Table 2.
Overview of the SARS-CoV-2 variants used in the study, reported with their corresponding mutations, the date of isolation, the lineage following Pangolin [10] and, where applicable, the WHO nomenclature [11].
| Strain Name | WHO Nomenclature |
Lineage (Pangolin) | Spike Mutations |
Spike Deletions | GISIAD |
|---|---|---|---|---|---|
| hCoV-19/Italy/LAZ-INMI1-isl/2020 | - | A | N679S | - | EPI_ISL_410545 |
| hCoV-19/Italy/LOM-INMI-10734/2020 | - | B.1 | S247R, D614G | - | EPI_ISL_568579 |
| hCoV-19/Italy/LOM-Pavia-10833/2020 | Alpha | B.1.1.7 | N501Y, A570D, D614G, P681H, R685H, T716I, S982A, D1118H | 69–70, 144 |
EPI_ISL_7043618 |
| hCoV-19/Italy/LOM-Pavia-10858/2021 | Gamma | P1 | L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F | - | EPI_ISL_7043637 |
| hCoV-19/Italy/LOM-Pavia-10860/2021 | Beta | B.1.351 | S171L, D80A, D215G, L242H, K417N, E484K, N501Y, D614G, A701V | 243–245 | EPI_ISL_7043650 |
| hCoV-19/Italy/LOM-Pavia-10870/2021 | - | B.1.258.17 | L189F, N439K, D614G, V772I | 69–70 | EPI_ISL_7043668 |
| hCoV-19/Italy/LOM-Pavia-10881/2021 | C.36.3(1) | S12F, W152R, R346S, L452R, T547I, D614G, Q677H, A899S | 69–70 | EPI_ISL_7043684 | |
| hCoV-19/Italy/LOM-Pavia-10882/2021 | Eta | B.1.525 | Q52R, A67V, E484K, D614G, Q677H, F888L | 69–70, 144 |
EPI_ISL_7043697 |
| hCoV-19/Italy/LOM-Pavia-10916/2021 | Delta | B.1.617.2 | T19R, G142D, E156G, A222V, L452R, T478K, D614G, P681R, R682W, D950N, E990A | 157–158 | EPI_ISL_7043718 |
| hCoV-19/Italy/LOM-Pavia-10919/2021 | Mu | B.1.621.1 | T95I, Y144T, R346K, N501Y, D614G, P681H, D950N | - | EPI_ISL_7462685 |
| hCoV-19/Italy/LOM-Pavia-10921/2021 | - | C.36.3(2) | S12F, W152R, R346S, L452R, D614G, A899S | 69–70, 675–679 |
EPI_ISL_7043733 |
| hCoV-19/Italy/LOM-Pavia-10924/2021 | Lambda | C.37 | G75V, T76I, R246N, L452Q, D614G, T859N | 247–253, 675–679 |
EPI_ISL_7043746 |
| hCoV-19/Italy/LOM-Pavia-10940/2021 | DeltaPlus | AY.4.2.3 | T19R, T95I, G142D, Y145H, R158G, A222V, L452R, T478K, D614G, P681R, D950N | 156–157 | Submitted |
| hCoV-19/Italy/LOM-Pavia-10943/2021 | Omicron | B.1.1.529 (BA.1) | A67V, T95I, Y145D, L212I, G339D, S371L, S373P, S375F, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981 | 69–70, 142–144, 211 | Submitted |