Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand.
Creators: name: Huang, Angkana
name: Salje, Henrik
name: Escoto, Ana Coello
name: Chowdhury, Nayeem
name: Chávez, Christian
name: Garcia-Carreras, Bernardo
name: Rutvisuttinunt, Wiriya
name: Maljkovic Berry, Irina
name: Gromowski, Gregory D
name: Wang, Lin
name: Klungthong, Chonticha
name: Thaisomboonsuk, Butsaya
name: Nisalak, Ananda
name: Trimmer-Smith, Luke M
name: Rodriguez-Barraquer, Isabel
name: Ellison, Damon W
name: Jones, Anthony R
name: Fernandez, Stefan
name: Thomas, Stephen J
name: Smith, Derek
name: Jarman, Richard
name: Whitehead, Stephen S
name: Cummings, Derek AT
name: Katzelnick, Leah C
Publisher: name: Apollo - University of Cambridge Repository
Year: 2022
Subjects: subject: Research Article
subject: Biology and life sciences
subject: Medicine and health sciences
subject: Computer and information sciences
subject: FOS: Computer and information sciences

description: Funder: Division of Intramural Research, National Institute of Allergy and Infectious Diseases; funder-id: http://dx.doi.org/10.13039/100006492
description: Funder: Military Infectious Disease Research Program
description: Funder: Armed Forces Health Surveillance Branch; funder-id: http://dx.doi.org/10.13039/100014035
description: Neutralizing antibodies are important correlates of protection against dengue. Yet, determinants of variation in neutralization across strains within the four dengue virus serotypes (DENV1-4) is imperfectly understood. Studies focus on structural DENV proteins, especially the envelope (E), the primary target of anti-DENV antibodies. Although changes in immune recognition (antigenicity) are often attributed to variation in epitope residues, viral processes influencing conformation and epitope accessibility also affect neutralizability, suggesting possible modulating roles of nonstructural proteins. We estimated effects of residue changes in all 10 DENV proteins on antigenic distances between 348 DENV collected from individuals living in Bangkok, Thailand (1994-2014). Antigenic distances were derived from response of each virus to a panel of twenty non-human primate antisera. Across 100 estimations, excluding 10% of virus pairs each time, 77 of 295 positions with residue variability in E consistently conferred antigenic effects; 52 were within ±3 sites of known binding sites of neutralizing human monoclonal antibodies, exceeding expectations from random assignments of effects to sites (p = 0.037). Effects were also identified for 16 sites on the stem/anchor of E which were only recently shown to become exposed under physiological conditions. For all proteins, except nonstructural protein 2A (NS2A), root-mean-squared-error (RMSE) in predicting distances between pairs held out in each estimation did not outperform sequences of equal length derived from all proteins or E, suggesting that antigenic signals present were likely through linkage with E. Adjusted for E, we identified 62/219 sites embedding the excess signals in NS2A. Concatenating these sites to E additionally explained 3.4% to 4.0% of observed variance in antigenic distances compared to E alone (50.5% to 50.8%); RMSE outperformed concatenating E with sites from any protein of the virus (ΔRMSE, 95%IQR: 0.01, 0.05). Our results support examining antigenic determinants beyond the DENV surface.