Table 1.
Similarity-based matches of TCR sequences from patient’s dominant clonotypes with validated SARS-CoV-2-specific TCR sequences.
| Seq ID | CDR3 AASeq | Global sequence identity (%) | Levenshtein distance | Seq source |
|---|---|---|---|---|
| Clonotypel | CASSYSSGFTDTQYF | NA | NA | Patient |
| P18688 | CASSYSSTDTQYF | 100 | 2 | lmmuneCODE |
| P19422 | CASSYSSGGTDTQYF | 93.33 | 1 | lmmuneCODE |
| P26312 | CASSFSGFTDTQYF | 92.86 | 2 | lmmuneCODE |
| P39473 | CASSESSGFTDTQYF | 93.33 | 1 | lmmuneCODE |
| P73013 | CASSYSTFTDTQYF | 92.86 | 2 | lmmuneCODE |
| P73132 | CASSYSSVTDTQYF | 92.86 | 2 | lmmuneCODE |
| P97143 | CASSYSGFTDTQYF | 100 | 1 | lmmuneCODE |
| P118904 | CASSYSSPTDTQYF | 92.86 | 2 | lmmuneCODE |
| P120946 | CASSYSPGFTDTQYF | 93.33 | 1 | lmmuneCODE |
| Clonotype2 | CASSRLAGRETQYF | NA | NA | Patient |
| P137116 | CASSRLAGREQYF | 100 | 1 | lmmuneCODE |
| Clonotype3 | CASSDSLLNQPQHF | NA | NA | Patient |
| P47858 | CASSDSLNQPQHF | 100 | 1 | lmmuneCODE |
| P119742 | CASSLLNQPQHF | 100 | 2 | lmmuneCODE |
CD-HIT-derived clusters that contain at least one CDR3 amino acid sequence from a dominant clonotype (1-3) as well as one ImmuneCode-based SARS-CoV-2-specific CDR3 sequence. The clustering threshold was 90% global sequence identity. Global sequence identity was defined by CD-HIT as the number of identical amino acids in alignment divided by the number of amino acids in the shorter sequence, allowing for a sequence length difference of up to two amino acids per alignment. Levenshtein distances between the patient clonotypes and the ImmuneCODE hits were computed using the R stringdist package. Levenshtein distance is defined as the minimum number of amino acid edits (insertions, deletions or substitutions) needed to change one amino acid sequence into the other. NA, Not applicable.