Recent SARS-CoV-2 evolution trajectories indicate the emergence of Omicron's several subvariants and the current rise of KP.3.1.1 and XEC

Abstract

The recent COVID-19 pandemic is one of the quickest-evolving pandemics in the world history. Therefore, the evolution of SARS-CoV-2 needs to be tracked consistently. Various VOIs, VOCs, and recent subvariants of Omicron have emerged from the dynamically evolving SARS-CoV-2. Various offspring of the Omicron subvariants have emerged since its origin, including lineages such as BA, BQ, and XBB, as well as more recent subvariants like BA.2.86, JN.1, JN.11.1, KP.3, KP.3.1.1, and XEC. The study evaluated the overall and one year evolutionary patterns, genome diversity, divergence event, transmission and geographical distributions, circulating frequency, entropy diversity, mutational diversity, risk mutations in S-protein and mutational fitness of the subvariants. The study estimated the substitution rate of all variants and subvariants of SARS-CoV-2 since its origin (32.001 × 10^-4 subs/year). The geographical distributions of the recent KP.3.1.1 and XEC subvariant indicated its distribution in North America, South America, Europe, and Southeast Asia. Simultaneously, genome mutational landscapes were noted, including Spike and RBD mutations. We found that JN.1, JN.1.11.1, KP.3, KP.3.1.1 and XEC subvariants have gained the highest mutational fitness in Europe and North America. Our study indicates that the rapid evolution and highest frequency of mutational fitness have created a variety of subvariants from Omicron. It also indicates a shift from waves to mini-waves. Finally, our possible explanation is that mutation-driven divergent evolution contributes to the emergence of recent subvariants.