Table 2.
Data obtained from whole genome sequencing of wastewater environmental RNA from August 2021 to January 2022 for Prince Albert.
| Date Collected | Nextclade (consensus) | Pangolin | % Breadth of coverage (≥ 5× depth) | Average depth of coverage | Median Depth of Coverage | VOC Detected (consensus) | Number of VOC mutations (consensus) | Frequencies of reads (> cov 30) with VOC mutation (consensus) | Number of mutations supporting presence of additional VOC (subconsensus) | Additional Delta sublineages or VOCs, VOIs detected in subconsensus sequences |
|---|---|---|---|---|---|---|---|---|---|---|
| 04/08/2021 | 21A (Delta) | AY.4 | 98 | 3444.43 | 1289 | B.1.617.2 (Delta) sublineage AY.12 | 10/12 12/12 (cov <30) |
0.61 cov < 30 = 0.99 |
B.1.1.7 = 4 (<0.1) P.1 = 16 (0.17) |
Confirmed P.1 (Gamma)- weak Possible B.1.1.7 (Alpha) |
| 11/08/2021 | 21A (Delta) | B.1.617.2 | 98.61 | 5949.44 | 8666 | B.1.617.2 (Delta) | 11/12 | 0.89 | <4 | IE |
| 23/08/2021 | 21A (Delta) | B.1.617.2 | 99.6 | 4270.86 | 3396 | B.1.617.2 (Delta) | 10/12 | 0.84 | <4 | IE |
| 30/08/2021 | 21A (Delta) | B.1.617.2 | 98.61 | 5306.34 | 4909 | B.1.617.2 (Delta) | 13/13 | 0.99 | AY.25 = 2 (<0.1) | AY.25 (weak signal) |
| 06/09/2021 | 21A (Delta) | B.1.617.2 | 99.41 | 5755.65 | 5254 | B.1.617.2 (Delta) | 12/13 | 0.91 | AY.25 = 2 AY.25.1 = 1 (< 0.1) | AY.25 (weak signal) |
| 13/09/2021 | 21A (Delta) | N_content:0.64 | 38.17 | 1384.15 | 2 | 21A (Delta) | 7/13 | 0.54 | <3 | IE |
| 04/10/2021 | 21J (Delta) | B.1.617.2 | 98.61 | 5705.11 | 5627 | B.1.617.2 | 12/13 | 0.92 | AY.25 = 4 (0.16) | IE |
| 11/10/2021 | 21J (Delta) | AY.39 | 99.39 | 3966.28 | 3495 | AY.39 | 11/13 | 0.84 | AY.4 = 1 (0.14) | IE |
| 22/10/2021 | 21J (Delta) | AY.93 | 99.33 | 4396.12 | 4682 | AY.93 | 11/13 | 0.84 | AY.27 = 3 (0.36) AY.25 = 1 (< 0.1) |
AY.25 |
| 22/10/2021 | 21J (Delta) | B.1.617.2 | 99.57 | 3807 | 3345 | B.1.617.2 (Delta) | 13/13 | 1.0 | AY.15 = 1 (< 0.1) AY.25 = 4 (0.33) AY.27 = 2 (0.31) |
AY.25, AY.27 |
| 15/11/2021 | 21J (Delta) | N_content:0.41 | 74.48 | 1662.91 | 140 | 21J (Delta) | 9/12 | 0.69 | AY.27 = 2 (0.15) AY.93 = 2 (0.5) AY.5.2 = 1 (0.38) |
AY.27, AY.93, AY.5.2. |
| 29/11/2021 | 21I (Delta) | N_content:0.55 | 45.85 | 2864.19 | 0 | 21I (Delta) | 11/13 | 0.78 | AY.103 = 1 (0.65) | AY.103 |
| 10/12/2021 | 21I (Delta) | AY.27 | 99.58 | 17,582.41 | 5403 | AY.27 | 11/13 | 0.85 | <4 | |
| 04/01/2022 | 21K (Omicron) | B.1.1.529 | 98.81 | 13,699.9 | 4514 | BA.1 (Omicron) | 46/51 | 0.58 | BA.2 = 4 (34/60)-0.34 Delta = 13 (0.3) AY.27 = 6 (< 0.1) |
Moderate presence of 4 BA.2 mutations Moderate presence of Delta (trace presence of AY.27) |
| 24/01/2022 | 21K (Omicron) | BA.1.1 | 98.89 | 98.89 | 98.89 | BA.1.1 (Omicron) | 50/51 | 0.81 | BA.2 = 3/28 (<0.1) | Trace presence of BA.2 |
| 31/01/2022 | 21K (Omicron) | BA.1.1 | 98.78 | 17,763.47 | 9845 | BA.1.1 (Omicron) | 51/51 | 0.97 | <4 |