Table 3 Summary table of sequences containing identifiable co-occurring mutations
From: CoMIT: a bioinformatic pipeline for risk-based prediction of COVID-19 test inclusivity
Frequencies of sequences containing identifiable co-occurring mutations | ||||||||
|---|---|---|---|---|---|---|---|---|
Pangolin lineage | #Assays Affected | Sequences by Lineage | ||||||
0 | 1 | 2 | 3 | 4 | 5 | ≥ 6 | ||
Variants of interest (VOI) | ||||||||
XBB.1.5 | 2 (0%) | 3,001 (92%) | 89 (3%) | 179 (5%) | 4 (0%) | 0 | 1 (0%) | 3,276 (13.2%) |
XBB.1.16 | 0 | 522 (90%) | 46 (8%) | 9 (2%) | 0 | 0 | 0 | 577 (2.3%) |
Variants under monitoring (VUM) | ||||||||
BA.2.75 | 0 | 2 (67%) | 0 | 1 (33%) | 0 | 0 | 0 | 3(0%) |
CH.1.1 | 2 (0%) | 986 (94%) | 24 (2%) | 40(4%) | 1(0%) | 0 | 0 | 1053(4.2%) |
BQ.l | 0 | 86 (88%) | 6 (6%) | 5 (5%) | 0 | 1 (1%) | 0 | 98 (0.4%) |
XBB | 0 | 50 (96%) | 0 | 2 (4%) | 0 | 0 | 0 | 52 (0.2%) |
XBB.1.9.1 | 1 (0%) | 349 (88%) | 28 (7%) | 15 (4%) | 2 (1%) | 0 | 0 | 395 (1.6%) |
XBF | 1 (0%) | 1182 (88%) | 56 (4%) | 107 (8%) | 0 | 1 (0%) | 0 | 1347 (5.4%) |
Variants not currently under monitoring by the WHO | ||||||||
Omicron Recombinant1 | 2 (0%) | 1,506 (77%) | 266 (14%) | 163 (8%) | 11 (1%) | 1 (0%) | 0 | 1.949 (7.8%) |
Other Omicron | 17 (0%) | 12,980 (85%) | 700 (5%) | 1,532 (10%) | 73 (0%) | 26 (0%) | 0 | 15,328 (61.5%) |
Non-Omicron | 8 (3%) | 284 (89%) | 13 (4%) | 14 (4%) | 0 | 0 | 0 | 319 (1.3%) |
Unassigned | 1 (0%) | 443 (86%) | 33 (6%) | 37 (7%) | 1 (0%) | 0 | 0 | 515 (2.1%) |
Summary: all sequences by assays | ||||||||
34 (0.1%) | 21,391 (85.9%) | 1,261 (5.1%) | 2,104 (8.4%) | 92 (0.4%) | 29 (0.1%) | 1(0%) | 24,912(100%) | ||