Seifert David, Beerenwinkel Niko
ETH Zurich, Basel, Switzerland.
Curr Top Microbiol Immunol. 2016;392:181-200. doi: 10.1007/82_2015_462.
The quasispecies model is ubiquitous in the study of viruses. While having lead to a number of insights that have stood the test of time, the quasispecies model has mostly been discussed in a theoretical fashion with little support of data. With next-generation sequencing (NGS), this situation is changing and a wealth of data can now be produced in a time- and cost-efficient manner. NGS can, after removal of technical errors, yield an exceedingly detailed picture of the viral population structure. The widespread availability of cross-sectional data can be used to study fitness landscapes of viral populations in the quasispecies model. This chapter highlights methods that estimate the strength of selection in selective sweeps, assesses marginal fitness effects of quasispecies, and finally infers the fitness landscape of a viral quasispecies, all on the basis of NGS data.
准种模型在病毒研究中无处不在。虽然它带来了许多经得起时间考验的见解，但准种模型大多是以理论方式进行讨论的，几乎没有数据支持。随着下一代测序（NGS）技术的出现，这种情况正在发生变化，现在可以以高效省时且经济的方式产生大量数据。在去除技术误差后，NGS能够提供关于病毒群体结构极其详细的情况。横断面数据的广泛可得性可用于在准种模型中研究病毒群体的适应度景观。本章重点介绍了一些方法，这些方法基于NGS数据来估计选择性清除中选择的强度、评估准种的边际适应度效应，并最终推断病毒准种的适应度景观。
