The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance

  1. Izumi Kimura
  2. Yusuke Kosugi
  3. Jiaqi Wu
  4. Jiri Zahradnik
  5. Daichi Yamasoba
  6. Erika P. Butlertanaka
  7. Yuri L. Tanaka
  8. Keiya Uriu
  9. Yafei Liu
  10. Nanami Morizako
  11. Kotaro Shirakawa
  12. Yasuhiro Kazuma
  13. Ryosuke Nomura
  14. Yoshihito Horisawa
  15. Kenzo Tokunaga
  16. Takamasa Ueno
  17. Akifumi Takaori-Kondo
  18. Gideon Schreiber
  19. Hisashi Arase
  20. Chihiro Motozono
  21. Akatsuki Saito
  22. So Nakagawa
  23. Kei Sato

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Abstract

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  3. Version published to 10.1016/j.celrep.2021.110218
  4. ScreenIT

    SciScore for 10.1101/2021.07.28.454085: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: EXPERIMENTAL MODEL AND SUBJECT DETAILS: Ethics Statement: For the use of human specimen, all protocols involving human subjects recruited at Kyoto University were reviewed and approved by the Institutional Review Boards of Kyoto University (approval number G0697).
    Consent: All human subjects provided written informed consent.
    Sex as a biological variableCollection of BNT162b2-Vaccinated Sera: Peripheral blood were collected four weeks after the second vaccination of BNT162b2 (Pfizer-BioNTech), and the sera of 18 vaccinees (average age: 40, range: 28-59, 22% male) were isolated from peripheral blood.
    RandomizationTo estimate the emerging time of the Lambda variant (C.37 lineage), we collected all Lambda sequences carrying the RSYLTPGD246-253N mutation that were sampled in 2020 (2 sequences) and randomly sampled 100 sequences in 2021.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Cell Culture: HEK293T cells (a human embryonic kidney cell line; ATCC CRL-3216), and HOS cells (a human osteosarcoma cell line; ATCC CRL-1543) were maintained in Dulbecco’s modified Eagle’s medium (high glucose) (Wako, Cat# 044-29765) containing 10% fetal calf serum and 1% PS.
    HOS
    suggested: None
    , luciferase-expressing reporter viruses pseudotyped with the SARS-CoV-2 S protein and its derivatives, HEK293T cells (1 × 106 cells) were cotransfected with 1 μg of psPAX2-IN/HiBiT (Ozono et al., 2020), 1 μg of pWPI-Luc2 (Ozono et al., 2020), and 500 ng of plasmids expressing parental S or its derivatives using Lipofectamine 3000 (Thermo Fisher Scientific, Cat# L3000015) or PEI Max (Polysciences, Cat# 24765-1) according to the manufacturer’s protocol.
    HEK293T
    suggested: None
    For the experiment, HOS-ACE2 cells and HOS-ACE2/TMPRSS2 cells (10,000 cells/50 ÎĽl) were seeded in 96-well plates and infected with 100 ÎĽl of the pseudoviruses prepared at 4 different doses.
    HOS-ACE2
    suggested: None
    HOS-ACE2/TMPRSS2
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    We also added the following 4 SARS-CoV-2 genomes as the outgroup: strain Wuhan-Hu-1 (GISAID ID: EPI_ISL_1532199, isolated on December 26, 2019), EPI_ISL_1093172 (isolated on August 25, 2020), and EPI_ISL_1534645 (isolated on November 30, 2020).
    Wuhan-Hu-1
    suggested: None
    Recombinant DNA
    SentencesResources
    Plasmids expressing the S proteins of the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Lambda (C.37) variants and the point mutants were generated by site-directed overlap extension PCR using pC-SARS2-S D614G (Ozono et al., 2021) as the template and the following primers listed in Table S4.
    pC-SARS2-S D614G
    suggested: None
    The resulting PCR fragment was digested with Acc65I or KpnI and NotI and inserted into the corresponding site of the pCAGGS vector (Niwa et al., 1991).
    pCAGGS
    suggested: RRID:Addgene_18926)
    Software and Algorithms
    SentencesResources
    We aligned entire genome sequences by using the FFT-NS-1 program in MAFFT suite v7.407 (Katoh and Standley, 2013) and deleted gapped regions in the 5’ and 3’ regions.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    We constructed a phylogenetic tree using IQ-TREE 2 v2.1.3 software (Minh et al., 2020) with 1,000 bootstraps (Figure S1A)
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    A timetree was summarized using TreeAnnotator software in the BEAST package and visualized by using FigTree v1.4.4 (Figure 1C and Figure S1B).
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    In Figures 2C and 2D, the crystal structure of SARS-CoV-2 S (PDB: 6ZGE) (Wrobel et al., 2020) was used as the template, and 40 homology models of the SARS-CoV-2 S of the Lambda variant were generated using Build Homology Model protocol MODELLER v9.24 (Fiser et al., 2000).
    MODELLER
    suggested: (MODELLER, RRID:SCR_008395)
    Nucleotide sequences were determined by DNA sequencing services (Fasmac or Eurofins), and the sequence data were analyzed by Sequencher v5.1 software (Gene Codes Corporation).
    Sequencher
    suggested: (Sequencher, RRID:SCR_001528)
    Then, the 80 μl mixture of pseudovirus and sera/antibodies was added into HOS-ACE2/TMPRSS2 cells (10,000 cells/50 μl) in a 96-well white plate and the luminescence was measured as described above (see “Pseudovirus Assay” above). 50% neutralization titer was calculated using Prism 9 (GraphPad Software)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: Thank you for sharing your data.

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  5. Version published to 10.1101/2021.07.28.454085v1 on bioRxiv