N440K variant of SARS-CoV-2 has Higher Infectious Fitness

  1. Dixit Tandel
  2. Divya Gupta
  3. Vishal Sah
  4. Krishnan Harinivas Harshan

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Abstract

Several variants of SARS-CoV-2 have been emerging across the globe, continuing to threaten the efforts to end COVID-19 pandemic. Recent data indicate the prevalence of variants with N440K Spike substitution in several parts of India, which is under the second wave of the pandemic. Here, we first analyze the prevalence of N440K variants within the sequences submitted from India and identify a rising trend of its spread across various clusters. We then compare the replicative fitness and infectivity of a prototype of this variant with two other previously prevalent strains. The N440K variant produced ten times higher infectious viral titers than a prevalent A2a strain, and over 1000 folds higher titers than a much less prevalent A3i strain prototype in Caco2 cells. Similar results were detected in Calu-3 cells as well, confirming the increased potency of the N440K variant. Interestingly, A3i strain showed the highest viral RNA levels, but the lowest infectious titers in the culture supernatants, indicating the absence of correlation between the RNA content and the infectivity of the sample. N440K mutation has been reported in several viral sequences across India and based on our results, we predict that the higher infectious titers achieved by N440K variant could possibly lead to its higher rate of transmission. Availability of more sequencing data in the immediate future would help understand the potential spread of this variant in more detail.

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  1. ScreenIT

    SciScore for 10.1101/2021.04.30.441434: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: Institutional ethics clearance: Institutional ethics clearance (IEC-82/2020) was obtained for the patient sample processing for virus culture.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationContamination: Cells were continuously passaged at 70-80% confluency and mycoplasma contamination was monitored periodically.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Cell culture: Vero (CCL-81) African green monkey kidney epithelial cells, Caco2 colorectal adenocarcinoma and Calu-3 lung adenocarcinoma cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; from Gibco) with Fetal Bovine Serum (FBS; from Hyclone) and 1× penicillin-streptomycin cocktail (Gibco, 15140-122) at 37°C and 5% CO2.
    Calu-3
    suggested: None
    The viruses were propagated in Vero (CCL-81) cells grown in 1×DMEM deficient in serum and antibiotics.
    Vero
    suggested: None
    Caco2 and Calu-3 cells were infected at 0.1 MOI for 2 hours in serum-free conditions after which the media was replaced with complete media and further incubated until the time of harvesting.
    Caco2
    suggested: CLS Cat# 300137/p1665_CaCo-2, RRID:CVCL_0025)
    Software and Algorithms
    SentencesResources
    Following this, the Venn diagram was made using Adobe photoshop.
    Adobe photoshop
    suggested: (Adobe Photoshop, RRID:SCR_014199)
    For the graph plotting of the infographs, Graphpad Prism was used.
    Graphpad
    suggested: (GraphPad, RRID:SCR_000306)

    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.

  2. Version published to 10.1101/2021.04.30.441434 on bioRxiv