Severe acute respiratory syndrome coronavirus 2 Raw sequence reads. Severe acute respiratory syndrome coronavirus 2

To evaluate the effects of T492I on the evolution of SARS-CoV-2, we constructed four variants as ancestors for our evolution experiments: the T492I mutant (aWT-I), which is based on the wild-type (WT) strain (GenBank accession No. MT020880); the wild-type strain (aWT-T); the Delta variant (EVAg: 009V-04187, aDelta-I); and the reversely mutated (I492T) Delta variant (aDelta-T). We chose aDelta-I and aDelta-T as ancestors in the evolution experiment to evaluate the effects of T492I on strains with adaptive mutations, such as Delta mutations. Experimental evolution was carried out over an incubation course of 90 days (30 transmission events) with three independent replicates performed in parallel (R1, R2 and R3), resulting in corresponding evolved populations (eWT-I, eWT-T, eDelta-I and eDelta-T). To develop a better understanding of the evolutionary process and confirm the findings, we also independently performed evolve-and-resequence experiments on the four constructed variants in a shorter experiment of 45 days (15 transmission events). RNA from the evolved viruses was extracted and analyzed via whole-genome sequencing (WGS).