Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
Viruses. 2019 Jul 24;11(8):677. doi: 10.3390/v11080677.
Viruses are known to have some of the highest and most diverse mutation rates found in any biological replicator, with single-stranded (ss) RNA viruses evolving the fastest, and double-stranded (ds) DNA viruses having rates approaching those of bacteria. As mutation rates are tightly and negatively correlated with genome size, selection is a clear driver of viral evolution. However, the role of intragenomic interactions as drivers of viral evolution is still unclear. To understand how these two processes affect the long-term evolution of viruses infecting humans, we comprehensively analyzed ssRNA, ssDNA, dsRNA, and dsDNA viruses, to find which virus types and which functions show evidence for episodic diversifying selection and correlated evolution. We show that selection mostly affects single stranded viruses, that correlated evolution is more prevalent in DNA viruses, and that both processes, taken independently, mostly affect viral replication. However, the genes that are jointly affected by both processes are involved in key aspects of their life cycle, favoring viral stability over proliferation. We further show that both evolutionary processes are intimately linked at the amino acid level, which suggests that it is the joint action of selection and correlated evolution, and not just selection, that shapes the evolutionary trajectories of viruses-and possibly of their epidemiological potential.
病毒的突变率在所有生物复制子中是最高且最多样的，其中单链（ss）RNA 病毒的进化速度最快，双链（ds）DNA 病毒的进化速度接近细菌。由于突变率与基因组大小呈紧密的负相关，因此选择是病毒进化的明显驱动力。然而，基因组内相互作用作为病毒进化驱动力的作用仍不清楚。为了了解这两个过程如何影响感染人类的病毒的长期进化，我们全面分析了 ssRNA、ssDNA、dsRNA 和 dsDNA 病毒，以发现哪些病毒类型和哪些功能显示出间断性多样化选择和相关进化的证据。我们表明，选择主要影响单链病毒，相关进化在 DNA 病毒中更为普遍，这两个过程单独作用时主要影响病毒复制。然而，共同受到这两个过程影响的基因涉及到它们生命周期的关键方面，有利于病毒的稳定性而不是增殖。我们进一步表明，这两个进化过程在氨基酸水平上密切相关，这表明是选择和相关进化的共同作用，而不仅仅是选择，塑造了病毒的进化轨迹——可能还有它们的流行病学潜力。
