Table 4.
Test of the West Nile virus set A primers with WNV-L1 homogenates. (* Samples with multiple viral species/WNV lineage).
| Viral Homogenate WNV L1—Sample Number | Host | RT-PCR Ct Value | Co-InfectionCt Value | # Total Trimmate Reads | # WNV L1 Reads | % HCoverage | VCoverage | Consensus Sequence Length |
|---|---|---|---|---|---|---|---|---|
| 1 | Accipiter gentilis | 15 | - | 2,037,215 | 591,954 | 100% | 6362.04 | 11,027 |
| 2 | Pica pica | 16 | - | 14,648,025 | 1,333,187 | 100% | 6381.67 | 11,016 |
| 3 | Corvus cornix | 16 | - | 6,447,209 | 657,948 | 99% | 5135.45 | 10,966 |
| 4 | Pica pica | 18 | - | 2,923,237 | 387,986 | 99% | 4264.56 | 10,966 |
| 5 | Phalacrocorax carbo | 19 | - | 11,441,518 | 1,107,291 | 99% | 5888.49 | 10,961 |
| 6 | Corvus cornix | 19 | - | 2,347,380 | 351,292 | 99% | 4177.69 | 10,963 |
| 7 | Culex pipiens | 20 | - | 3,495,685 | 744,562 | 99% | 5560.68 | 10,968 |
| 8 | Culex pipiens | 22 | - | 7,571,826 | 597,499 | 98% | 3973.2 | 10,967 |
| 9 | Corvus cornix | 22 | - | 5,382,363 | 629,364 | 99% | 4806.11 | 10,960 |
| 10 | Passer domesticus | 22 | - | 3,942,375 | 304,215 | 97% | 3084.4 | 10,962 |
| 11 | Culex pipiens | 23 | - | 4,560,711 | 283,771 | 93% | 2899.47 | 10,960 |
| 12 | Corvus Cornix | 24 | - | 3,052,530 | 342,271 | 93% | 3508.25 | 10,966 |
| 13 * | Culex pipiens | 25 | L2 Ct 28 | 3,576,787 | 403,166 | 94% | 3761.48 | 10,966 |
| 14 * | Culex pipiens | 25 | L2 Ct 28 | 1,557,373 | 263,149 | 90% | 2471.3 | 10,954 |
| 15 | Larus michahellis | 25 | - | 1,813,567 | 129,834 | 88% | 1805.95 | 10,952 |
| 16 | Streptopelia decaocto | 26 | - | 1,439,897 | 203,172 | 91% | 2592.09 | 10,961 |
| 17 | Pica pica | 26 | - | 7,677,172 | 251,982 | 81% | 2920.03 | 10,963 |
| 18 | Parus major | 26 | - | 755,951 | 38,780 | 69% | 747.61 | 9389 |
| 19 * | Culex pipiens | 27 | L2 Ct 32 | 3,371,541 | 369,610 | 96% | 3287.31 | 10,956 |
| 20 | Turdus merula | 27 | - | 2,710,572 | 66,229 | 82% | 1039.08 | 10,954 |
| 21 | Culex pipiens | 28 | - | 6,865,408 | 269,727 | 94% | 2618.84 | 10,962 |
| 22 * | Culex pipiens | 28 | L2 Ct 31 | 3,378,716 | 190,102 | 87% | 2201.29 | 10,966 |
| 23 | Streptopelia decaocto | 28 | - | 1,842,010 | 22,006 | 68% | 430.494 | 10,946 |
| 24 | Equus caballus | 28 | - | 1,805,957 | 159,703 | 92% | 2101.31 | 10,960 |
| 25 | Athene noctua | 29 | - | 3,394,989 | 15,767 | 34% | 404 | 10,802 |
| 26 | Columba palumbus | 31 | - | 835,362 | 9948 | 57% | 211.706 | 10,960 |
| 27 * | Culex pipiens | 33 | L2 Ct 25 | 4,662,340 | 220,508 | 91% | 2381.21 | 10,963 |
| 28 * (Alphavirus, Mesonivirus) | Culex neavei | 28.5 | - | 391,494 | 1,135,180 | 92.42% | 2514.3 | 10,194 |
| 29 * (Barkedji, Mesonivirus) | Culex poicilipes | 35.59 | - | 64,716 | 616,500 | 82.35% | 1789.36 | 9083 |
| 30 * (Barkedji) | Culex neavei | 29.52 | - | 302,175 | 1,394,466 | 89% | 2001.3 | 9819 |
| 31 * (Alphavirus, Barkedji, Usutu) | Culex neavei | 25.03 | - | 180,791 | 484,221 | 73.89% | 822.02 | 8150 |