Characterization of entry pathways, species-specific ACE2 residues determining entry, and antibody neutralization evasion of Omicron BA.1, BA.1.1, BA.2, and BA.3 variants

  1. Sabari Nath Neerukonda
  2. Richard Wang
  3. Russell Vassell
  4. Haseebullah Baha
  5. Sabrina Lusvarghi
  6. Shufeng Liu
  7. Tony Wang
  8. Carol D. Weiss
  9. Wei Wang

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Abstract

The SARS-CoV-2 Omicron variants were first detected in November 2021, and several Omicron lineages (BA.1, BA.2, BA.3, BA.4, and BA.5) have since rapidly emerged. Studies characterizing the mechanisms of Omicron variant infection and sensitivity to neutralizing antibodies induced upon vaccination are ongoing by several groups. In the present study, we used pseudoviruses to show that the transmembrane serine protease 2 (TMPRSS2) enhances infection of BA.1, BA.1.1, BA.2, and BA.3 Omicron variants to lesser extent compared to ancestral D614G. We further show that Omicron variants have higher sensitivity to inhibition by soluble angiotensin converting enzyme 2 (ACE2) and the endosomal inhibitor chloroquine compared to D614G. The Omicron variants also more efficiently used ACE2 receptors from nine out of ten animal species tested, and unlike the D614G variant, used mouse ACE2 due to the Q493R and Q498R spike substitutions. Finally, neutralization of the Omicron variants by antibodies induced by three doses of Pfizer/BNT162b2 mRNA vaccine was 7-8-fold less potent than the D614G, and the Omicron variants still evade neutralization more efficiently.

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  1. ScreenIT

    SciScore for 10.1101/2022.06.01.494385: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Sera were collected at the U.S. Food and Drug Administration with written consent under an approved Institutional Review Board (IRB) protocol (FDA IRB Study # 2021-CBER-045).
    IRB: Sera were collected at the U.S. Food and Drug Administration with written consent under an approved Institutional Review Board (IRB) protocol (FDA IRB Study # 2021-CBER-045).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Membranes were probed for the V5-tag and γ-actin using V5 epitope tag antibody (Novus Biologicals, Centennial, CO), and mouse gamma actin polyclonal antibody (Thermofisher), respectively.
    V5-tag
    suggested: (Novus Cat# NB100-62264, RRID:AB_965837)
    V5 epitope tag antibody (Novus Biologicals, Centennial, CO)
    suggested: None
    mouse gamma actin
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    ACE2 genes of various species (African green monkey (AGM), Chinese rufous horseshoe bat (Rhinolophus sinicus), ferret, mouse, Chinese hamster, Syrian golden hamster, white-tailed deer, swine, bovine, and pangolin) with a C-terminal V5 tag were synthesized by GenScript as described previously 42. 293T (ATCC, Manassas, VA, USA; Cat no: CRL-11268), 293T.ACE2 (BEI Resources, Manassas, VA, USA; Cat no: NR-52511) 64 and 293T.ACE2.TMPRSS2 cells stably expressing human angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) (BEI Resources, Manassas, VA, USA; Cat no: NR-55293) 34 were maintained at 37°C in Dulbecco’s modified eagle medium (DMEM) supplemented with high glucose, L-glutamine, minimal essential media (MEM) non-essential amino acids, penicillin/streptomycin, HEPES, and 10% fetal bovine serum (FBS).
    293T.ACE2.TMPRSS2
    suggested: None
    Pseudoviruses comprising the spike glycoprotein and a firefly luciferase (FLuc) reporter gene packaged within HIV capsid were produced in 293T cells by co-transfection of 5 μg of pCMVΔR8.2, 5 μg of pHR’CMVLuc and 0.5 μg of pVRC8400 or 4 μg of pcDNA3.1(+) encoding a codon-optimized spike gene.
    293T
    suggested: None
    Soluble ACE2 Protein Production: His-tagged soluble human ACE2 was produced in FreeStyle™ 293-F cells by transfecting soluble human ACE2 (1-741 aa) expression vector plasmid DNA using 293fectin (Thermo Fisher) and purified using HiTrap Chelating column charged with nickel (GE healthcare) according to the manufacturer’s instructions.
    293-F
    suggested: None
    Recombinant DNA
    SentencesResources
    Plasmids and Cell Lines: Codon-optimized, full-length open reading frames of the spike genes of B.1 (D614G) and Omicron variants in the study were synthesized into pVRC8400 (B.1, BA.1, BA.2, and BA.3) or pcDNA3.1(+) (BA.1.1) were obtained from the Vaccine Research Center (National Institutes of Health, Bethesda, MD) and GenScript (Piscataway, NJ, USA).
    pVRC8400
    suggested: RRID:Addgene_63163)
    pcDNA3.1
    suggested: RRID:Addgene_79663)
    The HIV gag/pol packaging (pCMVΔR8.2) and firefly luciferase encoding transfer vector (pHR’CMV-Luc) plasmids 62,63 were obtained from the Vaccine Research Center (National Institutes of Health, Bethesda, MD, USA).
    pHR’CMV-Luc
    suggested: None
    Pseudoviruses comprising the spike glycoprotein and a firefly luciferase (FLuc) reporter gene packaged within HIV capsid were produced in 293T cells by co-transfection of 5 μg of pCMVΔR8.2, 5 μg of pHR’CMVLuc and 0.5 μg of pVRC8400 or 4 μg of pcDNA3.1(+) encoding a codon-optimized spike gene.
    pCMVΔR8.2
    suggested: None
    Software and Algorithms
    SentencesResources
    Titers were calculated using a nonlinear regression curve fit (GraphPad Prism Software Inc., La Jolla, CA, USA).
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    The ACE2 concentration causing a 50% reduction of luciferase activity compared to untreated control was reported as the IC50 using a nonlinear regression curve fit (GraphPad Prism software Inc., La Jolla, CA).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: We detected the following sentences addressing limitations in the study:
    Our study has several caveats, including the use of pseudoviruses instead of authentic SARS-CoV-2 for conducting experiments. However, our findings using pseudoviruses agree with those reported using authentic SARS-CoV-2. For instance, authentic BA.1 /BA.1.1 VOCs were shown to undergo attenuated replication in TMPRSS2-expressing cells compared to ancestral Wuhan-Hu-1, and Alpha, Beta, and Delta VOCs 6,36. These reports also showed greater sensitivity of BA.1 pseudovirus entry to endosomal inhibitor E64d. While we used pseudovirus entry assays to determine Omicron variant usage of ACE2 receptors of various animal species, it remains unknown whether there may be intrinsic and/or innate host-specific factors that might act to inhibit live Omicron VOCs at an entry or post entry step. Furthermore, although we identified RBM substitutions in Omicron spike that conferred the ability to use mouse or horseshoe bat ACE2, we didn’t confirm ACE2 substitutions that permit or prevent Omicron spike binding. For instance, introducing K35E substitution in horseshoe bat ACE2 should permit Omicron variants’ usage. Finally, analysis of a limited number of serum samples and short follow up after the receipt of three doses of the Pfizer/BNT162b2 mRNA vaccine do not give us insights into the durability of the antibody response. While studies of antibody durability are ongoing, our findings indicate that three dose immunization with the Pfizer/BNT162b2 will likely contribute to protection from sever...

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

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

    About SciScore

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  2. Version published to 10.1101/2022.06.01.494385v1 on bioRxiv