未经批准:世界仍在与2019年冠状病毒病(COVID-19)的大流行作斗争,由严重急性呼吸综合征冠状病毒2(SARS-CoV-2)引起,2022年。变异株的间歇性出现促进了大流行,主要通过spike(S)基因的点突变模式进行了解释和分类。然而,大流行期间SARS-CoV-2基因组中插入/缺失(indel)的情况仍未得到评估.
未经批准:在这项研究中,我们首先通过多序列比对筛选多态性indel位点的基因组区域;然后,进行了NCBIBLAST搜索和GISAID数据库搜索,以全面调查多态性indel热点处的indel图谱,并阐明了indel在时间和地理分布上的出现和传播。
UNASSIGNED:在S基因的N末端结构域中大约22,200个核苷酸的位置鉴定出多态性indel热点,对应于SARS-CoV-2S蛋白的210-215个氨基酸位置。这个多态热点由相邻的3个碱基缺失(5'-ATT-3';Spike_N211del)和9个碱基插入(5'-AGCCAAG-3';Spike_ins214EPE)组成。通过执行NCBIBLAST搜索和GISAID数据库搜索,我们确定了几种类型的9碱基插入的串联重复,创建一个18基插入(Spike_ins214EPEEPE,斯派克_ins214EPDEPE)。搜索结果表明,9碱基插入的两个周期串联重复是在2021年11月在中欧创建的,而最初的单周期9基插入(Spike_ins214EPE)的出现可以追溯到2020年中期,并且远离中欧。在2021年11月至2022年4月之间收集了基于9碱基插入的2周期串联重复序列鉴定的18碱基插入,表明这些突变无法存活并且已经被消除。
UNASSIGNED:GISAID数据库搜索暗示,这种多态性indel热点是SARS-CoV-2S基因中掺入indel的最高耐受性之一。总之,本研究确定了SARS-CoV-2S基因N端结构域中9个碱基插入的可变数量的串联重复序列,并且重复可能发生在与原始9个碱基插入不同的插入时间。
UNASSIGNED: The world is still struggling against the pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in 2022. The pandemic has been facilitated by the intermittent emergence of variant strains, which has been explained and classified mainly by the patterns of point mutations of the spike (S) gene. However, the profiles of insertions/deletions (indels) in SARS-CoV-2 genomes during the pandemic remain largely unevaluated yet.
UNASSIGNED: In this study, we first screened for the genome regions of polymorphic indel sites by performing multiple sequence alignment; then, NCBI BLAST search and GISAID database search were performed to comprehensively investigate the indel profiles at the polymorphic indel hotspot and elucidate the emergence and spread of the indels in time and geographical distribution.
UNASSIGNED: A polymorphic indel hotspot was identified in the N-terminal domain of the S gene at approximately 22,200 nucleotide position, corresponding to 210-215 amino acid positions of SARS-CoV-2 S protein. This polymorphic hotspot was comprised of adjacent 3-base deletion (5\'-ATT-3\'; Spike_N211del) and 9-base insertion (5\'-AGCCAGAAG-3\'; Spike_ins214EPE). By performing NCBI BLAST search and GISAID database search, we identified several types of tandem repeats of the 9-base insertion, creating an 18-base insertion (Spike_ins214EPEEPE, Spike_ins214EPDEPE). The results of the searches suggested that the two-cycle tandem repeats of the 9-base insertion were created in November 2021 in Central Europe, whereas the emergence of the original one-cycle 9-base insertion (Spike_ins214EPE) would date back to the middle of 2020 and was away from the Central Europe. The identified 18-base insertions based on 2-cycle tandem repeat of the 9-base insertion were collected between November 2021 and April 2022, suggesting that these mutations could not survive and have been already eliminated.
UNASSIGNED: The GISAID database search implied that this polymorphic indel hotspot to be with one of the highest tolerability for incorporating indels in SARS-CoV-2 S gene. In summary, the present study identified a variable number of tandem repeat of 9-base insertion in the N-terminal domain of SARS-CoV-2 S gene, and the repeat could have occurred at different time from the insertion of the original 9-base insertion.