Table 2.
Low-complexity region (LCR) validation and entropy-level intra-host analysis in monkeypox virus (MPXV) genome sequence 353R
| Name | Repeat Unit | Pattern HQ | Number of repeats HQG | Nearest Gene | Variation | Type of Variation | Entropy threshold > 0.03 | Resolved correctly in RefSeq | Nanopore | MiSeq | NovaSeq | # Supporting Reads MiSeq | # Supporting Reads NovaSeq |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LCR4 | 16 | TAGTCATAAGTTAGTT [AAGTCATAAGTTAGTT]15 | 16 | OPG003 (ITR) | NR | Length | NA | Nob | Yes | No | No | NA | NA |
| LCR3 | 9 | ATAT [ACATTATAT]52 | 52 | OPG208 | Yes | Length | NA | Yes | Yes | No | No | NA | NA |
| LCR1 | 16 | [AACTAACTTATGACTT]15 AACTAACTTATGACTA | 16 | OPG003 (ITR) | NR | Length | NA | Nob | Yes | No | No | NA | NA |
| LCR2 | 2 | [AT]25 | 25 | NA | Yes | Length | 1.66 | No | Yes | Yes | Yes | 768 | 90 |
| LCR5 | 1 | [T]24 | 24 | OPG152 | Yes | Length | 1.535 | Yes | No | No | Yes | NA | 112 |
| LCR10 | 1 | [T]13 | 13 | OPG001 (ITR) | Yes | Length | 0.63 | Nob | Yes | No | No | 6561 | 11,945 |
| LCR11 | 1 | [T]13 | 13 | OPG001 (ITR) | Yes | Length | 0.627 | Nob | Yes | Yes | Yes | 6448 | 11,589 |
| LCR21 | 6 | [GATGAA]4 GATGA | 4.5 | OPG204 | Yes | Mutation | 0.207 | Yes | Yes | Yes | Yes | 6578 | 6661 |
| LCR7 | 3 | [ATC]14 TATGAT [ATC]3 | 19 | OPG153 | Yes | Length | 0.181 | Yes | Yes | Yes | Yes | 4541 | 6607 |
| LCR9 | 9 | [TATGAAG]1 [GATATGAT]1 [GATATGATG]5 [GATATGAT]1 | 8 | OPG176 | No | NA | 0 | Yes | Yes | Yes | Yes | 5208 | 5737 |
| LCR8 | 5 + 7 | [ATATTTT]1 [ATTTT]1 [ATATTTT]3 [ATTTT]1 [ATATTTT]2 [ATTTT]1 [ATATTTT]1 | 10 | OPG171 | No | NA | 0 | Yes | Yes | Yes | Yes | 6581 | 6790 |
| LCR6 | 10 | [CAATCTTTCT]1 | 1 | OPG152 | Yesa | NA | 0 | Noa | Yes | Yes | Yes | 4884 | 12,930 |
| LCR20 | 1 | [T]9 | 9 | OPG199 | No | NA | 0 | Yes | Yes | Yes | Yes | 10,106 | 13,315 |
| LCR19 | 6 | GATTCA [GATACA]8 GAT | 9.3 | OPG197 | No | NA | 0 | Yes | Yes | Yes | yes | 4119 | 4685 |
| LCR18 | 7 | [AATAATT]3 AATAA | 3 | OPG190 | No | NA | 0 | Yes | Yes | Yes | Yes | 9755 | 11,838 |
| LCR17 | 4 | [TAAC]6 T | 6.1 | OPG188 | No | NA | 0 | Yes | Yes | Yes | Yes | 7388 | 9474 |
| LCR16 | 1 | [A]9 | 9 | OPG180 | No | NA | 0 | Yes | Yes | Yes | Yes | 10,340 | 16,044 |
| LCR15 | 9 | [ATAACAATT]4 [ATAATTGTT]1 [ATAATAATT]1 [ATAATTGTT]1 | 7 | OPG159 | No | NA | 0 | Yes | Yes | Yes | Yes | 7067 | 6569 |
| LCR14 | 1 | [T]9 | 9 | OPG104 | No | NA | 0 | Yes | Yes | Yes | Yes | 7819 | 12,521 |
| LCR13 | 1 | [T]9 | 9 | OPG097/098 | No | NA | 0 | Yes | Yes | Yes | Yes | 7480 | 12,126 |
| LCR12 | 1 | [A]9 | 9 | OPG044 | No | NA | 0 | Yes | Yes | Yes | Yes | 9789 | 13,592 |
Listed are the type and number of supporting reads for each LCR. Definitions of quality: Yes, LCR is found entirely in the assembly in one contig; no, LCR is not assembled with the reported method. All LCRs with entropy levels above 0.15 are shaded in gray. OPG orthologous poxvirus gene.
aLCR6 is a 10-bp repeat that was reported early in the outbreak as an insertion (https://virological.org/t/first-german-genome-sequence-of-monkeypox-virus-associated-to-multi-country-outbreak-in-may-2022/812). In our dataset, we have not seen any variation in this area.
bLCR pairs 1/4 and 10/11 are located in ITRs. Given that no read covering this area reached a unique are outside of the ITRs, we cannot technically state that we solved the repeat. Nonetheless, the ITRs should be identical based on the know poxvirid replication mode.