Table 3. RT-qPCR and sequencing results for 11 mosquito pools.
| JCV RT-qPCR results | No. JCV sequencing reads | No. total sequencing reads | |||||
|---|---|---|---|---|---|---|---|
| Sample | Positive | Mean Ct | Mean copies/uL | Library 1 | Library 2 | Library 1 | Library 2 |
| No template controls | 2/75 | 35.5 | NA | NA | NA | NA | NA |
| Pool 1 | 1/3 | 36.6 | 0.8 | 0 | NA | 2,780,216 | NA |
| Pool 2 | 1/3 | 35.6 | 0.4 | 0 | NA | 3,436,372 | NA |
| Pool 3 | 0/3 | NA | NA | 0 | NA | 4,640,644 | NA |
| Pool 4 | 3/3 | 39.2 | <0.1 | 0 | NA | 2,796,224 | NA |
| Pool 5 | 3/3 | 34.1 | 0.4 | 0 | NA | 2,714,312 | NA |
| Pool 6 | 2/3 | 41 | <0.1 | 0 | NA | 2,390,196 | NA |
| Pool 7 | 3/3 | 36.1 | 0.1 | 0 | NA | 1,687,562 | NA |
| Pool 8 | 2/3 | 35.7 | 0.2 | 2 | 0 | 3,694,624 | 4,782,330 |
| Pool 9 | 3/3 | 37.1 | 0.4 | 6 | 4 | 3,725,980 | 5,849,716 |
| Pool 10 (screening) | 3/3 | 25.7 | 272.9 | 390 | >1000 | 1,597,522 | 7,602,802 |
| Pool 10 (deep sequencing) | >1500 | >4000 | 13,829,206 | 32,622,656 | |||
| Pool 11 | 1/3 | 33.4 | 2.7 | 0 | NA | 1,971,412 | NA |
Notes: Pool 10 was positive by RT-qPCR (all replicates positive, below the Ct of no template controls), while Pool 3 was a negative control and the remaining pools were negative for JCV by RT-qPCR, but showed some amplification close to the threshold. Based on sequencing results from both libraries combined, Pools 9 and 10 were confirmed as positive for JCV. Pool 10 underwent deeper sequencing in order to assemble a full JCV genome.