Zorian T Thornton, etc.,al. [preprint]antigen-prime: Simulating coupled genetic and antigenic evolution of influenza virus. https://doi.org/10.64898/2026.01.23.701420
Seasonal influenza virus undergoes rapid antigenic drift to escape population immunity. Computational methods can be used to organize viral genetic diversity into antigenically similar variants and estimate variant-specific growth rates. However, benchmarking these methods is challenging because it can be di?cult to accurately quantify antigenicity and growth rates in nature. Simulating viral evolution using defined selective pressures can provide ground-truth data for benchmarking. But, existing simulators do not link genetic sequences to antigenic phenotypes under selection from host populations. Here, we present a forward-time epidemic simulator called antigen-prime that links these factors. We use it to simulate viral evolution over 30 years and validate the simulation recapitulates genetic and antigenic patterns observed in natural influenza evolution. We then use the simulated data to benchmark methods for assigning variants and estimating their growth rates. We evaluated a sequence-based and a phylogenetics-based method for variant assignment, finding the former was slightly more e?ective at separating viruses into antigenically distinct groups. We also evaluated methods for estimating variant growth rates in one-year sliding windows. Estimates were accurate in most windows, but highly inaccurate in several others. Examining high- error windows revealed several examples of a previously unreported failure mode. In all, antigen-prime provides a simulation framework to benchmark models of influenza evolution, and could be used to help guide future development of these models. The source code is openly available at https://github.com/matsengrp/antigen-prime.
See Also:
Latest articles in those days:
- T cell help is a limiting factor for rare anti-influenza memory B cells to reenter germinal centers and generate potent broadly neutralizing antibodies 18 hours ago
- Wild birds drive the introduction, maintenance, and spread of H5N1 clade 2.3.4.4b high pathogenicity avian influenza viruses in Spain, 2021-2022 18 hours ago
- [preprint]FluNexus: a versatile web platform for antigenic prediction and visualization of influenza A viruses 19 hours ago
- Salpingitis and multiorgan lesions caused by highly pathogenic avian influenza A(H5N1) virus in a cat associated with consumption of recalled raw milk in California 19 hours ago
- Detection of highly pathogenic avian influenza A(H5N1) virus 2.3.4.4b in alpacas 19 hours ago
[Go Top] [Close Window]


