Table 5. Nanobody neutralization activity against spike variants; related to Figure 4.
Nanobodies were assayed for neutralization activity against a pseudotyped HIV-1 virus (PSV) expressing SARS-CoV-1 or SARS-CoV-2 wild-type or variant spike, with IC50s calculated from neutralization curves. Standard error of the mean (s.e.m.) is reported where replicates were available.
| ID | Epitope | SARS-CoV-2 PSV IC50 (s.e.m.)(nM) | SARS-CoV-1 PSV IC50 (s.e.m.) (nM) | SARS-CoV-2 20H/501Y.V2 PSV IC50 (s.e.m.) (nM) | SARS-CoV-2 20I/501Y.V1 PSV IC50 (s.e.m.) (nM) | SARS-CoV-2 20J/501Y.V3 PSV IC50 (s.e.m.) (nM) |
|---|---|---|---|---|---|---|
| S1-1 | RBD | 6.7 (1.0) | 8.6 (6.4) | 7.2 (1.6) | 8.5 (4.2) | 2.9 (0.2) |
| S1-3 | Non-RBD | 1030 (666) | 3598 (563) | – | – | – |
| S1-4 | RBD | 41.5 (3.7) | 179 | – | – | – |
| S1-6 | RBD | 56.1 (20.7) | 227 (205) | – | – | – |
| S1-17 | Non-RBD | 1271 (888) | NA | – | – | – |
| S1-20 | RBD | 51.8 (3.7) | NA | NA | 13.5 | NA |
| S1-23 | RBD | 5.7 (2.2) | NA | NA | 78.3 | NA |
| S1-24 | Non-RBD | 868 | NA | – | – | – |
| S1-27 | RBD | 19.5 (4.9) | NA | – | – | – |
| S1-30 | Non-RBD | 717.8 (387) | NA | – | – | – |
| S1-31 | RBD | 78.7 (3.5) | NA | – | – | – |
| S1-35 | RBD | 12.5 (0.1) | 386.8 (350) | – | – | – |
| S1-36 | RBD | 48.5 (21.1) | NA | – | – | – |
| S1-37 | RBD | 6.8 (0.7) | NA | NA | 13.5 | NA |
| S1-39 | RBD | 111 (4.0) | 22.1 (18.5) | – | – | – |
| S1-41 | Non-RBD | 679 (53.4) | NA | – | – | – |
| S1-48 | RBD | 5.82 (0.5) | NA | 20.9 (1.4) | 7.3 (1.5) | 14.2 (3.5) |
| S1-49 | Non-RBD | 356 (32.8) | NA | – | – | – |
| S1-51 | RBD | 555.8 (52.5) | NA | – | – | – |
| S1-58 | Non-RBD | 940 (795) | NA | – | – | – |
| S1-62 | RBD | 3.3 (0.8) | – | NA | 6.4 (4.5) | NA |
| S1-RBD-6 | RBD | 77.2 (21.8) | 89.7 (4.2) | 75.8 | 78.3 | 43.5 |
| S1-RBD-9 | RBD | 235 (97.5) | 149.4 (54.1) | 115.7 (18.9) | 35.9 (5.1) | 24.5 (5.8) |
| S1-RBD-11 | RBD | 13.5 (5.50) | NA | 40.4 (2.5) | 100.6 | 138.6 |
| S1-RBD-15 | RBD | 4.6 (1.2) | NA | 3.4 (1.4) | 5.2 (1.0) | 1.3 (0.03) |
| S1-RBD-16 | RBD | 79.2 (4.2) | – | 1612 (1303) | 81.2 (10.9) | 35.7 (23.1) |
| S1-RBD-20 | RBD | 12.4 (1.1) | NA | NA | 49.6 | NA |
| S1-RBD-21 | RBD | 17.3 (3.1) | NA | 128.5 (16.8) | 24.3 (0.7) | 40.7 (7.0) |
| S1-RBD-23 | RBD | 7.3 (0.4) | NA | 16.3 (1.9) | 2.8 | 5.7 |
| S1-RBD-27 | RBD | 163 (71.4) | NA | NA | 99.8 | NA |
| S1-RBD-29 | RBD | 9.5 (1.0) | NA | – | – | – |
| S1-RBD-35 | RBD | 12.3 (2.4) | NA | 51.2 (4.2) | 11.5 (1.1) | 17.7 (4.0) |
| S1-RBD-37 | RBD | 523 (93.4) | NA | NA | – | – |
| S1-RBD-40 | RBD | 25.6 (3.4) | NA | 299.8 (200) | 10.5 (0.2) | 32.2 (7.1) |
| S1-RBD-47 | RBD | 127 (11.6) | NA | NA | 206 (123) | NA |
| S1-RBD-48 | RBD | 68.7 (14.2) | NA | NA | 106.6 (65.6) | NA |
| S2-2 | S2 | 4460 (901) | NA | – | – | – |
| S2-3 | S2 | 2234 (751) | 6277 | – | – | – |
| S2-40 | S2 | 1712 (828) | NA | – | – | – |
| S2-62 | S2 | 7177 (5801) | 1954 (364) | – | – | – |
–, not determined; NA, no activity.