Insertions and deletions (InDels) are essential to protein evolution. In RNA viruses, InDels contribute to the emergence of viruses with new phenotypes, including altered host engagement and tropism. However, the tolerance of viral proteins for InDels has not been extensively studied. Here, we conduct deep mutational scanning to map and quantify the mutational tolerance of a complete viral proteome to insertion, deletion and substitution. We engineered approximately 45,000 insertions, 6,000 deletions and 41,000 amino acid substitutions across the nearly 2,200 coding positions of the Enterovirus A71 proteome, quantifying their effects on viral fitness by population sequencing. The vast majority of InDels are lethal to the virus, tolerated at only a few hotspots. Some of these hotspots overlap with sites of host recognition and immune engagement, suggesting tolerance at these sites reflects the important role InDels have played in the past phenotypic diversification of Enterovirus A.

插入和缺失 （InDel） 对蛋白质进化至关重要。在 RNA 病毒中，InDel 有助于出现具有新表型的病毒，包括改变宿主参与和趋向性。然而，病毒蛋白对 InDel 的耐受性尚未得到广泛研究。在这里，我们进行深度突变扫描，以绘制和量化完整病毒蛋白质组对插入、缺失和替换的突变耐受性。我们在肠道病毒 A71 蛋白质组的近 2,200 个编码位置设计了大约 45,000 个插入、6,000 个缺失和 41,000 个氨基酸替换，并通过群体测序量化了它们对病毒适应性的影响。绝大多数 InDel 对病毒是致命的，仅在少数热点地区被容忍。其中一些热点与宿主识别和免疫参与位点重叠，表明这些位点的耐受性反映了 InDels 在过去肠道病毒 A 表型多样化中发挥的重要作用。