Table 7. Nanobody neutralization of rVSV/SARS-CoV-2 and selected resistant mutants; related to Figure 6.
Neutralization assays were carried out using rVSV/SARS-CoV-2 and 293T/ACE2cl.22 target cells treated with the denoted nanobodies. Pseudovirus with either wild-type or variant spike (with escape mutants selected using the corresponding nanobody) was used. Escape mutants and IC50s are listed. Amino acid substitutions contributing to loss of neutralization activity are indicated in bold.
| Nanobody | Epitope | rVSV/SARS-CoV-2 variant | IC50 (nM)± s.e.m. |
|---|---|---|---|
| S1-1 | RBD | wt | 2.63 ± 0.23 |
| Y369N | 122 ± 3.0 | ||
| G404E | 40.8 ± 1.01 | ||
| S1-6 | RBD | wt | 13.0 ± 3.47 |
| D574N*, Q792H, Q992H | 587 ± 31.1 | ||
| S371P, H66R, N969T | 202 ± 29.9 | ||
| S1-23 | RBD | wt | 0.58 ± 0.02 |
| F490S, E484K, Q493K | > 1000 | ||
| Q493R, G252R | > 1000 | ||
| E484K† | > 1000 | ||
| S1-36 | RBD | wt | 3.69 ± 0.14 |
| W64R,L452F | 262 ± 10.1 | ||
| W64R,F490L,I931G | 870 ± 202 | ||
| W64R, F490S | >1000 | ||
| S1-37 | RBD | wt | 1.83 ± 0.59 |
| W64R, F490S | >1000 | ||
| S1-48 | RBD | wt | 1.75 ± 0.43 |
| Y449H, F490S, Q787R | >1000 | ||
| S494P | >1000 | ||
| S1-62 | RBD | wt | 0.65 ± 0.16 |
| E484K | >1000 | ||
| S1-3trimer | S1 non-RBD | wt | 60.0 |
| W64R, Y170H, V705M | >1000 | ||
| W64R, Y170H, Q787H | >1000 | ||
| S1-30trimer | S1 non-RBD | wt | 150 |
| T315I | 2400 | ||
| S1-49 | S1 non-RBD | wt | 146 ± 53.8 |
| S172G | >1000 | ||
| S1-49dimer | S1 non-RBD | wt | 3.38 ± 2.44 |
| S172G | >1000 | ||
| S1-49trimer | S1 non-RBD | wt | 0.47 ± 0.00 |
| S172G | >1000 | ||
| S2-10 | S2 | wt | 6649 ± 2,545 |
| W64R, S982R | >100,000 | ||
| S2-10dimer | S2 | wt | 1015 ± 236 |
| W64R, S982R | >40,000 | ||
| S1-RBD-9 | RBD | wt | 30.2 ± 7.43 |
| T259K, K378Q | >1000 | ||
| W64R, K378Q | >1000 | ||
| K378Q | >1000 | ||
| S1-RBD-11 | RBD | wt | 1.44 ± 0.53 |
| F486S | >1000 | ||
| T478R | >1000 | ||
| T478I | >1000 | ||
| S1-RBD-15 | RBD | wt | 1.21 ± 0.06 |
| Y508H | 549 ± 36.9 | ||
| S1-RBD-16 | RBD | wt | 268 ± 162 |
| N354S | >1000 | ||
| S1-RBD-21 | RBD | wt | 9.61 ± 1.90 |
| F486L | >1000 | ||
| Y489H | >1000 | ||
| S1-RBD-22 | RBD | wt | 31.5 ± 11.8 |
| K378Q | >1000 | ||
| S1-RBD-23 | RBD | wt | 14.8 ± 3.55 |
| L452R | >1000 | ||
| H245R, S349P, H1083Y | >1000 | ||
| S1-RBD-24 | RBD | wt | 58.0 ± 0.00 |
| P384Q | >1000 | ||
| K378Q† | >1000 | ||
| S1-RBD-29 | RBD | wt | 18.0 ± 1.80 |
| E484G | >1000 | ||
| E484K | >1000 | ||
| S1-RBD-35 | RBD | wt | 1.80 ± 0.15 |
| T478I | >1000 | ||
| F486L† | 306 ± 17.2 | ||
| Y489H† | 57.4 ± 4.5 | ||
| S1-RBD-40 | RBD | wt | 38.9 ± 11.7 |
| W64R, F490S | > 500 |
*
Residue 574 is outside the structurally covered region of the RBD (residues 333–526) and, therefore, was not used in the Integrative Modeling Platform modeling.
†
Variant was separately identified by selection against a different nanobody.