The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses innumerous challenges, like understanding what triggered the emergence of this new human virus, how this RNA virus is evolving or how the variability of viral genome may impact the primary structure of proteins that are targets for vaccine. We analyzed 19471 SARS-CoV-2 genomes available at the GISAID database from all over the world and 3335 genomes of other Coronoviridae family members available at GenBank, collecting SARS-CoV-2 high-quality genomes and distinct Coronoviridae family genomes. Additionally, we analyzed 199,984 spike glycoprotein sequences. Here, we identify a SARS-CoV-2 emerging cluster containing 13 closely related genomes isolated from bat and pangolin that showed evidence of recombination, which may have contributed to the emergence of SARS-CoV-2. The analyzed SARS-CoV-2 genomes presented 9632 single nucleotide variants (SNVs) corresponding to a variant density of 0.3 over the genome, and a clear geographic distribution. SNVs are unevenly distributed throughout the genome and hotspots for mutations were found for the spike gene and ORF 1ab. We describe a set of predicted spike protein epitopes whose variability is negligible. Additionally, all predicted epitopes for the structural E, M and N proteins are highly conserved. The amino acid changes present in the spike glycoprotein of variables of concern (VOCs) comprise between 3.4% and 20.7% of the predicted epitopes of this protein. These results favors the continuous efficacy of the available vaccines targeting the spike protein, and other structural proteins. Multiple epitopes vaccines should sustain vaccine efficacy since at least some of the epitopes present in variability regions of VOCs are conserved and thus recognizable by antibodies.

由严重急性呼吸系统综合症冠状病毒 2 (SARS-CoV-2) 引起的 2019 年冠状病毒病 (COVID-19) 大流行带来了无数挑战，例如了解是什么引发了这种新的人类病毒的出现、这种 RNA 病毒是如何进化的或如何进化的病毒基因组的变异性可能会影响作为疫苗靶标的蛋白质的一级结构。我们分析了 GISAID 数据库中来自世界各地的 19471 个 SARS-CoV-2 基因组和 GenBank 中其他冠状病毒科成员的 3335 个基因组，收集了 SARS-CoV-2 高质量基因组和不同的冠状病毒科基因组。此外，我们还分析了 199,984 个刺突糖蛋白序列。在这里，我们确定了一个 SARS-CoV-2 新兴簇，其中包含从蝙蝠和穿山甲中分离出的 13 个密切相关的基因组，这些基因组显示出重组的证据，这可能促成了 SARS-CoV-2 的出现。分析的 SARS-CoV-2 基因组呈现出 9632 个单核苷酸变异 (SNV)，对应于基因组中 0.3 的变异密度，并且具有清晰的地理分布。SNV 在整个基因组中分布不均，并且发现了刺突基因和 ORF 1ab 的突变热点。我们描述了一组预测的刺突蛋白表位，其可变性可以忽略不计。此外，结构 E、M 和 N 蛋白的所有预测表位都是高度保守的。关注变量 (VOC) 的刺突糖蛋白中存在的氨基酸变化占该蛋白质预测表位的 3.4% 至 20.7%。这些结果有利于针对刺突蛋白和其他结构蛋白的可用疫苗的持续功效。