were created by ClustalW implemented in MEGA6 with default parameters.
    ClustalW
    suggested: (ClustalW, RRID:SCR_017277)
    Maximum Likelihood and Neighbour-joining phylogenetic trees were generated using the Jukes-Cantor model with 1000 bootstrap replicates in the MEGA6 software package.
    MEGA6
    suggested: (MEGA Software, RRID:SCR_000667)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  2. Version published to 10.1101/2021.05.21.445091v1 on bioRxiv
  3. Version published to 10.1080/22221751.2021.1956373