Molecular Evolution of SARS-CoV-2 Structural Genes: Evidence of Positive Selection in Spike Glycoprotein

Abstract Background: SARS-CoV-2 has caused a global pandemic since early 2020 and is still a serious public health issue world-wide. Four structural proteins, envelope (E), membrane (M), nucleocapsid (N) and spike (S) glycoprotein, play a key role in controlling the entry into human cells and virion assembly of SARS-CoV-2. The evolution of these genes may determine the infectivity of SARS-CoV-2, but is largely unknown. Results: We analyzed roughly 3090 SARS-CoV-2 isolates from GenBank database. The distribution of four gene alleles is determined: 16 for E, 40 for M, 131 for N and 173 for S genes. Phylogenetic analysis shows that global SARS-CoV-2 isolates can be clustered into three to four major clades based on the protein sequence. Although intragenic recombination event isn’t detected among different alleles, purifying selection has conducted on the evolution of these genes. By analyzing full genomic sequences of these alleles, it reveals that codon 614 of S glycoprotein has subjected to strong positive selection pressure and a consistent D614G mutation is identified. Additionally, another potential positive selection site at codon 5 in the signal sequence of the S protein is also identified with consistent L5F mutation. The allele containing D614G mutation has undergone significant expansion during SARS-CoV-2 transmission, implying a better adaptability of isolates with the mutation. However, L5F allele expansion is relatively restricted. The D614G mutation is located at the subdomain 2 (SD2) of C-terminal portion (CTP) of the S1 subunit. Protein structural modeling shows that the D614G mutation may cause the disruption of a salt bridge between S protein monomers and increase their flexibility, and in turn promote receptor binding domain (RBD) opening, virus attachment and entry into host cells. Located at the signal sequence of S protein as it is, L5F mutation may facilitate the protein folding, assembly, and secretion of the virus. Conclusions: This is the first evidence of positive Darwinian selection in the spike gene of SARS-CoV-2, which contributes to a better understanding of the adaptive mechanism of this virus and help to provide insights for developing novel therapeutic approaches as well as effective vaccines by targeting on mutation sites.