Introductions and evolutions of SARS-CoV-2 strains in Japan

  1. Reitaro Tokumasu
  2. Dilhan Weeraratne
  3. Jane Snowdon
  4. Laxmi Parida
  5. Michiharu Kudo
  6. Takahiko Koyama

Reviewed by

Read the full article See related articles

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

Log in to save this article

Abstract

COVID-19 caused by SARS-CoV-2 was first identified in Japan on January 15 th , 2020, soon after the pandemic originated in Wuhan, China. Subsequently, Japan experienced three distinct waves of the outbreak in the span of a year and has been attributed to new exogenous strains and evolving existing strains. Japan engaged very early on in tracking different COVID-19 strains and have sequenced approximately 5% of all confirmed cases. While Japan has enforced stringent airport surveillance on cross-border travelers and returnees, some carriers appear to have advanced through the quarantine stations undetected. In this study 30493 genomes sampled in Japan were analyzed to understand the strains, heterogeneity and temporal evolution of different SARS-CoV-2 strains. We identified 12 discrete strains with a substantial number of cases with most strains possessing the spike (S) D614G and nucleocapsid (N) 203_204delinsKR mutations. 155 distinct strains have been introduced into Japan and 39 of them were introduced after strict quarantine policy was implemented. In particular, the B.1.1.7 strain, that emerged in the United Kingdom (UK) in September 2020, has been circulating in Japan since late 2020 after eluding cross-border quarantine stations. Similarly, the B.1.351 strain dubbed the South African variant, P.1 Brazilian strain and R.1 strain with the spike E484K mutation have been detected in Japan. At least 14 exogenous B.1.1.7 sub-strains have been independently introduced in Japan as of late March 2021, and these strains carry mutations that give selective advantage including N501Y, H69_V70del, and E484K that confer increased transmissibility, reduced efficacy to vaccines and possible increased virulence. Furthermore, various strains, which harbor multiple variants in the PCR primers and the probe developed by National Institute of Infectious Disease (NIID), are emerging. It is imperative that the quarantine policy be revised, cross-border surveillance reinforced, and new public health measures implemented to mitigate further transmission of this deadly disease and to identify strains that may engender resistance to vaccines.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2021.02.26.21252555: (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
    In brief, genomes were first aligned to the reference genome NC_045512 using The European Molecular Biology Open Software Suite (EMBOSS) needle(14) with open gap penalty of 100 to filter out fictitious frameshifts.
    EMBOSS
    suggested: (EMBOSS, RRID:SCR_008493)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    There are several limitations of this study. While the genomes from airport quarantine checkpoints were released in a timely manner; the genomes from Japanese domestic samples lagged behind by months. Furthermore, more precise information on collection dates is needed; most of the Japanese samples only carry year and month but not the date. Furthermore, specimen collection locations are not available on most instances. Therefore, it is challenging to evaluate spatial propagation of the virus and to assess the effect of a ‘go-to’ travel campaign to encourage business and leisure travel in an attempt to rescue the ailing travel industry. Therefore, while the study could not reveal unambiguous evidence, the campaign may have contributed to the resurgence of the virus across Japan and exacerbated the situation(23). It is imperative that the government mitigate the spread of new strains carrying the spike N501Y and E484K by reinforcing quarantine policies and further ramping up genome sequencing. In particular, wide spread of E484K variant strains may undermine vaccination efforts and discourage Japanese citizens from getting the vaccines. More aggressive genome sampling would facilitate understanding transmission dynamics of the virus including origins, routes, and rates, which is critical to its containment. Additional genomic analysis with clinical data as well as employing animal models will provide insights on infectivity, susceptibility, treatment resistance, vaccine evasion...

    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.

  2. Version published to 10.1101/2021.02.26.21252555 on medRxiv