The global scale of the COVID-19 pandemic has demonstrated the evolution of SARS-CoV-2 and the clues of adaptation. After two years and two months since the declaration of the pandemic, several variants have emerged and become fixed in the human population thanks to extrinsic selective pressures but also to the inherent mutational capacity of the virus. Here, we applied a neutral substitution evolution test to the spike (S) protein of Omicron’s protein and compared it to the others’ variant of concern (VOC) neutral evolution. We carried out comparisons among the interactions between the S proteins from the VOCs (Alpha, Beta, Gamma, Delta and Omicron) and the receptor ACE2. The shared amino acids among all the ACE2 binding S proteins remain constant, indicating that these amino acids are essential for the accurate binding to the receptor. The complexes of the RBD for every variant with the receptor were used to identify the amino acids involved in the protein—protein interaction (PPI). The RBD of Omicron establishes 82 contacts, compared to the 74 of the Wuhan original viral protein. Hence, the mean number of contacts per residue is higher, making the contact thermodynamically more stable. The RBDs of the VOCs are similar in sequence and structure; however, Omicron’s RBD presents the largest deviation from the structure by 1.11 Å RMSD, caused by a set of mutations near the glycosylation N343. The chemical properties and structure near the glycosylation N343 of the Omicron S protein are different from the original protein, which provoke reduced recognition by the neutralizing antibodies. Our results hint that selective pressures are induced by mass vaccination throughout the world and by the persistence of recurrent infections in immunosuppressed individuals, who did not eliminate the infection and ended up facilitating the selection of viruses whose characteristics are different from the previous VOCs, less pathogenic but with higher transmissibility.

As the SARS-CoV-2 has spread and the pandemic has dragged on, the virus continued to evolve rapidly resulting in the emergence of new highly transmissible variants that can be of public health concern. The evolutionary mechanisms that drove this rapid diversity are not well understood but neutral evolution should open the first insight. The neutral theory of evolution states that most mutations in the nucleic acid sequences are random and they can be fixed or disappear by purifying selection. Herein, we performed a neutrality test to better understand the selective pressures exerted over SARS-CoV-2 spike protein from homologue proteins of Betacoronavirus, as well as to the spikes from human clinical isolates of the virus. Specifically, Tyr and Asn have higher occurrence rates on the Receptor Binding Domain (RBD) and in the overall sequence of spike proteins of Betacoronavirus, whereas His and Arg have lower occurrence rates. The in vivo evolutionary phenomenon of SARS-CoV-2 shows that Glu, Lys, Phe, and Val have the highest probability of occurrence in the emergent viral particles. Amino acids that have higher occurrence than the expected by the neutral control, are favorable and are fixed in the sequence while the ones that have lower occurrence than expected, influence the stability and/or functionality of the protein. Our results show that most unique mutations either for SARS-CoV-2 or its variants of health concern are under selective pressures, which could be related either to the evasion of the immune system, increasing the virus’ fitness or altering protein – protein interactions with host proteins. We explored the consequences of those selected mutations in the structure and protein – protein interaction with the receptor. Altogether all these forces have shaped the spike protein and the continually evolving variants.

Coronaviruses interact with protein or carbohydrate receptors through their spike proteins to infect cells. Even if the known protein receptors for these viruses have no evolutionary relationships, they do share ontological commonalities that the virus might leverage to exacerbate the pathophysiology. ANPEP/CD13, DPP IV/CD26, and ACE2 are the three protein receptors that are known to be exploited by several human coronaviruses. These receptors are moonlighting enzymes involved in several physiological processes such as digestion, metabolism, and blood pressure regulation; moreover, the three proteins are expressed in kidney, intestine, endothelium, and other tissues/cell types. Here, we spot the commonalities between the three enzymes, the physiological functions of the enzymes are outlined, and how blocking either enzyme results in systemic deregulations and multi-organ failures via viral infection or therapeutic interventions is addressed. It can be difficult to pinpoint any coronavirus as the target when creating a medication to fight them, due to the multiple processes that receptors are linked to and their extensive expression.

As the SARS-CoV-2 has spread and the pandemic has dragged on, the virus continued to evolve rapidly resulting in the emergence of new highly transmissible variants that can be of public health concern. The evolutionary mechanisms that drove this rapid diversity are not well understood but neutral evolution should open the first insight. The neutral theory of evolution states that most mutations in the nucleic acid sequences are random and they can be fixed or disappear by purifying selection. Herein, we performed a neutrality test to better understand the selective pressures exerted over SARS-CoV-2 Spike protein, as well as in four of the identified health concern variants. Lys and Thr have higher occurrence rate on the Receptor Binding Domain (RBD) than in the overall sequence whereas Cys, His, and importantly Arg have low occurrence rate both in the whole protein and the RBD. Amino acids that have lower occurrence than the expected neutral control influence in the stability and or functionality of the protein. Our results show that most unique mutations either for SARS-CoV-2 or the variants of health concern are under selective pressures, which could be related either to the evasion of the immune system, increasing the virus’ fitness or altering protein – protein interactions with host proteins. Altogether all these forces have shaped the Spike protein. Understanding the evolutionary forces that act upon Spike protein may help designing better treatments and vaccines that target variants of health concern.