Case report: change of dominant strain during dual SARS-CoV-2 infection

  1. Andrei E. Samoilov
  2. Valeriia V. Kaptelova
  3. Anna Y. Bukharina
  4. Olga Y. Shipulina
  5. Elena V. Korneenko
  6. Stepan S. Saenko
  7. Alexander V. Lukyanov
  8. Antonina A. Grishaeva
  9. Antonina A. Ploskireva
  10. Anna S. Speranskaya
  11. Vasiliy G. Akimkin

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Abstract

Background

The dual infection with SARS-CoV-2 is poorly described and is currently under discussion. We present a study of two strains of SARS-CoV-2 detected in the same patient during the same disease presentation.

Case presentation

A patient in their 90 s was hospitalised with fever. Oropharyngeal swab obtained on the next day (sample 1) tested positive for SARS-CoV-2. Five days later, the patient was transferred to the ICU (intensive care unit) of the hospital specialising in the treatment of COVID-19 patients, where the patient's condition progressively worsened and continuous oxygen insufflation was required. Repeated oropharyngeal swab (sample 2), which was taken eight days after the first one, also tested positive for SARS-CoV-2. After 5 days of ICU treatment, the patient died. The cause of death was a coronavirus infection, which progressed unfavourably due to premorbid status. We have performed sequencing of full SARS-CoV-2 genomes from oropharyngeal swabs obtained eight days apart. Genomic analysis revealed the presence of two genetically distant SARS-CoV-2 strains in both swabs. Detected strains belong to different phylogenetic clades (GH and GR) and differ in seven nucleotide positions. The relative abundance of strains was 70% (GH) and 30% (GR) in the first swab, and 3% (GH) and 97% (GR) in the second swab.

Conclusions

Our findings suggest that the patient was infected by two genetically distinct SARS-CoV-2 strains at the same time. One of the possible explanations is that the second infection was hospital-acquired. Change of the dominant strain ratio during disease manifestation could be explained by the advantage or higher virulence of the GR clade strain.

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  1. Version published to 10.1186/s12879-021-06664-w
  2. ScreenIT

    SciScore for 10.1101/2020.11.29.20238402: (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
    Double-stranded cDNA was sheared in microTUBE-50 AFA Fiber Screw-Cap (PN 520166) using Covaris M220
    Covaris
    suggested: None
    Quality and fragment length distribution of the obtained libraries were evaluated with Agilent Bioanalyzer 2100 (Agilent Technologies, USA).
    Agilent Bioanalyzer
    suggested: None
    We performed adapter and quality trimming with Trimmomatic [12], removed PCR primers with cutadapt (for amplicon libraries) [13], and mapped reads to the reference sequence (strain hCoV-19/Wuhan/WIV04/2019, GISAID accession ID EPI_ISL_402124) using bowtie2 [14].
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    After that, we filtered out reads with low mapping quality using SAMtools [15], performed base-calling with GATK [16], filtered gvcf files were with BCFtools [17].
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    GATK
    suggested: (GATK, RRID:SCR_001876)
    BCFtools
    suggested: (SAMtools/BCFtools, RRID:SCR_005227)
    Finally, the consensus sequences were obtained with BEDTools [18].
    BEDTools
    suggested: (BEDTools, RRID:SCR_006646)
    All of the SARS-CoV-2 strains were aligned using mafft [19], the phylogenetic tree was built using IQtree 2 [20] using the GTR model.
    mafft
    suggested: (MAFFT, RRID:SCR_011811)

    Results from OddPub: Thank you for sharing your data.

    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.

    About SciScore

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  3. Version published to 10.1101/2020.11.29.20238402v1 on medRxiv