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Low-dose dengue virus 3 human challenge model: a phase 1 open-label study

Nature Microbiology (2024)Cite this article

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Abstract

Dengue human infection models present an opportunity to explore the potential of a vaccine, anti-viral or immuno-compound for clinical benefit in a controlled setting. Here we report the outcome of a phase 1 open-label assessment of a low-dose dengue virus 3 (DENV-3) challenge model (NCT04298138), in which nine participants received a subcutaneous inoculation with 0.5 ml of a 1.4 × 103 plaque-forming unit per ml suspension of the attenuated DENV-3 strain CH53489. The primary and secondary endpoints of the study were to assess the safety of this DENV-3 strain in healthy flavivirus-seronegative individuals. All participants developed RNAaemia within 7 days after inoculation with peak titre ranging from 3.13 × 104 to 7.02 × 108 genome equivalents per ml. Solicited symptoms such as fever and rash, clinical laboratory abnormalities such as lymphopenia and thrombocytopenia, and self-reported symptoms such as myalgia were consistent with mild-to-moderate dengue in all volunteers. DENV-3-specific seroconversion and memory T cell responses were observed within 14 days after inoculation as assessed by enzyme-linked immunosorbent assay and interferon-gamma-based enzyme-linked immunospot. RNA sequencing and serum cytokine analysis revealed anti-viral responses that overlapped with the period of viraemia. The magnitude and frequency of clinical and immunologic endpoints correlated with an individual’s peak viral titre.

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Fig. 1: Viral kinetics of CH53489 challenge.
Fig. 2: Timing and severity of clinically significant AEs in response to CH53489 challenge.
Fig. 3: Timing and magnitude of clinical laboratory abnormalities following CH53489 challenge.
Fig. 4: Kinetics and specificity of DENV-3-specific immunity elicited by CH53489 challenge.
Fig. 5: Kinetics and composition of DENV-3 elicited inflammation.
Fig. 6: Correlation analysis of a selection virologic, clinical and immunologic features post-CH53489 challenge.

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Data availability

The authors declare that all data supporting the findings of this study, including participant-level source data, are available within this article, in its Supplementary Information files or in a publicly accessible database. RNAseq gene expression data have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO GSE216328). The DENV strain used for this study was made available by the US Army Medical Research and Development Command under a material transfer agreement with the SUNY–UMU and SUNY Research Foundation. Requests for the challenge strain should be addressed to the US Army Medical Research and Development Command (heather.l.friberg-robertson.civ@health.mil). Please anticipate a response within 2 weeks.

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Acknowledgements

We gratefully acknowledge excellent technical assistance provided by K. Gentile of the UMU Molecular Analysis Core, L. Phelps of the SUNY–UMU Flow Cytometry Core, H. Chanatry and the members of the Institute for Global Health and Translational Science of SUNY–UMU. We also acknowledge C. Rooney from the US Army. We also wish to thank all the study participants for making this study possible. The following reagents were obtained through BEI Resources, NIAID, NIH: Peptide Array, DENV-3 Sleman/1978, E protein (NR-511), DENV-3 Philippines/H87/1956, E protein (NR-9228), DENV-3 Philippines/H87/1956, NS1 protein (NR-2753), DENV-3 Philippines/H87/1956, NS3 protein (NR-2754), DENV-3 Philippines/H87/1956 and NS5 protein (NR-4204). The opinions or assertions contained herein are the private views of the authors and are not to be construed as reflecting the official views of the US Army or the US Department of Defense. Material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The investigators have adhered to the policies for protection of human participants as prescribed in AR 70-25. The sponsor was involved in the design and conduct of the study and in the collection, management, analysis and interpretation of the data. All authors had full access to the data in the study. Funding: funding for this research was provided by the Department of Defense, Medical Research and Material Command, the Military Infectious Disease Research Program (S.J.T. and T.P.E.) and the State of New York (A.T.W.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

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Authors and Affiliations

  1. Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, NY, USA

    Adam T. Waickman, Krista Newell, Joseph Q. Lu, HengSheng Fang, Mitchell Waldran, Chad Gebo, Timothy P. Endy & Stephen J. Thomas

  2. Institute for Global Health and Translational Sciences, State University of New York Upstate Medical University, Syracuse, NY, USA

    Adam T. Waickman, Joseph Q. Lu, Michelle D. Klick, Lisa A. Ware & Stephen J. Thomas

  3. Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA

    Jeffrey R. Currier, Heather Friberg & Richard G. Jarman

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Contributions

Conceptualization: L.A.W., M.D.K., R.G.J., T.P.E. and S.J.T. Formal analysis: L.A.W. and A.T.W. Funding acquisition: H.F, R.G.J., T.P.E. and S.J.T. Investigation: A.T.W., J.Q.L., K.N., H.S.F., M.W., C.G., M.D.K., L.A.W., T.P.E. and S.J.T. Resources: H.F., R.G.J. and J.R.C. Visualization: K.N. and A.T.W. Writing—original draft: A.T.W. and S.J.T. Writing—review and editing: all authors.

Corresponding authors

Correspondence to Adam T. Waickman or Stephen J. Thomas.

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Nature Microbiology thanks Anna Durbin and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 NS1 opsonization assay.

a) Sequence and annotation of the DENV-3 NS1 expression construct used in this study. Yellow = signal peptide, green = NS1, blue = NS2A. b) Anti-NS1 staining mAb staining (clone FE8) of parental CEM.NKR cell line and DENV-3 NS1 expressing CEM.NKR cells. Unstained cells shown in blue, FE8 stained shown in red c) Representative NS1 opsonizing activity of serum collected at days 0, 24, and 90 days post DENV-3 challenge. Unstained cells shown in blue, serum stained shown in red.

Source data

Extended Data Fig. 2 DENV serology day 90 post challenge.

a) Quantification of DENV-1, −2, −3 and −4 E binding IgG antibody levels on day 90 post challenge using a multiplex antigen array. b) Quantification of DENV-1, −2, −3 and −4 E neutralizing antibody titers on 90 post challenge by FlowNT. * p < 0.05 paired one-way ANOVA with correction for multiple comparisons. Data are presented as mean values +/- SEM. n = 9 biologically independent samples.

Source data

Extended Data Fig. 3

Representative IFN-γ ELISPOT images.

Extended Data Fig. 4 Gene module identification from RNA-seq data.

Identification of gene modules with coordinated expression changes following DENV-3 challenge. a) Gene modules identified performing differential gene expression analysis between A) days 0 and 6 post infection, b) days 0 and 8 post infection, c) days 0 and 10 post infection, and d) days 0 and 14 post infection.

Extended Data Fig. 5 Select extended correlation analysis.

Correlation analysis between peak virama titers and T cell responses day 90 post infection. Relationship between peak viremia and a) DENV-3 E protein ELISPOT readout, b) DENV-3 NS1 protein ELISPOT readout, c) DENV-3 NS3 protein ELISPOT readout, d) DENV-3 NS5 protein ELISPOT readout on day 90 post.

Source data

Extended Data Table 1 Study demographics
Full size table

Supplementary information

Supplementary Information

Supplementary Figs. 1–7 and Tables 1–6.

Reporting Summary

Peer Review File

Supplementary Data 1

RNAseq differential gene expression data.

Supplementary Data 2

Study protocol.

Source data

Source Data

Statistical source data for Figs. 1–6 and Extended Figs. 1–2 and 5.

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Waickman, A.T., Newell, K., Lu, J.Q. et al. Low-dose dengue virus 3 human challenge model: a phase 1 open-label study. Nat Microbiol (2024). https://doi.org/10.1038/s41564-024-01668-z

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