Table 2.
PCR, metagenomics and viral WGS results from cases in which metagenomic sequencing was performed
| Case ID | Sample ID | PCR Ct values | Metagenomics reads | Viral WGS coverage (10×) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| DNA | RNA | ||||||||||||
| AAV2 | HAdV | HHV-6B | AAV2 | HAdV | HHV-6B | AAV2 | HAdV | HHV-6B | AAV2 | HAdV | HHV-6B | ||
| Liver | |||||||||||||
| 1 | JBL1 | 17 | 37 | 29 | 1,343 | 0 | 8 | 574 | 0 | 0 | 97 | − | 3 |
| 2 | JBL4 | 21 | 42 | 32 | 360 | 0 | 8 | 49 | 0 | 0 | 93 | − | 2 |
| 3 | JBL3 | 20 | 37 | 30 | 1,189 | 0 | 4 | 95 | 0 | 0 | 98 | − | 2 |
| 4 | JBL2 | 20 | 37 | 27 | 1,564 | 0 | 203 | 42 | 0 | 0 | 98 | − | 94 |
| 5 | JBL5 | 21 | 37 | 28 | 266 | 0 | 12 | F | F | F | − | − | − |
| Blood | |||||||||||||
| 6a | JBB14, JBB16, JBB9 | 24 | 36 | 37 | 151 | 0 | 0 | 77 | 0 | 0 | 95 | 35.5 | − |
| 7 | JBB10, JBB11 | 21 | 36 | 37 | 103 | 0 | 0 | F | F | F | 49 | F | − |
| 8 | JBPL1, JBB13 | 25 | P/N | −/N | 277 | 0 | 0 | 165 | 0 | 0 | 94 | F | − |
| 9 | JBB1 | 19 | P/− | P/− | 1,936 | 5 | 0 | 0 | 0 | 0 | 94 | F | − |
| 10 | JBB15 | −/N | N/N | 37 | 0 | 0 | 0 | F | F | F | − | F | − |
Where two results are shown, the first refers to the referring laboratory and the second to GOSH. Where there was a discrepancy, the positive result is shown. Where there is more than one sample for a single patient, Ct values represent the mean across the samples that were tested. De novo assembly of unclassified metagenomics reads was unremarkable. −, not tested (at GOSH due to insufficient residual material); F, failed; N, negative PCR result; P, positive PCR result in referring laboratory.
aFor metagenomics reads, the result of combining the datasets from two blood samples from the same case.