The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

  1. Zharko Daniloski
  2. Tristan X Jordan
  3. Juliana K Ilmain
  4. Xinyi Guo
  5. Gira Bhabha
  6. Benjamin R tenOever  Is a corresponding author
  7. Neville E Sanjana  Is a corresponding author
  1. New York Genome Center, United States
  2. Icahn School of Medicine at Mount Sinai, United States
  3. New York University School of Medicine, United States

Abstract

A novel variant of the SARS-CoV-2 virus carrying a point mutation in the Spike protein (D614G) has recently emerged and rapidly surpassed others in prevalence. This mutation is in linkage disequilibrium with an ORF1b protein variant (P314L), making it difficult to discern the functional significance of the Spike D614G mutation from population genetics alone. Here, we perform site-directed mutagenesis on wild-type human codon optimized Spike to introduce the D614G variant. Using multiple human cell lines, including human lung epithelial cells, we found that the lentiviral particles pseudotyped with Spike D614G are more effective at transducing cells than ones pseudotyped with wild-type Spike. The increased transduction with Spike D614G ranged from 1.3 to 2.4-fold in Caco-2 and Calu-3 cells expressing endogenous ACE2, and 1.5 to 7.7-fold in A549ACE2 and Huh7.5ACE2 overexpressing ACE2. Furthermore, trans-complementation of SARS-CoV-2 virus with Spike D614G showed an increased infectivity of human cells. Although there is minimal difference in ACE2 receptor binding between the D614 and G614 Spike variants, we show that the G614 variant is more resistant to proteolytic cleavage in human cells, suggesting a possible mechanism for the increased transduction.

Data availability

All data generated or analyzed in this study are included in this published article and its supplementary information files. The Spike D614G expression plasmid has been deposited to Addgene (#166850).

The following previously published data sets were used

Article and author information

Author details

  1. Zharko Daniloski

    New York Genome Center, New York, United States
    Competing interests
    No competing interests declared.
  2. Tristan X Jordan

    Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States
    Competing interests
    No competing interests declared.
  3. Juliana K Ilmain

    Cell Biology, New York University School of Medicine, New York, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9507-5069
  4. Xinyi Guo

    New York Genome Center, New York, United States
    Competing interests
    No competing interests declared.
  5. Gira Bhabha

    Department of Cell Biology, New York University School of Medicine, New York, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0624-6178
  6. Benjamin R tenOever

    Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States
    For correspondence
    benjamin.tenoever@mssm.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0324-3078
  7. Neville E Sanjana

    New York Genome Center, New York, United States
    For correspondence
    neville@sanjanalab.org
    Competing interests
    Neville E Sanjana, N.E.S. is an advisor to Vertex..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1504-0027

Funding

American Heart Association (20POST35220040)

  • Zharko Daniloski

Sidney Kimmel Foundation

  • Neville E Sanjana

National Institute of Allergy and Infectious Diseases (R01AI123155)

  • Tristan X Jordan

Pew Charitable Trusts (PEW-00033055)

  • Gira Bhabha

Searle Scholars Program (SSP-2018-2737)

  • Gira Bhabha

National Institute of Allergy and Infectious Diseases (R01AI147131)

  • Gira Bhabha

Defense Advanced Research Projects Agency (HR0011-20-2-0040)

  • Benjamin R tenOever

National Human Genome Research Institute (DP2HG010099)

  • Neville E Sanjana

National Cancer Institute (R01CA218668)

  • Neville E Sanjana

Defense Advanced Research Projects Agency (D18AP00053)

  • Neville E Sanjana

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Frank Kirchhoff, Ulm University Medical Center, Germany

Publication history

  1. Received: December 2, 2020
  2. Accepted: February 10, 2021
  3. Accepted Manuscript published: February 11, 2021 (version 1)
  4. Version of Record published: February 18, 2021 (version 2)

Copyright

© 2021, Daniloski et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Zharko Daniloski
  2. Tristan X Jordan
  3. Juliana K Ilmain
  4. Xinyi Guo
  5. Gira Bhabha
  6. Benjamin R tenOever
  7. Neville E Sanjana
(2021)
The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types
eLife 10:e65365.
https://doi.org/10.7554/eLife.65365

Further reading

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    Peter Bruun-Rasmussen, Morten Hanefeld Dziegiel ... Søren Brunak
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    Whether natural selection may have attributed to the observed blood group frequency differences between populations remains debatable. The ABO system has been associated with several diseases and recently also with susceptibility to COVID-19 infection. Associative studies of the RhD system and diseases are sparser. A large disease-wide risk analysis may further elucidate the relationship between the ABO/RhD blood groups and disease incidence.

    Methods:

    We performed a systematic log-linear quasi-Poisson regression analysis of the ABO/RhD blood groups across 1,312 phecode diagnoses. Unlike prior studies, we determined the incidence rate ratio for each individual ABO blood group relative to all other ABO blood groups as opposed to using blood group O as the reference. Moreover, we used up to 41 years of nationwide Danish follow-up data, and a disease categorization scheme specifically developed for diagnosis-wide analysis. Further, we determined associations between the ABO/RhD blood groups and the age at the first diagnosis. Estimates were adjusted for multiple testing.

    Results:

    The retrospective cohort included 482,914 Danish patients (60.4% females). The incidence rate ratios (IRRs) of 101 phecodes were found statistically significant between the ABO blood groups, while the IRRs of 28 phecodes were found statistically significant for the RhD blood group. The associations included cancers and musculoskeletal-, genitourinary-, endocrinal-, infectious-, cardiovascular-, and gastrointestinal diseases.

    Conclusions:

    We found associations of disease-wide susceptibility differences between the blood groups of the ABO and RhD systems, including cancer of the tongue, monocytic leukemia, cervical cancer, osteoarthrosis, asthma, and HIV- and hepatitis B infection. We found marginal evidence of associations between the blood groups and the age at first diagnosis.

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    Novo Nordisk Foundation and the Innovation Fund Denmark

    1. Epidemiology and Global Health
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    Methods: We constructed PRS using weights curated in the online PGS Catalog. PRS performance was evaluated by distribution, discrimination, predictive ability, and calibration. Hazard ratios (HR) and corresponding confidence intervals [CI] of the common cancers after 20 years of follow-up were estimated using Cox proportional hazard models for different levels of PRS.

    Results: A total of 495 breast, 308 prostate, 332 female-colorectal, 409 male-colorectal, 181 female-lung and 381 male-lung incident cancers were identified. The area under receiver operating characteristic curve for the best performing site-specific PRS were 0.61 (PGS000873, breast), 0.70 (PGS00662, prostate), 0.65 (PGS000055, female-colorectal), 0.60 (PGS000734, male-colorectal) and 0.56 (PGS000721, female-lung), and 0.58 (PGS000070, male-lung), respectively. Compared to the middle quintile, individuals in the highest cancer-specific PRS quintile were 64% more likely to develop cancers of the breast, prostate, and colorectal. For lung cancer, the lowest cancer-specific PRS quintile was associated with 28-34% decreased risk compared to the middle quintile. In contrast, the hazard ratios observed for quintiles 4 (female-lung: 0.95 [0.61-1.47]; male-lung: 1.14 [0.82-1.57]) and 5 (female-lung: 0.95 [0.61-1.47]) were not significantly different from that for the middle quintile.

    Conclusions: Site-specific PRSs can stratify the risk of developing breast, prostate, and colorectal cancers in this East Asian population. Appropriate correction factors may be required to improve calibration.

    Funding This work is supported by the National Research Foundation Singapore (NRF-NRFF2017-02), PRECISION Health Research, Singapore (PRECISE) and the Agency for Science, Technology and Research (A*STAR). WP Koh was supported by National Medical Research Council, Singapore (NMRC/CSA/0055/2013). CC Khor was supported by National Research Foundation Singapore (NRF-NRFI2018-01). Rajkumar Dorajoo received a grant from the Agency for Science, Technology and Research Career Development Award (A*STAR CDA - 202D8090), and from Ministry of Health Healthy Longevity Catalyst Award (HLCA20Jan-0022). The Singapore Chinese Health Study was supported by grants from the National Medical Research Council, Singapore (NMRC/CIRG/1456/2016) and the U.S. National Institutes of Health [NIH] (R01 CA144034 and UM1 CA182876).