Sequential Appearance and Isolation of a SARS-CoV-2 Recombinant between Two Major SARS-CoV-2 Variants in a Chronically Infected Immunocompromised Patient

  1. Emilie Burel
  2. Philippe Colson
  3. Jean-Christophe Lagier
  4. Anthony Levasseur
  5. Marielle Bedotto
  6. Philippe Lavrard-Meyer
  7. Pierre-Edouard Fournier
  8. Bernard La Scola
  9. Didier Raoult

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Abstract

Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but only a single patient’s sample was analyzed, and the virus was not isolated. Here, we report the gradual emergence of a hybrid genome of B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months, and we isolated the recombinant virus. The hybrid genome was obtained by next-generation sequencing, and the recombination sites were confirmed by PCR. This consisted of a parental B.1.160 backbone interspersed with two fragments, including the spike gene, from an Alpha variant. An analysis of seven sequential samples from the patient decoded the recombination steps, including the initial infection with a B.1.160 variant, then a concurrent infection with this variant and an Alpha variant, the generation of hybrid genomes, and eventually the emergence of a predominant recombinant virus isolated at the end of the patient’s follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying the genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more generally with several RNA viruses, as this may lead to the appearance of new viruses.

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  1. Version published to 10.3390/v14061266
  2. ScreenIT

    SciScore for 10.1101/2022.03.21.22272673: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Virus culture isolation: Culture isolation was performed on Vero E6 cells, as previously described [33].
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    Freebayes results were filtered with a threshold of 70% for the majority nucleotide.
    Freebayes
    suggested: (FreeBayes, RRID:SCR_010761)
    The clade was designated at the consensus level with the Nextclade online tool (https://clades.nextstrain.org/) [42,32] and an in-house Python script allowed detection of variants and hybrids of variants.
    Python
    suggested: (IPython, RRID:SCR_001658)
    Nucleotide diversity at genomic positions was calculated using the Microsoft Excel software (https://www.microsoft.com/en-us/microsoft-365/excel) with an in-house built file.
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)
    Reads were then filtered according to variant-specific nucleotide patterns using SAMtools combined with an in-house awk script.
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Sequences were aligned using MAFFT v.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    7 [44] with their 20 most similar hits identified with the BLAST tool [45] among SARS-CoV-2 genomes from our database that contains sequences obtained from clinical samples collected between February 2020 and February 2022 [27,14]
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Phylogeny reconstruction was performed using the IQ-TREE software with the GTR Model and 1,000 ultrafast bootstrap repetitions (http://www.iqtree.org) [46], and trees were visualized with iTOL (Interactive Tree Of Life) (https://itol.embl.de/) [47] and MEGA X (v10.2.6; https://www.megasoftware.net/) [47] softwares.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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.

    Results from scite Reference Check: We found no unreliable references.

    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.

  3. Version published to 10.1101/2022.03.21.22272673v1 on medRxiv