Evolutionary Trajectory for the Emergence of Novel Coronavirus SARS-CoV-2

Abstract

Over the last two decades, the world experienced three outbreaks of coronaviruses with elevated morbidity rates. Currently, the global community is facing emerging virus SARS-CoV-2 belonging to Betacoronavirus, which appears to be more transmissible but less deadly than SARS-CoV. The current study aimed to track the evolutionary ancestors and different evolutionary strategies that were genetically adapted by SARS-CoV-2. Our whole-genome analysis revealed that SARS-CoV-2 was the descendant of Bat SARS/SARS-like CoVs and bats served as a natural reservoir. SARS-CoV-2 used mutations and recombination as crucial strategies in different genomic regions including the envelop, membrane, nucleocapsid, and spike glycoproteins to become a novel infectious agent. We confirmed that mutations in different genomic regions of SARS-CoV-2 have specific influence on virus reproductive adaptability, allowing for genotype adjustment and adaptations in rapidly changing environments. Moreover, for the first time we identified nine putative recombination patterns in SARS-CoV-2, which encompass spike glycoprotein, RdRp, helicase and ORF3a. Six recombination regions were spotted in the S gene and are undoubtedly important for evolutionary survival, meanwhile this permitted the virus to modify superficial antigenicity to find a way from immune reconnaissance in animals and adapt to a human host. With these combined natural selected strategies, SARS-CoV-2 emerged as a novel virus in human society.

Keywords: SARS-CoV; SARS-CoV-2; evolutionary strategies; genomic structure; mutations; phylogeny; recombination or reassortment.

Figure 1

Classification of coronaviruses.

Figure 2

Evolutionary phylogenetic tree analysis of Coronaviruses: whole-genome sequences based on the phylogenetic tree of CoVs was constructed with the maximum-likelihood method using BEAST with GTR+I+G as the nucleotide substitution model with an applied posterior probability value of 0.5. Branches with different colors represent different genera of Coronaviruses; black, alpha coronavirus, blue, beta coronavirus; red, SARS-CoV-2; green, delta coronavirus; purple, gamma coronavirus.

Figure 3

Genomic and gene view of four coronaviruses genera.

Figure 4

Comparison of Spike (S) protein amino acid residue sequence of Wuhan-Hu-1-CoV and SARS-CoV; (a): Wuhan-Hu-1-CoV (Wuhan seafood market pneumonia virus) and SARS-CoV (GZ02) amino acid residue multiple sequence alignment with hierarchical clustering (b,c): Prediction of S protein structure by using homology protein modeling (b) (Wuhan-Hu-1-CoV) and (c) (SARS CoV GZ02). Secondary structure selection by representing color includes: red, helix; yellow, sheets; green, loops; pink, insertions.

Figure 4

Comparison of Spike (S) protein amino acid residue sequence of Wuhan-Hu-1-CoV and SARS-CoV; (a): Wuhan-Hu-1-CoV (Wuhan seafood market pneumonia virus) and SARS-CoV (GZ02) amino acid residue multiple sequence alignment with hierarchical clustering (b,c): Prediction of S protein structure by using homology protein modeling (b) (Wuhan-Hu-1-CoV) and (c) (SARS CoV GZ02). Secondary structure selection by representing color includes: red, helix; yellow, sheets; green, loops; pink, insertions.

Figure 5

Similarity plot of Wuhan-Hu-1-CoV with other Coronaviruses (Blue, Bat SARS Like-CoVs W1V, ZXC21, ZC45; green, Bat SARS-CoVs GZ02, RF1; and yellow, MERS-CoV).