Long SARS-CoV-2 nucleocapsid sequences in blood monocytes collected soon after hospital admission

  1. Nathan Pagano
  2. Maudry Laurent-Rolle
  3. Jack Chun-Chieh Hsu
  4. the Yale IMPACT Research Team
  5. Chantal BF Vogels
  6. Nathan D Grubaugh
  7. Laura Manuelidis

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Abstract

Many viruses infect circulating mononuclear cells thereby facilitating infection of diverse organs. Blood monocytes (PBMC) are being intensively studied as immunologic and pathologic responders to the new SARS-CoV-2 virus (CoV19) but direct evidence showing CoV19 in monocytes is lacking. Circulating myeloid cells that take up residence in various organs can harbor viral genomes for many years in lymphatic tissues and brain, and act as a source for re-infection and/or post-viral organ pathology. Because nucleocapsid (NC) proteins protect the viral genome we tested PBMC from acutely ill patients for the diagnostic 72bp NC RNA plus adjacent longer (301bp) transcripts. In 2/11 patient PBMC, but no uninfected controls, long NCs were positive as early as 2-6 days after hospital admission as validated by sequencing. Pathogenic viral fragments, or the infectious virus, are probably disseminated by rare myeloid migratory cells that incorporate CoV19 by several pathways. Predictably, these cells carried CoV19 to heart and brain educing the late post-viral pathologies now evident.

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  1. Version published to 10.1101/2020.12.16.423113v2 on bioRxiv
  2. ScreenIT

    SciScore for 10.1101/2020.12.16.423113: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Samples: Collection of de-identified control (“uninfected normal”) blood samples and those from patients with positive CoV19 nasopharyngeal swab tests, first assayed by the US CDC 2019-nCoV_N1 primer–probe set at the Yale-New Haven Hospital (YNHH), were approved by the Institutional Review Board of the Yale Human Research Protection Program (no. FWA00002571, Protocol ID 2000027690).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    For infection, high-titer stocks of SARS-CoV-2 virus (isolate USA-WA1/2020, CoV-2 WA1) from the BEI reagent repository were obtained by passaging in Vero E6 cells with viral titers determined by plaque assay on Vero E6 cells (ATCC).
    Vero E6
    suggested: RRID:CVCL_XD71)
    In addition, control mock-infected (V-) and infected (V+) Vero cell RNAs were used as paired standards with longer NC primer pairs.
    Vero
    suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
    Software and Algorithms
    SentencesResources
    Samples: Collection of de-identified control (“uninfected normal”) blood samples and those from patients with positive CoV19 nasopharyngeal swab tests, first assayed by the US CDC 2019-nCoV_N1 primer–probe set at the Yale-New Haven Hospital (YNHH), were approved by the Institutional Review Board of the Yale Human Research Protection Program (no. FWA00002571, Protocol ID 2000027690).
    Yale Human Research Protection Program
    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 16. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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 10.1101/2020.12.16.423113v1 on bioRxiv