Table 3.
Data obtained from whole genome sequencing of wastewater environmental RNA from August 2021 to January 2022 for North Battleford.
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| 06/08/2021 | 20B | None | 49.54 | 1176.78 | 2 | None detected | n/a | n/a | B.1.1.7 = 4 (0.21) B.1.617.2 = 2 (<0.1) |
Possible B.1.1.7 (Alpha) |
| 20/08/2021 | 21A (Delta) | B.1.617.2 | 98.98 | 4986.72 | 5603 | B.1.617.2 (Delta) sublineage AY.6 | 10/12 | 0.84 | <4 | IE |
| 30/08/2021 | 21A (Delta) | B.1.617.2 | 99.6 | 6319.17 | 6650 | B.1.617.2 (Delta) | 13/13 | 0.99 | AY.25 = 2 (0.14) AY.21 = 1 (0.18) |
AY.25 (weak signal) |
| 03/09/2021 | 21A (Delta) | B.1.617.2 | 99.6 | 4648.12 | 3777 | B.1.617.2 (Delta) | 11/13 | 0.84 | AY.25 = 2 (<0.1) | AY.25 (weak signal) |
| 09/09/2021 | 21A (Delta) | AY.12 | 97.71 | 5627.37 | 5480 | Delta sublineage AY.12 | 11/13 | 0.84 | AY.25 = 4 (0.13) | AY.25 (weak signal) |
| 16/09/2021 | 21J (Delta) | B.1.617.2 | 98.72 | 5194.09 | 4595 | B.1.617.2 (Delta) | 11/13 | 0.84 | AY.25 = 2 (0.11) AY.27 = 1 < 0.1) |
AY.25 |
| 03/10/2021 | 21J (Delta) | B.1.617.2 | 99.6 | 6164.71 | 6232 | B.1.617.2 | 13/13 | 1 | AY.25 = 4 (0.16) AY.27 = 3 (0.15) |
IE |
| 09/10/2021 | 21J (Delta) | AY.39 | 99.52 | 5031.35 | 5945 | AY.39 | 11/13 | 0.85 | <4 | IE |
| 22/10/2021 | 21I (Delta) | B.1.617.2 | 99.57 | 4949.38 | 5961 | B.1.617.2 | 11/13 | 0.84 | AY.25 = 2 (0.19) AY.27 = 3 (0.68) |
AY.25, AY.27 |
| 24/10/2021 | 21J (Delta) | B.1.617.2 | 99.57 | 5234.73 | 6593 | B.1.617.2 (Delta) | 13/13 | 1.0 | AY.25 = 3 (0.18) AY.27 = 3 (0.22) |
AY.25, AY.27 |
| 12/11/2021 | 21A (Delta) | AY.70 | 85.12 | 3017.02 | 1311 | AY.70 | 7/13 | 0.54 | AY.25 = 1 (0.18) AY.27 = 1 (0.38) AY.93 = 1 (0.72) |
AY.25, AY.27, AY.93 |
| 26/11/2021 | 21I (Delta) | AY.74 | 91.33 | 6001.55 | 2523 | AY.74 | 11/13 | 0.85 | AY.4.1 = 1 (0.5) | AY.4.1 |
| 11/12/2021 | 21I (Delta) | AY.27 | 89.34 | 7322.47 | 1723 | AY.27 | 11/13 | 0.84 | AY.103 = 1 (0.35) AY.25 = 1 (0.21) |
AY.103 AY.25 |
| 03/01/2022 | 21I (Delta) | AY.27 | 99.6 | 16,478.08 | 7917 | AY.27 (Delta) | 13/13 | 0.73 | Moderate presence of BA.1 (Omicron) | |
| 21/01/2022 | 21K (Omicron) | BA.1 | 98.69 | 98.69 | 98.69 | BA.1 (Omicron) | 50/51 | 0.9 | BA.2 = 27/28 (0.41) Delta = 3 (0.16); 2 mutations overlap with Omicron |
Moderate presence of BA.2 Trace presence of Delta |
| 28/01/2022 | 21K (Omicron) | BA.1 | 98.65 | 12,386.05 | 7772 | BA.1 (Omicron) | 50/51 | 0.77 | BA.2 = 27 (0.42) | Moderate presence of BA.2 |