SARS-like Coronaviruses in Horseshoe Bats (Rhinolophus spp.) in Russia, 2020

  1. Sergey Alkhovsky
  2. Sergey Lenshin
  3. Alexey Romashin
  4. Tatyana Vishnevskaya
  5. Oleg Vyshemirsky
  6. Yulia Bulycheva
  7. Dmitry Lvov
  8. Asya Gitelman

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Abstract

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.

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  1. Version published to 10.3390/v14010113
  2. Version published to 10.1101/2021.05.17.444362v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.05.17.444362: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: The samples from bats were collected in Sochi National Park (Sochi-Adler, Krasnodar krai, Russia) and surrounding areas in March-October 2020.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Obtained contig sequences were analyzed using blastx algorithm by DIAMOND software (11) against nr ‘Viruses’ database that included all reference viral sequences available in GenBank at December 2020.
    blastx
    suggested: (BLASTX, RRID:SCR_001653)
    DIAMOND
    suggested: (DIAMOND, RRID:SCR_009457)
    Nucleotide and deduced amino acid sequences were alignment by ClustalW implemented in MEGAX software (12).
    ClustalW
    suggested: (ClustalW, RRID:SCR_017277)
    Phylogenetic trees were inferred by ‘maximum likelihood’ method using appropriate model with 1000 bootstrap replicates by MEGAX software.
    MEGAX
    suggested: None

    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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  4. Version published to 10.1101/2021.05.17.444362v1 on bioRxiv