Table 1.
Data obtained from whole genome sequencing of wastewater environmental RNA from August 2021 to January 2022 for Saskatoon.
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| 01/08/2021 | 21A (Delta) | AY.12 | 93.91 | 2903.88 | – | B.1.617.2 (Delta) | 13/13 | 0.9 | <3 (only common mutations were detected) | IE |
| 04/08/2021 | 21A (Delta) | B.1.617.2 | 93.42 | 2712.42 | 961 | B.1.617.2 (Delta) | 10/12 12/12 (cov <30) |
0.83 cov < 30 = 0.97 | P.1 = 4 (0.1) | Possible P.1 (Gamma) |
| 15/08/2021 | 21A (Delta) | AY.4 | 99.6 | 6365.48 | 10,240 | B.1.617.2 (Delta) sublineage AY.12 | 12/12 | 0.89 | <4 | IE |
| 22/08/2021 | 21A (Delta) | AY.4 | 99.55 | 5543.97 | 7060 | B.1.617.2 (Delta) sublineage AY.6 | 10/12 | 0.84 | <4 | IE |
| 02/09/2021 | 21A (Delta) | B.1.617.2 | 99.6 | 6385.45 | 6504 | B.1.617.2 (Delta) | 13/13 | 0.97 | AY.25 = 2 (~0.24) AY.15 = 1 (<0.1) |
AY.25 |
| 05/09/2021 | 21A (Delta) | B.1.617.2 | 99.6 | 5396.24 | 4696 | B.1.617.2 (Delta) | 13/13 | 0.99 | AY.25 = 2 (0.18) | AY.25 (weak signal) |
| 12/09/2021 | 21A (Delta) | B.1.617.2 | 99.6 | 6342.31 | 6567 | B.1.617.2 (Delta) | 13/13 | 0.99 | AY.25 = 4 (0.37) | AY.25 |
| 19/09/2021 | 21J (Delta) | B.1.617.2 | 99.6 | 6157.97 | 6342 | B.1.617.2 (Delta) | 13/13 | 0.99 | AY.25 = 4 (0.26) AY.27 = 3 (0.23) |
AY.25, AY.27 |
| 03/10/2021 | 21J (Delta) | B.1.617.2 | 99.6 | 5876.3 | 5910 | B.1.617.2 | 13/13 | 1 | AY.25 = 2 (0.32) AY.27 = 3 (0.27) |
AY.25, AY.27 |
| 13/10/2021 | 21J (Delta) | B.1.617.2 | 99.57 | 4742.91 | 5408 | B.1.617.2 | 13/13 | 1.0 | AY.25 = 4 (0.26) AY.27 = 3 (0.57) |
AY.25, AY.27 |
| 24/10/2021 | 21J (Delta) | AY.23 | 93.04 | 4125.28 | 4082 | Delta sublineage AY.23 | 11/13 | 0.84 | AY.25 = 2 (0.55) AY.27 = 3 (0.78) AY.33 = 2 (<0.1) |
AY.25, AY.27 |
| 31/10/2021 | 21J (Delta) | AY.9.2 | 95.31 | 2391.4 | 441 | AY.9.2 | 9/12 | 0.69 | AY.25 = 1 (0.61) AY.27 = 1 (0.38) |
AY.25, AY.27 |
| 14/11/2021 | 21I (Delta) | AY.27 | 99.39 | 3879.32 | 3450 | AY.27 | 11/13 | 0.84 | AY.25 = 3 (0.24) AY.93 = 4 (0.11) AY.103 = 1 (0.31) |
AY.25, AY.93, AY.103 |
| 24/11/2021 | 21I (Delta) | N_content:0.55 | 47.18 | 4140.94 | 0 | 21I (Delta) | 9/13 | 0.69 | AY.25 = 1 (0.25) AY.27 = 1 (0.12) |
AY.25, AY.27 |
| 08/12/2021 | 21J (Delta) | N_content:0.66 | 35.21 | 3692 | 0 | 21J (Delta) | 5/12 | 0.38 | AY.25 = 2 (0.38) | |
| 17/12/2021 | 21J (Delta) | N_content:0.85 | 16.81 | 548.38 | 0 | 21J (Delta) | 3/13 | 0.23 | <4 | IE |
| 26/12/2021 | 21K (Omicron) | BA.1 | 96.94 | 11,418.2 | 3739 | BA.1 (Omicron) | 36/51 | 0.58 | Delta = 10/13 (0.27) AY.53 = 1 (0.15) |
AY.53 |
| 02/01/2022 | 21K (Omicron) | BA.1 | 99.57 | 13,755.92 | 5132 | BA.1 (Omicron) | 48/51 | 0.64 | BA.2 = 3 (37/60)-0.37 Delta = 11 (0.23) AY.25/AY.25.1 = 5 (0.1) |
Moderate presence of 3 BA.2 mutations Low presence of Delta (AY.25/AY.25.1) |
| 09/01/2022 | 21K (Omicron) | BA.1 | 99.29 | 14,499.08 | 5575 | BA.1 (Omicron) | 51/51 | 0.96 | Delta = 4 (< 0.1) | Trace presence of 4 Delta mutations |
| 23/01/2022 | 21K (Omicron) | BA.1 | 98.65 | 98.65 | 98.65 | BA.1 (Omicron) | 51/51 | 0.94 | BA.2 = 14/28 (0.12) Delta = 4 (0.16) |
Low presence of BA.2 Low presence of Delta |
| 30/01/2022 | 21K (Omicron) | BA.1.1 | 98.41 | 9983.54 | 4365 | BA.1.1 (Omicron) | 50/51 | 0.95 | BA.2 = 10 (< 0.1) | Trace presence of BA.2 |
IE – Insufficient evidence; () - frequencies of reads for mutations supporting subconsensus sequences.