SARS-CoV-2 Quasispecies provides insight into its genetic dynamics during infection

  1. Fengming Sun
  2. Xiuhua Wang
  3. Shun Tan
  4. Yunjie Dan
  5. Yanqiu Lu
  6. Juan Zhang
  7. Junli Xu
  8. Zhaoxia Tan
  9. Xiaomei Xiang
  10. Yi Zhou
  11. Weiwei He
  12. Xing Wan
  13. Wei Zhang
  14. Yaokai Chen
  15. Wenting Tan
  16. Guohong Deng

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

A novel coronavirus disease (COVID-19) caused by SARS-CoV-2 has been pandemic worldwide. The genetic dynamics of quasispecies afford RNA viruses a great fitness on cell tropism and host range. However, no quasispecies data of SARS-CoV-2 have been reported yet. To explore quasispecies haplotypes and its transmission characteristics, we carried out single-molecule real-time (SMRT) sequencing of the full-length of SARS-CoV-2 spike gene within 14 RNA samples from 2 infection clusters, covering first-to third-generation infected-patients. We observed a special quasispecies structure of SARS-CoV-2 (modeled as ‘One-King’): one dominant haplotype (mean abundance ~70.15%) followed by numerous minor haplotypes (mean abundance < 0.10%). We not only discovered a novel dominant haplotype of F 1040 but also realized that minor quasispecies were also worthy of attention. Notably, some minor haplotypes (like F 1040 and currently pandemic one G 614 ) could potentially reveal adaptive and converse into the dominant one. However, minor haplotypes exhibited a high transmission bottleneck (~6% could be stably transmitted), and the new adaptive/dominant haplotypes were likely originated from genetic variations within a host rather than transmission. The evolutionary rate was estimated as 2.68-3.86 × 10 −3 per site per year, which was larger than the estimation at consensus genome level. The ‘One-King’ model and conversion event expanded our understanding of the genetic dynamics of SARS-CoV-2, and explained the incomprehensible phenomenon at the consensus genome level, such as limited cumulative mutations and low evolutionary rate. Moreover, our findings suggested the epidemic strains may be multi-host origin and future traceability would face huge difficulties.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.08.20.258376: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: All the samples were from our previous study 35, which was approved by the ethics committee of CPHMC (document no. 2020-002-01-KY, 2020-003-01-KY) and conducted in accordance with Declaration of Helsinki principles.
    Consent: Written informed consent was obtained from each subject.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableThe first case FG1 (a 70-year-old male) was a local resident in Wuhan, and came to Chongqing to visit his younger sister’s family (FG2, FG2’s husband: FG3, FG2’s son: FG4, FG2’s grandson: FG5) in Jan 15 of 2020 by taking a train and then they lived together from that day.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Through direct contact, two family members of SG2 were also infected and revealed viral RNA positive on 19 Jan, including SG2’s wife SG4 and SG4’s mother SG3.
    SG2’s
    suggested: None
    After size selection, full-length DNA of S gene was quantified using The Qubit 2.0 Fluorometer and Qubit dsDNA HS Assay Kit (Thermofisher No. Q32851).
    Thermofisher No.
    suggested: None
    Seven samples could be obtained the next-generation sequencing reads from metagenomic sequencing, which was used to access the amplification bias by BWA software 36 (
    BWA
    suggested: (BWA, RRID:SCR_010910)
    Meanwhile, SNV information were extracted using PERL scripts based on the BLAST results.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our study had some limitations. Firstly, due to technical limitations, it was currently difficult to obtain a haplotype with full-length of genome (~29Kb), and the spike gene (~4Kb) may be partially reflected the genome-wide quasispecies information. Secondly, insufficient number of samples made it difficult to observe the dynamics in a relatively large scope such as the intermediate transition state. Thirdly, the current study only focuses on SNVs, and other mutation types such as insertions, deletions, and structural variations need to be further studied. The ‘One-King’ structure of SARS-CoV-2 quasispecies reflected a novel quasispecies genetic fitness mechanism. Behind the dominant haplotype, there were countless minor fitness haplotypes that could be survived as dominant one in different hosts. Although these haplotypes may be suppressed and unable overcome the transmission bottleneck, the advantage mutations within them could be high-frequently obtained by virus mutations. Future molecular epidemiologic investigations, clinical interventions and vaccine designs need to consider the potential advantage SARS-CoV-2 quasispecies and its related mutations, which are missed by routine single concensus genotype 34 (Supplementary Tables 3 and 4).

    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 10.1101/2020.08.20.258376v1 on bioRxiv