SARS-CoV-2的新变种,即omicron的出现,由于其基因组中的高传播率和突变率,引起了全球关注。全世界的研究人员都在试图了解这种变异的进化和出现,以了解突变级联事件。
我们已经考虑了直到2021年12月2日在GISAID的公共存储库中提供的所有omicron基因组(n=302基因组)以及关注变体(VOC)的代表,即,阿尔法,beta,gamma,delta,和omicron;感兴趣的变体(VOI)mu和lambda;和受监测的变体(VUM)。进行了基于全基因组的系统发育和突变分析,以了解导致omicron变体出现的SARSCoV-2的进化。
基于全基因组的系统发育描绘了两个系统群(PG-I和PG-II)形成变体特异性进化枝,除了γ和VUGH。突变分析在omicron变体中检测到18,261个突变,其中大多数是刺突中的非同义突变(A67,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H),其次是RNA依赖性RNA聚合酶(rdrp)(A1892T,I189V,P314L,K38R,T492I,V57V),ORF6(M19M)和核衣壳卵白(RG203KR)。
Delta和omicron已经进化成不同的系统组,并且没有共同的祖先。同时,omicron与VOIlambda有着共同的祖先,其进化主要是由非同义突变产生的。
Emergence of new variant of SARS-CoV-2, namely omicron, has posed a global concern because of its high rate of transmissibility and mutations in its genome. Researchers worldwide are trying to understand the evolution and emergence of such variants to understand the mutational cascade events.
We have considered all omicron genomes (n = 302 genomes) available till 2nd December 2021 in the public repository of GISAID along with representatives of variants of concern (VOC), i.e., alpha, beta, gamma, delta, and omicron; variant of interest (VOI) mu and lambda; and variant under monitoring (VUM). Whole genome-based phylogeny and mutational analysis were performed to understand the evolution of SARS CoV-2 leading to emergence of omicron variant.
Whole genome-based phylogeny depicted two phylogroups (PG-I and PG-II) forming variant specific clades except for gamma and VUM GH. Mutational analysis detected 18,261 mutations in the omicron variant, majority of which were non-synonymous mutations in spike (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), followed by RNA dependent RNA polymerase (rdrp) (A1892T, I189V, P314L, K38R, T492I, V57V), ORF6 (M19M) and nucleocapsid protein (RG203KR).
Delta and omicron have evolutionary diverged into distinct phylogroups and do not share a common ancestry. While, omicron shares common ancestry with VOI lambda and its evolution is mainly derived by the non-synonymous mutations.