Estimating the elevated transmissibility of the B.1.1.7 strain over previously circulating strains in England using GISAID sequence frequencies

  1. Chayada Piantham
  2. Natalie M. Linton
  3. Hiroshi Nishiura
  4. Kimihito Ito

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Abstract

The B.1.1.7 strain, also referred to as Alpha variant, is a variant strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The Alpha variant is considered to possess higher transmissibility compared to the strains previously circulating in England. This paper proposes a new method to estimate the selective advantage of a mutant strain over another strain using the time course of strain frequencies and the distribution of the serial interval of infections. This method allows the instantaneous reproduction numbers of infections to vary over calendar time. The proposed method also assumes that the selective advantage of a mutant strain over previously circulating strains is constant. Applying the method to SARS-CoV-2 sequence data from England, the instantaneous reproduction number of the B.1.1.7 strain was estimated to be 26.6–45.9% higher than previously circulating strains in England. This result indicates that control measures should be strengthened by 26.6–45.9% when the B.1.1.7 strain is newly introduced to a country where viruses with similar transmissibility to the preexisting strain in England are predominant.

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  2. Rapid Reviews Infectious Diseases

    Christine Tedijanto

    Review of "Estimating the increased transmissibility of the B.1.1.7 strain over previously circulating strains in England using fractions of GISAID sequences and the distribution of serial intervals"

    Reviewers: Christine Tedijanto (UCSF) | 📗📗📗📗◻️ 

  3. Version published to 10.1101/2021.03.17.21253775v4 on medRxiv
  4. Version published to 10.1101/2021.03.17.21253775v3 on medRxiv
  5. Version published to 10.1101/2021.03.17.21253775v2 on medRxiv
  6. ScreenIT

    SciScore for 10.1101/2021.03.17.21253775: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Nucleotide sequences that determined from viruses detected in England were selected and aligned to the reference amino acid sequence of S protein of SARS-CoV-2 virus (YP_009724390) using DIAMOND (Buchfink et al., 2015).
    DIAMOND
    suggested: (DIAMOND, RRID:SCR_009457)
    The aligned nucleotide sequences were translated into amino acid sequences, then were aligned with the reference amino acid sequence of S protein using MAFFT (Katoh et al., 2002).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    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.

  7. Version published to 10.1101/2021.03.17.21253775v1 on medRxiv