A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel

  1. Neta Zuckerman
  2. Shay Fleishon
  3. Efrat Bucris
  4. Dana Bar-Ilan
  5. Michal Linial
  6. Itay Bar-Or
  7. Victoria Indenbaum
  8. Merav Weil
  9. Yaniv Lustig
  10. Ella Mendelson
  11. Michal Mandelboim
  12. Orna Mor
  13. Neta Zuckerman
  14. on behalf of the Israel National Consortium for SARS-CoV-2 Sequencing

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

The routine detection, surveillance, and reporting of novel SARS-CoV-2 variants is crucial, as these threaten to hinder global vaccination efforts. Herein we report a novel local variant with a non-synonymous mutation in the spike (S) protein P681H. This local Israeli variant was not associated with a higher infection rate or higher prevalence. Furthermore, the local variant was successfully neutralized by sera from fully vaccinated individuals at a comparable level to the B.1.1.7 variant and an Israel wild-type strain. While it is not a variant of concern, routine monitoring by sequencing is still required.

Article activity feed

  1. Version published to 10.3390/vaccines9060616
  2. ScreenIT

    SciScore for 10.1101/2021.03.25.21253908: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Virus-serum mixtures were added to the Vero E-6 cells and incubated for five days at 33ºC, after which Gentain violet staining (1%) was used to stain and fix the cell culture layer.
    Vero E-6
    suggested: None
    Software and Algorithms
    SentencesResources
    Bioinformatics analysis: Fastq files were subjected to quality control using FastQC (www.bioinformatics.babraham.ac.uk/ projects/fastqc/) and MultiQC [6] and low-quality sequences were filtered using trimmomatic [7].
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    MultiQC
    suggested: (MultiQC, RRID:SCR_014982)
    trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Sequences were mapped to the SARS-CoV-2 reference genomes (NC_045512.2) using Burrows-Wheeler aligner (BWA) mem [8]
    BWA
    suggested: (BWA, RRID:SCR_010910)
    Resulting BAM files were sorted, indexed and subjected to quality control using SAMtools suite [9].
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Sequences were aligned to SARS-CoV-2 reference genome (NC_045512.2) using MAFFT [10].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Phylogenetic trees were constructed using the Augur pipeline [2].
    Augur
    suggested: None
    Sequences were aligned to SARS-CoV-2 reference genome (NC_045512.2) using MAFFT [10], and a time-resolved phylogenetic tree was constructed with IQ-Tree [13] and TreeTime [14] under the GTR substitution model and visualized with auspice [2].
    IQ-Tree
    suggested: (IQ-TREE, RRID:SCR_017254)
    Analysis of sewage samples was conducted using a custom R code and the Bioconductor package Rsamtools [16].
    Bioconductor
    suggested: (Bioconductor, RRID:SCR_006442)
    Rsamtools
    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.

    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 10.1101/2021.03.25.21253908v1 on medRxiv