Molecular evolution of SARS-CoV-2 structural genes: evidence of positive selection in spike glycoprotein

SARS-CoV-2 caused a global pandemic in early 2020 and has resulted in more than 8,000,000 infections as well as 430,000 deaths in the world so far. 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. However, how these genes evolve during its human to human transmission is largely unknown. In this study, we screened and analyzed roughly 3090 SARS-CoV-2 isolates from GenBank database. The distribution of the 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 sequences of these genes. Intragenic recombination event isnt detected among different alleles. However, purifying selection has conducted on the evolution of these genes. By analyzing full genomic sequences of these alleles using codon-substitution models (M8, M3 and M2a) and likelihood ratio tests (LRTs) of codeML package, it reveals that codon 614 of S glycoprotein has subjected to strong positive selection pressure and a persistent D614G mutation is identified. The definitive positive selection of D614G mutation is further confirmed by internal fixed effects likelihood (IFEL) and Evolutionary Fingerprinting methods implemented in Hyphy package. In addition, another potential positive selection site at codon 5 in the signal sequence of the S protein is also identified. The allele containing D614G mutation has undergone significant expansion during SARS-CoV-2 global pandemic, 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 salt bridge among S protein monomers 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. 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.

Relationship of the phosphodiesterase 4D gene rs153031 polymorphism and the susceptibility of unstable angina pectoris / 重庆医学

Objective To investigate the association between the phosphodiesterase 4D(PDE4D) gene rs153031 polymorphism and the susceptibility of unstable angina pectoris(UAP) in Chinese Han population of Changwu region .Methods The PDE4D gene rs153031 polymorphism was genotyped by Taqman probe in 172 UAP patients(UAP group) ,as well as in gender-and-age-matched 220 subjects without coronary heart disease(CHD)(control group) .Results In this crowd ,there was PDE4D gene rs153031 poly-morphism in patients with UAP and in subjects without CHD .Compared with control group ,frequencies of GG ,GA ,AA genotypes and G allele of rs153031 in UAP group showed no statistical differences (P> 0 .05) .Conclusion In Chinese Han population of Changwu region ,PDE4D gene rs153031 polymorphism shows no association with the susceptibility of UAP .

The relevance among serum CRP level,CRP gene C+1444T polymorphism and the risk with acute myocardial infarction * / 重庆医学

Objective To investigate the relationship between serum C-reactive protein(CRP) level ,CRP gene C+1444T poly-morphism and the risk with Acute myocardial infarction (AMI) in Chinese Han population in Sunan region .Methods The CRP gene C+1444T polymorphism was genotyped by Polymerase reaction restriction-fragment length polymorphism (PCR-RFLP) and the serum CRP level was measured by enzyme linked immunosorbent assay (ELISA) between 227 patients with AMI(AMI group) and 161 control subjects .Results No differences were found in genotype distribution between AMI group and controls (CC 82 .38% ,CT 17 .62% ,TT 0% vs 86 .96% ,13 .04% ,0% )(P>0 .05) .The serum CRP level in AMI group was significantly higher than controls(P< 0 .01) .There was no differences in the serum level between any genotypes of the CRP gene C + 1444T (P<0 .05) .Conclusion The CRP gene C+1444T polymorphism is not associate with increased risk of AMI ,and it have no effect with the serum level in Chinese Han population in Sunan region .