Table 1.
Abundance of SNP A288P quantified by digital PCR (dPCR) and detection by SANGER-Sequencing.
| material | week | Target | A288P fraction | Partitions (valid) | Partitions positive | Partitions negative | A288P (SANGER) |
|---|---|---|---|---|---|---|---|
| Lesional swab | 2 | A288P | 0.00 % | 25405 | 0 | 25405 | Not detected |
| WT | – | 25405 | 25405 | 0 | |||
| Lesional swab | 4 | A288P | 0.92 % | 25498 | 10 | 25488 | Not detected |
| WT | – | 25494 | 1049 | 24445 | |||
| Lesional swab | 7 | A288P | 0.12 % | 25496 | 212 | 25284 | Not detected |
| WT | – | 25496 | 25474 | 22 | |||
| blood | 8 | A288P | 28.78 % | 25391 | 19 | 25372 | Detected |
| WT | – | 25391 | 47 | 25344 | |||
| Lesional swab | 8 | A288P | 54.60 % | 25470 | 490 | 24980 | Detected |
| WT | – | 25468 | 408 | 25060 | |||
| Lesional swab | 9 | A288P | 0.00 % | 25349 | 3 | 25346 | Not detected |
| WT | – | 25349 | 24482 | 867 | |||
| Tissue biopsie, sample 1 | 9 | A288P | 0.00%o | 25481 | 0 | 25481 | Not detected |
| WT | – | 25481 | 25481 | 0 | |||
| Tissue biopsie, sample 2 | 9 | A288P | 0.00 % | 25466 | 0 | 25466 | Not detected |
| WT | – | 25466 | 25466 | 0 | |||
| Lesional swab | 11 | A288P | 80.90 % | 25479 | 249 | 25230 | Sequencing failed |
| WT | 25479 | 59 | 25420 | ||||
| MPXV tissue derived isolate 1 | 9 | A288P | 0.00 % | 25418 | 0 | 25418 | Not detected |
| WT | – | 21637 | 18731 | 2906 | |||
| MPXV tissue derived isolate 2 | 9 | A288P | 0.02 % | 25497 | 3 | 25494 | Not detected |
| WT | – | 25497 | 13339 | 12158 | |||
| MPXV tissue derived isolate 3 | 9 | A288P | 0.00 % | 25380 | 1 | 25379 | Not detected |
| WT | – | 25380 | 14803 | 10577 | |||
| MPXV tissue derived isolate 4 | 9 | A288P | 0.01 % | 25466 | 2 | 25464 | Not detected |
| WT | – | 25309 | 18910 | 6399 | |||
| MPXV tissue derived isolate 5 | 9 | A288P | 0.01 % | 25340 | 2 | 25338 | nd |
| WT | – | 25340 | 19580 | 5760 | |||
| MPXV tissue derived isolate 6 | 9 | A288P | 0.01 % | 25340 | 2 | 25338 | nd |
| WT | – | 25340 | 19580 | 5760 | |||
| MPXV tissue derived isolate 7 | 9 | A288P | 0.01 % | 25488 | 1 | 25487 | nd |
| WT | – | 25488 | 11192 | 14296 | |||
| MPXV tissue derived isolate 8 | 9 | A288P | 0.00 % | 25471 | 0 | 25471 | nd |
| WT | – | 25471 | 22452 | 3019 | |||
| MPXV tissue derived isolate 9 | 9 | A288P | 0.00 % | 25472 | 0 | 25472 | nd |
| WT | – | 25472 | 18573 | 6899 | |||
| MPXV tissue derived isolate 10 | 9 | A288P | 0.00 % | 25475 | 0 | 25475 | nd |
| WT | – | 25475 | 18383 | 7092 | |||
| Lesional swab (patient B) | na | A288P | 0.00 % | 25459 | 0 | 25459 | Not detected |
| WT | – | 25082 | 8293 | 16789 | |||
| Negative control | na | A288P | 0.00 % | 25451 | 0 | 0 | nd |
| WT | – | 25451 | 0 | 0 |
Table 1: By applying dPCR, the relative proportion of the VP37 A288P SNP compared to ancestral epidemic MPXV sequence was assessed in clinical samples and 10 of the MPXV isolates (MPXV tissue derived isolates 1–10, all rescued from tissue obtained during chirurgical intervention in week 9), therein those used for the in vitro tests. A newly designed SNP-specific and a reference sequence-specific probe were used and dPCR was performed on the QIAcuity platform. As controls, a different patient (patient B) and a negative sample are included.
The table lists the type of material, in the case of patient samples the week of the observation period, gives the share of the A288P SNP compared to the reference sequence (percentage), indicates the overall number of positive partitions per sample (e.g. partitions with MPXV DNA detected by either probe) and gives the share of target specific partitions. Additionally, A288P detection in SANGER-Sequencing is indicated (A288P SANGER).
Nd = not done.