The SARS-CoV-2 virus causing the global pandemic is a coronavirus with a genome of about 30Kbase length. The design of vaccines and choice of therapies depends on the structure and mutational stability of encoded proteins in the open reading frames (ORFs) of this genome. In this study, we computed, using Expectation Reflection, the genome-wide covariation of the SARS-CoV-2 genome based on an alignment of $\approx 130000$ SARS-CoV-2 complete genome sequences obtained from GISAID. We used this covariation to compute the Direct Information between pairs of positions across the whole genome, investigating potentially important relationships within the genome, both within each encoded protein and between encoded proteins. We then computed the covariation within each clade of the virus. The covariation detected recapitulates all clade determinants and each clade exhibits distinct covarying pairs.

引起全球大流行的SARS-CoV-2病毒是一种基因组长度约为30Kbase的冠状病毒。疫苗的设计和疗法的选择取决于该基因组开放阅读框 (ORF) 中编码蛋白的结构和突变稳定性。在这项研究中，我们使用期望反射计算了 SARS-CoV-2 基因组的全基因组协变，该协变基于比对$\approx 130000$从 GISAID 获得的 SARS-CoV-2 完整基因组序列。我们使用这种协变来计算整个基因组中位置对之间的直接信息，研究基因组内潜在的重要关系，包括每个编码蛋白质内和编码蛋白质之间的关系。然后我们计算了病毒每个进化枝内的协变。检测到的协变概括了所有进化枝的决定因素，每个进化枝都表现出不同的协变对。