Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy

  1. Francesca Di Giallonardo
  2. Ilaria Puglia
  3. Valentina Curini
  4. Cesare Cammà
  5. Iolanda Mangone
  6. Paolo Calistri
  7. Joanna C. A. Cobbin
  8. Edward C. Holmes
  9. Alessio Lorusso

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Abstract

Italy’s second wave of SARS-CoV-2 has hit hard, with more than three million cases and over 100,000 deaths, representing an almost ten-fold increase in the numbers reported by August 2020. Herein, we present an analysis of 6515 SARS-CoV-2 sequences sampled in Italy between 29 January 2020 and 1 March 2021 and show how different lineages emerged multiple times independently despite lockdown restrictions. Virus lineage B.1.177 became the dominant variant in November 2020, when cases peaked at 40,000 a day, but since January 2021 this is being replaced by the B.1.1.7 ‘variant of concern’. In addition, we report a sudden increase in another documented variant of concern—lineage P.1—from December 2020 onwards, most likely caused by a single introduction into Italy. We again highlight how international importations drive the emergence of new lineages and that genome sequencing should remain a top priority for ongoing surveillance in Italy.

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  1. Version published to 10.3390/v13050794
  2. ScreenIT

    SciScore for 10.1101/2021.03.24.21254277: (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.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Three separate alignments were performed using MAFFT implementing the L-INS-I algorithm and manually inspected for accuracy using Geneious Prime(r) 2021.1.1 (https://www.geneious.com)24.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Geneious Prime(r
    suggested: None
    A maximum likelihood tree was estimated for each lineage using IQ-TREE implementing the following: Hasegawa-Kishino-Yano nucleotide substitution model with a gamma distributed rate variation among sites (HKY+Γ) and an ultrafast bootstrap method (1000 repetitions)25,26.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)

    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 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 10.1101/2021.03.24.21254277v1 on medRxiv