TABLE 2.
Characteristics of SARS-CoV-2 co-infections
| Patient # | Clades | Lineages | Relative abundancea | 2.5 kb haplotypesb | GISAID |
|---|---|---|---|---|---|
| 1 | 21J/21K | B.1.617.2/BA.1.1 | 50%/50% | B.1.617.2 (52%) / BA.1.1 (48%) | EPI_ISL_16507432 |
| 2 | 21J/21K | B.1.617.2/BA.1.1 | 50%/50% | B.1.617.2 (57%) / BA.1.1 (43%) | EPI_ISL_16507433 |
| 3 | 21J/21K | AY.4/BA.1.1 | 75%/25% | AY.4 (72%) / BA.1.1 (28%) | EPI_ISL_16507434 |
| 4 | 21K/21L | BA.1.1/BA.2 | 70%/30% | BA.1.1 (83%) / BA.2 (17%) | EPI_ISL_16507435 |
| 5 | 21K/21L | BA.1/BA.2 | 25%/75% | BA.1 (16%) / BA.2 (84%) | EPI_ISL_16507436 |
| 6 | 21K/21L | BA.1.1/BA.2 | 50%/50% | BA.1.1 (45%) / BA.2 (55%) | EPI_ISL_16507437 |
| 7 | 21K/21L | BA.1.1/BA.2 | 35%/65% | BA.1.1 (40%) / BA.2 + E340A (60%) | EPI_ISL_16507438 |
| 8 | 21L/22A | BA.2/BA.4 | 25%/75% | BA.2 + L452M (12%) BA.4 (66%) recombinant BA.4/BA.2 (L452M) (12%) recombinant BA.2/BA.4 (10%) |
EPI_ISL_13502102 |
| 9 | 21L/22B | BA.2/BA.5 | 35%/65% | BA.2 (41%) / BA.5 (59%) | EPI_ISL_16507439 |
| 10 | 22A/22B | BA.4/BA.5 | 15%/85% | BA.4 and/or BA.5 (100%) | EPI_ISL_13950692 |
| 11 | 21L/22B | BA.2/BA.5 | 25%/75% | BA.2 (24%) / BA.5 (76%) | EPI_ISL_13950697 |
| 12 | 22B/22C | BA.5/BA.2.12.1 | 35%/65% | BA.2.12.1 (58%) BA.5 (20%) recombinant BA.2.12.1/ BA.5 (L452Q) (9%) recombinant BA.2.12.1/ BA.5 (L452R) (6%) recombinant BA.5/BA.2.12.1 (7%) |
EPI_ISL_13974755 |
| 13 | 22B/22C | BA.5/BA.2.12.1 | 60%/40% | BA.2.12.1 (46%) BA.5 (37%) recombinant BA.2.12.1/ BA.5 (12%) recombinant BA.5/BA.2.12.1 (5%) |
EPI_ISL_16507440 |
| 14 | 22A/22B | BA.4/BA.5 | 50%/50% | BA.4 (63%) / BA.5 (37%) | EPI_ISL_14232543 |
| 15 | 22A/22B | BA.4.6/BA.5 | 80%/20% | Inconclusive | EPI_ISL_14232544 |
| 16 | 22A/22B | BA.4.4/BA.5.1 | 20%/80% | BA.4 (19%) / BA.5 (81%) | EPI_ISL_14497373 |
| 17 | 22B/22E | BA.5.1/BQ.1.1 | 25%/75% | BA.5.1 wild type (9%) BA.5.1 + K444Q (12%) BQ.1.1 (79%) |
EPI_ISL_15777849 |
a
Relative abundance was calculated from the variant calling results throughout the whole SARS-CoV-2 genome: the abundance of each strain is the mean of the prevalence values of mutations specific to its lineage.
b
Based on S gene sequencing. The abundance of each haplotype was calculated as the number of reads of this haplotype/total number of reads of the sample.