Identification of super-transmitters of SARS-CoV-2

  1. Xuemei Yang
  2. Ning Dong
  3. Edward Wai-Chi Chan
  4. Sheng Chen

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Abstract

A newly emerged coronavirus, SARS-CoV-2, caused severe outbreaks of pneumonia in China in December 2019 and has since spread to various countries around the world. To probe the origin and transmission dynamics of this virus, we performed phylodynamic analysis of 247 high quality genomic sequences of viruses available in the GISAID platform as of March 05, 2020. A substantial number of earliest sequences reported in Wuhan in December 2019, including those of viruses recovered from the Huanan Seafood Market (HNSM), the site of the initial outbreak, were genetically diverse, suggesting that viruses of multiple sources were involved in the original outbreak. The viruses were subsequently disseminated to different parts of China and other countries, with diverse mutational profiles being recorded in strains recovered subsequently. Interestingly, four genetic clusters defined as Super-transmitters (STs) were found to become dominant and were responsible for the major outbreaks in various countries. Among the four clusters, ST1 is widely disseminated in Asia and the US and mainly responsible for outbreaks in the states of Washington and California in the US as well as those in South Korea at the end of February and early March, whereas ST4 contributed to the pandemic in Europe. Each ST cluster carried a signature mutation profile which allowed us to trace the origin and transmission patterns of specific viruses in different parts of the world. Using the signature mutations as markers of STs, we further analysed 1539 genome sequences reported after February 29, 2020. We found that around 90% of these genomes belonged to STs with ST4 being the dominant one and their contribution to pandemic in different continents were also depicted. The identification of these super-transmitters provides insight into the control of further transmission of SARS-CoV-2.

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  1. ScreenIT

    SciScore for 10.1101/2020.04.19.20071399: (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

    Experimental Models: Organisms/Strains
    SentencesResources
    Nucleotide and amino acid mutations of all genome and separate proteins were analyzed by blast (https://blast.ncbi.nlm.nih.gov/) using the sequence of strain Wuhan-Hu-1 as reference.
    Wuhan-Hu-1
    suggested: None
    Software and Algorithms
    SentencesResources
    The pipeline involved the sequence alignment module with MAFFT [14], phylogenetic analysis with IQ-TREE [15], maximum-likelihood phylodynamic analysis with Treetime [16], identification of nucleotide and amino acid mutations with Augur, and result visualization with Auspice [13].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    The outputs were edited by Inkscape 0.91 [
    Inkscape
    suggested: (Inkscape, RRID:SCR_014479)
    Phylogenetic tree of all SARS-CoV-2 was built with RAxML version 8.2.4 [18].
    RAxML
    suggested: (RAxML, RRID:SCR_006086)

    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:
    One limitation of the study is that we can only utilize currently available genome sequences. The lack of genome sequence of ST4 in other continent does not necessarily mean that ST4 viruses are not present in other continents. A second limitation of this study is the lack of data to explain the mechanisms underlying the evolution of these genetic clusters into super-transmitters. Every ST cluster carried at least one amino acid mutation in different protein. Whether such mutational changes were the key step that enabled SARS-CoV-2 to evolve into super-transmitters must be investigated in future research studies. Lastly, our data also provided insight into the major transmitting viruses in current pandemic areas in the world. For example, in Italy, ST2, ST3 were reported in the end of January, while ST4 was reported in February and early March. Similar trends were seen in other countries with exception that a higher proportion of the original viral genomes were reported in Netherland. In the US, the original viruses were reported in other states, while ST1 was the major virus that caused outbreak in Washington and California States. Other ST genomes were also sporadically reported in the US. Although data from Iran is not available, two genomes reported from Australia with travel history from Iran were shown to belong to ST3, suggesting that this cluster was responsible for the pandemic in Iran. In Australia, all genomes were reported except ST4. Using the signature mutations...

    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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  2. Version published to 10.1101/2020.04.19.20071399 on medRxiv