Early phylogenetic estimate of the effective reproduction number of SARS‐CoV‐2

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Abstract

To reconstruct the evolutionary dynamics of the 2019 novel‐coronavirus recently causing an outbreak in Wuhan, China, 52 SARS‐CoV‐2 genomes available on 4 February 2020 at Global Initiative on Sharing All Influenza Data were analyzed. The two models used to estimate the reproduction number (coalescent‐based exponential growth and a birth‐death skyline method) indicated an estimated mean evolutionary rate of 7.8 × 10 −4 subs/site/year (range, 1.1 × 10 −4 ‐15 × 10 −4 ) and a mean tMRCA of the tree root of 73 days. The estimated R value was 2.6 (range, 2.1‐5.1), and increased from 0.8 to 2.4 in December 2019. The estimated mean doubling time of the epidemic was between 3.6 and 4.1 days. This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections even as the epidemic is growing.

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  1. SciScore for 10.1101/2020.02.19.20024851: (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
    The sequences were aligned using the ClustalW Multiple Alignment program included in the accessory application of Bioedit software, manually controlled, and cropped to a final length of 29,774 bp using BioEdit v.
    ClustalW
    suggested: (ClustalW, RRID:SCR_017277)
    Bioedit
    suggested: (BioEdit, RRID:SCR_007361)
    Phylodynamic analysis: The simplest evolutionary model best fitting the sequence data was selected using software JmodelTest v.
    JmodelTest
    suggested: (jModelTest, RRID:SCR_015244)
    1.84 of the BEAST package.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    7 The final trees were summarised by selecting the tree with the maximum product of posterior probabilities (pp) (maximum clade credibility or MCC) after a 10% burn-in using Tree Annotator v.1.84 (included in the BEAST package), and were visualised using FigTree v.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    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: We detected the following sentences addressing limitations in the study:
    This preliminary study has some limitations. The R values and doubling times were estimated phylogentically using all of the whole genomes available in a public database at the time the study was carried out (https://www.gisaid.org/). Given the small number of sequences and the relatively short sampling period, the credibility intervals are wide and limit the precision of the estimates. Moreover, the analysis included isolates collected outside mainland China as it is assumed that they all belong to the same epidemic originating in Wuhan. Serial intervals were used to estimate the duration of infectiousness, although we do not yet have any information concerning the possible existence and duration of a latent (pre-infectious) period that would contribute to the serial interval. More detailed and accurate analyses can be made when a larger number of genomes and more precise data on the infectious period become available. However, although the R0 calculated on the basis of the direct observation of the number of infected individuals may be affected by omissions or delayed notifications of cases,16 a phylogenetic estimate of the same parameter may be more reliable. This became particularly evident recently (on February 12, 2020) when the change in diagnosis classification led to a sudden increase in the reported cases by Hubei, China (https://myemail.constantcontact.com/COVID-19-Updates---Feb-12.html?soid=1107826135286&aid=Kdg8a0rBTAk). In conclusion, these results allowed us to...

    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

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