Data_Sheet_1_Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil.pdf

Recombination events have been described in the Coronaviridae family. Since the beginning of the SARS-CoV-2 pandemic, a variable degree of selection pressure has acted upon the virus, generating new strains with increased fitness in terms of viral transmission and antibody scape. Most of the SC2 variants of concern (VOC) detected so far carry a combination of key amino acid changes and indels. Recombination may also reshuffle existing genetic profiles of distinct strains, potentially giving origin to recombinant strains with altered phenotypes. However, co-infection and recombination events are challenging to detect and require in-depth curation of assembled genomes and sequencing reds. Here, we present the molecular characterization of a new SARS-CoV-2 recombinant between BA.1.1 and BA.2.23 Omicron lineages identified in Brazil. We characterized four mutations that had not been previously described in any of the recombinants already identified worldwide and described the likely breaking points. Moreover, through phylogenetic analysis, we showed that the newly named XAG lineage groups in a highly supported monophyletic clade confirmed its common evolutionary history from parental Omicron lineages and other recombinants already described. These observations were only possible thanks to the joint effort of bioinformatics tools auxiliary in genomic surveillance and the manual curation of experienced personnel, demonstrating the importance of genetic, and bioinformatic knowledge in genomics.

冠状病毒科（Coronaviridae）中已被报道存在重组事件。自新冠病毒（SARS-CoV-2）大流行伊始，不同程度的选择压力持续作用于该病毒，催生了在病毒传播能力与抗体逃逸方面适应性更强的新型毒株。截至目前检测到的绝大多数新冠病毒关切变异株（VOC，Variants of Concern），均携带着关键氨基酸突变与插入缺失（indels）的组合特征。重组还可对不同毒株已有的遗传特征进行重新组合，有可能产生表型发生改变的重组毒株。不过，共感染与重组事件的检测难度较大，需要对组装后的基因组进行深度整理分析，并对测序读段（sequencing reads）进行核验。本研究针对在巴西检出的一株新型新冠病毒重组毒株（其为BA.1.1与BA.2.23奥密克戎（Omicron）支系的重组体）进行了分子特征解析。我们鉴定出4种此前在全球已报道的重组毒株中均未出现的突变，并明确了其潜在的重组断裂位点。此外，通过系统发育分析，我们证实新命名的XAG支系隶属于一个支持度极高的单系群（monophyletic clade），确认其与亲本奥密克戎支系及已有报道的其他重组毒株共享共同的演化历史。本研究的上述结论得益于基因组监测辅助工具与专业人员的人工整理分析共同协作，由此凸显了遗传学与生物信息学知识在基因组学研究中的重要价值。