Table 1.
WNV samples studied and some statistics on the viral sequencing process. Samples came from Hospital Virgen del Rocío (HUVR), Seville, and Hospital Puerto Real (HPR), Cádiz. Depth refers to the mean number of reads covering each position. High-confidence variants (HCV) refer to the variants unambiguously identified by the calling algorithm of the nf-core/viralrecon pipeline used, and the last column refers to the percentage of the viral genome covered in the sequencing process.
| Date | Code | Hospital | Sample | PCR | Culture | SAMPLE_ID | Depth | HCV | Coverage |
|---|---|---|---|---|---|---|---|---|---|
| 13 August 2020 | 44013531 | HUVR | Urine | Positive | No | 1_44013531 | 835x | 351 | 57.00% |
| 13 August 2020 | 44013532 | HUVR | Urine | Positive | No | 2_44013532 | 1190x | 461 | 96.10% |
| 2013 Au-gust 2020 | 44013536 | HUVR | Urine | Positive | No | 3_44013536 | 465x | 88 | 19.10% |
| 2013 Au-gust 2020 | 44013537 | HUVR | Urine | Positive | No | 4_44013537 | 1043x | 420 | 79.70% |
| 2013 Au-gust 2020 | 44013538 | HUVR | Urine | Positive | Negative | 5_44013538 | 1205x | 453 | 94.50% |
| 9 September 2020 | 44025400 | HPR | CSF | Positive | Negative | - | |||
| 9 September 2020 | 44025400 | HPR | Urine | Positive | Positive | 6_44025400 | 1145x | 451 | 94.70% |