Table 3.
Prolonged viral shedding and genomic changes.
| PID | Positives | Sequenced | HQ Genomes | Days between first and last positives | Days between first and last HQ Genomes | First HQ genome lineage | last HQ genome lineage | Number Acquired subs/dels | Acquired AA substitutions/deletions | Vaccinated | Immunosuppressed | Monoclonal antibody | Convalescent Plasma |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PIDVWVGDCM | 2 | 2 | 2 | 5 | 5 | B.1.2 | B.1.2 | 4 | S:G142del,S:V143del,S:Y144del,S:L141del | No | Yes | Yes | |
| PIDWUGBIZH | 5 | 4 | 3 | 14 | 7 | B.1.637 | B.1.637 | 1 | S:H146Q | No | Yes | Yes | |
| PIDCXIYIPP | 6 | 5 | 4 | 20 | 9 | B.1.243 | B.1.243 | 1 | NSP8:F6L | No | Yes | Yes | |
| PIDLUEEQYV | 5 | 4 | 2 | 13 | 13 | B.1.1.7 | B.1.1.7 | 1 | NSP14:D126Y | No | Yes | ||
| PIDEAUSZWF | 2 | 2 | 2 | 15 | 15 | B.1.2 | B.1.2 | 2 | NSP2:E490K,S:E484K | No | |||
| PIDRSHNQNS | 12 | 8 | 5 | 51 | 17 | B.1.2 | B.1.2 | 1 | E:V70F | No | Yes | Yes | |
| PIDGBIBYYQ | 7 | 4 | 4 | 24 | 24 | Q.4 | Q.4 | 3 | NSP4:H313Y,N:F307L,S:R102G | No | Yes | Yes | |
| PIDBXQZZLV | 5 | 4 | 4 | 26 | 26 | B.1.526 | B.1.526 | 2 | S:G446V,S:E406Q | Yes | Yes | Yes | |
| PIDLCYVIUV | 2 | 2 | 2 | 37 | 37 | B.1.564 | B.1 | 2 | S:L270F,NSP2:T85I | No | |||
| PIDFTUQFAV | 7 | 3 | 2 | 81 | 43 | A.3 | A.3 | 7 | S:R190S,S:L244del,NSP4:F317S,S:T1006I,NSP3:F1646I,NSP4:G232V,S:A243del | No | Yes | ||
| PIDSDHALQC | 5 | 4 | 4 | 49 | 49 | B.1.637 | B.1.637 | 8 | S:T95I,S:G142del,NSP13:T115K,S:V143del,S:L141del,S:E484Q,NSP8:T123I,S:W152R | No | Yes | ||
| PIDHCPHTBW | 3 | 2 | 2 | 53 | 53 | B.1.369 | B.1.369 | 2 | NSP5:Q192stop,N:T271I | No | |||
| PIDXTTUNJN | 9 | 5 | 4 | 57 | 57 | B.1.2 | B.1.2 | 2 | S:E484K,NSP6:L37F | No | Yes | Yes | |
| PIDNXQFFZG | 6 | 4 | 3 | 77 | 61 | B.1.409 | B.1.409 | 2 | NSP8:I156L,NS6:E13K | No | Yes | Yes | Yes |
| PIDHNGFDXK | 7 | 4 | 3 | 84 | 67 | B.1 | B.1 | 4 | NSP8:T148I,S:P1079S,NSP3:T820I,N:P326L | No | Yes | ||
| PIDLYROPCD | 4 | 3 | 3 | 70 | 70 | B.1.520 | B.1 | 2 | NSP6:M86I,N:T205I | No | Yes | ||
| PIDLVBEHYS | 11 | 9 | 6 | 139 | 117 | B.1.1.434 | B.1.1.434 | 4 | NSP2:K534R,S:N334K,NSP13:D56G,S:S939F | No | Yes | Yes |
PID, patient identifier; HPID, identification of samples with whole genome sequencing; HQ, High quality genomes were defined as sequences with coverage >90% and a mean depth of >100. Subs/dels, substitutions/deletions; AA, amino acid.