The evolution of circulating viruses is shaped by their need to evade antibody response, which mainly targets the glycoprotein (spike). However, not all antigenic sites are targeted equally by antibodies, leading to complex immunodominance patterns. We used 3D computational models to estimate antibody pressure on the seasonal influenza H1N1 and SARS spikes. Analyzing publically available sequences, we show that antibody pressure, through the geometrical organization of spikes on the viral surface, shaped their mutability. Studying the mutability patterns of SARS-CoV-2 and the 2009 H1N1 pandemic spikes, we find that they are not predominantly shaped by antibody pressure. However, for SARS-CoV-2, we find that over time, it acquired mutations at antibody-accessible positions, which could indicate possible escape as define by our model. We offer a geometry-based approach to predict and rank the probability of surface resides of SARS-CoV-2 spike to acquire antibody escaping mutations.

中文翻译：

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病毒表面几何形状通过抗体压力塑造流感和冠状病毒尖峰进化

循环病毒的进化是由于它们需要逃避主要针对糖蛋白（尖峰）的抗体反应。然而，并非所有抗原位点都被抗体同等靶向，从而导致复杂的免疫优势模式。我们使用 3D 计算模型来估计季节性流感 H1N1 和 SARS 峰值的抗体压力。通过分析公开可用的序列，我们表明抗体压力通过病毒表面上尖峰的几何结构塑造了它们的可变性。研究 SARS-CoV-2 和 2009 年 H1N1 大流行的变异模式，我们发现它们并非主要受抗体压力的影响。然而，对于 SARS-CoV-2，我们发现随着时间的推移，它会在抗体可接近的位置发生突变，这可能表明我们模型定义的可能逃逸。