Code and scripts used to generate results for: Designing transmissible viral vaccines for evolutionary robustness and maximum efficiency

The danger posed by infectious agents necessitates the development of new tools to both predict and manage emerging diseases. One promising approach is the development of recombinant viral vaccines that are themselves infectious. Transmissible vaccines have been shown to greatly reduce the effort required to control the spread of zoonotic pathogens in their animal reservoirs, thereby limiting the chances of human infection. While this approach can be immensely useful in combating emerging diseases, the ability to self-replicate exposes vaccines to evolutionary change. As a recombinant transmissible vaccine mutates, selection is expected to favor variants with reduced efficacy against the pathogen and increased transmission rates. This creates a trade-off in vaccine design priorities between efficacy, reduction in transmission, and evolutionary stability. Here we ask how such trade-offs influence the overall performance of transmissible vaccines. We find that evolutionary instability can...

传染性病原体（infectious agents）所带来的威胁，推动了可同时预测与管控新发传染病的新型工具研发。其中一种颇具前景的技术路径，是开发具备自主感染性的重组病毒疫苗（recombinant viral vaccines）。研究证实，可传播疫苗（transmissible vaccines）可大幅降低管控动物宿主内人畜共患病原体（zoonotic pathogens）传播所需的工作投入，进而降低人类感染风险。尽管该方法在对抗新发传染病领域极具应用价值，但疫苗的自主复制能力使其面临进化变异的潜在影响。当重组可传播疫苗发生突变时，自然选择将更青睐那些对靶标病原体效力减弱、但传播能力提升的变异株。这使得疫苗研发的优先级在效力、传播抑制效果与进化稳定性之间形成权衡取舍。本研究旨在探究此类权衡如何影响可传播疫苗的整体性能。我们发现，进化不稳定性可……