Fig. 4. The potential effect of APOBEC-mediated editing on SARS-CoV-2 mutations and fitness.

(A) The number of mutational events (all single nucleotide variants) on SARS-CoV-2 RNA segment 5’UTR-Orf1a (segment 1 in Fig. 1A) from the SARS-CoV-2 genome sequence data (the Nextstrain datasets from Dec. 2019 to Jan. 22nd, 2022 downloaded from the GISAID database, https://www.gisaid.org/hcov19-variants/ and https://nextstrain.org/ncov/global). The C203, C222, and C241 represent many of the C-to-U mutational events (asterisks) with the A3A-editing UC motif in the SARS-CoV-2 variants. (B) The A3A-mediated C-to-U editing rate on UC motif in the same 5’UTR-Orf1a region obtained from our cell-based editing system and the SSS analysis. The Ctrl (EV) editing levels (or background error rates) of the corresponding region are presented as negative values (%). The C203, C222, and C241 (asterisks) all showed significant editing by A3A. (C) The C-to-U mutation prevalence over time at C203, C222, and C241. The sequencing frequency is represented by C in blue and U in yellow (referred to the Nextstrain datasets: https://nextstrain.org/ncov/global). This analysis showed that SARS-CoV-2 started to acquire the C-to-U mutation at C241 in January 2020. By July 2020, 90% of the circulating viral variants carry this mutation at C241. By March 2021, almost all circulating viral variants have this mutation, suggesting the C241 to U mutation in the 5’UTR is beneficial to the viral fitness (see Fig. S9).