Abstract Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Many of these engineered viruses are viable and express heterologous proteins at high levels, but the inserted sequences often prove to be unstable over time and are rapidly lost, limiting heterologous protein expression. Although virologists are aware that inserted sequences can be unstable, processes leading to insert instability are rarely considered from an evolutionary perspective. Here, we review experimental work on the stability of inserted sequences over a broad range of viruses, and we present some theoretical considerations concerning insert stability. Different virus genome organizations strongly impact insert stability, and factors such as the position of insertion can have a strong effect. In addition, we argue that insert stability not only depends on the characteristics of a particular genome, but that it will also depend on the host environment and the demography of a virus population. The interplay between all factors affecting stability is complex, which makes it challenging to develop a general model to predict the stability of genomic insertions. We highlight key questions and future directions, finding that insert stability is a surprisingly complex problem and that there is need for mechanism-based, predictive models. Combining theoretical models with experimental tests for stability under varying conditions can lead to improved engineering of viral modified genomes, which is a valuable tool for understanding genome evolution as well as for biotechnological applications, such as gene therapy.

中文翻译：

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关于插入病毒基因组的序列的稳定性

摘要 病毒被广泛用作在培养细胞或自然宿主中表达异源基因的载体，因此大量将外源序列插入其基因组的病毒被设计出来。许多这些工程病毒都是可行的，并且高水平表达异源蛋白，但插入的序列往往随着时间的推移而不稳定并迅速丢失，从而限制了异源蛋白的表达。尽管病毒学家意识到插入序列可能不稳定，但很少从进化角度考虑导致插入不稳定的过程。在这里，我们回顾了各种病毒中插入序列稳定性的实验工作，并提出了一些有关插入稳定性的理论考虑。不同的病毒基因组组织强烈影响插入稳定性，插入位置等因素也会产生很大的影响。此外，我们认为插入稳定性不仅取决于特定基因组的特征，而且还取决于宿主环境和病毒种群的人口统计学。影响稳定性的所有因素之间的相互作用很复杂，这使得开发一个通用模型来预测基因组插入的稳定性具有挑战性。我们强调了关键问题和未来方向，发现刀片稳定性是一个令人惊讶的复杂问题，并且需要基于机制的预测模型。将理论模型与不同条件下稳定性的实验测试相结合，可以改进病毒修饰基因组的工程设计，这是了解基因组进化以及基因治疗等生物技术应用的宝贵工具。