A novel coronavirus, SARS-CoV-2, has caused a pandemic of COVID-19. The evolutionary trend of the virus genome may have implications for infection control policy but remains obscure. We introduce an estimation of fold change of translational efficiency based on synonymous variant sites to characterize the adaptation of the virus to hosts. The increased translational efficiency of the M and N genes suggests that the population of SARS-CoV-2 benefits from mutations toward favored codons, while the ORF1ab gene has slightly decreased the translational efficiency. In the coding region of the ORF1ab gene upstream of the -1 frameshift site, the decreasing of the translational efficiency has been weakening parallel to the growth of the epidemic, indicating inhibition of synthesis of RNA-dependent RNA polymerase and promotion of replication of the genome. Such an evolutionary trend suggests that multiple infections increased virulence in the absence of social distancing.

中文翻译：

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SARS-CoV-2基因的同义位点显示影响翻译效率的趋势

新型冠状病毒SARS-CoV-2导致了COVID-19的大流行。病毒基因组的进化趋势可能对感染控制策略有影响，但仍不清楚。我们引入了基于同义变异位点的翻译效率倍数变化的估计，以表征病毒对宿主的适应性。M和N基因的翻译效率提高表明SARS-CoV-2群体受益于朝着偏爱密码子的突变，而ORF1ab基因则略有降低了翻译效率。在-1移码位点上游的ORF1ab基因的编码区中，翻译效率的下降与流行病的增长平行而减弱，表明抑制了RNA依赖性RNA聚合酶的合成并促进了基因组的复制。