Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes revealed its epidemic trend and possible origins

  1. Yunmeng Bai
  2. Dawei Jiang
  3. Jerome R Lon
  4. Xiaoshi Chen
  5. Meiling Hu
  6. Shudai Lin
  7. Zixi Chen
  8. Xiaoning Wang
  9. Yuhuan Meng
  10. Hongli Du

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Abstract

Objectives

To reveal epidemic trend and possible origins of SARS-CoV-2 by exploring its evolution and molecular characteristics based on a large number of genomes since it has infected millions of people and spread quickly all over the world.

Methods

Various evolution analysis methods were employed.

Results

The estimated Ka/Ks ratio of SARS-CoV-2 is 1.008 or 1.094 based on 622 or 3624 SARS-CoV-2 genomes, and the time to the most recent common ancestor (tMRCA) was inferred in late September 2019. Further 9 key specific sites of highly linkage and four major haplotypes H1, H2, H3 and H4 were found. The Ka/Ks, detected population size and development trends of each major haplotype showed H3 and H4 subgroups were going through a purify evolution and almost disappeared after detection, indicating H3 and H4 might have existed for a long time, while H1 and H2 subgroups were going through a near neutral or neutral evolution and globally increased with time. Notably the frequency of H1 was generally high in Europe and correlated to death rate (r>0.37).

Conclusions

In this study, the evolution and molecular characteristics of more than 16000 genomic sequences provided a new perspective for revealing epidemiology of SARS-CoV-2.

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  1. Version published to 10.1101/2020.04.24.058933v3 on bioRxiv
  2. ScreenIT

    SciScore for 10.1101/2020.04.24.058933: (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
    Finally, 624 high quality genomes with precise collection time were selected and aligned using MAFFT v7 with automatic parameters.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Estimate of evolution rate and the time to the most recent common ancestor for SARS-CoV, MERS-CoV, and SARS-CoV-2: The average Ka, Ks and Ka/Ks for all coding sequences were calculated using KaKs_Calculator v1.2(Zhang, et al., 2006), and the substitution rate and tMRCA were estimated using BEAST v2.6.2(Bouckaert, et al., 2019).
    KaKs_Calculator
    suggested: None
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    The temporal signal with root-to-tip divergence was visualized in TempEst v1.5.3(Rambaut, et al., 2016) using a ML whole genome tree with bootstrap value as input.
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    The output was examined in Tracer v1.6 (http://tree.bio.ed.ac.uk/software/tracer/).
    Tracer
    suggested: (Tracer, RRID:SCR_019121)
    Variants calling of SARS-CoV-2 genome sequences: Each genome sequence was aligned to the reference genome (NC_045512.2) using bowtie2 with default parameters(Langmead and Salzberg, 2012), and variants were called by samtools (sort; mpileup -gf) and bcftoots (call -vm).
    bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    The SMS method was used to select GTR+G as the base substitution model(Lefort, et al., 2017), and the PhyML 3.1(Guindon, et al., 2010) and MEGA(Kumar, et al., 2018) were used to construct the no-root phylogenetic tree by the maximum likelihood method with the bootstrap value of 100.
    PhyML
    suggested: (PhyML, RRID:SCR_014629)
    Phylogenetic network of haplotype subgroups: The phylogenetic networks were inferred by PopART package v1.7.2(Leigh, et al., 2015) using TCS and minimum spanning network (MSN) methods respectively.
    PopART
    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.

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  3. Version published to 10.1101/2020.04.24.058933v2 on bioRxiv
  4. Version published to 10.1101/2020.04.24.058933v1 on bioRxiv