Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in December, 2019 and have spread around the world. Within less than two years, delta variant of SARS-CoV-2 became the current dominant strain in Europe, USA and many countries. This study aimed to understand potential protein structural features that result each dominant variants in United Kingdom, Israel, South Africa, Brazil and Peru. We collected vaccination data from Our World in Data (https://ourworldindata.org/), variants frequency data in each country from CoVariants (https://ourworldindata.org/) and COVID-19 policy in each country from Reuters (https://graphics.reuters.com/world-coronavirus-tracker-and-maps/). The crystal structure of S1RBD with hACE2 from PDB databank (PDB ID: 6M0J, 7A91) were used. We mutated the amino acids on S1RBD to several variants (alpha, beta, delta, delta+, gamma, epsilon, lambda) by Schrödinger Maestro. Then, molecular dynamics simulations were conducted for 100ns with GROMACS under physiological conditions (310K, 142 mM NaCl, pH 7.4). In each competitive analysis, variants frequency data and also major types around variants turning point at each country were used. We found that delta variant beat alpha, beta, gamma or lambda variant under low infection trend whether vaccination coverage is over 50%. Also, dominant variant preferred short hydrogen bonds relaxation time when it competed with alpha, beta, gamma and lambda variant were fund during dynamic simulation studies. Each dominant type preferred small RMSD at first but large RMSD at the end when competing with alpha, beta, gamma. With our results, SARS-CoV-2 variants might be classified into two variant groups (delta-tend group, alpha-tend group) and each group might compete with the other. Moreover, the competitive studies hint that lambda-based variant might be next dominant in delta-dominant regions and delta variant would be dominant in alpha-tend-group-dominant regions. Our study provided structural features and competition strategy from dominant variants to explain why it became more contagious.

Competitive analysis of different SARS-CoV-2 variants in United Kingdom, Israel, South Africa, Brazil and Peru

ACS Spring 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.