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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 681-687 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T2 970-981 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T3 1086-1090 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T4 1265-1271 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T5 1305-1312 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T6 1414-1419 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T7 2635-2640 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T8 2838-2842 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T9 2997-3001 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T10 3217-3221 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T11 3619-3630 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T12 3664-3668 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T13 3924-3932 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T14 4176-4185 Body_part denotes leukocyte http://purl.org/sig/ont/fma/fma62852
T15 4195-4198 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T16 4430-4438 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T17 4582-4586 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T18 4645-4649 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T19 4698-4706 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T20 4813-4817 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T21 5006-5010 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T22 5184-5188 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T23 6138-6141 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T24 6294-6298 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T25 6382-6387 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T26 6545-6549 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T27 6591-6595 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T28 7081-7087 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T29 7166-7170 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T30 7310-7314 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T31 7784-7794 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T32 7843-7854 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T33 7918-7928 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T34 8114-8124 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T35 8257-8267 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T36 8302-8311 Body_part denotes aminoacid http://purl.org/sig/ont/fma/fma82739
T37 8692-8695 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T38 8915-8926 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T39 9025-9028 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T40 9356-9367 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T41 9550-9559 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T42 9625-9634 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T43 9733-9744 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T44 10025-10032 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T45 10473-10481 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T46 10587-10595 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T47 10612-10618 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T48 10843-10850 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T49 10940-10950 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T50 11617-11620 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T51 11729-11733 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T52 11778-11785 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T53 11880-11883 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T54 12060-12070 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T55 12102-12109 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T56 12134-12140 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T57 12141-12151 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T58 12318-12329 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T59 12502-12509 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T60 12510-12522 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T61 12896-12900 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T62 13055-13066 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T63 13361-13372 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T64 14027-14035 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T65 14054-14059 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T66 14255-14261 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T67 14377-14388 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T68 14433-14439 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T69 14529-14535 Body_part denotes Genome http://purl.org/sig/ont/fma/fma84116
T70 14745-14748 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T71 14940-14943 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T72 14996-15006 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T73 15111-15115 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T74 15134-15144 Body_part denotes Amino acid http://purl.org/sig/ont/fma/fma82739
T75 15297-15307 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T76 15329-15336 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T77 15790-15800 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T78 15836-15842 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T79 15854-15865 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T80 15968-15971 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T81 16011-16019 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T82 16162-16166 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T83 16504-16511 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T84 16680-16687 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T85 16862-16873 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T86 17205-17209 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T87 17284-17288 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T88 17894-17898 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T89 18730-18734 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T90 18868-18872 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T91 19237-19241 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T92 19318-19323 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T93 19512-19522 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T94 19675-19678 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T95 19741-19744 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T96 20315-20320 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T97 20415-20419 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T98 20530-20537 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T99 20765-20772 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T100 21517-21520 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T101 21771-21774 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T102 21901-21905 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T103 22425-22436 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T104 22744-22751 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T105 22862-22866 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T106 23348-23352 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T107 23456-23460 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T108 24130-24136 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T109 24608-24612 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T110 24809-24813 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T111 25180-25184 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T112 25273-25277 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T113 25300-25305 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T114 25907-25911 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T115 26047-26055 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T116 26216-26220 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T117 26325-26329 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T118 26862-26867 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T119 26952-26956 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T120 27114-27124 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T121 28581-28591 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T122 28760-28767 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T123 28790-28800 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T124 28984-28988 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T125 29002-29009 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T126 29172-29179 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T127 29286-29289 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T128 29300-29303 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T129 29421-29433 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T130 29528-29535 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T131 29680-29687 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T132 29775-29787 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T133 29875-29882 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T134 29924-29931 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T135 29973-29980 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T136 30071-30078 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T137 30326-30333 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 9382-9391 Body_part denotes extension http://purl.obolibrary.org/obo/UBERON_2000106
T2 23348-23352 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T69 25628-25636 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T1 0-8 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 75-82 Disease denotes COVID19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 553-561 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T4 564-573 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T5 594-602 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 734-742 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 1064-1072 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 1561-1569 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 1685-1693 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T10 1770-1778 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 1940-1948 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T12 2113-2121 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T13 2260-2267 Disease denotes sterile http://purl.obolibrary.org/obo/MONDO_0005047
T14 2396-2405 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T15 2476-2484 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 2532-2541 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T17 2764-2772 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 3119-3127 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 3130-3139 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T20 3533-3541 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 3638-3646 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 3796-3804 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 3870-3878 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 3913-3921 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 4377-4385 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 4495-4503 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 4717-4725 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 4738-4754 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T29 4922-4938 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T30 6114-6130 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094
T31 6563-6571 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 6626-6634 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 6839-6847 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 7541-7549 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 9293-9301 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 10151-10159 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 10660-10668 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 10684-10695 Disease denotes common cold http://purl.obolibrary.org/obo/MONDO_0005709
T39 11388-11396 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 12091-12099 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 12785-12793 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 14888-14896 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 15729-15737 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 15825-15833 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 17529-17537 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 17716-17724 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 17883-17891 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 18468-18476 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 18503-18512 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T50 18759-18767 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 19133-19141 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 21180-21188 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 22052-22060 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 23068-23078 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T55 23145-23155 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T56 23219-23230 Disease denotes common cold http://purl.obolibrary.org/obo/MONDO_0005709
T57 23323-23331 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T58 23625-23634 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T59 23649-23657 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 23719-23727 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 24087-24095 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 24303-24322 Disease denotes autoimmune diseases http://purl.obolibrary.org/obo/MONDO_0007179
T63 24332-24355 Disease denotes Guillain-Barré syndrome http://purl.obolibrary.org/obo/MONDO_0016218
T64 24595-24603 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 25197-25205 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T66 25387-25395 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T67 25513-25521 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 25561-25569 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T70 25803-25811 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T71 25814-25823 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T72 25924-25932 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T73 25961-25969 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T74 25972-25981 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T75 26234-26242 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T76 27181-27189 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T77 27204-27212 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T78 28909-28917 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T79 30887-30895 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 55-63 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptides
T2 350-351 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 438-442 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T4 592-593 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 896-903 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T6 948-956 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T7 967-969 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T8 1014-1016 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T9 1084-1090 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T10 1412-1419 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T11 1460-1467 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T12 1517-1525 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T13 1866-1867 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 2008-2011 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T15 2030-2031 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 2633-2640 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T17 2821-2826 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T18 2836-2842 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T19 2995-3001 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T20 3215-3221 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T21 3259-3266 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T22 3341-3346 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T23 3553-3556 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T24 3662-3668 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T25 4170-4175 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T26 4481-4482 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 4565-4570 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T28 4580-4586 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T29 4643-4649 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T30 4756-4758 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T31 4779-4782 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T32 4811-4817 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T33 4989-4994 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T34 5004-5010 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T35 5154-5161 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T36 5182-5188 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T37 5301-5306 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T38 5337-5339 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T39 5369-5373 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T40 5468-5469 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 5818-5825 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T42 6080-6081 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 6108-6113 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T44 6131-6136 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T45 6222-6230 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T46 6277-6282 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T47 6292-6298 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T48 6360-6367 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T49 6382-6387 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T50 6481-6482 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 6490-6494 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T52 6543-6549 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T53 6589-6595 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T54 6784-6785 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 7028-7029 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 7123-7130 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T57 7164-7170 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T58 7308-7314 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T59 7359-7360 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 7368-7372 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T61 7513-7514 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T62 7753-7754 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 7777-7779 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T64 7782-7783 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T65 8299-8301 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T66 8479-8486 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptide
T67 8560-8568 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T68 8717-8719 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T69 8760-8767 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T70 9330-9331 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 9353-9355 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T72 9530-9532 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T73 9623-9624 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 9682-9689 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T75 9974-9982 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptides
T76 10069-10070 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 10365-10366 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 10430-10433 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T79 10490-10497 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T80 10629-10634 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T81 10728-10733 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T82 10800-10806 http://purl.obolibrary.org/obo/UBERON_0001630 denotes MUSCLE
T83 10800-10806 http://purl.obolibrary.org/obo/UBERON_0005090 denotes MUSCLE
T84 10800-10806 http://www.ebi.ac.uk/efo/EFO_0000801 denotes MUSCLE
T85 10800-10806 http://www.ebi.ac.uk/efo/EFO_0001949 denotes MUSCLE
T86 10828-10830 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T87 11048-11055 http://purl.obolibrary.org/obo/CLO_0003453 denotes gap per
T88 11111-11119 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T89 11302-11305 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T90 11342-11347 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T91 11565-11572 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T92 11599-11611 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Homo sapiens
T93 11727-11733 http://purl.obolibrary.org/obo/CL_0000236 denotes B-cell
T94 11763-11764 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 12127-12128 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T96 12400-12402 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T97 12493-12501 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T98 12671-12679 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptides
T99 12718-12719 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 12750-12758 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T101 12820-12827 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T102 12856-12863 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T103 12894-12900 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T104 12982-12990 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T105 13052-13054 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T106 13226-13227 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 13245-13253 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T108 13293-13294 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 13358-13360 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T110 13403-13413 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing is
T111 13603-13611 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T112 13682-13690 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T113 13692-13694 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T114 13828-13830 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T115 13909-13910 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 13989-13990 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T117 13998-14003 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T118 14054-14059 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T119 14075-14079 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T120 14163-14165 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T121 14183-14185 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T122 14218-14219 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 14249-14254 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T124 14333-14334 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T125 14427-14432 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T126 14612-14617 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T127 14679-14682 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T128 14761-14762 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T129 15109-15115 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T130 15273-15275 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T131 15429-15431 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T132 16122-16123 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T133 16141-16148 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T134 16160-16166 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T135 16207-16212 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T136 16282-16283 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T137 16466-16468 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T138 16585-16588 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes Pan
T139 16792-16795 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T140 16818-16819 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T141 17021-17024 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T142 17099-17104 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T143 17203-17209 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T144 17282-17288 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T145 17348-17356 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T146 17705-17714 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T147 17705-17714 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T148 17726-17728 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T149 17730-17735 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T150 17774-17778 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1: 1
T151 17803-17815 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Homo sapiens
T152 17892-17898 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T153 17958-17964 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T154 18109-18114 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T155 18236-18244 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T156 18381-18389 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T157 18546-18549 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T158 18585-18587 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T159 18585-18587 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T160 18634-18635 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T161 18728-18734 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T162 18866-18872 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T163 18938-18939 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T164 18964-18965 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T165 19004-19006 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T166 19221-19224 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T167 19230-19233 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T168 19235-19241 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T169 19258-19260 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T170 19283-19290 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T171 19318-19323 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T172 19370-19374 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T173 19375-19383 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T174 19554-19561 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T175 19723-19731 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T176 19745-19746 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T177 19747-19749 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T178 19752-19753 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T179 19897-19905 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T180 20160-20161 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T181 20178-20186 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T182 20238-20246 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T183 20315-20320 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T184 20337-20339 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T185 20398-20403 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T186 20413-20419 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T187 20961-20969 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T188 20971-20979 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T189 21210-21211 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T190 21317-21321 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T191 21439-21441 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T192 21531-21534 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T193 21775-21782 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T194 21810-21815 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T195 21853-21854 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T196 21899-21905 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T197 22094-22099 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T198 22242-22249 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T199 22283-22291 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T200 22357-22364 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T201 22393-22400 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T202 22496-22497 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T203 22503-22510 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T204 22539-22540 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T205 22808-22811 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T206 22860-22866 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T207 22881-22884 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T208 22963-22968 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T209 23088-23093 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T210 23217-23218 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T211 23454-23460 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T212 23544-23545 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T213 23546-23549 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T214 23592-23593 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T215 23803-23809 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T216 23834-23835 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T217 23836-23839 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T218 23942-23945 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T219 24124-24129 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T220 24264-24265 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T221 24569-24572 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T222 24593-24594 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T223 24604-24612 http://purl.obolibrary.org/obo/CLO_0001272 denotes 2 T cell
T224 24613-24617 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T225 24807-24813 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T226 24855-24858 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T227 24901-24909 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T228 25012-25019 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T229 25046-25049 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T230 25116-25123 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T231 25144-25145 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T232 25178-25184 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T233 25271-25277 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T234 25298-25305 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T235 25905-25911 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T236 26035-26036 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T237 26214-26220 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T238 26308-26313 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T239 26323-26329 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T240 26705-26706 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T241 26860-26867 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T242 26888-26889 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T243 26950-26956 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T244 27075-27077 http://purl.obolibrary.org/obo/CLO_0050050 denotes s1
T245 27086-27088 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T246 27200-27202 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T247 27200-27202 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T248 27265-27267 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T249 27281-27288 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T250 28296-28299 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T251 28430-28431 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T252 28481-28484 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T253 28984-28988 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T254 29104-29107 http://purl.obolibrary.org/obo/CLO_0001003 denotes 163
T255 29435-29437 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T256 29449-29451 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T257 29449-29451 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T258 29766-29774 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T259 30505-30507 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T260 30513-30515 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T261 30550-30552 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T262 30553-30555 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T263 30557-30559 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T264 30561-30563 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T265 30571-30573 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T266 30635-30638 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes Pan
T267 30678-30683 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T268 30897-30902 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T269 31006-31010 http://purl.obolibrary.org/obo/CLO_0001407 denotes 5 2
T270 31641-31645 http://purl.obolibrary.org/obo/CLO_0053794 denotes 4 1

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2 0-10 Species denotes SARS-CoV-2 Tax:2697049
3 75-82 Disease denotes COVID19 MESH:C000657245
15 594-604 Species denotes SARS-CoV-2 Tax:2697049
16 630-635 Species denotes CoV-2 Tax:2697049
17 734-744 Species denotes SARS-CoV-2 Tax:2697049
18 1064-1074 Species denotes SARS-CoV-2 Tax:2697049
19 1114-1119 Species denotes CoV-2 Tax:2697049
20 1334-1345 Species denotes coronavirus Tax:11118
21 1474-1481 Species denotes new CoV Tax:2697049
22 1685-1695 Species denotes SARS-CoV-2 Tax:2697049
23 1561-1571 Species denotes SARS-CoV-2 Tax:2697049
24 475-483 Disease denotes infected MESH:D007239
25 553-573 Disease denotes SARS-CoV-2 infection MESH:C000657245
37 1940-1950 Species denotes SARS-CoV-2 Tax:2697049
38 2113-2123 Species denotes SARS-CoV-2 Tax:2697049
39 2454-2467 Species denotes coronaviruses Tax:11118
40 2476-2484 Species denotes SARS-CoV Tax:694009
41 2666-2672 Species denotes people Tax:9606
42 2764-2774 Species denotes SARS-CoV-2 Tax:2697049
43 1770-1778 Disease denotes COVID-19 MESH:C000657245
44 2396-2405 Disease denotes infection MESH:D007239
45 2491-2495 Disease denotes MERS MESH:D018352
46 2532-2541 Disease denotes infection MESH:D007239
47 3119-3139 Disease denotes SARS-CoV-2 infection MESH:C000657245
63 3533-3543 Species denotes SARS-CoV-2 Tax:2697049
64 3638-3648 Species denotes SARS-CoV-2 Tax:2697049
65 3796-3806 Species denotes SARS-CoV-2 Tax:2697049
66 3848-3861 Species denotes coronaviruses Tax:11118
67 3870-3878 Species denotes SARS-CoV Tax:694009
68 3913-3923 Species denotes SARS-CoV-2 Tax:2697049
69 4326-4339 Species denotes coronaviruses Tax:11118
70 4377-4385 Species denotes SARS-CoV Tax:694009
71 4495-4505 Species denotes SARS-CoV-2 Tax:2697049
72 4717-4727 Species denotes SARS-CoV-2 Tax:2697049
73 4170-4175 Species denotes human Tax:9606
74 3181-3189 Disease denotes infected MESH:D007239
75 4392-4396 Disease denotes MERS MESH:D018352
76 4738-4754 Disease denotes viral infections MESH:D001102
77 4922-4938 Disease denotes viral infections MESH:D001102
81 5167-5180 Species denotes coronaviruses Tax:11118
82 5796-5825 Species denotes replication competent viruses Tax:353210
83 6108-6136 Species denotes human immunodeficiency virus Tax:12721
90 6563-6573 Species denotes SARS-CoV-2 Tax:2697049
91 6626-6636 Species denotes SARS-CoV-2 Tax:2697049
92 6839-6849 Species denotes SARS-CoV-2 Tax:2697049
93 6851-6856 Species denotes CoV-2 Tax:2697049
94 7070-7075 Species denotes CoV-2 Tax:2697049
95 7183-7188 Species denotes CoV-2 Tax:2697049
97 7541-7551 Species denotes SARS-CoV-2 Tax:2697049
101 9293-9303 Species denotes SARS-CoV-2 Tax:2697049
102 9550-9559 Chemical denotes glutamine MESH:D005973
103 9625-9634 Chemical denotes glutamine MESH:D005973
118 10100-10111 Species denotes coronavirus Tax:11118
119 10151-10161 Species denotes SARS-CoV-2 Tax:2697049
120 10186-10197 Species denotes coronavirus Tax:11118
121 10434-10445 Species denotes coronavirus Tax:11118
122 10515-10530 Species denotes Betacoronavirus Tax:694002
123 10538-10554 Species denotes beta-coronavirus Tax:694002
124 10629-10634 Species denotes human Tax:9606
125 10635-10648 Species denotes coronaviruses Tax:11118
126 10660-10668 Species denotes SARS-CoV Tax:694009
127 10670-10678 Species denotes MERS-CoV Tax:1335626
128 10728-10745 Species denotes human-coronavirus Tax:694448
129 10716-10720 Species denotes 229E Tax:11137
130 10691-10695 Disease denotes cold MESH:D000067390
131 10722-10726 CellLine denotes HKU1 CVCL:B526
133 11194-11199 Species denotes CoV-2 Tax:2697049
141 11287-11300 Species denotes coronaviruses Tax:11118
142 11306-11317 Species denotes coronavirus Tax:11118
143 11319-11336 Species denotes betacoronaviruses Tax:694002
144 11342-11347 Species denotes human Tax:9606
145 11348-11361 Species denotes coronaviruses Tax:11118
146 11388-11398 Species denotes SARS-CoV-2 Tax:2697049
147 11599-11611 Species denotes Homo sapiens Tax:9606
149 11985-11990 Species denotes CoV-2 Tax:2697049
153 12524-12525 Gene denotes M Gene:43740571
154 12034-12039 Species denotes CoV-2 Tax:2697049
155 12091-12101 Species denotes SARS-CoV-2 Tax:2697049
159 12785-12795 Species denotes SARS-CoV-2 Tax:2697049
160 14249-14254 Species denotes human Tax:9606
161 14427-14432 Species denotes human Tax:9606
163 14463-14468 Species denotes CoV-2 Tax:2697049
166 14888-14898 Species denotes SARS-CoV-2 Tax:2697049
167 14624-14632 Disease denotes infected MESH:D007239
170 15322-15328 Gene denotes ORF1ab Gene:43740578
171 15415-15420 Species denotes CoV-2 Tax:2697049
173 15691-15696 Species denotes CoV-2 Tax:2697049
178 15949-15955 Gene denotes ORF1ab Gene:43740578
179 15998-16006 Gene denotes Helicase Gene:164045
180 15729-15739 Species denotes SARS-CoV-2 Tax:2697049
181 15825-15835 Species denotes SARS-CoV-2 Tax:2697049
184 16537-16548 Species denotes Coronavirus Tax:11118
185 16589-16600 Species denotes Coronavirus Tax:11118
206 17736-17778 Gene denotes coronavirus 229E: 1, Alphacoronavirus 1: 1
207 16712-16723 Species denotes coronavirus Tax:11118
208 16796-16807 Species denotes coronavirus Tax:11118
209 17025-17036 Species denotes coronavirus Tax:11118
210 17058-17074 Species denotes beta-coronavirus Tax:694002
211 17099-17116 Species denotes human coronavirus Tax:694448
212 17372-17377 Species denotes CoV-2 Tax:2697049
213 17529-17537 Species denotes SARS-CoV Tax:694009
214 17716-17724 Species denotes SARS-CoV Tax:694009
215 17803-17815 Species denotes Homo sapiens Tax:9606
216 17883-17891 Species denotes SARS-CoV Tax:694009
217 17958-17964 Species denotes humans Tax:9606
218 18033-18044 Species denotes coronavirus Tax:11118
219 18109-18114 Species denotes human Tax:9606
220 18177-18193 Species denotes beta-coronavirus Tax:694002
221 18344-18355 Species denotes Coronavirus Tax:11118
222 18468-18478 Species denotes SARS-CoV-2 Tax:2697049
223 18524-18537 Species denotes coronaviruses Tax:11118
224 18550-18561 Species denotes coronavirus Tax:11118
225 18503-18512 Disease denotes infection MESH:D007239
230 18636-18641 Species denotes CoV-2 Tax:2697049
231 18759-18769 Species denotes SARS-CoV-2 Tax:2697049
232 18940-18945 Species denotes CoV-2 Tax:2697049
233 19133-19143 Species denotes SARS-CoV-2 Tax:2697049
239 19221-19224 Gene denotes CD4 Gene:920
240 19230-19233 Gene denotes CD8 Gene:925
241 19741-19746 Gene denotes HLA-B Gene:3106
242 20260-20278 Chemical denotes dimethyl sulfoxide MESH:D004121
243 20280-20284 Chemical denotes DMSO MESH:D004121
250 20659-20664 Species denotes CoV-2 Tax:2697049
251 21180-21190 Species denotes SARS-CoV-2 Tax:2697049
252 21771-21782 Species denotes DNA viruses Tax:2080735
253 21797-21815 Species denotes Epstein Barr Virus Tax:10376
254 22052-22062 Species denotes SARS-CoV-2 Tax:2697049
255 22094-22099 Species denotes human Tax:9606
280 22788-22799 Species denotes coronavirus Tax:11118
281 22963-22980 Species denotes human coronavirus Tax:694448
282 23088-23093 Species denotes human Tax:9606
283 23094-23107 Species denotes coronaviruses Tax:11118
284 23195-23208 Species denotes coronaviruses Tax:11118
285 23323-23333 Species denotes SARS-CoV-2 Tax:2697049
286 23421-23432 Species denotes coronavirus Tax:11118
287 23550-23561 Species denotes coronavirus Tax:11118
288 23649-23659 Species denotes SARS-CoV-2 Tax:2697049
289 23702-23713 Species denotes coronavirus Tax:11118
290 23719-23727 Species denotes SARS-CoV Tax:694009
291 23754-23771 Species denotes new coronaviruses Tax:2697049
292 23803-23809 Species denotes humans Tax:9606
293 23840-23851 Species denotes coronavirus Tax:11118
294 23946-23957 Species denotes coronavirus Tax:11118
295 24087-24097 Species denotes SARS-CoV-2 Tax:2697049
296 24124-24129 Species denotes human Tax:9606
297 24229-24242 Species denotes coronaviruses Tax:11118
298 23068-23078 Disease denotes infections MESH:D007239
299 23145-23155 Disease denotes infections MESH:D007239
300 23226-23230 Disease denotes cold MESH:D000067390
301 23625-23634 Disease denotes infection MESH:D007239
302 23734-23738 Disease denotes MERS MESH:D018352
303 24303-24322 Disease denotes autoimmune diseases MESH:D001327
309 24431-24436 Species denotes CoV-2 Tax:2697049
310 24595-24605 Species denotes SARS-CoV-2 Tax:2697049
311 25197-25207 Species denotes SARS-CoV-2 Tax:2697049
312 24524-24532 Disease denotes infected MESH:D007239
313 25387-25395 Disease denotes COVID-19 MESH:C000657245
325 25513-25523 Species denotes SARS-CoV-2 Tax:2697049
326 25561-25571 Species denotes SARS-CoV-2 Tax:2697049
327 25628-25638 Species denotes SARS-CoV-2 Tax:2697049
328 25924-25934 Species denotes SARS-CoV-2 Tax:2697049
329 26234-26244 Species denotes SARS-CoV-2 Tax:2697049
330 26345-26350 Species denotes CoV-2 Tax:2697049
331 26721-26734 Species denotes coronaviruses Tax:11118
332 26812-26825 Species denotes coronaviruses Tax:11118
333 26904-26917 Species denotes coronaviruses Tax:11118
334 25803-25823 Disease denotes SARS-CoV-2 infection MESH:C000657245
335 25961-25981 Disease denotes SARS-CoV-2 infection MESH:C000657245
338 27181-27191 Species denotes SARS-CoV-2 Tax:2697049
339 27204-27214 Species denotes SARS-CoV-2 Tax:2697049
352 27823-27824 Gene denotes M Gene:43740571
353 27803-27804 Gene denotes M Gene:43740571
354 27750-27751 Gene denotes M Gene:43740571
355 27730-27731 Gene denotes M Gene:43740571
356 27679-27680 Gene denotes M Gene:43740571
357 27659-27660 Gene denotes M Gene:43740571
358 27587-27588 Gene denotes M Gene:43740571
359 27567-27568 Gene denotes M Gene:43740571
360 27474-27475 Gene denotes M Gene:43740571
361 27451-27452 Gene denotes M Gene:43740571
362 27424-27425 Gene denotes M Gene:43740571
363 27401-27402 Gene denotes M Gene:43740571
365 28516-28521 Species denotes CoV-2 Tax:2697049
547 28605-28611 Gene denotes ORF1ab Gene:43740578
574 29036-29041 Gene denotes ORF1a Gene:43740578
575 29087-29092 Gene denotes ORF1a Gene:43740578
576 29191-29200 Gene denotes nsp2 nsp3 Gene:43740578
577 29225-29229 Gene denotes nsp6 Gene:43740578
578 29230-29233 Gene denotes nsp Gene:43740578
579 29235-29238 Gene denotes nsp Gene:43740578
580 29240-29244 Gene denotes nsp9 Gene:43740578
581 29245-29250 Gene denotes nsp10 Gene:43740578
582 29251-29256 Gene denotes nsp11 Gene:43740578
583 29257-29334 Gene denotes ORF1ab 13468 21555 pp1ab RNA-dependent RNA polymerase Canonical helicase Gene:55354
584 29501-29506 Gene denotes ORF3a Gene:43740569
585 29522-29527 Gene denotes ORF3a Gene:43740569
586 29550-29555 Gene denotes ORF3a Gene:43740569
587 29602-29607 Gene denotes ORF3a Gene:43740569
588 29850-29854 Gene denotes ORF6 Gene:43740572
589 29870-29874 Gene denotes ORF6 Gene:43740572
590 29995-30000 Gene denotes ORF7b Gene:43740574
591 30248-30253 Gene denotes ORF10 Gene:43740576
592 30093-30097 Gene denotes ORF8 Gene:43740577
593 30066-30070 Gene denotes ORF8 Gene:43740577
594 30046-30050 Gene denotes ORF8 Gene:43740577
595 30320-30325 Gene denotes ORF10 Gene:43740576
596 30299-30304 Gene denotes ORF10 Gene:43740576
597 29918-29923 Gene denotes ORF7a Gene:43740573
598 29897-29902 Gene denotes ORF7a Gene:43740573
599 29749-29750 Gene denotes M Gene:43740571
601 28909-28919 Species denotes SARS-CoV-2 Tax:2697049
603 30446-30451 Species denotes CoV-2 Tax:2697049
607 30887-30895 Species denotes SARS-CoV Tax:694009
608 30897-30902 Species denotes Human Tax:9606
609 30910-30921 Species denotes Coronavirus Tax:11118
614 30619-30630 Species denotes coronavirus Tax:11118
615 30639-30650 Species denotes coronavirus Tax:11118
616 30656-30671 Species denotes Betacoronavirus Tax:694002
617 30678-30695 Species denotes Human coronavirus Tax:694448

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
6114-6130 Phenotype denotes immunodeficiency http://purl.obolibrary.org/obo/HP_0002721|http://purl.obolibrary.org/obo/HP_0002960
24303-24322 Phenotype denotes autoimmune diseases http://purl.obolibrary.org/obo/HP_0002721|http://purl.obolibrary.org/obo/HP_0002960

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 443-459 http://purl.obolibrary.org/obo/GO_0006955 denotes immune responses
T2 1580-1589 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T3 1896-1911 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T4 2745-2760 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T5 4738-4754 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T6 4922-4938 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T7 5184-5200 http://purl.obolibrary.org/obo/GO_0008037 denotes cell recognition
T8 6360-6377 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T9 6368-6377 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T10 7264-7273 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T11 9682-9699 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T12 9690-9699 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T13 12820-12837 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T14 12828-12837 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T15 16109-16118 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T16 18449-18464 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T17 18735-18750 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T18 19283-19300 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T19 19291-19300 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T20 19554-19571 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T21 19562-19571 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T22 22210-22219 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T23 22357-22374 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T24 22365-22374 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T25 22393-22410 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T26 22401-22410 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T27 29214-29224 http://purl.obolibrary.org/obo/GO_0004175 denotes proteinase

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-121 Sentence denotes SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development
T2 123-131 Sentence denotes Abstract
T3 132-335 Sentence denotes Synthetic antigens based on consensus sequences that represent circulating viral isolates are sensitive, time saving and cost-effective tools for in vitro immune monitoring and to guide immunogen design.
T4 336-520 Sentence denotes When based on a representative sequence database, such consensus sequences can effectively be used to test immune responses in exposed and infected individuals at the population level.
T5 521-838 Sentence denotes To accelerate immune studies in SARS-CoV-2 infection, we here describe a SARS-CoV-2 2020 consensus sequence (CoV-2-cons) which is based on more than 1700 viral genome entries in NCBI and encompasses all described SARS-CoV-2 open reading frames (ORF), including recently described frame-shifted and length variant ORF.
T6 839-1100 Sentence denotes Based on these sequences, we created curated overlapping peptide (OLP) lists containing between 1500 to 3000 peptides of 15 and 18 amino acids in length, overlapping by 10 or 11 residues, as ideal tools for the assessment of SARS-CoV-2-specific T cell immunity.
T7 1101-1272 Sentence denotes In addition, CoV-2-cons sequence entropy values are presented along with variant sequences to provide increased coverage of the most variable sections of the viral genome.
T8 1273-1468 Sentence denotes The identification of conserved protein fragments across the coronavirus family and the corresponding OLP facilitate the identification of T cells potentially cross-reactive with related viruses.
T9 1469-1729 Sentence denotes This new CoV-2-cons sequence, together with the peptides sets, should provide the basis for SARS-CoV-2 antigen synthesis to facilitate comparability between ex-vivo immune analyses and help to accelerate research on SARS-CoV-2 immunity and vaccine development.
T10 1731-1733 Sentence denotes 1.
T11 1734-1746 Sentence denotes Introduction
T12 1747-1951 Sentence denotes Since the start of the COVID-19 pandemic in December 2019, researchers around the world have put major efforts towards a better understanding of the immune response to its causative agent, the SARS-CoV-2.
T13 1952-2139 Sentence denotes Although an impressive amount of scientific information has been generated in a very short period of time, there remain significant gaps in our understanding of SARS-CoV-2 immune control.
T14 2140-2406 Sentence denotes In particular, it remains unclear what kind of adaptive immunity should be triggered by vaccination in order to achieve sterile immunity, or at least lead to an ameliorated disease course, in cases where vaccination cannot provide absolute protection from infection.
T15 2407-2719 Sentence denotes We know from the available literature on other coronaviruses (mainly SARS-CoV-1 and MERS) that antibodies can neutralize the infection, although these humoral responses are short lived in many individuals, and that long-lived T cells responses are present in people with less severe disease outcomes [1,2,3,4,5].
T16 2720-2958 Sentence denotes The emerging data on the immune response to SARS-CoV-2 demonstrate the essential contribution of the virus-specific T-cell responses, possibly in addition to the action of neutralizing antibodies, in viral control [3,6,7,8,9,10,11,12,13].
T17 2959-3140 Sentence denotes Thus, improved tools to assess host T cell immunity in detail are urgently needed to better identify these responses and to define their role in the outcome of SARS-CoV-2 infection.
T18 3141-3267 Sentence denotes Ex-vivo immune analyses of samples from infected individuals can identify T cell responses to specific pathogens like viruses.
T19 3268-3399 Sentence denotes Such analyses can help to better understand the role of host immunity in virus control and to guide successful vaccine development.
T20 3400-3505 Sentence denotes However, they rely on the use of the correct recall antigens that can elicit specific responses in vitro.
T21 3506-3974 Sentence denotes The urgency of the current SARS-CoV-2 pandemic has led researchers to tackle the problem of screening the 10,000 amino acids of the SARS-CoV-2 proteome for T cell responses by selecting viral sequences based on different criteria: (i) bioinformatically predicted epitopes, (ii) homology of SARS-CoV-2 sequences with epitopes defined in other coronaviruses (mainly SARS-CoV) or (iii) selecting some specific SARS-CoV-2 proteins over others [5,7,9,11,14,15,16,17,18,19].
T22 3975-4032 Sentence denotes However, all these approaches have intrinsic limitations.
T23 4033-4268 Sentence denotes Bioinformatic prediction tools are trained on sets of previously described epitopes, but since the available epitope repertoire for many human leukocyte antigen (HLA) alleles is limited, its prediction capacity is also limited [20,21].
T24 4269-4439 Sentence denotes Inferences based on epitope sequence homology with other coronaviruses are hampered because past studies on SARS-CoV-1 and MERS only included few selected viral proteins.
T25 4440-4596 Sentence denotes This is of concern, since screening only a part of the SARS-CoV-2 proteome will potentially miss an important portion of the virus-specific T cell response.
T26 4597-4760 Sentence denotes Indeed, recent data indicate the existence of T cell responses against structural and non-structural proteins [5,9] for SARS-CoV-2 and other viral infections [22].
T27 4761-4953 Sentence denotes Finally, no study has considered the existence of T cell responses to epitopes encoded by open-reading frames (ORF) in alternative frames, as reported for other viral infections [23,24,25,26].
T28 4954-5181 Sentence denotes In order to reliably measure total virus-specific T cell immunity, the recall antigens used need to be as representative as possible of the worldwide viral sequences, even for genetically more stable viruses like coronaviruses.
T29 5182-5341 Sentence denotes T cell recognition of epitopes is very sensitive to mismatches and not matching the recall antigen with the autologous virus can lead to missed responses [27].
T30 5342-5519 Sentence denotes For this reason, different test antigen design strategies, trying to cope with the diversity of circulating viral isolates in a single sequence, have been developed in the past.
T31 5520-5826 Sentence denotes These strategies include central sequence designs such as Center of Tree (COT) [28,29,30,31,32], Ancestral [33,34,35,36] or Consensus sequences [29,30,31,32,35,37,38,39,40,41,42,43]; which may (Ancestral, COT) or may not (Consensus) represent naturally occurring sequences of replication competent viruses.
T32 5827-5989 Sentence denotes All these designs are sensitive to the underlying sequence database and may change over time as new sequence information on additional isolates becomes available.
T33 5990-6317 Sentence denotes Direct comparisons of these different central sequence approaches have been performed for a highly variable pathogen (human immunodeficiency virus, HIV) and shown that the different designs yielded comparable results when synthetic peptides covering these sequences were used to measure virus-specific T cell responses [42,43].
T34 6318-6499 Sentence denotes However, the additional costs in terms of peptide synthesis and cells needed for ex-vivo experiments, may not warrant inclusion of all the different variants into a single test set.
T35 6500-6759 Sentence denotes Thus, the characterization of the complete T cell responses to SARS-CoV-2 urgently needs T cell antigens that cover the whole SARS-CoV-2 proteome while covering sequence diversity, and which can be combined in different experimental set-ups and immune assays.
T36 6760-6937 Sentence denotes To this end, we created a consensus sequence to cover the genetic diversity of SARS-CoV-2 (CoV-2-cons) for all ORF, including those described in alternative open reading frames.
T37 6938-7178 Sentence denotes Given the computational ease for its initial generation and periodic updates, we designed a consensus sequence using more than 1700 CoV-2 full-genome sequences and designed overlapping peptide (OLP) sets as recall antigens in T cell assays.
T38 7179-7436 Sentence denotes The CoV-2-cons OLP sets are presented here in different designs, balancing costs for synthesis with the sensitivity of detecting T cell responses and with the intention to provide a common test antigen that will allow data comparability across laboratories.
T39 7438-7440 Sentence denotes 2.
T40 7441-7448 Sentence denotes Methods
T41 7450-7454 Sentence denotes 2.1.
T42 7455-7512 Sentence denotes Consensus Sequence ORF Generation and Entropy Calculation
T43 7513-7674 Sentence denotes A total of 1731 full-length SARS-CoV-2 sequences were downloaded from NCBI (30 April 2020, txid2697049, minimum length = 29,000 bp) and aligned using MAFFT [44].
T44 7675-7781 Sentence denotes The alignment was visually inspected and curated using Genbank NC_045512.2 as a coordinate reference [45].
T45 7782-7913 Sentence denotes A nucleotide consensus sequence was generated by keeping all nucleotides present in at least 25% of the sequences in the alignment.
T46 7914-8107 Sentence denotes The amino acid consensus sequence was then created by using NC_045512.2 annotated Open Reading Frames (ORFs) plus additional ORFs described in Finkel et al. [46] using the Biostrings R package.
T47 8108-8215 Sentence denotes Mixed nucleotide positions were either resolved if they were synonymous or flagged for downstream analysis.
T48 8216-8460 Sentence denotes Positional entropy was calculated at the amino acid level both as the standard and 22-aminoacid-normalized Shannon entropy for every ORF using Bio3d R package on the alignment [47], and afterward, the mean OLP normalized entropy was calculated.
T49 8462-8466 Sentence denotes 2.2.
T50 8467-8519 Sentence denotes Overlapping Peptide Set Design and Variability Plots
T51 8520-8721 Sentence denotes For the automated design of overlapping peptides with variable length, we used the previously described Peptgen algorithm available at the Los Alamos National Laboratories HIV Immunology database [48].
T52 8722-8829 Sentence denotes This OLP generator allows predefining peptide length and level of the desired overlap between adjacent OLP.
T53 8830-9061 Sentence denotes Peptgen is also set up to exclude from the C-terminal end of OLP certain “forbidden” amino acids (G, P, E, D, Q, N, T, S and C) that are rarely seen to serve as the C-terminal anchor position of HLA class I presented epitopes [49].
T54 9062-9258 Sentence denotes Using this optional modification can lead to length variation in the OLP set, which can be controlled by limiting the maximal length of an OLP in regions with numerous serial “forbidden” residues.
T55 9259-9466 Sentence denotes The settings used for the present SARS-CoV-2 consensus OLP design were a) OLP length of 15 or 18 amino acids, with maximal extension or truncation of up to ±3 residues to avoid forbidden C-terminal residues.
T56 9467-9542 Sentence denotes In addition, the overlap between adjacent OLP was set at 10 or 11 residues.
T57 9543-9700 Sentence denotes The no-glutamine at N-terminal setting was applied to prevent OLP starting with a glutamine residue as this can lead to complications with peptide synthesis.
T58 9701-9863 Sentence denotes For positions where two or more amino acids were present above 25% of the sequences in the alignment, two or more sequence variants for those OLPs were generated.
T59 9864-9944 Sentence denotes Sequence logos were generated for these cases with the ggseqlogo R package [50].
T60 9946-9950 Sentence denotes 2.3.
T61 9951-10000 Sentence denotes Detection of Conserved Peptides Among Coronavirus
T62 10001-10208 Sentence denotes In an attempt to detect protein fragments that are conserved across a wide range of members of the coronavirus family, full-length consensus ORF from SARS-CoV-2 were aligned with other coronavirus sequences.
T63 10209-10757 Sentence denotes Three alignments were performed based on different sequence selection criteria: (i) 50 reference sequences (RefSeq) with the lowest E-values resulting from a pBLAST search [51] using the ORF-specific consensus sequences (pan-coronavirus alignment) (ii) homologous proteins from 17 viruses representing the Betacoronavirus taxon (beta-coronavirus alignment) or, (iii) homologous proteins from the 7 full-genome sequenced human coronaviruses (including SARS-CoV, MERS-CoV, and common cold species OC43, NL63, 229E, HKU1, human-coronavirus alignment).
T64 10758-10832 Sentence denotes Selected sequences were aligned using the MUSCLE algorithm in MEGA X [52].
T65 10833-11064 Sentence denotes Conserved protein fragments were identified using BioEdit with the following criteria: minimum length of 8 amino acid, maximum average entropy of 0.25, maximum entropy per position of 1 and limiting the search to 1 gap per segment.
T66 11065-11136 Sentence denotes Sequence logos were generated for the aligned peptides on Weblogo [53].
T67 11138-11142 Sentence denotes 2.4.
T68 11143-11217 Sentence denotes Identification of Previously Described Epitopes in CoV-2 Conserved Regions
T69 11218-11519 Sentence denotes To identify previously reported epitopes in the conserved regions of coronaviruses (pan-coronavirus, betacoronaviruses, and human coronaviruses), and match them with the SARS-CoV-2 consensus sequence, searches for experimentally described epitopes were carried out in the Immune Epitope Database [54].
T70 11520-11587 Sentence denotes The search criteria were as follows: “linear peptide; blast option:
T71 11588-11598 Sentence denotes 90%; Host:
T72 11599-11681 Sentence denotes Homo sapiens; Any MHC restriction; Positive assays only; All assays; Any disease”.
T73 11682-11799 Sentence denotes The search yielded 141 epitopes, of which 14 B-cell epitopes and 2 epitopes from a hypothetical protein were removed.
T74 11800-11920 Sentence denotes The remaining identified epitopes were subsequently used to generate an epitope map of the respective conserved regions.
T75 11922-11924 Sentence denotes 3.
T76 11925-11932 Sentence denotes Results
T77 11934-11938 Sentence denotes 3.1.
T78 11939-12013 Sentence denotes Open Reading Frames and Sequence Isolates for CoV-2-Cons Sequence Creation
T79 12014-12330 Sentence denotes For creation of the CoV-2 Consensus sequence, nucleotide sequences from 1731 SARS-CoV-2 genomes were aligned and a full genome nucleotide consensus was created, 23 open reading frames (ORF) were then located in the alignment using the NC_045512.2 and the Finkel et al. [46] coordinates and translated to amino acids.
T80 12331-12475 Sentence denotes Of the 23 ORF, 12 were canonical ORF as annotated in NC_045512.2 and 11 in alternative reading frames described by Finkel et al. [46] (Table 1).
T81 12476-12652 Sentence denotes In addition, the membrane protein glycoprotein (M), is completely embedded inside an extended ORF (exORFM) without any frameshifts and was not used for separate OLP set design.
T82 12654-12658 Sentence denotes 3.2.
T83 12659-12697 Sentence denotes Overlapping Peptides (OLP) Sets Design
T84 12698-12973 Sentence denotes In order to achieve a balance between the number of peptides needed to cover the whole SARS-CoV-2 proteome, the costs for peptide synthesis and the design of peptide sets that allow for detecting T cell responses with high sensitivity, three OLP sets were designed (Table 2).
T85 12974-13191 Sentence denotes Shorter peptides (15 mers) with longer sequence overlap between adjacent OLP (11 amino acids) offer high resolution detection of responses, thus lowering the risk of missing longer epitopes located in the OLP overlap.
T86 13192-13311 Sentence denotes The consequence, however, will be a higher number of peptides to synthesize and screen, in this case a set of 2821 OLP.
T87 13312-13499 Sentence denotes When the overlap between OLP was reduced from 11 amino acids to 10, the sensitivity of OLP testing is maintained, but some longer epitopes located in the overlap of two OLP may be missed.
T88 13500-13663 Sentence denotes With this caveat in mind, an OLP set of 15-mers overlapping by 10 residues helped reduce the number of peptides needed by 560 OLP (total number OLP required 2262).
T89 13664-13804 Sentence denotes Similarly, longer peptides (18 mers) significantly reduce the number of OLP to be synthesized, but tend to reduce in vitro sensitivity [55].
T90 13805-13885 Sentence denotes This approach, with an 11 mer overlap, reduced the number of needed OLP to 1561.
T91 13886-14095 Sentence denotes The final decision for a specific design may also be driven by the assay system used for screening, an a-priori focus on fewer or more viral proteins and the available cells and funding to test immunogenicity.
T92 14096-14166 Sentence denotes The three full OLP sets with their entropies are included in Table S1.
T93 14167-14332 Sentence denotes Of note, the 15–11 OLP sequences were subjected to a search for homologies in the human genome to predict molecular mimicry events related to the autoimmune process.
T94 14333-14456 Sentence denotes A blastp search (>8aa consecutive identical amino acids per OLP) of the whole set against the human genome yielded no hits.
T95 14458-14462 Sentence denotes 3.3.
T96 14463-14535 Sentence denotes CoV-2-Cons Variability Analysis by Entropy Scores across the Full Genome
T97 14536-14673 Sentence denotes Mismatches between the sequence of in vitro antigen sets and the autologous virus in an infected individual can lead to missed responses.
T98 14674-14856 Sentence denotes This has been described for highly variable pathogens, such as HCV and HIV, and showed a direct relationship between sequence entropy and the frequency of detected responses [56,57].
T99 14857-15133 Sentence denotes Even though the variability of SARS-CoV-2 reported is substantially lower than for HIV and HCV, the sequence entropy was calculated at the amino acid level and as the mean OLP entropy in order to identify positions and OLP that may escape detection in T cell screening assays.
T100 15134-15317 Sentence denotes Amino acid positional Shannon entropies were generally highly conserved, although specific more variable positions were identified (Figure S1), linked to specific amino acid variants.
T101 15318-15407 Sentence denotes The ORF1ab protein, including three of the most variable positions, is shown in Figure 1.
T102 15408-15495 Sentence denotes In the CoV-2-cons 15–11 OLP set, mean OLP normalized entropies were overall low (Range:
T103 15496-15570 Sentence denotes 0.947–0.758) and comparable between OLP covering the canonical ORF (Range:
T104 15571-15639 Sentence denotes 0.947–0.879) and OLP matching the alternative frameshift ORF (Range:
T105 15640-15653 Sentence denotes 0.932–0.758).
T106 15655-15659 Sentence denotes 3.4.
T107 15660-15715 Sentence denotes Variant OLP Sequences to Cover CoV-2 Sequence Diversity
T108 15716-15918 Sentence denotes Based on the SARS-CoV-2 alignment used to design the consensus, only nine amino acid positions in the entire SARS-CoV-2 genome showed two amino acids present in at least 25% of the sequences (Figure 2).
T109 15919-16020 Sentence denotes Three of them were located in ORF1ab, one in the RNA polymerase and two in the Helicase sub-proteins.
T110 16021-16097 Sentence denotes None of them were located close enough to each other to affect the same OLP.
T111 16098-16251 Sentence denotes Still, the synthesis of a single consensus peptide could miss T cell responses in individuals exposed to the virus with the subdominant sequence variant.
T112 16252-16487 Sentence denotes To prevent missing responses, a small number of additional OLP containing each of the variants were generated to cover the variability of these OLP, creating an additional set of 31 different variant OLP in the 15–11 OLP set (Table 2).
T113 16489-16493 Sentence denotes 3.5.
T114 16494-16610 Sentence denotes Conserved Protein Sequences Matching Other Coronavirus Family Member and Identification of Pan-Coronavirus Sequences
T115 16611-16817 Sentence denotes In addition to variable positions, we also evaluated the presence of protein regions conserved among coronavirus species, as these may support the design of immunogen sequences for pan-coronavirus vaccines.
T116 16818-16979 Sentence denotes A total of 26 regions, ranging from 8 to 23 amino acids, were identified as being conserved in at least one of the three different sequence alignments (Table 3).
T117 16980-17127 Sentence denotes Fifteen fragments were identified in the pan-coronavirus alignment, 17 in the beta-coronavirus alignment and 12 in the human coronavirus alignment.
T118 17128-17180 Sentence denotes Seven of them were detected in all three alignments.
T119 17181-17397 Sentence denotes To identify potential T cell epitopes in these conserved regions, we searched the IEDB for described T-cell epitopes similar (>90% sequence identity) to the conserved peptides present in the CoV-2 consensus sequence.
T120 17398-17538 Sentence denotes Interestingly, the majority of the conserved regions contained several matches, most of which were described epitopes derived from SARS-CoV.
T121 17539-17639 Sentence denotes In total, 125 similar epitopes were identified, from all but two of the conserved regions (Table 3).
T122 17640-17725 Sentence denotes The similar epitopes were found to be derived from the following organisms; SARS-CoV:
T123 17726-17753 Sentence denotes 71, Human coronavirus 229E:
T124 17754-17776 Sentence denotes 1, Alphacoronavirus 1:
T125 17777-17795 Sentence denotes 1, Unknown origin:
T126 17796-17816 Sentence denotes 3, and Homo sapiens:
T127 17817-17820 Sentence denotes 47.
T128 17821-18069 Sentence denotes Interestingly, 24 out of 26 fragments contained the described SARS-CoV T cell epitopes, indicating that these regions are immunogenic in humans and reinforcing the idea that some degree of cross-reactivity among coronavirus can be expected [11,58].
T129 18070-18217 Sentence denotes Also, the majority, i.e., 40 of the 47 human epitopes, clustered around one single region conserved in the beta-coronavirus alignment (QGPPGTGKSH).
T130 18218-18364 Sentence denotes Several conserved peptides have thus been identified, which could potentially contain epitopes cross-reactive among different Coronavirus species.
T131 18365-18589 Sentence denotes These conserved peptides can thus provide valuable information to understand if the immune response to SARS-CoV-2 is affected by previous infection with other coronaviruses and for pan-coronavirus vaccine design (Figure S2).
T132 18591-18593 Sentence denotes 4.
T133 18594-18604 Sentence denotes Discussion
T134 18605-18770 Sentence denotes We here report the design of a CoV-2-cons sequence and the matched OLP sets for the comprehensive analysis of the adaptive T cell immune response against SARS-CoV-2.
T135 18771-18907 Sentence denotes Three sets of OLP reported here provide enough flexibility to balance exhaustive screening for T cell responses and available resources.
T136 18908-19166 Sentence denotes Ideally, the wide use of such a CoV-2-cons sequence and a specific OLP set (ideally 15 mer with 11 overlap) would ensure the comparability and reproducibility of immunological data across laboratories worldwide to accelerate SARS-CoV-2 immunological studies.
T137 19167-19353 Sentence denotes Fifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings.
T138 19354-19470 Sentence denotes However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping.
T139 19471-19607 Sentence denotes For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity.
T140 19608-19769 Sentence denotes This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others).
T141 19770-19884 Sentence denotes Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges.
T142 19885-20106 Sentence denotes How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required.
T143 20107-20341 Sentence denotes The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11].
T144 20342-20591 Sentence denotes Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46].
T145 20592-20783 Sentence denotes Canonical and alternative frame ORF were considered in the present CoV-2-consensus sequence design to ensure an as broad as possible screening for all potentially expressed protein sequences.
T146 20784-20860 Sentence denotes Whether all these putative ORF are indeed expressed remains to be confirmed.
T147 20861-21013 Sentence denotes If shown that not all these sequences are indeed expressed, the OLP set could be reduced by some 65 peptides, focusing exclusively on the canonical ORF.
T148 21014-21127 Sentence denotes Consensus sequence design is highly dependent on the sequences included in the alignments used to construct them.
T149 21128-21254 Sentence denotes We used publicly available sequences in the growing SARS-CoV-2 NCBI repository as a representative set of worldwide sequences.
T150 21255-21443 Sentence denotes As noted, coverage of sequence diversity for in-vitro antigen test sets is critical as responses to autologous viral variants may be missed if these variant sequences are not matched [27].
T151 21444-21717 Sentence denotes This may be most critical for highly variable pathogens, such as HCV and HIV, where it has been shown that sequence entropy was directly related to the frequency of OLP reactivity in vitro and essential to identify the potential emergence of immune escape variants [59,60].
T152 21718-21933 Sentence denotes However, even genetically more stable pathogens such DNA viruses (for instance Epstein Barr Virus, EBV) have been reported to exist as a swarm of quasi-species and to lose specific T cell epitopes over time [61,62].
T153 21934-22116 Sentence denotes This is also supported by recent data showing some degree of adaptation to host immunity and sequence variability for SARS-CoV-2 as it moves through the global human population [63].
T154 22117-22178 Sentence denotes To cover these variant sites, variant OLP can be synthesized.
T155 22179-22375 Sentence denotes An alternative approach to the synthesis of individual variant peptide sequences is the use of “toggled peptides”, where the sequence variation is directly incorporated into the peptide synthesis.
T156 22376-22596 Sentence denotes To achieve this, peptide synthesis uses mixes of amino acids at variable positions, so that the resulting OLP resembles a mini-peptide library that can achieve an a-priori set coverage of circulating viral variants [64].
T157 22597-22726 Sentence denotes This would readily allow to cover more sequence diversity beyond the 25% frequency cut-off that was applied in the present study.
T158 22727-22833 Sentence denotes The existence of protein fragments conserved among different coronavirus species has several implications.
T159 22834-22988 Sentence denotes For the interpretation of T cell responses, it has to be taken into account that some degree of cross-reactivity can exist among human coronavirus [5,65].
T160 22989-23231 Sentence denotes This implies that responses to these regions could be associated with previous infections by other human coronaviruses, some of them triggering much milder infections that can pass unnoticed, like those by coronaviruses causing a common cold.
T161 23232-23334 Sentence denotes This observation will need to be taken into consideration when interpreting immune data on SARS-CoV-2.
T162 23335-23586 Sentence denotes On the other hand, the existence of conserved sequences among beta- or even the whole coronavirus family suggests that T cell responses to these regions could provide broad protection and that the creation of a pan-coronavirus vaccine may be feasible.
T163 23587-23810 Sentence denotes Such a vaccine could allow to prevent infection not only with SARS-CoV-2, but also with other, clinically relevant coronavirus like SARS-CoV-1 and MERS, and even with new coronaviruses jumping the species barrier to humans.
T164 23811-23935 Sentence denotes However, the design of a pan-coronavirus vaccine will critically depend on the identification of epitopes shared among them.
T165 23936-24051 Sentence denotes These pan-coronavirus epitopes are likely to exist in conserved sequences, but need to be experimentally validated.
T166 24052-24370 Sentence denotes At the same time, the existence of SARS-CoV-2 homologous regions in the human genome, together with the existence of described epitopes in these regions raise some concern that coronaviruses could be involved in a molecular mimicry process triggering autoimmune diseases like the Guillain-Barré syndrome [66,67,68,69].
T167 24371-24545 Sentence denotes The present study is currently limited to the design of the CoV-2 consensus sequence, without functional immune analyses of the OLP sets in samples from infected individuals.
T168 24546-24758 Sentence denotes However, the principal aim here was to provide a SARS-CoV-2 T cell test reagent, including all described ORF and covering as much viral variability as possible, for its implementation in future screening efforts.
T169 24759-25097 Sentence denotes In addition, the OLP sets will certainly elicit T cell responses in vitro as partial evaluation has been performed by others in studies using peptides spanning some of the regions covered by the present consensus sequence [5,9,11] and since the current peptide designs (length, overlap) has been shown to be effective in the past [55,70].
T170 25098-25470 Sentence denotes Thus, the present peptide designs will afford a high-resolution analysis of the T cell response to SARS-CoV-2, the nature of the targeted epitopes and the functionality and T cell receptor use of the T cells targeting these epitopes, thereby increasing our knowledge of factors that drive COVID-19 disease progression and which could be implemented in vaccine development.
T171 25472-25474 Sentence denotes 5.
T172 25475-25486 Sentence denotes Conclusions
T173 25487-25700 Sentence denotes We here present the first SARS-CoV-2 Consensus sequence for all described SARS-CoV-2 ORF, including those in alternative frames covering the SARS-CoV-2 sequence variability represented by 1700 available sequences.
T174 25701-25872 Sentence denotes The description of this sequence and of the matching OLP sets will aid the further immune analyses in SARS-CoV-2 infection and ensure reproducibility between laboratories.
T175 25873-25982 Sentence denotes In light of recent studies, the T cell response to SARS-CoV-2 can be crucial to control SARS-CoV-2 infection.
T176 25983-26139 Sentence denotes To date, published studies are generally limited to a few viral proteins, using recall antigens that do not reflect sequence diversity nor alternative ORFs.
T177 26140-26340 Sentence denotes To overcome these limitations, the description of the global landscape of T cell responses to SARS-CoV-2 urgently needs unbiased, comparable, full-proteome screens for virus-specific T cell responses.
T178 26341-26486 Sentence denotes The CoV-2-cons and matched OLP sets described here will allow to integrate data globally, generating crucial information for vaccine development.
T179 26487-26630 Sentence denotes We also include measures of sequence entropy to identify the most variable segments and design additional OLP sequences that cover these sites.
T180 26631-26826 Sentence denotes Of note, these entropy analyses, together with sequence alignments across a wide range of coronaviruses, also allowed the identification of highly conserved regions among different coronaviruses.
T181 26827-26972 Sentence denotes These regions may be targeted by T cells, which could target a wide range of coronaviruses and may be relevant targets for T cell vaccine design.
T182 26974-26997 Sentence denotes Supplementary Materials
T183 26998-27089 Sentence denotes The following are available online at https://www.mdpi.com/2076-393X/8/3/444/s1, Figure S1:
T184 27090-27268 Sentence denotes Shannon entropy plot by amino acid position for all canonical and alternative frame ORF of SARS-CoV-2, Figure S2: SARS-CoV-2 ORF fragments containing conserved regions, Table S1:
T185 27269-27295 Sentence denotes Overlapping peptide lists.
T186 27296-27332 Sentence denotes Click here for additional data file.
T187 27334-27354 Sentence denotes Author Contributions
T188 27355-27842 Sentence denotes Conceptualization, A.O.; Data curation, A.O., M.N.-J., A.K. and L.R.-M.; Formal analysis, A.O., M.N.-J., A.K. and L.R.-M.; Funding acquisition, J.G.P. and C.B.; Investigation, A.K. and J.G.P.; Methodology, A.O., M.N.-J., A.K., L.R.-M., J.G.P. and C.B.; Supervision, J.G.P. and C.B.; Visualization, A.O., M.N.-J., A.K., L.R.-M., J.G.P. and C.B.; Writing—original draft, A.O., M.N.-J., A.K., L.R.-M., J.G.P. and C.B.; Writing—review & editing, A.O., M.N.-J., A.K., L.R.-M., J.G.P. and C.B.
T189 27843-27919 Sentence denotes All authors have read and agreed to the published version of the manuscript.
T190 27921-27928 Sentence denotes Funding
T191 27929-28158 Sentence denotes This study was supported in part by grants from the National Health Institute Carlos III (ISCIII) COV20/00660, PI17/000164 and RETIC RD16/0025/0041 (Co-funded by European Regional Development Fund/European Social Fund) for J.G.P.
T192 28159-28284 Sentence denotes The funders had no role in study design, data collection and analysis, the decision to publish or drafting of the manuscript.
T193 28285-28381 Sentence denotes This study has received partial funding from Grifols and the crowdfunding initiative YoMeCorono.
T194 28383-28404 Sentence denotes Conflicts of Interest
T195 28405-28536 Sentence denotes The authors declare that a patent application (application number 63051925) has been submitted that covers the CoV-2-cons sequence.
T196 28538-28612 Sentence denotes Figure 1 Standard Shannon entropy plot by amino acid position for ORF1ab.
T197 28613-28681 Sentence denotes Zero entropy indicates total conservation at each specific position.
T198 28682-28759 Sentence denotes Figure 2 Sequence Logos for epitopes encompassing variable (>25%) positions.
T199 28760-28844 Sentence denotes Protein location and starting amino acid positions are indicated on top of the logo.
T200 28845-28983 Sentence denotes Table 1 Canonical and alternative open reading frames (ORF) in SARS-CoV-2. iORF: internal OPF, extORF: extended ORF, upORF: upstream ORF.
T201 28984-29035 Sentence denotes Gene Start End Protein Protease Products Frame
T202 29036-29086 Sentence denotes ORF1a.iORF1.ext 59 136 upORF1a1 - Alternative
T203 29087-29138 Sentence denotes ORF1a.iORF2.ext 163 264 upORF1a2 - Alternative
T204 29139-29190 Sentence denotes ORF1ab 266 13483 pp1a leader protein Canonical
T205 29191-29195 Sentence denotes nsp2
T206 29196-29200 Sentence denotes nsp3
T207 29201-29205 Sentence denotes nsp4
T208 29206-29224 Sentence denotes 3C-like proteinase
T209 29225-29229 Sentence denotes nsp6
T210 29230-29234 Sentence denotes nsp7
T211 29235-29239 Sentence denotes nsp8
T212 29240-29244 Sentence denotes nsp9
T213 29245-29250 Sentence denotes nsp10
T214 29251-29256 Sentence denotes nsp11
T215 29257-29325 Sentence denotes ORF1ab 13468 21555 pp1ab RNA-dependent RNA polymerase Canonical
T216 29326-29334 Sentence denotes helicase
T217 29335-29355 Sentence denotes 3′-to-5′ exonuclease
T218 29356-29365 Sentence denotes endoRNAse
T219 29366-29395 Sentence denotes 2′-O-ribose methyltransferase
T220 29396-29448 Sentence denotes S 21563 25384 surface glycoprotein S1 Canonical
T221 29449-29451 Sentence denotes S2
T222 29452-29500 Sentence denotes ORFS.iORF1 21744 21863 inORFS - Alternative
T223 29501-29549 Sentence denotes ORF3a 25393 26220 ORF3a protein - Canonical
T224 29550-29601 Sentence denotes ORF3a.iORF1 25457 25582 inORF3a1 - Alternative
T225 29602-29653 Sentence denotes ORF3a.iORF2 25596 25697 inORF3a2 - Alternative
T226 29654-29701 Sentence denotes E 26245 26472 envelope protein - Canonical
T227 29702-29748 Sentence denotes ORFM.ext 26484 27191 exORFM - Alternative
T228 29749-29801 Sentence denotes M 26523 27191 membrane glycoprotein - Canonical
T229 29802-29849 Sentence denotes ORFM.iORF 27151 27195 inORFM - Alternative
T230 29850-29896 Sentence denotes ORF6 27202 27387 ORF6 protein - Canonical
T231 29897-29945 Sentence denotes ORF7a 27394 27759 ORF7a protein - Canonical
T232 29946-29994 Sentence denotes ORF7b 27756 27887 ORF7b protein - Canonical
T233 29995-30045 Sentence denotes ORF7b.iORF2 27862 27897 inORF7b - Alternative
T234 30046-30092 Sentence denotes ORF8 27894 28259 ORF8 protein - Canonical
T235 30093-30140 Sentence denotes ORF8.iORF 27965 27994 inORF8 - Alternative
T236 30141-30199 Sentence denotes N 28274 29533 nucleocapsid phosphoprotein - Canonical
T237 30200-30247 Sentence denotes ORFN.iORF1 28284 28577 ORF9b - Alternative
T238 30248-30298 Sentence denotes ORF10.upORF 29538 29570 upORF10 - Alternative
T239 30299-30347 Sentence denotes ORF10 29558 29674 ORF10 protein - Canonical
T240 30348-30411 Sentence denotes ORF position is referred to the NC_045512.2 reference sequence.
T241 30412-30461 Sentence denotes Table 2 Description of the three CoV-2 OLP sets.
T242 30462-30501 Sentence denotes Set Length Overlapp Number Variants
T243 30502-30525 Sentence denotes 15–11 15 11 2821 31
T244 30526-30549 Sentence denotes 15–10 15 10 2262 23
T245 30550-30573 Sentence denotes 18–11 18 11 1561 22
T246 30574-30631 Sentence denotes Table 3 Conserved sequences among different coronavirus.
T247 30632-30634 Sentence denotes I:
T248 30635-30655 Sentence denotes Pan-coronavirus, II:
T249 30656-30677 Sentence denotes Betacoronavirus, III:
T250 30678-30706 Sentence denotes Human coronavirus alignment.
T251 30707-30790 Sentence denotes The black squares that indicted which alignments contained the conserved sequences.
T252 30791-30865 Sentence denotes Consensus Sequence ORF Consensus Start Position Alignment Hit Epitopes
T253 30866-30921 Sentence denotes I II III Unknown SARS-CoV Human Other Coronavirus
T254 30922-30962 Sentence denotes VGVLTLDNQDLNG ORF1b 193 1 4 - -
T255 30963-31013 Sentence denotes TQMNLKYAISAKNRARTVAGVSI ORF1b 530 - 5 2 -
T256 31014-31052 Sentence denotes VIGTSKFYGGW ORF1b 580 - 3 - -
T257 31053-31095 Sentence denotes LMGWDYPKCDRAMPN ORF1b 605 1 3 - -
T258 31096-31132 Sentence denotes LANECAQVL ORF1b 646 - 1 - -
T259 31133-31175 Sentence denotes YVKPGGTSSGDATTA ORF1b 665 - 3 - -
T260 31176-31220 Sentence denotes KHFSMMILSDDAVVCFN ORF1b 743 - 2 1 -
T261 31221-31258 Sentence denotes LYYQNNVFMS ORF1b 778 - - - -
T262 31259-31296 Sentence denotes GPHEFCSQHT ORF1b 800 - 2 - -
T263 31297-31334 Sentence denotes LPYPDPSRIL ORF1b 820 - 2 3 -
T264 31335-31375 Sentence denotes ERFVSLAIDAYPL ORF1b 849 - 5 - 1
T265 31376-31411 Sentence denotes SQTSLRCG ORF1b 934 - 1 - -
T266 31412-31448 Sentence denotes LYLGGMSYY ORF1b 986 - 3 - -
T267 31449-31485 Sentence denotes LKLFAAET ORF1b 1054 - 4 - -
T268 31486-31525 Sentence denotes QGPPGTGKSH ORF1b 1205 1 2 40 -
T269 31526-31569 Sentence denotes TACSHAAVDALCEKA ORF1b 1231 - 1 - -
T270 31570-31608 Sentence denotes GDPAQLPAPR ORF1b 1324 - 3 - -
T271 31609-31648 Sentence denotes AVFISPYNSQN ORF1b 1432 - 4 1 -
T272 31649-31687 Sentence denotes NRFNVAITRA ORF1b 1483 - 2 - -
T273 31688-31724 Sentence denotes CNLGGAVC ORF1b 2002 - 1 - -
T274 31725-31763 Sentence denotes KYTQLCQYLN ORF1b 2443 - 3 - -
T275 31764-31800 Sentence denotes RSFIEDLLF Spike 815 - 2 - -
T276 31801-31838 Sentence denotes QIDRLITGRL Spike 993 - 5 - 1
T277 31839-31875 Sentence denotes KWPWYIWL Spike 1211 - - - -
T278 31876-31907 Sentence denotes WSFNPETN M 110 - 3 - -
T279 31908-31943 Sentence denotes PRWYFYYLGTGP N 106 - 7 - -