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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 51-55 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T2 95-103 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T3 406-418 Body_part denotes venous blood http://purl.org/sig/ont/fma/fma83067
T4 430-435 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T5 461-468 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T6 532-536 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T7 563-571 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T8 765-769 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T9 1094-1098 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T10 1216-1221 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T11 1373-1381 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T12 1409-1416 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T13 1506-1514 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T14 1969-1973 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T15 2000-2008 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T16 2038-2042 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T17 2364-2367 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 2387-2393 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T19 2443-2446 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T20 2471-2477 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T21 2610-2618 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T22 2665-2673 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T23 2685-2697 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T24 2718-2730 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T25 2745-2757 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T26 2784-2791 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T27 2817-2825 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T28 3031-3041 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T29 3159-3167 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T30 3243-3246 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T31 3257-3260 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T32 3302-3307 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T33 3365-3374 Body_part denotes leukocyte http://purl.org/sig/ont/fma/fma62852
T34 3384-3387 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T35 3493-3510 Body_part denotes cytotoxic T cells http://purl.org/sig/ont/fma/fma70573
T36 3505-3510 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T37 3523-3537 Body_part denotes T helper cells http://purl.org/sig/ont/fma/fma70572
T38 3532-3537 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T39 3570-3573 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T40 3595-3600 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T41 3658-3662 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T42 3740-3743 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T43 3771-3776 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T44 3883-3888 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T45 4069-4077 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T46 4165-4173 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T47 4241-4245 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T48 4315-4319 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T49 4396-4400 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T50 4605-4610 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T51 4926-4934 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T52 5273-5277 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T53 5310-5314 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T54 6161-6168 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T55 6242-6245 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T56 6252-6255 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T57 6489-6492 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T58 6688-6696 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T59 6778-6786 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T60 7110-7119 Body_part denotes histidine http://purl.org/sig/ont/fma/fma82755
T61 7241-7249 Body_part denotes arginine http://purl.org/sig/ont/fma/fma82763
T62 7674-7677 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T63 7877-7888 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T64 7897-7900 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T65 7912-7915 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T66 8161-8167 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T67 8356-8362 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T68 8524-8527 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T69 8776-8779 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T70 8862-8865 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T71 8923-8926 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T72 9011-9014 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T73 9463-9471 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T74 10016-10027 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T75 10045-10055 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T76 10200-10203 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T77 10343-10346 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T78 10449-10452 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T79 10761-10764 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T80 10897-10900 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T81 11010-11013 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T82 11020-11023 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T83 11052-11055 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T84 11559-11562 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T85 11632-11635 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T86 11812-11820 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T87 12222-12230 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T88 12368-12373 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T89 12498-12508 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T90 12604-12611 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T91 12669-12679 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T92 12954-12957 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T93 12971-12974 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T94 13197-13208 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T95 13236-13244 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T96 13317-13327 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T97 13387-13390 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T98 13401-13404 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T99 13471-13475 Body_part denotes ExoN http://purl.org/sig/ont/fma/fma84120
T100 13903-13907 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T101 13997-14004 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T102 14050-14054 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T103 14233-14240 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T104 14362-14373 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T105 14419-14427 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T106 14494-14497 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T107 14715-14722 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T108 14742-14749 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T109 14836-14847 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T110 14893-14901 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T111 15013-15016 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T112 15049-15056 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T113 15163-15170 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T114 15190-15197 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T115 15284-15295 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T116 15341-15349 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T117 15425-15432 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T118 15547-15550 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T119 15583-15590 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T120 15697-15704 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T121 15724-15731 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T122 15818-15829 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T123 15892-15899 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T124 15966-15969 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T125 16002-16009 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T126 16457-16461 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T127 16489-16497 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T128 16568-16575 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T129 16767-16770 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T130 16816-16819 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T131 16875-16878 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T132 16905-16908 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T133 17043-17051 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T134 17107-17115 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T135 17214-17221 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T136 17247-17250 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T137 17275-17282 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T138 17321-17328 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T139 17351-17354 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T140 17421-17424 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T141 17684-17692 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T142 17826-17830 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T143 17892-17900 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T144 18142-18146 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T145 18414-18417 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T146 18439-18442 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T147 18449-18452 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T148 18468-18471 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T149 18504-18509 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T150 18535-18538 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T151 18569-18572 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T152 18671-18676 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T153 18971-18979 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T154 19079-19083 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T155 19107-19114 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T156 19195-19202 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T157 19525-19530 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T158 20184-20198 Body_part denotes immune systems http://purl.org/sig/ont/fma/fma9825
T159 20280-20285 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T160 20418-20431 Body_part denotes immune system http://purl.org/sig/ont/fma/fma9825
T161 21219-21222 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T162 21269-21272 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T163 21318-21321 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T164 21365-21368 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T165 21421-21424 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T166 21455-21461 Body_part denotes groove http://purl.org/sig/ont/fma/fma75037
T167 21476-21479 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T168 21588-21591 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T169 22161-22171 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T170 22209-22220 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T171 22227-22238 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T172 22421-22428 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T173 22448-22458 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T174 22625-22636 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T175 22666-22669 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T176 22835-22843 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T177 22870-22883 Body_part denotes immune system http://purl.org/sig/ont/fma/fma9825
T178 23405-23409 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T179 23579-23583 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T180 23692-23695 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T181 24195-24200 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T182 24419-24427 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T183 24563-24570 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T184 24841-24848 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T185 24904-24911 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T186 25117-25124 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T187 25448-25455 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T188 25513-25520 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T189 25610-25613 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T190 25661-25668 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T191 26270-26273 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T192 26391-26399 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T193 26795-26805 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T194 26823-26833 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T195 26864-26875 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T196 26933-26944 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T197 26985-26996 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T198 27140-27148 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T199 27370-27377 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T200 27492-27495 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T201 28359-28366 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T202 28764-28771 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T203 30628-30635 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T204 33098-33105 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T205 33249-33256 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T206 33321-33328 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 406-418 Body_part denotes venous blood http://purl.obolibrary.org/obo/UBERON_0013756
T2 413-418 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T3 2038-2042 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T4 17200-17204 Body_part denotes tail http://purl.obolibrary.org/obo/UBERON_0002415
T5 20184-20198 Body_part denotes immune systems http://purl.obolibrary.org/obo/UBERON_0002405
T6 20418-20431 Body_part denotes immune system http://purl.obolibrary.org/obo/UBERON_0002405
T7 22870-22883 Body_part denotes immune system http://purl.obolibrary.org/obo/UBERON_0002405

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 84-92 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 152-160 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T3 448-456 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T4 602-610 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 638-646 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 1081-1089 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 1194-1202 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 1253-1261 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 1461-1469 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T10 1583-1607 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T11 1609-1617 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T12 1645-1692 Disease denotes severe acute respiratory syndrome coronavirus-2 http://purl.obolibrary.org/obo/MONDO_0100096
T13 1645-1678 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T14 1694-1702 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 1738-1746 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 1749-1759 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T17 1837-1846 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T18 2107-2115 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 2161-2169 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 2279-2290 Disease denotes common cold http://purl.obolibrary.org/obo/MONDO_0005709
T21 2460-2468 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 3854-3862 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 4085-4093 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 4154-4162 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 4184-4193 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T26 4374-4382 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 4559-4567 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 4634-4644 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T29 4655-4663 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 5054-5063 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T31 5134-5142 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 5173-5177 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T33 5374-5383 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T34 5411-5421 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T35 5612-5621 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T36 5914-5922 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 5997-6010 Disease denotes infections in http://purl.obolibrary.org/obo/MONDO_0005550
T38 6279-6287 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 6767-6775 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 6972-6980 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 7790-7798 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 8538-8546 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 8812-8821 Disease denotes varicella http://purl.obolibrary.org/obo/MONDO_0005700
T44 8822-8828 Disease denotes zoster http://purl.obolibrary.org/obo/MONDO_0005609
T45 8933-8942 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T46 9018-9026 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 9680-9689 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T48 9739-9747 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 9812-9820 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 10318-10326 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 10750-10758 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 10945-10953 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 11188-11196 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 11203-11211 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 11408-11416 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T56 12180-12188 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 12346-12354 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T58 12454-12462 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 13137-13145 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 13342-13350 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 13951-13959 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 14125-14133 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 14281-14289 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 14377-14385 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 14519-14527 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T66 14755-14763 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T67 14851-14859 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 15036-15044 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T69 15203-15211 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T70 15299-15307 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T71 15570-15578 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T72 15737-15745 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T73 15833-15841 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T74 15989-15997 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 16679-16687 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T76 16999-17003 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T77 17673-17681 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T78 17786-17794 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T79 17941-17951 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T80 18174-18182 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T81 18226-18234 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 18357-18365 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T83 18482-18490 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 18643-18651 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 18830-18838 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 18894-18902 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T87 19241-19249 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T88 19365-19377 Disease denotes tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076
T89 19425-19433 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T90 19497-19505 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T91 19766-19774 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T92 19778-19786 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T93 20967-20986 Disease denotes respiratory disease http://purl.obolibrary.org/obo/MONDO_0005087
T94 21083-21103 Disease denotes respiratory diseases http://purl.obolibrary.org/obo/MONDO_0005087
T95 23144-23152 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T96 23239-23247 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T97 23542-23550 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T98 23897-23905 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T99 24294-24302 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T100 24370-24374 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T101 24553-24557 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T102 25199-25208 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T103 25378-25386 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T104 25469-25477 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T105 25651-25655 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T106 26153-26161 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T107 26758-26766 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T108 27237-27245 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T109 27359-27367 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T110 30469-30477 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T111 30617-30625 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T112 31421-31423 Disease denotes Ns http://purl.obolibrary.org/obo/MONDO_0009735
T113 33170-33178 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 49-55 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T2 163-168 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T3 226-231 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T4 232-235 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T5 413-418 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T6 413-418 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T7 428-435 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T8 518-519 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 530-536 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T10 763-769 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T11 967-968 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1028-1033 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T13 1090-1098 http://purl.obolibrary.org/obo/CLO_0001272 denotes 2 T cell
T14 1214-1221 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T15 1765-1766 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 1969-1973 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T17 2038-2042 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T18 2038-2042 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T19 2368-2375 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T20 2385-2386 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 2411-2413 http://purl.obolibrary.org/obo/CLO_0007074 denotes kb
T22 2411-2413 http://purl.obolibrary.org/obo/CLO_0051988 denotes kb
T23 2447-2454 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T24 2583-2584 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 2732-2740 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T26 2922-2923 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 3300-3307 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T28 3318-3326 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T29 3359-3364 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T30 3421-3429 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptides
T31 3488-3491 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T32 3503-3510 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T33 3518-3521 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T34 3523-3537 http://purl.obolibrary.org/obo/CL_0000912 denotes T helper cells
T35 3548-3556 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T36 3593-3600 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T37 3647-3648 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 3656-3662 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T39 3685-3693 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T40 3769-3776 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T41 3865-3870 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T42 3879-3880 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 3881-3888 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T44 3923-3925 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T45 4029-4037 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T46 4121-4122 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 4175-4176 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T48 4202-4205 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T49 4239-4245 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T50 4313-4319 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T51 4394-4400 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T52 4470-4471 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 4603-4610 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T54 4971-4975 http://purl.obolibrary.org/obo/CLO_0001360 denotes 4–12
T55 5112-5113 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 5256-5257 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 5271-5277 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T58 5308-5314 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T59 5622-5623 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T60 5844-5849 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T61 5878-5879 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 5958-5959 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 6097-6104 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T64 6106-6108 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T65 6119-6127 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria
T66 6325-6326 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 6636-6637 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 6709-6714 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T69 6911-6912 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T70 7003-7006 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T71 7007-7008 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 7528-7535 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T73 7604-7611 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T74 7737-7744 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T75 7749-7757 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria
T76 7763-7771 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T77 7894-7895 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 7909-7910 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T79 8289-8290 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T80 8334-8343 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T81 8334-8343 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T82 8437-8442 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T83 8780-8785 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T84 8786-8791 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T85 8829-8834 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T86 8866-8871 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T87 8882-8883 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T88 8927-8932 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T89 8943-8944 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T90 8951-8953 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2a
T91 9047-9048 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 9109-9114 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T93 9148-9153 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T94 9211-9216 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T95 9324-9329 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T96 9486-9491 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T97 9499-9506 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T98 9690-9691 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T99 10488-10491 http://purl.obolibrary.org/obo/CLO_0001376 denotes 464
T100 10488-10491 http://purl.obolibrary.org/obo/CLO_0001378 denotes 464
T101 10634-10635 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T102 11014-11015 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T103 11034-11035 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 11056-11057 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T105 11079-11082 http://purl.obolibrary.org/obo/CLO_0001000 denotes 3–5
T106 11132-11133 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 11540-11541 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T108 11579-11580 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 11613-11614 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T110 11653-11654 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 11921-11922 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 11978-11985 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T113 12366-12373 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T114 12378-12385 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T115 13438-13441 http://purl.obolibrary.org/obo/CLO_0003679 denotes Hel
T116 13448-13452 http://purl.obolibrary.org/obo/CLO_0001000 denotes 3′–5
T117 13754-13755 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 13899-13900 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 13901-13907 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T120 14048-14054 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T121 14217-14218 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T122 14550-14551 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 14694-14701 http://purl.obolibrary.org/obo/PR_000010213 denotes M’. (b)
T124 16455-16461 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T125 16498-16501 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T126 16548-16550 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T127 16548-16550 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T128 16972-16974 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T129 16972-16974 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T130 17122-17124 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4c
T131 17200-17204 http://purl.obolibrary.org/obo/UBERON_0002415 denotes tail
T132 17227-17228 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T133 17400-17401 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T134 17443-17445 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4c
T135 17802-17804 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T136 17824-17830 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T137 18131-18132 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T138 18140-18146 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T139 18331-18334 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T140 18443-18444 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T141 18502-18509 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T142 18550-18553 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T143 18585-18588 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T144 18669-18676 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T145 18841-18846 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T146 19077-19083 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T147 19217-19218 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T148 19523-19530 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T149 19603-19606 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T150 19686-19687 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T151 19688-19693 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T152 19868-19874 http://purl.obolibrary.org/obo/NCBITaxon_9837 denotes camels
T153 20054-20061 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T154 20151-20152 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T155 20184-20198 http://purl.obolibrary.org/obo/UBERON_0002405 denotes immune systems
T156 20208-20214 http://purl.obolibrary.org/obo/NCBITaxon_9837 denotes camels
T157 20240-20246 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T158 20278-20285 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T159 20365-20370 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T160 20371-20372 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T161 20418-20431 http://purl.obolibrary.org/obo/UBERON_0002405 denotes immune system
T162 20884-20891 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T163 21130-21131 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T164 21234-21237 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T165 21439-21446 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T166 21483-21484 http://purl.obolibrary.org/obo/CLO_0001020 denotes ɑ
T167 21724-21725 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T168 21750-21758 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T169 21968-21969 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T170 22093-22098 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T171 22386-22387 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T172 22870-22883 http://purl.obolibrary.org/obo/UBERON_0002405 denotes immune system
T173 22958-22959 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T174 23403-23409 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T175 23507-23508 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T176 23509-23516 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T177 23540-23541 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T178 23575-23576 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T179 23577-23583 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T180 23600-23601 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T181 23602-23609 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T182 23739-23744 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T183 23748-23749 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T184 24195-24200 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T185 24214-24219 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T186 24530-24538 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T187 24648-24650 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T188 24752-24757 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T189 24988-24990 http://purl.obolibrary.org/obo/CLO_0002709 denotes db
T190 25209-25210 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T191 25212-25217 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T192 25248-25249 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T193 25255-25260 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T194 26175-26176 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 26198-26199 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T196 26314-26322 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T197 26558-26559 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T198 26610-26611 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 26775-26776 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T200 26948-26952 http://purl.obolibrary.org/obo/CLO_0001022 denotes L, I
T201 26948-26952 http://purl.obolibrary.org/obo/CLO_0007314 denotes L, I
T202 27121-27129 http://purl.obolibrary.org/obo/OBI_0100026 denotes organism
T203 27121-27129 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organism
T204 27297-27298 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T205 27819-27822 http://purl.obolibrary.org/obo/CLO_0008491 denotes p,s
T206 27855-27858 http://purl.obolibrary.org/obo/CLO_0008491 denotes p,s
T207 27898-27904 http://purl.obolibrary.org/obo/CLO_0008954 denotes s} + C
T208 27927-27933 http://purl.obolibrary.org/obo/CLO_0007079 denotes k} + C
T209 27976-27980 http://purl.obolibrary.org/obo/CLO_0009124 denotes Sp,s
T210 27993-27997 http://purl.obolibrary.org/obo/CLO_0007122 denotes k/Tp
T211 28000-28002 http://purl.obolibrary.org/obo/CLO_0008491 denotes Ps
T212 28287-28290 http://purl.obolibrary.org/obo/CLO_0008491 denotes p,s
T213 28309-28311 http://purl.obolibrary.org/obo/CLO_0008192 denotes Np
T214 28693-28696 http://purl.obolibrary.org/obo/CLO_0008491 denotes p,s
T215 29075-29078 http://purl.obolibrary.org/obo/CLO_0008491 denotes p,s
T216 29107-29109 http://purl.obolibrary.org/obo/CLO_0008192 denotes Np
T217 29112-29116 http://purl.obolibrary.org/obo/CLO_0007122 denotes k/Tp
T218 29495-29497 http://purl.obolibrary.org/obo/CLO_0008491 denotes Ps
T219 30262-30264 http://purl.obolibrary.org/obo/CLO_0008491 denotes Ps
T220 30274-30275 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T221 30377-30378 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T222 30545-30550 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T223 30608-30609 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T224 31018-31024 http://purl.obolibrary.org/obo/CLO_0008954 denotes s} + C
T225 31047-31053 http://purl.obolibrary.org/obo/CLO_0007079 denotes k} + C
T226 31111-31113 http://purl.obolibrary.org/obo/CLO_0037066 denotes Tk
T227 31114-31116 http://purl.obolibrary.org/obo/CLO_0008491 denotes Ps
T228 31814-31816 http://purl.obolibrary.org/obo/CLO_0037066 denotes Tk
T229 32547-32549 http://purl.obolibrary.org/obo/CLO_0009141 denotes St
T230 32547-32549 http://purl.obolibrary.org/obo/CLO_0050980 denotes St
T231 32550-32554 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T232 32673-32675 http://purl.obolibrary.org/obo/CLO_0051741 denotes C1
T233 33048-33057 http://purl.obolibrary.org/obo/OBI_0000245 denotes organized
T234 33311-33313 http://purl.obolibrary.org/obo/CLO_0002709 denotes db
T235 33460-33461 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 537-543 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T2 770-776 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T3 825-831 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T4 1099-1105 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T5 2148-2157 http://purl.obolibrary.org/obo/GO_0016032 denotes virulence
T6 2148-2157 http://purl.obolibrary.org/obo/GO_0009405 denotes virulence
T7 2968-2979 http://purl.obolibrary.org/obo/GO_0006412 denotes translation
T8 4320-4326 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T9 5315-5321 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T10 7213-7221 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange
T11 17817-17823 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T12 18032-18041 http://purl.obolibrary.org/obo/GO_0016032 denotes virulence
T13 18032-18041 http://purl.obolibrary.org/obo/GO_0009405 denotes virulence
T14 18133-18139 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T15 22967-22982 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 1837-1846 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 1857-1877 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T3 2038-2055 Phenotype denotes lung infiltrating http://purl.obolibrary.org/obo/HP_0002113
T4 5401-5421 Phenotype denotes recurrent infections http://purl.obolibrary.org/obo/HP_0002719

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-103 Sentence denotes Epitope similarity cannot explain the pre-formed T cell immunity towards structural SARS-CoV-2 proteins
T2 105-113 Sentence denotes Abstract
T3 114-279 Sentence denotes The current pandemic is caused by the SARS-CoV-2 virus and large progress in understanding the pathology of the virus has been made since its emergence in late 2019.
T4 280-503 Sentence denotes Several reports indicate short lasting immunity against endemic coronaviruses, which contrasts studies showing that biobanked venous blood contains T cells reactive to SARS-CoV-2 S-protein even before the outbreak in Wuhan.
T5 504-613 Sentence denotes This suggests a preformed T cell memory towards structural proteins in individuals not exposed to SARS-CoV-2.
T6 614-777 Sentence denotes Given the similarity of SARS-CoV-2 to other members of the Coronaviridae family, the endemic coronaviruses appear likely candidates to generate this T cell memory.
T7 778-949 Sentence denotes However, given the apparent poor immunological memory created by the endemic coronaviruses, immunity against other common pathogens might offer an alternative explanation.
T8 950-1106 Sentence denotes Here, we utilize a combination of epitope prediction and similarity to common human pathogens to identify potential sources of the SARS-CoV-2 T cell memory.
T9 1107-1417 Sentence denotes Although beta-coronaviruses are the most likely candidates to explain the pre-existing SARS-CoV-2 reactive T cells in uninfected individuals, the SARS-CoV-2 epitopes with the highest similarity to those from beta-coronaviruses are confined to replication associated proteins—not the host interacting S-protein.
T10 1418-1556 Sentence denotes Thus, our study suggests that the observed SARS-CoV-2 pre-formed immunity to structural proteins is not driven by near-identical epitopes.
T11 1558-1570 Sentence denotes Introduction
T12 1571-1737 Sentence denotes The current coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)1 with devastating consequences.
T13 1738-1888 Sentence denotes SARS-CoV-2 infections have a broad spectrum of manifestations, ranging from asymptomatic to severe pneumonia and acute respiratory distress syndrome2.
T14 1889-2131 Sentence denotes The reason for this broad range is still unclear, but markedly decreased immune cell numbers3,4, together with cytokine storm5, and dysregulation of lung infiltrating immune cells6–9 have been associated with critical COVID-19 manifestations.
T15 2132-2320 Sentence denotes The more severe virulence of SARS-CoV-2 is in contrast to the four endemic coronaviruses OC43, HKU1, 229E, and NL63, which are responsible for the common cold with usually mild symptoms10.
T16 2321-2455 Sentence denotes Coronaviruses are single positive stranded RNA viruses and with a genome size of about 30 kb are the largest of the known RNA-viruses.
T17 2456-2567 Sentence denotes The SARS-CoV-2 genome contains 14 open reading frames (ORFs), where the ORF10 is not translated into protein11.
T18 2568-2792 Sentence denotes In addition to a number of non-structural proteins, the ORFs translates into the four structural proteins: spike (S) glycoprotein, small envelope (E) glycoprotein, membrane (M) glycoprotein, and the nucleocapsid (N) protein.
T19 2793-3067 Sentence denotes The most non-structural proteins are encoded by ORF1a and ORF1b, where ORF1a is translated into the polyprotein pp1a and through a slippery sequence near the end of ORF1a the translation is continued into the ORF1b which produce the 7096 amino acid long polyprotein pp1ab12.
T20 3068-3212 Sentence denotes The autoproteolytic cleavage of the polyproteins pp1a and pp1ab creates the non-structural proteins, which form the complex replicase machinery.
T21 3213-3299 Sentence denotes Among these are the essential RNA-dependent RNA polymerase (RdRp) embedded in ORF1b11.
T22 3300-3420 Sentence denotes T cells recognize peptides presented in the context of the human leukocyte antigen (HLA) class I and class II molecules.
T23 3421-3592 Sentence denotes Peptides presented on the class I HLAs are generally recognized by CD8+ cytotoxic T cells, while CD4+ T helper cells recognize peptides bound on the HLA class II molecule.
T24 3593-3754 Sentence denotes T cells are known to be cross reactive13,14, that is, a single T cell can recognize similar peptides derived from different pathogens presented by HLA molecules.
T25 3755-3849 Sentence denotes Additionally, T cells are known to be promiscuous and can recognize many different epitopes15.
T26 3850-3926 Sentence denotes The SARS-CoV-2 virus elicits a T cells response during the infection6,16–18.
T27 3927-4174 Sentence denotes However, mounting evidence suggests that 20–50% of unexposed individuals are capable of responding to peptides derived from the S-, N-, and M-proteins of the SARS-CoV-2 virus6,16–24, indicating a pre-existing immunity to these SARS-CoV-2 proteins.
T28 4175-4348 Sentence denotes A single influenza epitope has been identified by comparison of T cell receptors25, but the original pathogenic source of this pre-formed T cell memory is generally unclear.
T29 4349-4514 Sentence denotes Interestingly, identical SARS-CoV-2 specific T cell receptors were observed in multiple convalescent donors17 indicating a similar source of the pre-formed immunity.
T30 4515-4690 Sentence denotes There is also some evidence of pre-existing SARS-CoV-2 antibodies26, which like for the T cells indicate that previous infections can cause SARS-CoV-2 cross-reactive immunity.
T31 4691-4861 Sentence denotes Given the high sequence similarity, endemic coronaviruses have been suggested likely inducers of the observed pre-existing immunity although other sources are possible27.
T32 4862-5004 Sentence denotes However, immunity to these coronaviruses appears short-lived as antibody titers return to baseline levels at 4–12 months after infection28–30.
T33 5005-5128 Sentence denotes Importantly, it can also not be excluded that re-infection with the same coronavirus type can occur within a single year31.
T34 5129-5290 Sentence denotes Both SARS-CoV-1, which caused the 2002–2004 SARS epidemic, and MERS-CoV, which emerged in 2012, have both been shown to elicit a long lasting T cell memory20,32.
T35 5291-5369 Sentence denotes In contrast, the T cell memory towards the endemic coronaviruses is not clear.
T36 5370-5518 Sentence denotes For influenza it is clear that recurrent infections and epidemics are due to the accumulation of mutations in the hemagglutinin and neuraminidase33.
T37 5519-5635 Sentence denotes However, the genetic drift of endemic coronaviruses seems to be considerably slower than for Influenza A and B34,35.
T38 5636-5789 Sentence denotes Collectively, this indicates that other frequently encountered pathogens besides the endemic coronaviruses could have generated the preexisting immunity.
T39 5790-5934 Sentence denotes In the present report, we evaluate commonly occurring human pathogens for epitopes with a very high similarity to potential SARS-CoV-2 epitopes.
T40 5936-5943 Sentence denotes Results
T41 5944-6062 Sentence denotes We identified a number of pathogens commonly causing infections in the European population (Supplementary Tables 2–5).
T42 6063-6144 Sentence denotes The list of pathogens included 32 viruses, 11 fungi, 26 bacteria and 2 parasites.
T43 6145-6427 Sentence denotes We obtained all protein sequences for these pathogens from NCBI, and compared these to predicted HLA-I and HLA-II binding epitopes in SARS-CoV-2, and ranked the pathogens based on a relevance score (see Methods; Fig. 1a) based on short exact sequence matches of length k ("k-mers").
T44 6428-6606 Sentence denotes We limited the analysis to include only the five most common HLA alleles in the European population as reported in the Allele Frequency Net Database36 (Supplementary Tables 6–7).
T45 6607-6787 Sentence denotes Figure 1 Analysis approach. (a) k-mers for k ϵ {6, 7, 8} were extracted from the proteins of relevant human pathogens and compared to epitopes predicted in the SARS-CoV-2 proteins.
T46 6788-6844 Sentence denotes The epitope prediction was by netMHCpan and netMHCIIpan.
T47 6845-6967 Sentence denotes Pathogens were ranked based on exact k-mer hits to the epitopes. (b) Principle of edit distance determination of epitopes.
T48 6968-7138 Sentence denotes The SARS-CoV-2 epitope MKFSDRPFMLH has a edit distance of 1 when compared to the putative pathogen epitope MKFSDRPFML_ because of the missing histidine at the C-terminus.
T49 7139-7268 Sentence denotes The distance between MKFSDRPFMLH and MKFSDAPFMLHR is 2 because of the D6A exchange and the additional arginine at the C-terminus.
T50 7269-7372 Sentence denotes The K2L, D5I, and F8S exchanges give rise to an edit distance of 3 between MKFSDRPFMLH and MLFSIRPSMLH.
T51 7373-7499 Sentence denotes We observed different relevance scores for the same pathogen, depending on the length of k-mers (Supplementary Figs. 1 and 2).
T52 7500-7645 Sentence denotes For k = 6 we found that all viruses were in the upper half when ranking the relevance scores, while the viruses were in the lower half for k = 8.
T53 7646-7722 Sentence denotes This was independent of the HLA-class epitopes (Supplementary Fig. 1 and 2).
T54 7723-7810 Sentence denotes Figure 2 Some viruses and bacteria have peptides (k-mers) matching SARS-CoV-2 epitopes.
T55 7811-7919 Sentence denotes The top 10 pathogen relevance scores were averaged over k = 6,7,8 amino acids for (a) HLA-I, and (b) HLA-II.
T56 7920-8014 Sentence denotes Pathogen relevance score for each pathogen and k are presented in Supplementary Figs. 1 and 2.
T57 8015-8142 Sentence denotes Given the overall similarity between coronaviruses, the endemic coronaviruses are expected to have the highest relevance score.
T58 8143-8308 Sentence denotes Given the compact genome size and highly optimized proteins37 it seems likely that only short stretches will have an exact match, even when using a reduced alphabet.
T59 8309-8423 Sentence denotes Conversely, more complex organisms have larger genome, why the probability of matching longer stretches increases.
T60 8424-8483 Sentence denotes We therefore focus on pathogens with short (k = 6) matches.
T61 8484-8683 Sentence denotes Within the top 10 ranking pathogens for HLA-I binding SARS-CoV-2 epitopes based on k = 6, we find the two fungi Candida tropicalis and Cryptococcus neoformans, and the parasite Trichomonas vaginalis.
T62 8684-8955 Sentence denotes Apart from the endemic coronaviruses HKU1, OC43, 229E, and NL63 we find the double-stranded DNA virus Human alphaherpesvirus 3 (varicella-zoster virus, VZV), the double-stranded RNA virus Rotavirus A (RV), and the single-stranded negative RNA virus Influenza B (Fig. 2a).
T63 8956-9204 Sentence denotes When scoring the relevance based on matches to predict HLA-II SARS-CoV-2 epitopes, we find a similar result, the only difference being the appearance of Human Gammaherpesvirus 4 (Epstein-Barr virus, EBV) in place of Trichomonas vaginalis (Fig. 2b).
T64 9205-9275 Sentence denotes Viral genes can be expressed at different times during an infection38.
T65 9276-9374 Sentence denotes However, during the multiplication phase of the virus, the viral products are expressed in excess.
T66 9375-9533 Sentence denotes To avoid selection of pathogens based on highly similar, but rarely or poorly expressed proteins, we therefore focus on the viruses in the following analysis.
T67 9534-9710 Sentence denotes Using netMHCpan and netMHCIIpan we predicted the epitopes in the reference sequences for the coronaviruses OC43, HKU1, 229E, and NL63, as well as Influenza B, EBV, RV, and VZV.
T68 9711-9901 Sentence denotes Assessing the similarity to SARS-CoV-2 predicted epitopes, we calculated the edit distance from each SARS-CoV-2 epitope to each of the predicted epitopes in the selected pathogens (Fig. 1b).
T69 9902-10078 Sentence denotes The edit distance – also known as the Levenshtein distance – accounts for addition, deletion, and substitution of amino acids to transform one amino acid sequence into another.
T70 10079-10153 Sentence denotes We opted for this distance metric to allow differences in epitope lengths.
T71 10154-10204 Sentence denotes The edit distance was calculated per analyzed HLA.
T72 10205-10338 Sentence denotes We found that the beta-coronaviruses OC43 and HKU1 had the highest number of epitopes identical to the predicted SARS-CoV-2 epitopes.
T73 10339-10444 Sentence denotes For HLA-I bound epitopes we found 211 and 195 identical epitopes in HKU1 and OC3, respectively (Fig. 3a).
T74 10445-10552 Sentence denotes For HLA-II bound epitopes we found 493 and 464 identical epitopes in OC43 and HKU1, respectively (Fig. 3b).
T75 10553-10661 Sentence denotes When the similarity threshold was relaxed to an edit distance of 1 or 2 we found a similar pattern (Fig. 3).
T76 10662-10870 Sentence denotes Interestingly, if we accept an edit distance of 3 we find the highest number of similar SARS-CoV-2 HLA-I epitopes in VZV, followed by OC43, and HKU1 with 1292, 1189, and 1163 epitopes, respectively (Fig. 3a).
T77 10871-10919 Sentence denotes This was not reflected in HLA-II bound epitopes.
T78 10920-11084 Sentence denotes The strong occurrence of SARS-CoV-2 similar VZV epitopes was mainly driven by epitopes on HLA-B and HLA-C, and to a minor degree on HLA-A (Supplementary Figs. 3–5).
T79 11085-11237 Sentence denotes In agreement with previous reports39, we found a large number of identical or similar epitopes between SARS-CoV-1 and SARS-CoV-2 (Supplementary Fig. 6).
T80 11238-11300 Sentence denotes Figure 3 OC43 and HKU1 epitopes can be presented on many HLAs.
T81 11301-11379 Sentence denotes Epitopes were predicted using netMHCpan and netMHCIIpan in selected pathogens.
T82 11380-11685 Sentence denotes The similarity between each SARS-CoV-2 epitope and pathogen epitope was calculated using the edit distance, and the number of shortest matches was enumerated. (a) Total number of HLA-I epitopes with a edit distance between 0 and 3. (b) Total number of HLA-II epitopes with a edit distance between 0 and 3.
T83 11686-11779 Sentence denotes The pathogens are ordered per plot from highest to lowest, while the fill color is preserved.
T84 11780-11875 Sentence denotes We next asked which coronavirus proteins might be the most likely inducers of cross reactivity.
T85 11876-12017 Sentence denotes Arguably, the epitopes most likely to elicit a cross-reactive response are those found in many corona viruses and are presented by many HLAs.
T86 12018-12145 Sentence denotes The latter constraint is important, since the current studies demonstrating cross-reactivity do not distinguish HLAs6,16,18–23.
T87 12146-12254 Sentence denotes We first enumerated the number of SARS-CoV-2 epitopes for each of the viral proteins (Supplementary Fig. 7).
T88 12255-12416 Sentence denotes Given that the OC43 and HKU1 coronavirus strains appear the most likely pathogen to create SARS-CoV-2 reactive T cells, we focused the analysis on these strains.
T89 12417-12564 Sentence denotes We found that only epitopes from the SARS-CoV-2 polyprotein pp1ab have identical amino acid sequences to epitopes identified in both OC43 and HKU1.
T90 12565-12731 Sentence denotes Interestingly, the epitopes from the S-protein are different at three positions or more compared to the amino acid sequences for the predicted OC43 and HKU1 epitopes.
T91 12732-12907 Sentence denotes Since not only the number of epitopes but also the probability of the epitope to be presented, we also enumerated the number of epitope-presenting HLAs (Supplementary Fig. 8).
T92 12908-13045 Sentence denotes The highest number of possible HLAs is 15 for HLA-I and 80 for HLA-II (50 DPA1-DPB1 combinations, 25 DQA1-DQB1 combinations, and 5 DRB1).
T93 13046-13166 Sentence denotes Again, we found the highest number of HLAs and the highest similarity in epitopes from the SARS-CoV-2 polyprotein pp1ab.
T94 13167-13292 Sentence denotes The polyprotein pp1ab is 7096 amino acids long, and 15 nonstructural proteins are created through autoproteolytic cleavage12.
T95 13293-13577 Sentence denotes Comparison of the pp1ab amino acid sequence from SARS-CoV-2, HKU1, and OC43 revealed that the RNA-dependent RNA polymerase (RdRp), the helicase (Hel), the 3′–5′ exoribonuclease (ExoN), and the 2′-O-ribose methyltransferase generally have the highest similarity (Fig. 4a; upper panel).
T96 13578-13721 Sentence denotes It is also in these regions that the near identical epitopes, as determined by an edit distance of 1 or less, are found (Fig. 4a; lower panel).
T97 13722-13832 Sentence denotes An experimental study evaluated a set of 117 epitopes form HKU1 and OC43 for their cross reactive potential24.
T98 13833-13990 Sentence denotes Two epitopes from HKU1 OC43 were identified as capable of raising a T cell response, and were nearly identical to two SARS-CoV-2, marked with ‘M’ in Fig. 4a.
T99 13991-14115 Sentence denotes The S-protein epitopes previously found to expand public T cell clonotypes17, were not found to be shared with HKU1 or OC43.
T100 14116-14232 Sentence denotes Figure 4 SARS-CoV-2 epitopes from conserved regions are nearly identical to OC43 and HKU1 epitopes. (a) Upper panel:
T101 14233-14403 Sentence denotes Protein sequence for the polyprotein pp1ab from SARS-CoV-2, OC43, and HKU1 were aligned and the similarity between OC43 and HKU1 amino acids to SARS-CoV-2 was calculated.
T102 14404-14466 Sentence denotes The individual proteins are marked above the similarity graph.
T103 14467-14479 Sentence denotes Lower panel:
T104 14480-14623 Sentence denotes The number of HLA-alleles that present SARS-CoV-2 pp1ab epitopes with a edit distance of 1 or less to epitopes predicted in both OC43 and HKU1.
T105 14624-14714 Sentence denotes Two epitopes previously identified as cross reactive24 are marked by ‘M’. (b) Upper panel:
T106 14715-14877 Sentence denotes Protein sequence for the S-protein from SARS-CoV-2, OC43, and HKU1 were aligned and the similarity between OC43 and HKU1 amino acids to SARS-CoV-2 was calculated.
T107 14878-14985 Sentence denotes The individual proteins are marked above the similarity graph, where RBD gives the receptor binding domain.
T108 14986-14998 Sentence denotes Lower panel:
T109 14999-15162 Sentence denotes The number of HLA-alleles presenting SARS-CoV-2 S-protein epitopes with an edit distance of 3 or less to epitopes predicted in both OC43 and HKU1. (c) Upper panel:
T110 15163-15325 Sentence denotes Protein sequence for the M-protein from SARS-CoV-2, OC43, and HKU1 were aligned and the similarity between OC43 and HKU1 amino acids to SARS-CoV-2 was calculated.
T111 15326-15519 Sentence denotes The individual proteins are marked above the similarity graph: ‘VS’ indicates the portion of the M-protein on the virion surface, ‘Tr’ the transmembrane region, and ‘IV’ the intraviron portion.
T112 15520-15532 Sentence denotes Lower panel:
T113 15533-15696 Sentence denotes The number of HLA-alleles presenting SARS-CoV-2 M-protein epitopes with an edit distance of 3 or less to epitopes predicted in both OC43 and HKU1. (d) Upper panel:
T114 15697-15859 Sentence denotes Protein sequence for the N-protein from SARS-CoV-2, OC43, and HKU1 were aligned and the similarity between OC43 and HKU1 amino acids to SARS-CoV-2 was calculated.
T115 15860-15938 Sentence denotes The individual domains of the N-protein are marked above the similarity graph.
T116 15939-15951 Sentence denotes Lower panel:
T117 15952-16098 Sentence denotes The number of HLA-alleles presenting SARS-CoV-2 N-protein epitopes with an edit distance of 3 or less to epitopes predicted in both OC43 and HKU1.
T118 16099-16329 Sentence denotes The height and color of the similarity graphs designate similarity such that white bars indicate no similarity, light blue bars with half height indicate 50% similarity and dark blue bars with full height indicate 100% similarity.
T119 16330-16408 Sentence denotes The width of the bar in the lower panels indicates the length of the epitopes.
T120 16409-16454 Sentence denotes Darker regions indicate overlapping epitopes.
T121 16455-16543 Sentence denotes T cell immunity to the structural proteins has received substantial attention6,16,18–24.
T122 16544-16729 Sentence denotes The S2 portion of the S-protein, which constitutes the stalk of the host interacting receptor12, shares the highest similarity between SARS-CoV-2, HKU1, and OC43 (Fig. 4b; upper panel).
T123 16730-16854 Sentence denotes Interestingly, we found some similar HLA-I epitopes (edit distance of 3) but only one HLA-II epitope (Fig. 4b; lower panel).
T124 16855-16975 Sentence denotes The majority of the HLA-I epitopes and the single HLA-II epitope fall within the relatively conserved portion of the S2.
T125 16976-17141 Sentence denotes The similarity between SARS–CoV–2, HKU1, and OC43 for the M- and N-proteins is most prominent around position 110 in either of the proteins (Fig. 4c,d; upper panel).
T126 17142-17283 Sentence denotes This corresponds to the N-terminus of the long intraviron tail of the M-protein, and a small part of the RNA-binding domain of the N-protein.
T127 17284-17462 Sentence denotes Similar to the observation for the S-protein, we find some similar HLA-I epitopes (edit distance of 3) but only one a single position of HLA-II epitopes (Fig. 4c,d; lower panel).
T128 17463-17515 Sentence denotes These epitopes also appear in the conserved regions.
T129 17516-17693 Sentence denotes Collectively, these data indicate that near identical epitopes derived from endemic coronaviruses cannot explain the observed cross-reactivity to structural SARS-CoV-2 proteins.
T130 17695-17705 Sentence denotes Discussion
T131 17706-17805 Sentence denotes There is mounting evidence for preformed immunity against the novel coronavirus SARS-CoV-216,19–22.
T132 17806-18073 Sentence denotes Reports on memory T cell response to the endemic coronaviruses are lacking, but since antibody titers appear transient and frequent re-infections cannot be excluded28–31, it is probable that the endemic coronaviruses with low virulence do not create lasting immunity.
T133 18074-18185 Sentence denotes This then begs the question, which pathogen can generate a memory T cell response cross-reactive to SARS-CoV-2.
T134 18186-18292 Sentence denotes Through in silico analysis of predicted SARS-CoV-2 epitopes and common pathogens we address this question.
T135 18293-18382 Sentence denotes When allowing some dissimilarity, VZV has the highest number of SARS-CoV-2 like epitopes.
T136 18383-18475 Sentence denotes However, this we only find for HLA-I, and in particular HLA-B and HLA-C, but not for HLA-II.
T137 18476-18677 Sentence denotes Since SARS-CoV-2 specific T cells are found among both the HLA-I reactive CD8+ and among the HLA-II reactive CD4+ it is not likely that VZV is the pathogen behind the SARS-CoV-2 cross reactive T cells.
T138 18678-18847 Sentence denotes Rather, only the endemic coronaviruses, and in particular the beta-coronaviruses, have the highest number of epitopes similar to those predicted in the SARS-CoV-2 virus.
T139 18848-18980 Sentence denotes However, the similarity between epitopes from SARS-CoV-2 and endemic coronaviruses was concentrated in replication related proteins.
T140 18981-19115 Sentence denotes Thus, it appears unlikely that endemic coronaviruses should give rise to the observed preformed T cell immunity towards the S-protein.
T141 19116-19216 Sentence denotes This notion is supported by experimental findings, where cross-reactivity to S-protein is rare24,40.
T142 19217-19378 Sentence denotes A set of near-identical SARS-CoV-2 epitopes have been identified in Mycobacterium bovis27 which, in its attenuated form, is used as vaccine against tuberculosis.
T143 19379-19586 Sentence denotes Although the efficacy of this vaccine against SARS-CoV-2 remains unclear41,42, the findings indicate nonetheless that SARS-CoV-2 cross-reactive T cells can have sources widely different from viral pathogens.
T144 19587-19705 Sentence denotes It appears that bat coronaviruses require an intermediate host to attain the potential of becoming a human pathogen10.
T145 19706-19894 Sentence denotes For 229E these intermediate hosts are likely camelids while SARS-CoV-1, SARS-CoV-2, and MERS-CoV find intermediate zoonotic hosts in civets, dog or pangolin, and camels, respectively10,43.
T146 19895-19939 Sentence denotes The intermediate host for NL63 is not known.
T147 19940-20076 Sentence denotes In this context it is interesting that OC43 and HKU1 are the most likely candidates, as the natural host of these viruses are rodents43.
T148 20077-20170 Sentence denotes The effect of these hosts on the pathogenicity of the coronavirus remains a source of debate.
T149 20171-20381 Sentence denotes However, the immune systems of dogs, camels, pangolins, rodents, and humans have marked differences—murine B cells for instance express the pattern recognition receptor TLR4, which is absent in human B cells44.
T150 20382-20515 Sentence denotes Because of these differences in the immune system, it is unlikely that the same evasive strategy can be applied in different species.
T151 20516-20645 Sentence denotes The lack of general epidemiological interest in the endemic coronaviruses render information on the prevalence in Europe elusive.
T152 20646-20892 Sentence denotes Data collected by the Karolinska Institute in Stockholm, Sweden between 2010 and 2017, and by the West of Scotland Specialist Virology Centre, Greater Glasgow and Clyde, Scotland between 2005 and 2017, show seasonal variation of the four viruses.
T153 20893-21034 Sentence denotes The peak season is between December and April where 2–4% of patients with respiratory disease were positive for any of the four viruses45,46.
T154 21035-21194 Sentence denotes Though the data is obtained among patients with respiratory diseases, it can be expected to be a reasonable proxy for the prevalence in the greater population.
T155 21195-21326 Sentence denotes While the prediction of HLA-I epitopes has high accuracy, the accuracy of HLA-II epitope prediction is lower than that for HLA-I47.
T156 21327-21462 Sentence denotes One reason for this lower accuracy of HLA-II epitope prediction is the dimer structure of the HLA-II making the peptide binding groove.
T157 21463-21551 Sentence denotes In fact, the HLA-II ɑβ-chain combinations have been estimated to be over 4000 in number.
T158 21552-21674 Sentence denotes In contrast, the combination of the HLA-I and β2-microglobulin chains yields less combinatorial variation on the receptor.
T159 21675-21746 Sentence denotes The epitope prediction with netMHCpan depends on a proper training set.
T160 21747-21862 Sentence denotes By focusing on the most frequent European HLAs, inaccuracies in the epitope prediction are reduced or even avoided.
T161 21863-22016 Sentence denotes We did not utilize epitope databases like VDJDB48 and IEDB49, the reason being that these databases have a natural bias towards laboratory model antigen.
T162 22017-22156 Sentence denotes For instance, the most frequent epitopes in the Immune Epitope Database are human auto antigen and epitopes derived from Trypanosoma cruzi.
T163 22157-22299 Sentence denotes The amino acid set was reduced from the 20 standard amino acids to 15 amino acids by combining molecules with similar hydrophobic side chains.
T164 22300-22429 Sentence denotes The advantage is the ease of sequence comparison without alignment since the k-mer is a complete substring of the target protein.
T165 22430-22582 Sentence denotes While the reduced amino acid alphabet is derived from structural considerations50, it cannot be excluded that alphabet reduction might skew the results.
T166 22583-22710 Sentence denotes However, given the requirements of anchor amino acids, which are buried within the HLA-molecule, the results should not change.
T167 22711-22884 Sentence denotes One limitation to the study is that we do not consider the frequency of pathogens nor the potential expression level of the proteins and accessibility for the immune system.
T168 22885-22983 Sentence denotes Both arguably have an effect on the likelihood that an epitope can raise a robust immune response.
T169 22984-23052 Sentence denotes However, both variables can only be assessed with great uncertainty.
T170 23053-23267 Sentence denotes Additionally, our analysis hone in on pathogens with the largest number of k-mers matching SARS-CoV-2 epitopes, which may exclude relevant pathogens producing few but highly immunogenic SARS-CoV-2 similar epitopes.
T171 23268-23445 Sentence denotes Another limitation to the study is the reliance on sequence similarity; although related epitopes are likely to interact with the same T cell receptor, this is not guaranteed51.
T172 23446-23639 Sentence denotes This is also observed in the report by Mateus et al.24 where a peptide with 80% similarity to a SARS-CoV-2 epitope did not raise a T cell response, while a peptide with only 33% similarity did.
T173 23640-23720 Sentence denotes The presentation of different epitopes on different HLA-molecules is well known.
T174 23721-23798 Sentence denotes In this study, we focus on a small handful of HLAs with prevalence in Europe.
T175 23799-23967 Sentence denotes Since patient HLAs are rarely evaluated, it is not possible to know if the patients with observed SARS-CoV-2 cross-reactivity carry the same epitopes as evaluated here.
T176 23968-24101 Sentence denotes Given the prevalence in Europe, it is possible that there is an overlap with some studies, but the specifics are essentially unknown.
T177 24102-24251 Sentence denotes It is therefore important that the HLAs are disclosed in studies evaluating antigen specific cells, in order to focus in silico studies such as this.
T178 24252-24428 Sentence denotes In conclusion, epitope similarity between SARS-CoV-2 and other endemic beta-coronaviruses cannot explain the observed SARS-CoV2 pre-formed immunity towards structural proteins.
T179 24429-24539 Sentence denotes We conjecture that this observation of preformed immunity is likely driven by structurally different peptides.
T180 24541-24548 Sentence denotes Methods
T181 24549-24674 Sentence denotes The SARS-CoV2 protein sequences were downloaded from ViralZone (https://viralzone.expasy.org/89966)52, accessed May 29, 2020.
T182 24675-24740 Sentence denotes Uniprot IDs and common names are listed in Supplementary Table 1.
T183 24741-24831 Sentence denotes The common human pathogens evaluated in this study are listed in Supplementary Tables 2–5.
T184 24832-25014 Sentence denotes Pathogen protein sequences were extracted from the NCBI "non-redundant" protein database ("nr", version 5, downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA on May 31, 2020).
T185 25015-25088 Sentence denotes The extraction was per pathogen name, as stored in the Taxonomy database.
T186 25089-25367 Sentence denotes For epitope comparison, the protein reference sequences for the coronaviruses OC43, HKU1, 229E, and NL63, and Influenza B, Human Gammaherpesvirus 4, Rotavirus A, and Human alphaherpesvirus 3, were downloaded from https://ftp.ncbi.nlm.nih.gov/refseq/release/viral on 26.Jun.2020.
T187 25368-25447 Sentence denotes Validated SARS-CoV-1 epitopes were obtained from IEDB (https://www.iedb.org)49.
T188 25448-25595 Sentence denotes Protein segments for SARS-CoV-2 pp1ab (identifier: P0DTD1) and S-protein (identifier: P0DTC2) were obtained from UniProt (https://www.uniprot.org).
T189 25596-25834 Sentence denotes All potential MHC class I and class II epitopes in the SARS-CoV2 protein sequences, and selected pathogen reference sequences, were identified using netMHCpan version 4.1 and netMHCIIpan version 4.0, respectively, with default settings53.
T190 25835-26068 Sentence denotes For this step, the evaluated HLAs listed in Supplementary Tables 6 and 7 were selected based on frequency in the European population as reported in the Allele Frequency Net Database36; https://www.allelefrequencies.net, June 1, 2020.
T191 26069-26233 Sentence denotes The edit distance was calculated as the Levenshtein distance between each predicted SARS-CoV-2 epitope to a predicted epitope in a selected pathogen was calculated.
T192 26234-26307 Sentence denotes The calculation as per pathogen and HLA and only the best match was used.
T193 26308-26677 Sentence denotes Short peptides of length k (k-mers) of lengths 6, 7, and 8 were extracted from the proteins of each of the relevant pathogens and counted, for each value of k separately Each such multiset of k-mers was pre-filtered so that k-mers found only once in a pathogen were removed if those k-mers constituted a small fraction (1%) or less of all k-mers found for the pathogen.
T194 26678-26817 Sentence denotes The resulting k-mers were matched to the k-mers from the predicted epitopes for SARS-CoV-2 using a reduced 15 letter amino acid alphabet50.
T195 26818-27100 Sentence denotes This amino acid alphabet allows mismatches of amino acids with similar properties by letting the large hydrophobic amino acids V, L, I, and M be represented by L, the amino acids Y and F, which are hydrophobic with aromatic side chains by F, and the positively charged K and R by K.
T196 27101-27163 Sentence denotes The more complex an organism, the more proteins are expressed.
T197 27164-27258 Sentence denotes This means that the probability of finding k-mers matching epitopes from SARS-CoV-2 increases.
T198 27259-27534 Sentence denotes To overcome this problem we developed a pathogen relevance score to be evaluated for each triple of SARS-CoV-2 protein p, pathogen species s and value of k (note that the quantity also depends on the considered set of epitopes, i.e. HLA class I or class II only or combined).
T199 27535-29911 Sentence denotes We thus define\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ S_{p,s,k } : = log_{2} \left[ \left(N_{p,s,k} / T_{p,k} \right) / \left( \left(P_{s} + C \right) / \left( {15^{k} + C} \right) \right) \right], $$\end{document}Sp,s,k:=log2Np,s,k/Tp,k/Ps+C/15k+C, where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N_{p,s,k}$$\end{document}Np,s,k is the number of k-mer matched epitopes of protein p in species s, and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$T_{p,k} : = \mathop \sum \limits_{s} N_{p,s,k}$$\end{document}Tp,k:=∑sNp,s,k is the number of such epitopes of protein p across all species; their ratio \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N_{p,s,k} / T_{p,k}$$\end{document}Np,s,k/Tp,k is viewed in relation to the "richness" of the k-mer set of the pathogen species s, i.e. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$P_{s}$$\end{document}Ps, the number of distinct k-mers in pathogen s, divided by the total number of possible k-mers over the reduced alphabet (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$15^{k}$$\end{document}15k).
T200 29912-30358 Sentence denotes To avoid bias in favor of underrepresented species (very small \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$P_{s}$$\end{document}Ps), we add a regularizing constant C when computing the fraction of k-mers used by the species.
T201 30359-30541 Sentence denotes Thus the score is a log-observed-vs-expected-ratio indicating whether species s matches unproportionally many SARS-CoV-2 epitopes that cannot be explained by its proteome size alone.
T202 30542-31875 Sentence denotes To focus on possibly relevant pathogens in general rather than on a single SARS-CoV-2 protein, we also considered an aggregated score\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ S_{s,k } : = log_{2} \left[ \left(N_{s,k} / T_{k} \right) / \left( \left(P_{s} + C \right) / \left( {15^{k} + C} \right) \right) \right], $$\end{document}Ss,k:=log2Ns,k/Tk/Ps+C/15k+C, where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N_{s,k}$$\end{document}Ns,k is the total number of k-mer matched epitopes in species s, and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$T_{k} : = \mathop \sum \limits_{s} N_{s,k}$$\end{document}Tk:=∑sNs,k is the number of such epitopes across all species.
T203 31876-32033 Sentence denotes The pathogens were then ranked according to score (the highest score obtaining rank 1, the lowest score rank n, where n is the number of considered species).
T204 32034-32120 Sentence denotes Then the average rank is computed over the different parameter combinations k = 6,7,8.
T205 32122-32147 Sentence denotes Supplementary information
T206 32149-32174 Sentence denotes Supplementary Information
T207 32176-32192 Sentence denotes Publisher's note
T208 32193-32311 Sentence denotes Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
T209 32312-32346 Sentence denotes These authors contributed equally:
T210 32347-32378 Sentence denotes Ulrik Stervbo and Sven Rahmann.
T211 32380-32405 Sentence denotes Supplementary information
T212 32406-32464 Sentence denotes is available for this paper at 10.1038/s41598-020-75972-z.
T213 32466-32482 Sentence denotes Acknowledgements
T214 32483-32676 Sentence denotes This work was supported by grants from the Mercator Foundation (St-2018-0014), BMBF e:KID (01ZX1612A), BMBF NoChro (FKZ 13GW0338B), and DFG Collaborative Research Center SFB 876, subproject C1.
T215 32678-32698 Sentence denotes Author contributions
T216 32699-32959 Sentence denotes Conceptualization: U.S. and T.R.; Data curation: U.S. and S.R.; Formal analysis: U.S. and S.R.; Funding acquisition: S.R. and N.B.; Investigation: U.S. and S.R.; Methodology: S.R.; Resources: T.H.W.; Visualization: U.S.; Writing – original draft: U.S. and S.R.
T217 32960-33006 Sentence denotes Writing—review & editing: U.S., T.R., and S.R.
T218 33008-33015 Sentence denotes Funding
T219 33016-33074 Sentence denotes Open Access funding enabled and organized by Projekt DEAL.
T220 33076-33093 Sentence denotes Data availability
T221 33094-33398 Sentence denotes The protein sequences used in this study are available from public sources: SARS-CoV-2 sequences: https://viralzone.expasy.org/89966, NCBI "non-redundant" protein database, version 5: ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA, Protein reference sequences: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral.
T222 33399-33539 Sentence denotes The workflow and accompanying Python scripts is available as a Snakefile for use with Snakemake under https://gitlab.com/svenrahmann/corona.
T223 33541-33560 Sentence denotes Competing interests
T224 33561-33604 Sentence denotes The authors declare no competing interests.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 84-94 Species denotes SARS-CoV-2 Tax:2697049
19 1407-1416 Gene denotes S-protein Gene:43740568
20 459-468 Gene denotes S-protein Gene:43740568
21 152-162 Species denotes SARS-CoV-2 Tax:2697049
22 344-357 Species denotes coronaviruses Tax:11118
23 448-458 Species denotes SARS-CoV-2 Tax:2697049
24 602-612 Species denotes SARS-CoV-2 Tax:2697049
25 638-648 Species denotes SARS-CoV-2 Tax:2697049
26 673-686 Species denotes Coronaviridae Tax:11118
27 707-720 Species denotes coronaviruses Tax:11118
28 855-868 Species denotes coronaviruses Tax:11118
29 1028-1033 Species denotes human Tax:9606
30 1081-1091 Species denotes SARS-CoV-2 Tax:2697049
31 1116-1134 Species denotes beta-coronaviruses Tax:694002
32 1194-1204 Species denotes SARS-CoV-2 Tax:2697049
33 1253-1263 Species denotes SARS-CoV-2 Tax:2697049
34 1315-1333 Species denotes beta-coronaviruses Tax:694002
35 1461-1471 Species denotes SARS-CoV-2 Tax:2697049
48 1645-1692 Species denotes severe acute respiratory syndrome coronavirus-2 Tax:2697049
49 1694-1704 Species denotes SARS-CoV-2 Tax:2697049
50 2161-2171 Species denotes SARS-CoV-2 Tax:2697049
51 2207-2220 Species denotes coronaviruses Tax:11118
52 2221-2225 Species denotes OC43 Tax:31631
53 1583-1607 Disease denotes coronavirus disease 2019 MESH:C000657245
54 1609-1617 Disease denotes COVID-19 MESH:C000657245
55 1738-1759 Disease denotes SARS-CoV-2 infections MESH:C000657245
56 1837-1846 Disease denotes pneumonia MESH:D011014
57 1851-1886 Disease denotes acute respiratory distress syndrome MESH:D012128
58 2107-2115 Disease denotes COVID-19 MESH:C000657245
59 2279-2290 Disease denotes common cold MESH:D003139
72 2528-2533 Gene denotes ORF10 Gene:43740576
73 2675-2757 Gene denotes spike (S) glycoprotein, small envelope (E) glycoprotein, membrane (M) glycoprotein
74 2841-2846 Gene denotes ORF1a Gene:43740578
75 2851-2856 Gene denotes ORF1b Gene:43740578
76 2864-2869 Gene denotes ORF1a Gene:43740578
77 2958-2963 Gene denotes ORF1a Gene:43740578
78 3002-3007 Gene denotes ORF1b Gene:43740578
79 3117-3121 Gene denotes pp1a Gene:5499
80 3273-3277 Gene denotes RdRp Gene:43740578
81 3291-3296 Gene denotes ORF1b Gene:43740578
82 2321-2334 Species denotes Coronaviruses Tax:11118
83 2460-2470 Species denotes SARS-CoV-2 Tax:2697049
87 3488-3491 Gene denotes CD8 Gene:925
88 3518-3521 Gene denotes CD4 Gene:920
89 3359-3364 Species denotes human Tax:9606
99 4067-4068 Gene denotes M Gene:43740571
100 3854-3864 Species denotes SARS-CoV-2 Tax:2697049
101 4085-4095 Species denotes SARS-CoV-2 Tax:2697049
102 4154-4164 Species denotes SARS-CoV-2 Tax:2697049
103 4374-4384 Species denotes SARS-CoV-2 Tax:2697049
104 4655-4665 Species denotes SARS-CoV-2 Tax:2697049
105 4559-4569 Species denotes SARS-CoV-2 Tax:2697049
106 3909-3918 Disease denotes infection MESH:D007239
107 4634-4644 Disease denotes infections MESH:D007239
120 5502-5515 Gene denotes neuraminidase Gene:4758
121 4735-4748 Species denotes coronaviruses Tax:11118
122 4889-4902 Species denotes coronaviruses Tax:11118
123 5078-5089 Species denotes coronavirus Tax:11118
124 5134-5142 Species denotes SARS-CoV Tax:694009
125 5192-5200 Species denotes MERS-CoV Tax:1335626
126 5342-5355 Species denotes coronaviruses Tax:11118
127 5557-5570 Species denotes coronaviruses Tax:11118
128 5729-5742 Species denotes coronaviruses Tax:11118
129 4989-4998 Disease denotes infection MESH:D007239
130 5054-5063 Disease denotes infection MESH:D007239
131 5411-5421 Disease denotes infections MESH:D007239
134 5844-5849 Species denotes human Tax:9606
135 5914-5924 Species denotes SARS-CoV-2 Tax:2697049
143 6709-6714 Species denotes human Tax:9606
144 6767-6777 Species denotes SARS-CoV-2 Tax:2697049
145 6972-6982 Species denotes SARS-CoV-2 Tax:2697049
146 6818-6827 Chemical denotes netMHCpan
147 6832-6843 Chemical denotes netMHCIIpan
148 7209-7212 Chemical denotes D6A
149 7241-7249 Chemical denotes arginine MESH:D001120
152 6279-6289 Species denotes SARS-CoV-2 Tax:2697049
153 5997-6007 Disease denotes infections MESH:D007239
155 7790-7800 Species denotes SARS-CoV-2 Tax:2697049
157 7694-7720 Gene denotes Supplementary Fig. 1 and 2
160 8052-8065 Species denotes coronaviruses Tax:11118
161 8079-8092 Species denotes coronaviruses Tax:11118
176 8538-8548 Species denotes SARS-CoV-2 Tax:2697049
177 8596-8614 Species denotes Candida tropicalis Tax:5482
178 8619-8642 Species denotes Cryptococcus neoformans Tax:5207
179 8661-8682 Species denotes Trichomonas vaginalis Tax:5722
180 8707-8720 Species denotes coronaviruses Tax:11118
181 8786-8810 Species denotes Human alphaherpesvirus 3 Tax:10335
182 8812-8834 Species denotes varicella-zoster virus Tax:10335
183 8872-8883 Species denotes Rotavirus A Tax:28875
184 9018-9028 Species denotes SARS-CoV-2 Tax:2697049
185 9109-9133 Species denotes Human Gammaherpesvirus 4 Tax:10376
186 9135-9153 Species denotes Epstein-Barr virus Tax:10376
187 9172-9193 Species denotes Trichomonas vaginalis Tax:5722
188 8727-8731 Species denotes OC43 Tax:31631
189 8885-8887 Species denotes RV Tax:28875
191 9263-9272 Disease denotes infection MESH:D007239
199 9627-9640 Species denotes coronaviruses Tax:11118
200 9739-9749 Species denotes SARS-CoV-2 Tax:2697049
201 9812-9822 Species denotes SARS-CoV-2 Tax:2697049
202 9641-9645 Species denotes OC43 Tax:31631
203 9698-9700 Species denotes RV Tax:28875
204 9540-9549 Chemical denotes netMHCpan
205 9554-9565 Chemical denotes netMHCIIpan
210 11408-11418 Species denotes SARS-CoV-2 Tax:2697049
211 11247-11251 Species denotes OC43 Tax:31631
212 11331-11340 Chemical denotes netMHCpan
213 11345-11356 Chemical denotes netMHCIIpan
227 10416-10419 Gene denotes OC3 Gene:390874
228 11010-11015 Gene denotes HLA-B Gene:3106
229 11020-11025 Gene denotes HLA-C Gene:3107
230 11052-11057 Gene denotes HLA-A Gene:3105
231 10223-10241 Species denotes beta-coronaviruses Tax:694002
232 10318-10328 Species denotes SARS-CoV-2 Tax:2697049
233 10750-10760 Species denotes SARS-CoV-2 Tax:2697049
234 10945-10955 Species denotes SARS-CoV-2 Tax:2697049
235 11188-11196 Species denotes SARS-CoV Tax:694009
236 11203-11213 Species denotes SARS-CoV-2 Tax:2697049
237 10242-10246 Species denotes OC43 Tax:31631
238 10514-10518 Species denotes OC43 Tax:31631
239 10796-10800 Species denotes OC43 Tax:31631
245 11800-11811 Species denotes coronavirus Tax:11118
246 12180-12190 Species denotes SARS-CoV-2 Tax:2697049
247 12284-12295 Species denotes coronavirus Tax:11118
248 12346-12356 Species denotes SARS-CoV-2 Tax:2697049
249 12270-12274 Species denotes OC43 Tax:31631
259 12602-12611 Gene denotes S-protein Gene:43740568
260 12987-12991 Gene denotes DPB1 Gene:3115
261 13009-13013 Gene denotes DQA1 Gene:3117
262 13014-13018 Gene denotes DQB1 Gene:3119
263 13039-13043 Gene denotes DRB1 Gene:3123
264 12454-12464 Species denotes SARS-CoV-2 Tax:2697049
265 13137-13147 Species denotes SARS-CoV-2 Tax:2697049
266 12550-12554 Species denotes OC43 Tax:31631
267 12708-12712 Species denotes OC43 Tax:31631
299 14740-14749 Gene denotes S-protein Gene:43740568
300 15188-15197 Gene denotes M-protein Gene:9172
301 15423-15432 Gene denotes M-protein Gene:9172
302 15047-15056 Gene denotes S-protein Gene:43740568
303 15581-15582 Gene denotes M Gene:43740571
304 14125-14135 Species denotes SARS-CoV-2 Tax:2697049
305 14281-14291 Species denotes SARS-CoV-2 Tax:2697049
306 14377-14387 Species denotes SARS-CoV-2 Tax:2697049
307 14519-14529 Species denotes SARS-CoV-2 Tax:2697049
308 14755-14765 Species denotes SARS-CoV-2 Tax:2697049
309 14851-14861 Species denotes SARS-CoV-2 Tax:2697049
310 15036-15046 Species denotes SARS-CoV-2 Tax:2697049
311 15203-15213 Species denotes SARS-CoV-2 Tax:2697049
312 15299-15309 Species denotes SARS-CoV-2 Tax:2697049
313 15570-15580 Species denotes SARS-CoV-2 Tax:2697049
314 15737-15747 Species denotes SARS-CoV-2 Tax:2697049
315 15833-15843 Species denotes SARS-CoV-2 Tax:2697049
316 15989-15999 Species denotes SARS-CoV-2 Tax:2697049
317 14192-14196 Species denotes OC43 Tax:31631
318 14293-14297 Species denotes OC43 Tax:31631
319 14348-14352 Species denotes OC43 Tax:31631
320 14609-14613 Species denotes OC43 Tax:31631
321 14767-14771 Species denotes OC43 Tax:31631
322 14822-14826 Species denotes OC43 Tax:31631
323 15131-15135 Species denotes OC43 Tax:31631
324 15215-15219 Species denotes OC43 Tax:31631
325 15270-15274 Species denotes OC43 Tax:31631
326 15665-15669 Species denotes OC43 Tax:31631
327 15749-15753 Species denotes OC43 Tax:31631
328 15804-15808 Species denotes OC43 Tax:31631
329 16084-16088 Species denotes OC43 Tax:31631
339 13417-13421 Gene denotes RdRp Gene:43740578
340 13428-13436 Gene denotes helicase Gene:164045
341 13995-14004 Gene denotes S-protein Gene:43740568
342 13976-13977 Gene denotes M Gene:43740571
343 13342-13352 Species denotes SARS-CoV-2 Tax:2697049
344 13951-13961 Species denotes SARS-CoV-2 Tax:2697049
345 13364-13368 Species denotes OC43 Tax:31631
346 13790-13794 Species denotes OC43 Tax:31631
347 14110-14114 Species denotes OC43 Tax:31631
357 16566-16575 Gene denotes S-protein Gene:43740568
358 17212-17221 Gene denotes M-protein Gene:9172
359 17319-17328 Gene denotes S-protein Gene:43740568
360 16679-16689 Species denotes SARS-CoV-2 Tax:2697049
361 16999-17009 Species denotes SARS–CoV–2 Tax:2697049
362 17600-17613 Species denotes coronaviruses Tax:11118
363 17673-17683 Species denotes SARS-CoV-2 Tax:2697049
364 16701-16705 Species denotes OC43 Tax:31631
365 17021-17025 Species denotes OC43 Tax:31631
373 17768-17785 Species denotes novel coronavirus Tax:2697049
374 17786-17796 Species denotes SARS-CoV-2 Tax:2697049
375 17855-17868 Species denotes coronaviruses Tax:11118
376 18009-18022 Species denotes coronaviruses Tax:11118
377 18174-18184 Species denotes SARS-CoV-2 Tax:2697049
378 18226-18236 Species denotes SARS-CoV-2 Tax:2697049
379 17941-17951 Disease denotes infections MESH:D007239
400 18439-18444 Gene denotes HLA-B Gene:3106
401 18449-18454 Gene denotes HLA-C Gene:3107
402 18550-18553 Gene denotes CD8 Gene:925
403 18585-18588 Gene denotes CD4 Gene:920
404 19105-19114 Gene denotes S-protein Gene:43740568
405 19193-19202 Gene denotes S-protein Gene:43740568
406 18357-18367 Species denotes SARS-CoV-2 Tax:2697049
407 18482-18492 Species denotes SARS-CoV-2 Tax:2697049
408 18643-18653 Species denotes SARS-CoV-2 Tax:2697049
409 18703-18716 Species denotes coronaviruses Tax:11118
410 18740-18758 Species denotes beta-coronaviruses Tax:694002
411 18830-18840 Species denotes SARS-CoV-2 Tax:2697049
412 18894-18904 Species denotes SARS-CoV-2 Tax:2697049
413 18917-18930 Species denotes coronaviruses Tax:11118
414 19020-19033 Species denotes coronaviruses Tax:11118
415 19241-19251 Species denotes SARS-CoV-2 Tax:2697049
416 19285-19304 Species denotes Mycobacterium bovis Tax:1765
417 19425-19435 Species denotes SARS-CoV-2 Tax:2697049
418 19497-19507 Species denotes SARS-CoV-2 Tax:2697049
419 19365-19377 Disease denotes tuberculosis MESH:D014376
436 20340-20344 Gene denotes TLR4 Gene:21898
437 19607-19620 Species denotes coronaviruses Tax:11118
438 19688-19693 Species denotes human Tax:9606
439 19766-19774 Species denotes SARS-CoV Tax:694009
440 19778-19788 Species denotes SARS-CoV-2 Tax:2697049
441 19794-19802 Species denotes MERS-CoV Tax:1335626
442 19847-19850 Species denotes dog Tax:9615
443 19868-19874 Species denotes camels Tax:9837
444 20131-20142 Species denotes coronavirus Tax:11118
445 20202-20206 Species denotes dogs Tax:9615
446 20208-20214 Species denotes camels Tax:9837
447 20240-20246 Species denotes humans Tax:9606
448 20271-20277 Species denotes murine Tax:10090
449 20365-20370 Species denotes human Tax:9606
450 19979-19983 Species denotes OC43 Tax:31631
451 19821-19829 Disease denotes zoonotic MESH:D015047
457 20576-20589 Species denotes coronaviruses Tax:11118
458 20953-20961 Species denotes patients Tax:9606
459 21069-21077 Species denotes patients Tax:9606
460 20967-20986 Disease denotes respiratory disease MESH:D012140
461 21083-21103 Disease denotes respiratory diseases MESH:D012140
466 21598-21614 Gene denotes β2-microglobulin Gene:567
467 22138-22155 Species denotes Trypanosoma cruzi Tax:5693
468 22093-22098 Species denotes human Tax:9606
469 21703-21712 Chemical denotes netMHCpan
471 22618-22636 Disease denotes anchor amino acids MESH:D000592
475 23144-23154 Species denotes SARS-CoV-2 Tax:2697049
476 23239-23249 Species denotes SARS-CoV-2 Tax:2697049
477 23542-23552 Species denotes SARS-CoV-2 Tax:2697049
481 23805-23812 Species denotes patient Tax:9606
482 23874-23882 Species denotes patients Tax:9606
483 23897-23907 Species denotes SARS-CoV-2 Tax:2697049
487 24294-24304 Species denotes SARS-CoV-2 Tax:2697049
488 24323-24341 Species denotes beta-coronaviruses Tax:694002
489 24370-24379 Species denotes SARS-CoV2 Tax:2697049
500 25511-25520 Gene denotes S-protein Gene:43740568
501 24553-24562 Species denotes SARS-CoV2 Tax:2697049
502 24752-24757 Species denotes human Tax:9606
503 25153-25166 Species denotes coronaviruses Tax:11118
504 25212-25236 Species denotes Human Gammaherpesvirus 4 Tax:10376
505 25238-25249 Species denotes Rotavirus A Tax:28875
506 25255-25279 Species denotes Human alphaherpesvirus 3 Tax:10335
507 25378-25386 Species denotes SARS-CoV Tax:694009
508 25469-25479 Species denotes SARS-CoV-2 Tax:2697049
509 25167-25171 Species denotes OC43 Tax:31631
514 25651-25660 Species denotes SARS-CoV2 Tax:2697049
515 25610-25613 Gene denotes MHC Gene:3107
516 25745-25754 Chemical denotes netMHCpan
517 25771-25782 Chemical denotes netMHCIIpan
519 26153-26163 Species denotes SARS-CoV-2 Tax:2697049
522 26958-26959 Gene denotes M Gene:43740571
523 26758-26768 Species denotes SARS-CoV-2 Tax:2697049
527 27237-27247 Species denotes SARS-CoV-2 Tax:2697049
528 27359-27369 Species denotes SARS-CoV-2 Tax:2697049
529 30469-30479 Species denotes SARS-CoV-2 Tax:2697049
531 30617-30627 Species denotes SARS-CoV-2 Tax:2697049
533 33170-33180 Species denotes SARS-CoV-2 Tax:2697049