Evolution of the SARS-CoV-2 Mutational Spectrum.
Evolution of the SARS-CoV-2 Mutational Spectrum.
复制标题
DOI：
10.1093/molbev/msad085
复制
发表时间：
2023-04-04
影响因子：
10.7
通讯作者：
Harris, Kelley
中科院分区：
文献类型：
--
作者：
Bloom, Jesse D.;Beichman, Annabel C.;Neher, Richard A.;Harris, Kelley
SARS-CoV-2进化迅速，部分原因是其突变率高。在这里，我们研究这种突变过程本身是否在病毒进化过程中发生了变化。为了做到这一点，我们量化了数百万个人类SARS-CoV-2序列中病毒基因组中4倍退化位点不同类型单核苷酸突变的相对比率。我们发现，在SARS-CoV-2进化过程中，几种类型的突变率发生了明显的变化。最引人注目的趋势是，与早期进化枝相比，基因组中G→T突变的相对比率大约下降了2倍，这是Ruis等人最近指出的（2022）。突变谱区分SARS-CoV-2复制位。bioRxiv, doi: 10.1101 / 2022.09.27.509649)。在Delta中，C→T突变的相对比率也有所下降，突变谱沿系统发育发生了其他微妙的变化。我们推测，这些突变谱的变化可能是由影响基因组复制、包装和宿主先天免疫因子拮抗的病毒突变引起的，尽管环境因素也可能起作用。有趣的是，与早期SARS-CoV-2进化枝的突变谱相比，Omicron的突变谱更类似于形成sarbecovirus长期进化的谱。总体而言，我们的工作表明，突变过程本身是SARS-CoV-2进化过程中的一个动态变量，并表明人类SARS-CoV-2可能趋向于更类似于其他动物sarbecovirus的突变谱。
SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here, we examine whether this mutational process itself has changed during viral evolution. To do this, we quantify the relative rates of different types of single-nucleotide mutations at 4-fold degenerate sites in the viral genome across millions of human SARS-CoV-2 sequences. We find clear shifts in the relative rates of several types of mutations during SARS-CoV-2 evolution. The most striking trend is a roughly 2-fold decrease in the relative rate of G→T mutations in Omicron versus early clades, as was recently noted by Ruis et al. (2022. Mutational spectra distinguish SARS-CoV-2 replication niches. bioRxiv, doi:10.1101/2022.09.27.509649). There is also a decrease in the relative rate of C→T mutations in Delta, and other subtle changes in the mutation spectrum along the phylogeny. We speculate that these changes in the mutation spectrum could arise from viral mutations that affect genome replication, packaging, and antagonization of host innate-immune factors, although environmental factors could also play a role. Interestingly, the mutation spectrum of Omicron is more similar than that of earlier SARS-CoV-2 clades to the spectrum that shaped the long-term evolution of sarbecoviruses. Overall, our work shows that the mutation process is itself a dynamic variable during SARS-CoV-2 evolution and suggests that human SARS-CoV-2 may be trending toward a mutation spectrum more similar to that of other animal sarbecoviruses.
登录
查看更多内容
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
7.7
作者：
Jiang P;Ollodart AR;Sudhesh V;Herr AJ;Dunham MJ;Harris K
通讯作者：
Harris K
影响因子：
16
作者：
Huston NC;Wan H;Strine MS;de Cesaris Araujo Tavares R;Wilen CB;Pyle AM
通讯作者：
Pyle AM
DOI：
10.1073/pnas.1418652112
发表时间：
2015-03-17
影响因子：
11.1
作者：
Harris, Kelley
通讯作者：
Harris, Kelley
影响因子：
3.3
作者：
Goldberg ME;Harris K
通讯作者：
Harris K