Table 2.
Information on mutations identified in immunosuppressed patients in this study and in other studies and SARS-CoV-2 lineages, consistent with sites of convergent evolution
| Patient ID | Accumulated mutations | Relevant immunosuppressed patient case studies | Relevant mAb and/or antiviral studiesa | Convergent mutations fixed in variantsb |
|---|---|---|---|---|
|
P29 BA.1.1 |
ORF1a:T1567I (nsp3) | This study | N/R | Kappa |
| ORF1a:V1574I (nsp3) | This study | N/R | / | |
| S:E484T (RBD) | Halfmann et al. 2023 [28] reported in a patient treated with bamlanivimab | Resistance to bamlanivimab [28] | Beta, Gamma, and all Omicron sublineages (convergent mutations: S: E484K/A/R) | |
| S:D574N | This study | Among the most recurrent G-A mutations related to molnupiravir [29] | / | |
|
P78 BA.2.9 |
ORF1a:P2739S (nsp3) | This study | N/R | / |
| S: 68/69-(NTD; RDR1) | S:69/70- convergent deletion mutation by Kemp et al. 2021 [7] and Sonnleitner et al. 2022 [30], etc. | S:69/70- increases viral entry efficiency and infectivity [31] | Alpha, BA.1, BA.3, BA.4, BA.5, and CK, BE, BF, BQ.1 sublineages (convergent mutation: S:69/70-) | |
| S:K444N (RBD) | Ordaya et al. 2023 [32] on reduced susceptibility to bebtelovimab | In vitro confirmed sites confer a reduction in susceptibility to bebtelovimab [33, 34] | Later Omicron BQ.1, CH.1, BE.9, BR.1, CL.1, CK, CM, DL.1 sublineages (convergent mutations: S: K444T/M/N/R) | |
| S:G446R (RBD) | Convergent mutation reported by Ordaya et al. 2023 [32] on reduced susceptibility to bebtelovimab | In vitro confirmed sites confer a reduction in susceptibility to bebtelovimab [33] | Omicron BA.1.1, BA.1.12.1, BA.2.75, BA.5.2.43, and later BN, BM, CH.1, XBB (e.g., XBB.1.★, EG, FL, FK, FU, GK, HK, HV), XBC.1.★, XBF, BA.2.86.1 and its descendent JN.★ sublineages (convergent mutations: S: G446S/D) | |
|
P126 BA.5.5 |
ORF1a:L3829F (nsp6) | Morita et al. 2023 [35] | N/R | Later Omicron BQ.1, XBB.2.3.8, and XBB.1.16 sublineages |
| S: 138/145- (NTD, RDR2) | Convergent deletion mutations by Hensley et al. [36] and Sonnleitner et al. 2022 [30] | Y144- and similar deletions confer to resistance to NTD-directed mAbs [27, 37] | Alpha, Omicron BA.1, and later BQ.1, XBB (e.g., XBB.1.★, EG, FL, FU, GK, HK, HV), XBC.1.★, BA.2.86.1 and its descendent JN.★ sublineages (convergent mutations: S:Y144- / 144/145- / 143/145-) | |
| S: 242/243- (NTD, RDR4) | Convergent deletion mutation by Nussenblatt et al. 2022 [38] | 243/244- and similar deletions confer to resistance to NTD-directed mAbs [27] | Beta and later Omicron XBC.1.3 lineages (convergent mutations: S:243/244- / 241/243-) | |
| S:G1085A (S2 CD) | This study | N/R | / | |
| N:M234I | Díaz et al. 2021[39], Shoji et al. 2022 [40] | N/R | B.1 lineage | |
|
P148 BA.5.1 |
ORF1a:E938G (nsp3) | This study | N/R | / |
aN/R not previously reported
bVariants and sublineages reported here are of > 90% frequency of the convergent mutations and > 1,000 counts in the GISAID database as of January 26, 2024; data was queried using the outbreakinfo R package