PDF(Pubmed)
Abstract：
Since its introduction in the human population, SARS-CoV-2 has evolved into multiple clades, but the events in its intrahost diversification are not well understood. Here, we compare three-dimensional (3D) self-organized neural haplotype maps (SOMs) of SARS-CoV-2 from thirty individual nasopharyngeal diagnostic samples obtained within a 19-day interval in Madrid (Spain), at the time of transition between clades 19 and 20. SOMs have been trained with the haplotype repertoire present in the mutant spectra of the nsp12- and spike (S)-coding regions. Each SOM consisted of a dominant neuron (displaying the maximum frequency), surrounded by a low-frequency neuron cloud. The sequence of the master (dominant) neuron was either identical to that of the reference Wuhan-Hu-1 genome or differed from it at one nucleotide position. Six different deviant haplotype sequences were identified among the master neurons. Some of the substitutions in the neural clouds affected critical sites of the nsp12-nsp8-nsp7 polymerase complex and resulted in altered kinetics of RNA synthesis in an in vitro primer extension assay. Thus, the analysis has identified mutations that are relevant to modification of viral RNA synthesis, present in the mutant clouds of SARS-CoV-2 quasispecies. These mutations most likely occurred during intrahost diversification in several COVID-19 patients, during an initial stage of the pandemic, and within a brief time period.
摘要：
自从它引入人类以来，SARS-CoV-2已经演变成多个分支，但是其宿主内多样化的事件还没有得到很好的理解。这里,我们比较了在马德里（西班牙）19天间隔内获得的30个单独的鼻咽诊断样本中SARS-CoV-2的三维（3D）自组织神经单倍型图（SOM），在进化枝19和20之间过渡的时候。已经用存在于nsp12和刺突（S）编码区的突变光谱中的单倍型库对SOM进行了训练。每个SOM由一个显性神经元（显示最大频率）组成，被低频神经元云包围.主（显性）神经元的序列与参考武汉-Hu-1基因组的序列相同或在一个核苷酸位置上与之不同。在主神经元中鉴定出六种不同的异常单倍型序列。神经云中的某些取代会影响nsp12-nsp8-nsp7聚合酶复合物的关键位点，并导致体外引物延伸测定中RNA合成的动力学改变。因此，分析已经确定了与病毒RNA合成修饰相关的突变，存在于SARS-CoV-2准种的突变云中。这些突变很可能发生在一些COVID-19患者的宿主内多样化过程中，在大流行的初始阶段，在一个短暂的时间内。
