Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques

  1. Vincent J. Munster
  2. Meaghan Flagg
  3. Manmeet Singh
  4. Brandi N. Williamson
  5. Friederike Feldmann
  6. Lizzette Pérez-Pérez
  7. Beniah Brumbaugh
  8. Myndi G. Holbrook
  9. Danielle R. Adney
  10. Atsushi Okumura
  11. Patrick W. Hanley
  12. Brian J. Smith
  13. Jamie Lovaglio
  14. Sarah L. Anzick
  15. Craig Martens
  16. Neeltje van Doremalen
  17. Greg Saturday
  18. Emmie de Wit

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Abstract

The emergence of several SARS-CoV-2 variants has caused global concerns about increased transmissibility, increased pathogenicity, and decreased efficacy of medical countermeasures. Animal models can be used to assess phenotypical changes in the absence of confounding factors that affect observed pathogenicity and transmissibility data in the human population. Here, we studied the pathogenicity of variants of concern (VOC) B.1.1.7 and B.1.351 in rhesus macaques and compared it to a recent clade B.1 SARS-CoV-2 isolate containing the D614G substitution in the spike protein. The B.1.1.7 VOC behaved similarly to the D614G with respect to clinical disease, virus shedding and virus replication in the respiratory tract. Inoculation with the B.1.351 isolate resulted in lower clinical scores in rhesus macaques that correlated with lower virus titers in the lungs, less severe histologic lung lesions and less viral antigen detected in the lungs. We observed differences in the local innate immune response to infection. In bronchoalveolar lavages, cytokines and chemokines were upregulated on day 4 in animals inoculated with D614G and B.1.1.7 but not in those inoculated with B.1.351. In nasal samples, we did not detect upregulation of cytokines and chemokines in D614G or B.1.351-inoculated animals. However, cytokines and chemokines were upregulated in the noses of B.1.1.7-inoculated animals. Taken together, our comparative pathogenicity study suggests that ongoing circulation under diverse evolutionary pressure favors transmissibility and immune evasion rather than an increase in intrinsic pathogenicity.

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    SciScore for 10.1101/2021.05.07.443115: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: Ethics and biosafety statement: All animal experiments were approved by the Institutional Animal Care and Use Committee of Rocky Mountain Laboratories, NIH and carried out in an Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International accredited facility, according to the institution’s guidelines for animal use, following the guidelines and basic principles in the NIH Guide for the Care and Use of Laboratory Animals, the Animal Welfare Act, United States Department of Agriculture and the United States Public Health Service Policy on Humane Care and Use of Laboratory Animals.
    Sex as a biological variableAll but one of the older animals were male.
    RandomizationSamples from animals inoculated with different variants were randomized across plates to mitigate batch effects.
    BlindingThe animals were observed and scored daily according to a standardized scoring sheet (23); the same person, blinded to the isolate the animals received, assessed the animals throughout the study.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    The inocula were titered on Vero E6 cells to confirm the correct dose was administered.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    Remaining reads were mapped to the the respective hCOV_19/England/204820464/2020, hCoV-19/USA/MD-HP01542/2021, and SARS-CoV-2/human/USA/RML-7/2020 genomes using Bowtie2 version 2.2.9 with parameters --local --no-mixed -X 1500.
    Bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    PCR duplicates were removed using picard MarkDuplicates (Broad Institute) and variants were called using GATK HaplotypeCaller version 4.1.2.0 (27) with parameter-ploidy 2.
    GATK
    suggested: (GATK, RRID:SCR_001876)
    Data were analyzed using Python (version 3.8.5) and GraphPad Prism (version 8.2.1).
    Python
    suggested: (IPython, RRID:SCR_001658)
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Unsupervised hierarchical clustering (Ward’s) was performed on Euclidean pairwise distance matrices calculated from the mean of the log2 fold change or concentration of analytes from animals in each group at each available timepoint using SciPy (version 1.6.0) and Seaborn (version 0.11.1) packages in Python.
    SciPy
    suggested: (SciPy, RRID:SCR_008058)
    Sequences have been deposited in NCBI under BioProject Accession number PRJNA727012.
    BioProject
    suggested: (NCBI BioProject, RRID:SCR_004801)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    One limitation of our study is the lack of comorbidities and severe disease manifestations in the rhesus macaque model. However, the age range of the animals used in this study (age range 2-16 years old) is probably a fair reflection of the population currently exhibiting the highest prevalence of SARS-CoV-2 infections, which appears to be younger than early during the COVID-19 pandemic (37). Despite the lower pathogenicity of B.1.351 overall, severe disease is still expected to occur in individuals with comorbidities. More targeted epidemiological studies are needed to clarify the impact of variants of concern on the disease burden in various subpopulations with and without comorbidities, while excluding the effect of confounding factors such as the overall number of cases and changes in human behavior. The B.1.351 lineage has been associated with reduced neutralization by convalescent sera of humans previously infected with SARS-CoV-2 and in people vaccinated against SARS-CoV-2 (38). In addition, reduced vaccine efficacy against mild-to-moderate COVID-19 was observed with the B.1.351 variant for vaccines tested in multi-center clinical trials in South Africa and Qatar (39, 40). Rechallenge studies in hamsters suggest that prior exposure with SARS-CoV-2 protects against disease but not re-infection of the upper respiratory tract (41). These studies, together with our side-by-side comparison of three SARS-CoV-2 variants in the most relevant animal model for preclinical develo...

    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

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  2. Version published to 10.1101/2021.05.07.443115 on bioRxiv