在其漫长的进化历史中，病毒通过一种称为“套印”的机制从头产生了许多蛋白质。套印是一种过程，其中预先存在的基因中的关键核苷酸取代可以通过翻译替代开放阅读框（ORF）来诱导新蛋白质的表达。重叠的基因代表了适应性冲突的一个有趣的例子，因为它们同时编码两种蛋白质，它们的变化自由受到彼此的限制。然而,重叠基因也是遗传新奇的来源，作为替代ORF进化的约束可以产生具有不寻常序列特性的蛋白质，最重要的是新功能的潜力。从在感染大肠杆菌的噬菌体中发现重叠基因开始，这篇综述涵盖了一系列研究，涉及在小型真核病毒（基因组长度低于30kb）中检测重叠基因，以及识别它们在致病性进化中的关键作用。重叠基因的起源，哪些因素有利于他们的出生和保留，以及他们如何管理其固有的适应性冲突被广泛审查。特别注意将重叠基因组装到临时数据库中，适合未来的研究，以及探索病毒基因组序列以寻找未被发现的重叠的统计方法的发展。
During their long evolutionary history viruses generated many proteins de novo by a mechanism called \"overprinting\". Overprinting is a process in which critical nucleotide substitutions in a pre-existing gene can induce the expression of a novel protein by translation of an alternative open reading frame (ORF). Overlapping genes represent an intriguing example of adaptive conflict, because they simultaneously encode two proteins whose freedom to change is constrained by each other. However, overlapping genes are also a source of genetic novelties, as the constraints under which alternative ORFs evolve can give rise to proteins with unusual sequence properties, most importantly the potential for novel functions. Starting with the discovery of overlapping genes in phages infecting Escherichia coli, this
review covers a range of studies dealing with detection of overlapping genes in small eukaryotic viruses (genomic length below 30 kb) and recognition of their critical role in the evolution of pathogenicity. Origin of overlapping genes, what factors favor their birth and retention, and how they manage their inherent adaptive conflict are extensively reviewed. Special attention is paid to the assembly of overlapping genes into ad hoc databases, suitable for future studies, and to the development of statistical methods for exploring viral genome sequences in search of undiscovered overlaps.
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