Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant

  1. Xianding Deng
  2. Miguel A. Garcia-Knight
  3. Mir M. Khalid
  4. Venice Servellita
  5. Candace Wang
  6. Mary Kate Morris
  7. Alicia Sotomayor-González
  8. Dustin R. Glasner
  9. Kevin R. Reyes
  10. Amelia S. Gliwa
  11. Nikitha P. Reddy
  12. Claudia Sanchez San Martin
  13. Scot Federman
  14. Jing Cheng
  15. Joanna Balcerek
  16. Jordan Taylor
  17. Jessica A. Streithorst
  18. Steve Miller
  19. Bharath Sreekumar
  20. Pei-Yi Chen
  21. Ursula Schulze-Gahmen
  22. Taha Y. Taha
  23. Jennifer M. Hayashi
  24. Camille R. Simoneau
  25. G. Renuka Kumar
  26. Sarah McMahon
  27. Peter V. Lidsky
  28. Yinghong Xiao
  29. Peera Hemarajata
  30. Nicole M. Green
  31. Alex Espinosa
  32. Chantha Kath
  33. Monica Haw
  34. John Bell
  35. Jill K. Hacker
  36. Carl Hanson
  37. Debra A. Wadford
  38. Carlos Anaya
  39. Donna Ferguson
  40. Phillip A. Frankino
  41. Haridha Shivram
  42. Liana F. Lareau
  43. Stacia K. Wyman
  44. Melanie Ott
  45. Raul Andino
  46. Charles Y. Chiu

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Abstract

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  1. Version published to 10.1016/j.cell.2021.04.025
  2. ScreenIT

    SciScore for 10.1101/2021.03.07.21252647: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Clinical samples from UCSF were collected for a biorepository and sequenced according to protocols approved by the UCSF Institutional Review Board (protocol number 10-01116, 11-05519).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    In short, Illumina raw paired-end reads were first screened for SARS-CoV-2 sequences using BLASTn (BLAST+ package 2.9.0) alignment against viral reference genome NC_045512, and then processed using the BBTools suite, v38.87 (Bushnell, 2021).
    BLASTn
    suggested: (BLASTN, RRID:SCR_001598)
    BLAST+
    suggested: (Japan Bioinformatics, RRID:SCR_012250)
    Adapter sequences were trimmed and low-quality reads were removed using BBDuk, and then mapped to the NC_045512 reference genome using BBMap.
    BBMap
    suggested: (BBmap, RRID:SCR_016965)
    Multiple sequence alignment of 6 B.1.427/B.1.429 genomes and the Wuhan Hu-1 prototypical genome (GISAID ID: EPI_ISL_402125, GenBank accession number MN908947) was performed using the MAFFT aligner v7.388 (Katoh and Standley, 2013) as implemented in Geneious v11.1.5 (Kearse et al., 2012).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Geneious
    suggested: (Geneious, RRID:SCR_010519)
    Phylogenetic Analysis: High-quality SARS-CoV-2 genomes (n=2,519, 2,172 generated in the current study and 347 used as representative global genomes) were downloaded from the Global Initiative on Sharing of All Influenza Data (GISAID) database and processed using the NextStrain bioinformatics pipeline Augur using IQTREE v1.6.
    IQTREE
    suggested: None
    Molecular clock analysis of SARS-CoV-2 for estimating the TMRCA (time to most recent common ancestor) and divergence dates for the B.1.426/B.1.427 variant was performed using the Markov chain Monte Carlo (MCMC) method implemented by Bayesian Evolutionary Analysis on Sampling Trees (BEAST) software v.2.63 (Drummond et al., 2012).
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    Convergence was evaluated using Tracer v1.7.1 (Rambaut et al., 2018).
    Tracer
    suggested: (Tracer, RRID:SCR_019121)
    2.6.3 (Drummond et al., 2012) and visualized using FigTree v.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    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.

    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.

  3. Version published to 10.1101/2021.03.07.21252647v1 on medRxiv