Table 2 Patient sequence/specimen characteristics of validated SARS-CoV-2 co- infections. Bold rows correspond to the specimen that revealed the co-infection event. Non-bold rows correspond to replicates (-BIS) or independent specimens from the same patient. *Lineage assigned after discarding segregated positions with lower confidence. %: Percentage, HZ: heterozygous, COV: Coverage, STD: Standard deviation
Patient | Sample | Gen N2 Ct | % COV>30X | HZ calls (N) | mean HZ proportion | std HZ proportion | % SNPs within STD | Minority lineage | Majority lineage | Sample Date |
|---|---|---|---|---|---|---|---|---|---|---|
1 | ERS14369070 | n.a | 99.69 | 12 | 0.66 | 0.04 | 83 | A.5 | B.1 | 2020-03-09 |
ERS14369071 (-BIS) | n.a | 99.58 | 12 | 0.67 | 0.02 | 83 | A.5 | B.1 | 2020-03-09 | |
2 | ERS14369072 | n.a | 99.08 | 11 | 0.64 | 0.03 | 91 | A.5 | B.1 | 2020-03-09 |
ERS14369073 (-BIS) | n.a | 99.58 | 12 | 0.63 | 0.07 | 92 | A.5 | B.1 | 2020-03-09 | |
3 | ERS14369074 | n.a | 99.02 | 8 | 0.73 | 0.03 | 88 | B.1 | B.1 | 2020-04-08 |
ERS14369075 (-BIS) | n.a | 99.1 | 8 | 0.66 | 0.05 | 88 | B.1 | B.1 | 2020-04-08 | |
4 | ERS14369076 | 20 | 99.66 | 8 | 0.66 | 0.04 | 75 | B.1.177 | B.1.177 | 2020-08-11 |
ERS14369077 (-BIS) | 20 | 99.58 | 8 | 0.67 | 0.03 | 88 | B.1.177 | B.1.177 | 2020-08-11 | |
5 | ERS14369078 | 25 | 98.71 | 9 | 0.54 | 0.03 | 100 | B.1.177 | B.1.177 | 2020-11-01 |
ERS14369079 (-BIS) | 25 | 99.02 | 9 | 0.55 | 0.04 | 89 | B.1.177 | B.1.177 | 2020-11-01 | |
6 | ERS14369080 | 31 | 99.02 | 37 | 0.6 | 0.05 | 76 | B.1.177 | B.1 | 2021-01-18 |
ERS14369081 | 14 | 98.97 | 37 | 0.76 | 0.06 | 89 | B.1 | B.1.177 | 2021-01-27 | |
ERS14369082 | 22 | 99.58 | 1 | 0.52 | 0 | 100 | B.1.177 | B.1.177 | 2021-02-01 | |
7 | ERS14369083 | 16 | 99.58 | 19 | 0.78 | 0.03 | 95 | B.1.177 | B.1.177 | 2021-01-21 |
ERS14369084 | 18 | 99.67 | 19 | 0.61 | 0.04 | 84 | B.1.177 | B.1.177 | 2021-01-21 | |
8 | ERS14369085 | 25 | 98.79 | 30 | 0.55 | 0.06 | 90 | B.1.617.2 | B.1.617.2 | 2021-08-08 |
ERS14369086 (-BIS) | 25 | 99.56 | 32 | 0.57 | 0.04 | 91 | B.1.617.2 | B.1.617.2 | 2021-08-08 | |
9 | ERS14369087 | 26 | 99.67 | 15 | 0.58 | 0.03 | 93 | AY.5.5 | AY.43 | 2021-08-25 |
ERS14369088 (-BIS) | 26 | 99.66 | 15 | 0.64 | 0.03 | 73 | AY.5.5 | AY.43 | 2021-08-25 | |
10 | ERS14369089 | 12 | 98.44 | 9 | 0.71 | 0.03 | 89 | BA.1.17 | BA.1.1.1 | 2021-12-14 |
ERS14369090 (-BIS) | 12 | 98.41 | 9 | 0.74 | 0.05 | 89 | BA.1.17 | BA.1.1.1 | 2021-12-14 | |
11 | ERS14369091 | 16 | 99.62 | 85 | 0.71 | 0.07 | 74 | AY.121 | BA.1 | 2021-12-17 |
ERS14369092 (-BIS) | 16 | 99.58 | 89 | 0.76 | 0.04 | 79 | AY.121 | BA.1 | 2021-12-17 | |
ERS14369093 | 29 | 99.58 | 1 | 0.81 | 0 | 100 | AY.121 | AY.121 | 2021-12-23 | |
12 | ERS14369094 | 18 | 98.73 | 9 | 0.7 | 0.07 | 67 | BA.1.1 | BA.1.1 | 2022-02-09 |
ERS14369095 | 31 | 98.91 | 11 | 0.73 | 0.04 | 73 | BA.1.1 | BA.1.1 | 2022-02-11 | |
13 | ERS14369096 | 14 | 99.3 | 12 | 0.57 | 0.07 | 92 | BA.2 | BA.2 | 2022-05-12 |
ERS14369097 | 23 | 98.69 | 11 | 0.53 | 0.02 | 91 | BA.2 | BA.2 | 2022-05-17 | |
14 | ERS14369098 | 18 | 98.61 | 22 | 0.7 | 0.05 | 82 | BA.5* | BE.1.1 | 2022-06-27 |
ERS14369099 | 28 | 95 | 14 | 0.79 | 0.05 | 86 | BA.5 | BE.1.1 | 2022-07-08 |