Rijal, K. R. et al. Epidemiology of dengue virus infections in Nepal, 2006–2019. Infect. Dis. Poverty 10, 52 (2021).
Hou, J. et al. Current Development and Challenges of Tetravalent Live-Attenuated Dengue Vaccines. Front Immunol. https://doi.org/10.3389/fimmu.2022.840104 (2022).
Low, J. G. et al. Efficacy and safety of celgosivir in patients with dengue fever (CELADEN): a phase 1b, randomised, double-blind, placebo-controlled, proof-of-concept trial. Lancet Infect. Dis. 14, 706–715 (2014).
Nguyen, N. M. et al. A randomized, double-blind placebo controlled trial of Balapiravir, a Polymerase inhibitor, in adult dengue patients. J. Infect. Dis. 207, 1442–1450 (2013).
Low, J. G., Gatsinga, R., Vasudevan, S. G. & Sampath, A. Dengue antiviral development: a continuing journey. Adv. Exp. Med. Biol. 1062, 319–332 (2018).
Natali, E. N., Babrak, L. M. & Miho, E. Prospective artificial intelligence to dissect the dengue immune response and discover therapeutics. Front. Immunol. 12, 574411 (2021).
Miho, E. et al. Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires. Front. Immunol. 9, 83369 (2018).
Greiff, V., Miho, E., Menzel, U. & Reddy, S. T. Bioinformatic and statistical analysis of adaptive immune repertoires. Trends Immunol. 36, 738–749 (2015).
Robinson, W. H. Sequencing the functional antibody repertoire—diagnostic and therapeutic discovery. Nat. Rev. Rheumatol. 11, 171–182 (2015).
Miho, E., Roškar, R., Greiff, V. & Reddy, S. T. Large-scale network analysis reveals the sequence space architecture of antibody repertoires. Nat. Commun. 10, 1–11 (2019).
Briney, B., Inderbitzin, A., Joyce, C. & Burton, D. R. Commonality despite exceptional diversity in the baseline human antibody repertoire. Nature 566, 393–397 (2019).
Elhanati, Y. et al. Inferring processes underlying B-cell repertoire diversity. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140243 (2015).
Horst, A. et al. Machine learning detects anti-DENV signatures in antibody repertoire sequences. Front. Artif. Intell. 4, 115 (2021).
Akbar, R. et al. In silico proof of principle of machine learning-based antibody design at unconstrained. bioRxiv https://doi.org/10.1101/2021.07.08.451480 (2021).
Greiff, V., Yaari, G. & Cowell, L. G. Mining adaptive immune receptor repertoires for biological and clinical information using machine learning. Curr. Opin. Syst. Biol. 24, 109–119 (2020).
Haque, A., Engel, J., Teichmann, S. A. & Lönnberg, T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genom. Med. 9, 75 (2017).
Dupic, T. et al. Immune fingerprinting through repertoire similarity. PLoS Genet. 17, e1009301 (2021).
Slamanig, S. A. & Nolte, M. A. The bone marrow as sanctuary for plasma cells and memory T-cells: implications for adaptive immunity and vaccinology. Cells 10, 1508 (2021).
Xu, J. L. & Davis, M. M. Diversity in the CDR3 region of V(H) is sufficient for most antibody specificities. Immunity 13, 37–45 (2000).
Akbar, R. et al. A finite vocabulary of antibody-antigen interaction enables predictability of paratope-epitope binding. bioRxiv https://doi.org/10.1101/759498 (2019).
Rajewsky, K., Förster, I. & Cumano, A. Evolutionary and somatic selection of the antibody repertoire in the mouse. Science 238, 1088–1094 (1987).
Crispin, M., Ward, A. B. & Wilson, I. A. Structure and immune recognition of the HIV glycan shield. Annu Rev. Biophys. 47, 499–523 (2018).
Wimmerová, M. et al. Stacking interactions between carbohydrate and protein quantified by combination of theoretical and experimental methods. PLoS One 7, e46032 (2012).
Hudson, K. L. et al. Carbohydrate–aromatic interactions in proteins. J. Am. Chem. Soc. 137, 15152–15160 (2015).
Bashford-Rogers, R. J. M. et al. Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations. Genome Res. 23, 1874–1884 (2013).
Hoehn, K. B. et al. Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals. Philos. Trans. R. Soc. Lond. B Biol. Sci. 370, 20140241 (2015).
Russell. P. J. iGenetics 3rd edn Vol. 2 (San Francisco Benjamin Cummings, 2011).
Parameswaran, P. et al. Convergent antibody signatures in human dengue. Cell Host Microb. 13, 691–700 (2013).
Rouvinski, A. et al. Recognition determinants of broadly neutralizing human antibodies against dengue viruses. Nature 520, 109–113 (2015).
Dejnirattisai, W. et al. A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus. Nat. Immunol. 16, 170–177 (2015).
Zanini, F. et al. Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue. Proc. Natl Acad. Sci. USA 115, E12363–E12369 (2018).
Hoang, L. T. et al. The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults. J. Virol. 84, 12982–12994 (2010).
Robinson, M. et al. A 20-gene set predictive of progression to severe dengue. Cell Rep. 26, 1104–1111.e4 (2019).
Zhao, E. et al. Bone marrow and the control of immunity. Cell Mol. Immunol. 9, 11–19 (2012).
Pioli, P. D. Plasma cells, the next generation: beyond antibody secretion. Front. Immunol. 10, 2768 (2019).
Pioli, P. D., Casero, D., Montecino-Rodriguez, E., Morrison, S. L. & Dorshkind, K. Plasma cells are obligate effectors of enhanced myelopoiesis in aging bone marrow. Immunity 51, 351–366.e6 (2019).
Kennedy, D. E. & Knight, K. L. Inflammatory changes in bone marrow microenvironment associated with declining B lymphopoiesis. J. Immunol. 198, 3471–3479 (2017).
Gazon, H., Barbeau, B., Mesnard, J.M. & Peloponese, J.M. Hijacking of the AP-1 signaling pathway during development of ATL. Front. Microbiol. 8, 961–985 (2018).
Antoine, M. & Kiefer, P. Functional characterization of transcriptional regulatory elements in the upstream region and intron 1 of the human S6 ribosomal protein gene. Biochem. J. 336, 327–335 (1998).
Ishii, K. et al. Characteristics and clustering of human ribosomal protein genes. BMC Genom. 7, 37 (2006).
Perry, R. P. The architecture of mammalian ribosomal protein promoters. BMC Evol. Biol. 5, 15 (2005).
Schieffelin, J. S. et al. Neutralizing and non-neutralizing monoclonal antibodies against dengue virus E protein derived from a naturally infected patient. Virol. J. 7, 28 (2010).
Appanna, R. et al. Plasmablasts during acute dengue infection represent a small subset of a broader virus-specific memory B cell pool. EBioMedicine 12, 178–188 (2016).
Rajamanonmani, R. et al. On a mouse monoclonal antibody that neutralizes all four dengue virus serotypes. J. Gen. Virol. 90, 799–809 (2009).
Midgley, C. M. et al. Structural analysis of a dengue cross-reactive antibody complexed with envelope domain III reveals the molecular basis of cross-reactivity. J. Immunol. 188, 4971–4979 (2012).
Lok, S.-M. et al. Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins. Nat. Struct. Mol. Biol. 15, 312–317 (2008).
Xu, M. et al. A potent neutralizing antibody with therapeutic potential against all four serotypes of dengue virus. NPJ Vaccines 2, e00445 (2017).
Pavlović, M. et al. The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nat. Mach. Intell. 3, 936–944 (2021).
Wang, Y. et al. Heavy chain sequence-based classifier for the specificity of human antibodies. Brief. Bioinform. 23, bbab516 (2022).
Devulapally, P. R. et al. Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes. Genom. Med. 10, 34 (2018).
Ren, J. et al. The role of the light chain in the structure and binding activity of two cattle antibodies that neutralize bovine respiratory syncytial virus. Mol. Immunol. 112, 123–130 (2019).
Goldstein, L. D. et al. Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies. Commun. Biol. 2, 1–10 (2019).
Sangesland, M. et al. Germline-encoded affinity for cognate antigen enables vaccine amplification of a human broadly neutralizing response against influenza virus. Immunity 51, 735–749.e8 (2019).
Niu, X. et al. Longitudinal analysis of T and B cell receptor repertoire transcripts reveal dynamic immune response in COVID-19 patients. Front. Immunol. 11, 2590 (2020).
Tucci, F. A. et al. Biased IGH VDJ gene repertoire and clonal expansions in B cells of chronically hepatitis C virus–infected individuals. Blood 131, 546–557 (2018).
Kalinke, U., Oxenius, A., López-Macías, C., Zinkernagel, R. M. & Hengartner, H. Virus neutralization by germ-line vs. hypermutated antibodies. PNAS 97, 10126–10131 (2000).
Godoy-Lozano, E. E. et al. Lower IgG somatic hypermutation rates during acute dengue virus infection is compatible with a germinal center-independent B cell response. Genom. Med. 8, e00499 (2016).
Wrammert, J. et al. Rapid and massive virus-specific plasmablast responses during acute dengue virus infection in humans. J. Virol. 86, 2911–2918 (2012).
Hyatt, J. G. et al. Molecular changes in dengue envelope protein domain III upon interaction with glycosaminoglycans. Pathogens 9, 935 (2020).
Wahala, W. M. P. B., Huang, C., Butrapet, S., White, L. J. & de Silva, A. M. Recombinant dengue type 2 viruses with altered E protein domain III epitopes are efficiently neutralized by human immune sera. J. Virol. 86, 4019–4023 (2012).
de Alwis, R. et al. Identification of human neutralizing antibodies that bind to complex epitopes on dengue virions. Proc. Natl Acad. Sci. USA 109, 7439–7444 (2012).
Strouts, F. R. et al. Early transcriptional signatures of the immune response to a live attenuated tetravalent dengue vaccine vandidate in non-human primates. PLoS Neglect.Trop. Dis. 10, e0004731 (2016).
Rouers, A. et al. CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function. iScience 24, 102482 (2021).
Fontana, M. F. et al. JUNB is a key transcriptional modulator of macrophage activation. J. Immunol. 194, 177–186 (2015).
Hop, H. T. et al. The key role of c-Fos for immune regulation and bacterial dissemination in brucella infected macrophage. Front. Cell. Infect. Microbiol. 8, 4332–4462 (2018).
Hoogenboom, H. R. Selecting and screening recombinant antibody libraries. Nat. Biotechnol. 23, 1105–1116 (2005).
Reddy, S. T. et al. Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat. Biotechnol. 28, 965–969 (2010).
Huang, C.H. et al. Shared IgG infection signatures vs. hemorrhage-restricted IgA clusters in human dengue: a phenotype of differential class-switch via TGFβ1. Front. Immunol. 8, 88321 (2017).
Corrie, B. D. et al. iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories. Immunol. Rev. 284, 24–41 (2018).
Brochet, X., Lefranc, M.-P. & Giudicelli, V. IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nuc. Acids Res. 36, W503–W508 (2008).
Smakaj, E. et al. Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. Bioinformatics 36, 1731–1739 (2020).
Vander Heiden, J. A. et al. Dysregulation of B cell repertoire formation in myasthenia gravis patients revealed through deep sequencing. J. Immunol. 198, 1460–1473 (2017).
Greiff, V. et al. Learning the high-dimensional immunogenomic features that predict public and private antibody repertoires. J. Immunol. 199, 2985–2997 (2017).
Greiff, V. et al. Systems analysis reveals high genetic and antigen-driven predetermination of antibody repertoires throughout B cell development. Cell Rep. 19, 1467–1478 (2017).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).
Gillespie, C. S. Fitting heavy tailed distributions: the poweRlaw package. J. Stat. Softw. 64, 1–16 (2015).
Van Rossum, G. & Drake, F. L. The Python Language Reference Manual (Scotts Valley CA, 2009).
R, Development Core Team. A Language and Environment for Statistical Computing. https://www.R-project.org/ (2009).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2009).
Dusa, A. Package “Venn* https://github.com/dusadrian/venn (2021).
Wagih, O. ggseqlogo: a versatile R package for drawing sequence logos. Bioinformatics 33, 3645–3647 (2017).
Wei, T. et al. Corrplot: Visualization of a Correlation Matrix. https://cran.r-project.org/web/packages/ (2021).
Kolde, R. Pheatmap: Pretty Heatmaps. https://rdrr.io/cran/pheatmap/ (2019).
Tennekes, M. & Ellis, P. Treemap: Treemap Visualization. https://2021.help.altair.com/2021/panopticon/vizguide/ (2021).
Li, J. et al. Structural and functional characterization of a cross-reactive dengue virus neutralizing antibody that recognizes a cryptic epitope. Structure 26, 51–59.e4 (2018).
Thullier, P. et al. A recombinant Fab neutralizes dengue virus in vitro. J. Biotechnol. 69, 183–190 (1999).
Deng, Y.-Q. et al. A broadly flavivirus cross-neutralizing monoclonal antibody that recognizes a novel epitope within the fusion loop of E protein. PLoS One 6, e16059 (2011).
Smith, S. A. et al. The potent and broadly neutralizing human dengue virus-specific monoclonal antibody 1C19 reveals a unique cross-reactive epitope on the bc loop of domain II of the envelope protein. MBio 4, e00873–00813 (2013).
Li, L. et al. Potent neutralizing antibodies elicited by dengue vaccine in rhesus macaque target diverse epitopes. PLoS Pathog. 15, e1007716 (2019).
Durham, N. D. et al. Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics. eLife 8, e52384 (2019).
Injampa, S. et al. Generation and characterization of cross neutralizing human monoclonal antibody against 4 serotypes of dengue virus without enhancing activity. PeerJ 5, e4021 (2017).
Shi, X. et al. A bispecific antibody effectively neutralizes all four serotypes of dengue virus by simultaneous blocking virus attachment and fusion. mAbs 8, 574–584 (2016).
Teoh, E. P. et al. The structural basis for serotype-specific neutralization of dengue virus by a human antibody. Sci. Transl. Med. 4, 139ra83–139ra83 (2012).
