CoDe: a web-based tool for codon deoptimization

CocoVax: a web server for codon-based deoptimization of viral genes in live attenuated vaccine design

Viral infections pose major economic and public health challenges worldwide, with vaccines as a critical tool for prevention. Synonymous recoding of viral genes through codon and codon-pair deoptimization offers a promising approach to design live attenuated vaccines (LAVs) by reducing viral fitness without altering protein sequences. This strategy has been successfully applied to develop vaccines for a range of pathogens affecting human and livestock. To support this approach, we developed CocoVax, the first web server dedicated to codon and codon-pair deoptimization for LAV design. CocoVax features four modules, Virus Database, Gene Recoder, Sequence Evaluator, and Reference Library, guiding users through the entire vaccine development process. With its intuitive interface, CocoVax enables rapid generation of vaccine candidates using only a pathogen's gene sequence, providing a valuable resource for researchers in virology and vaccine development. CocoVax is freely accessible at https://comics.med.sustech.edu.cn/cocovax with no login required.

Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production

We present the first complete stochastic model of vesicular stomatitis virus (VSV) intracellular replication. Previous models developed to capture VSV's intracellular replication have either been ODE-based or have not represented the complete replicative cycle, limiting our ability to understand the impact of the stochastic nature of early cellular infections on virion production between cells and how these dynamics change in response to mutations. Our model accurately predicts changes in mean virion production in gene-shuffled VSV variants and can capture the distribution of the number of viruses produced. This model has allowed us to enhance our understanding of intercellular variability in virion production, which appears to be influenced by the duration of the early phase of infection, and variation between variants, arising from balancing the time the genome spends in the active state, the speed of incorporating new genomes into virions, and the production of viral components. Being a stochastic model, we can also assess other effects of mutations beyond just the mean number of virions produced, including the probability of aborted infections and the standard deviation of the number of virions produced. Our model provides a biologically interpretable framework for studying the stochastic nature of VSV replication, shedding light on the mechanisms underlying variation in virion production. In the future, this model could enable the design of more complex viral phenotypes when attenuating VSV, moving beyond solely considering the mean number of virions produced.