Viruses can modify the usage of their synonymous codons to mimic that of their hosts: investigation of codon usage may therefore help increase our understanding of virus biology. The similarity index (SiD or (D(A,B)) is a recent method for estimating the resemblance of the overall codon usage of the hosts to that of a certain virus. Here we report that this index has been systematically misinterpreted in the literature. We first review its mathematical meaning to show that a high value of SiD indicates low codon usage similarity, and not the opposite as frequently reported. We further compared SiD with four other metrics - nCAI, nRCDI, I_TE and tAI - using Zika and West Nile arboviruses in relation to various vectors and hosts. We highlight some differences between the five metrics and present a first bioinformatic evidence that Zika virus is poorly adapted to Culex quinquefasciatus, in accordance with the known biology of this virus. We conclude that SiD, if correctly interpreted, is a useful tool for codon studies, but we advocate that the results from this and other methods are context and time dependent and should be taken with care. A script to automatically calculate SiD from two codon usage tables is available at https://github.com/andrea-silverj/SiDcal.

病毒可以修改其同义词密码子的用法以模仿其宿主的密码：因此，对密码子用法的研究可能有助于增进我们对病毒生物学的了解。相似性指数（SiD或（D（A，B））是一种估计宿主的总体密码子使用率与某种病毒的相似性的最新方法，在此我们报道该索引在文献中被系统地误解了我们首先回顾一下它的数学含义表明SID的高值表示低的密码子使用的相似性，而不是相反频繁地报道我们进一步比较SID与其他四个指标- NCAI，nRCDI，我_TE和tAI-使用Zika和West Nile虫媒病毒与各种载体和宿主相关。我们强调的五个指标之间的一些差异，并呈现第一生物信息学的证据表明，寨卡病毒是很难适应致倦库蚊，按照这种病毒的已知生物。我们得出的结论是，如果正确解释了SiD，则它是进行密码子研究的有用工具，但我们主张这种方法和其他方法的结果取决于上下文和时间，因此应谨慎使用。可从https://github.com/andrea-silverj/SiDcal获得一个脚本，该脚本可根据两个密码子使用表自动计算SiD。