Table 3.
Genome classification using an ASV inference strategy with sequencing data for one or two variants of the SARS-CoV-2 virus (PERF: performance of the VOC prediction regarding the expected VOC class).
| Samples | Expected genotype | Predicted genotype | PERF | |||
|---|---|---|---|---|---|---|
| Type | ID | Expected lineage | Expected VOC class | Score by iterations | Predicted VOC class | |
| Single lineage | S1 | B.1.1.389 | Non-VOC | 5 | Non-VOC | ✔ |
| S2 | C.36.3 | Non-VOC | 5 | Non-VOC | ✔ | |
| S3 | P.2 | Non-VOC | 5 | Non-VOC | ✔ | |
| S4 | B.1.625 | Non-VOC | 5 | Non-VOC | ✔ | |
| S5 | B.1.429 | Non-VOC | 5 | Non-VOC | ✔ | |
| S6 | B.1.525 | Non-VOC | 5 | Non-VOC | ✔ | |
| S7 | B.1.1.519 | Non-VOC | 5 | Non-VOC | ✔ | |
| S8 | B.1.1.7 | Alpha | 5 | Alpha | ✔ | |
| S9 | B.1.351 | Beta | 5 | Beta | ✔ | |
| S10 | P.1 | Gamma | 5 | Gamma | ✔ | |
| S11 | AY.113 | Delta | 5 | Delta | ✔ | |
| S12 | B.1.1.529 | Omicron | 5 | Omicron | ✔ | |
| Double lineage | D1 (S4 + S6) | B.1.625 + B.1.525 | Non-VOC (+ Non-VOC) | 5 | Non-VOC (+ Non-VOC) | ✔ |
| D2 (S1 + S8) | B.1.1.389 + B.1.1.7 | Alpha (+ Non-VOC) | 4 | Alpha (+ Non-VOC) | ✔ | |
| D3 (S8 + S9) | B.1.1.7 + B.1.351 | Alpha + Beta | 3 | Alpha + Beta | ✔ | |
| D4 (S8 + S10) | B.1.1.7 + P.1 | Alpha + Gamma | 4 | Alpha + Gamma | ✔ | |
| D5 (S8 + S11) | AY.113 + B.1.1.7 | Alpha + Delta | 4 | Alpha + Delta | ✔ | |
| D6 (S8 + S12) | B.1.1.7 + B.1.1.529 | Alpha + Omicron | 5 | Alpha + Omicron | ✔ | |
| D7 (S9 + S11) | AY.113 + B.1.351 | Beta + Delta | 5 | Beta + Delta | ✔ | |
| D8 (S9 + S10) | P.1 + B.1.351 | Beta + Gamma | 5 | Beta + Gamma | ✔ | |
| D9 (S9 + S12) | B.1.351 + B.1.1.529 | Beta + Omicron | 5 | Beta + Omicron | ✔ | |
| D10 (S11 + S10) | AY.113 + P.1 | Delta + Gamma | 5 | Delta + Gamma | ✔ | |
| D11 (S10 + S12) | P.1 + B.1.1.529 | Gamma + Omicron | 5 | Gamma + Omicron | ✔ | |
| D12 (S11 + S2) | AY.113 + C.36.3 | Delta (+ Non-VOC) | 5 | Delta (+ Non-VOC) | ✔ | |
| D13 (S7 + S11) | AY.113 + B.1.1.519 | Delta (+ Non-VOC) | 0 | Beta | ✘ | |
| D14 (S11 + S12) | AY.113 + B.1.1.529 | Delta + Omicron | 5 | Delta + Omicron | ✔ | |