> top > docs > PMC:7519301 > annotations

PMC:7519301 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 558-565 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T2 592-599 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T3 1017-1024 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T4 1450-1457 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T5 1746-1756 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T6 1779-1786 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T7 2014-2021 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T8 3224-3227 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T9 3261-3267 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T10 3273-3279 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T11 3354-3362 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T12 3383-3391 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T13 3577-3582 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T14 3617-3625 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T15 3838-3843 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T16 4283-4289 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T17 4315-4325 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T18 4514-4525 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T19 4587-4594 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T20 4809-4816 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T21 5053-5057 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T22 6617-6620 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T23 6808-6818 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T24 6932-6935 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T25 6984-6994 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T26 7770-7776 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T27 8053-8060 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 8243-8251 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T29 8338-8346 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T30 8715-8722 Body_part denotes Genomes http://purl.org/sig/ont/fma/fma84116
T31 8833-8839 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T32 9196-9203 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T33 9208-9216 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T34 9284-9291 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T35 9433-9439 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T36 9625-9633 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T37 9662-9670 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T38 9754-9760 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T39 10129-10135 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T40 10158-10169 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T41 10485-10492 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T42 10596-10602 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T43 11429-11435 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T44 11562-11569 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T45 11688-11695 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T46 11843-11850 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T47 11937-11945 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T48 11996-12003 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T49 12438-12446 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T50 12565-12571 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T51 12613-12623 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T52 12656-12666 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T53 12725-12735 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T54 13996-14003 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T55 14008-14016 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T56 14033-14040 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T57 15752-15756 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T58 15792-15800 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T59 16090-16100 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T60 16221-16229 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T61 16392-16400 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T62 16407-16411 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T63 16535-16543 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T64 16609-16616 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T65 17275-17279 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T66 17308-17312 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T67 17413-17421 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T68 17476-17485 Body_part denotes leukocyte http://purl.org/sig/ont/fma/fma62852
T69 17495-17498 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T70 17629-17633 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T71 17694-17702 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T72 17829-17837 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T73 17879-17885 Body_part denotes Genome http://purl.org/sig/ont/fma/fma84116
T74 18122-18129 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T75 18320-18328 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T76 18773-18789 Body_part denotes structural genes http://purl.org/sig/ont/fma/fma74402
T77 19181-19189 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T78 19477-19483 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T79 19623-19627 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T80 19869-19873 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T81 20022-20037 Body_part denotes structural gene http://purl.org/sig/ont/fma/fma74402
T82 20724-20731 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T83 20824-20831 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T84 21693-21701 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T85 22111-22119 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T86 22710-22725 Body_part denotes structural gene http://purl.org/sig/ont/fma/fma74402
T87 23060-23064 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T88 23259-23265 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T89 23536-23542 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T90 24881-24889 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T91 25686-25692 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T92 25723-25733 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T93 25759-25765 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T94 26075-26087 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T95 26089-26096 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T96 26537-26547 Body_part denotes Amino acid http://purl.org/sig/ont/fma/fma82739
T97 27159-27171 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T98 27310-27318 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T99 27539-27547 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T100 28831-28839 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T101 29445-29449 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T102 29754-29758 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T103 30600-30612 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T104 30686-30691 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T105 30776-30780 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T106 31745-31753 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T107 31775-31783 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T108 31824-31832 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T109 31958-31966 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T110 33370-33377 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T111 33865-33868 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T112 33982-33990 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T113 36735-36743 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T114 38318-38322 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T115 38355-38359 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T116 38421-38425 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T117 39037-39041 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T118 40691-40695 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T119 40916-40920 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T120 41363-41367 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T121 43421-43427 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T122 44392-44399 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T123 44437-44444 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T124 44482-44492 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T125 45033-45044 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T126 45062-45072 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T127 45390-45397 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T128 45594-45598 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T129 45625-45629 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T130 45685-45693 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T131 45818-45822 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T132 45903-45906 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T133 45951-45966 Body_part denotes neural networks http://purl.org/sig/ont/fma/fma74616
T134 46018-46021 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T135 46031-46034 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T136 46046-46049 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T137 46079-46082 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T138 46097-46100 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T139 46250-46253 Body_part denotes hla http://purl.org/sig/ont/fma/fma84795
T140 46381-46385 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T141 46463-46466 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T142 46475-46478 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T143 46490-46493 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T144 46497-46500 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T145 46508-46511 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T146 46678-46681 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T147 46834-46838 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T148 46971-46974 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T149 47092-47099 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T150 47184-47187 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T151 47196-47199 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T152 47209-47212 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T153 47216-47219 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T154 47227-47230 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T155 47299-47302 Body_part denotes hla http://purl.org/sig/ont/fma/fma84795
T156 47359-47362 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T157 47372-47375 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T158 47399-47402 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T159 47409-47412 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T160 47428-47431 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T161 47496-47499 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T162 47570-47573 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T163 49226-49234 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 5522-5527 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T2 9880-9885 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T3 36139-36142 Body_part denotes tip http://purl.obolibrary.org/obo/UBERON_2001840

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 2-10 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 2-6 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T3 137-145 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 147-155 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 147-151 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T6 390-398 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 390-394 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T8 547-555 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 547-551 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T10 785-793 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 785-789 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T12 898-906 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 1150-1197 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T14 1150-1183 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T15 1199-1207 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 1199-1203 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T17 1439-1447 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 1439-1443 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T19 1610-1618 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 1610-1614 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T21 2363-2371 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 2363-2367 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T23 2503-2550 Disease denotes Severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T24 2552-2560 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 2552-2556 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T26 2587-2595 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T27 2998-3006 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 2998-3002 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T29 3072-3105 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T30 3107-3111 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T31 3118-3126 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 3118-3122 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T33 3170-3178 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 3170-3174 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T35 3874-3882 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T36 4187-4195 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 4187-4191 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T38 4340-4348 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 4340-4344 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T40 4416-4424 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 4416-4420 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T42 4648-4656 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 4648-4652 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T44 4936-4944 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 4936-4940 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T46 5337-5345 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 5337-5341 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T48 5467-5475 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 5467-5471 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T50 5584-5592 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 5584-5588 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T52 5769-5777 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 5769-5773 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T54 5883-5891 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 5883-5887 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T56 6219-6227 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T57 6302-6311 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T58 6464-6472 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 6464-6468 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T60 6764-6772 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 6764-6768 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T62 6880-6888 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 6880-6884 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T64 7235-7243 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 7235-7239 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T66 7904-7913 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T67 7936-7941 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T68 8077-8085 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T69 8077-8081 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T70 8423-8431 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T71 8423-8427 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T72 8477-8485 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T73 8477-8481 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T74 8704-8712 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 8704-8708 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T76 8740-8748 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T77 8740-8744 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T78 8822-8830 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T79 8822-8826 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T80 9185-9193 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T81 9185-9189 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T82 9249-9257 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T83 9249-9253 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T84 11032-11042 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T85 11459-11467 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 11459-11463 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T87 13985-13993 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T88 13985-13989 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T89 14756-14764 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T90 14756-14760 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T91 17425-17433 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T92 17425-17429 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T93 17868-17876 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T94 17868-17872 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T95 19466-19474 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T96 19466-19470 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T97 21796-21804 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T98 21796-21800 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T99 22161-22169 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T100 22161-22165 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T101 22397-22405 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T102 22397-22401 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T103 22494-22502 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T104 22494-22498 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T105 23242-23250 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T106 23242-23246 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T107 23519-23527 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T108 23519-23523 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T109 23776-23784 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T110 23776-23780 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T111 24354-24362 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T112 24354-24358 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T113 24365-24376 Disease denotes S sequences http://purl.obolibrary.org/obo/MONDO_0007821
T114 24465-24473 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T115 24465-24469 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T116 24498-24506 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T117 24498-24502 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T118 24959-24967 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T119 24959-24963 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T120 25350-25361 Disease denotes S sequences http://purl.obolibrary.org/obo/MONDO_0007821
T121 25879-25887 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T122 25879-25883 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T123 25890-25901 Disease denotes S sequences http://purl.obolibrary.org/obo/MONDO_0007821
T124 25920-25928 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T125 25920-25924 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T126 25956-25964 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T127 25956-25960 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T128 26062-26070 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T129 26062-26066 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T130 26713-26721 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T131 26713-26717 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T132 26805-26813 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T133 26805-26809 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T134 27039-27047 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T135 27039-27043 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T136 27135-27143 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T137 27363-27371 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T138 27363-27367 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T139 27434-27442 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T140 27434-27438 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T141 27597-27605 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T142 27597-27601 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T143 28197-28205 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T144 28197-28201 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T145 28709-28717 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T146 28709-28713 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T147 28900-28909 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T148 29001-29009 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T149 29001-29005 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T150 29149-29157 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T151 29149-29153 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T152 29630-29638 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T153 29630-29634 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T154 29736-29744 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T155 29736-29740 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T156 29787-29795 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T157 29787-29791 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T158 30460-30465 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T159 30632-30640 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T160 30632-30636 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T161 32304-32312 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T162 32304-32308 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T163 32625-32635 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T164 33063-33071 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T165 33063-33067 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T166 33423-33431 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T167 33423-33427 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T168 33637-33645 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T169 33637-33641 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T170 33687-33695 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T171 33687-33691 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T172 33872-33881 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T173 33886-33892 Disease denotes Dengue http://purl.obolibrary.org/obo/MONDO_0005502
T174 33959-33967 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T175 33959-33963 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T176 34136-34144 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T177 34136-34140 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T178 34281-34289 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T179 34281-34285 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T180 34618-34626 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T181 34618-34622 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T182 43329-43337 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T183 43329-43333 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T184 43410-43418 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T185 43410-43414 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T186 43743-43751 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T187 43743-43747 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T188 43806-43814 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T189 43806-43810 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T190 44079-44087 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T191 44079-44083 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T192 44142-44150 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T193 44142-44146 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T194 44509-44517 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T195 44509-44513 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T196 44619-44627 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T197 44619-44623 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T198 45663-45671 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T199 45663-45667 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 0-1 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T2 123-128 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T3 201-202 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 238-243 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T5 258-259 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 620-623 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T7 816-817 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 944-945 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 998-1003 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T10 1081-1082 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 1464-1466 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T12 1728-1729 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 1950-1955 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T14 2413-2414 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 2569-2574 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T16 2600-2601 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 2638-2639 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 2657-2662 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T19 2707-2713 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T20 2967-2972 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T21 3155-3160 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T22 3161-3166 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T23 3191-3192 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 3228-3233 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T25 3433-3441 http://purl.obolibrary.org/obo/UBERON_0000158 denotes Membrane
T26 3542-3547 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T27 3577-3582 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T28 3675-3677 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T29 3682-3684 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T30 3682-3684 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T31 3759-3764 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T32 3838-3843 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T33 3892-3895 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T34 3903-3904 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 4221-4222 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 4232-4239 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T37 4259-4263 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bats
T38 4279-4282 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T39 4297-4300 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T40 4559-4561 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T41 4566-4568 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T42 4566-4568 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T43 4601-4603 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T44 4604-4606 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T45 4604-4606 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T46 4620-4621 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 4758-4760 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T48 4896-4899 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T49 4984-4986 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T50 4987-4989 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T51 4987-4989 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T52 5053-5057 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T53 5238-5241 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T54 5242-5249 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T55 5261-5262 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 5288-5289 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 5299-5304 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T58 5390-5395 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T59 5405-5411 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T60 5426-5433 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T61 5504-5510 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T62 5603-5609 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T63 5616-5617 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 5865-5866 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 5897-5898 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 6057-6062 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T67 6621-6628 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T68 6649-6650 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 6834-6835 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 6936-6943 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T71 6957-6965 http://purl.obolibrary.org/obo/CLO_0001040 denotes 1 × 10−5
T72 7072-7074 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T73 7295-7300 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T74 7312-7318 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T75 7485-7486 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 7548-7553 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T77 7644-7645 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 7696-7697 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 7947-7954 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T80 7984-7985 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 7986-7991 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T82 8145-8150 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T83 8167-8173 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T84 8452-8458 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T85 9106-9107 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 9159-9160 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87 9223-9225 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T88 9294-9295 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T89 9368-9369 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T90 9957-9964 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T91 9985-9987 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T92 10069-10072 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T93 10073-10074 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T94 10205-10206 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 10334-10336 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T96 10549-10550 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T97 10648-10653 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T98 10766-10769 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T99 10871-10872 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T100 11283-11284 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 11470-11477 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T102 11759-11760 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 11787-11788 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 11903-11904 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T105 11952-11954 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T106 11952-11954 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T107 12046-12047 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T108 12094-12095 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 12355-12356 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 12398-12399 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 12453-12455 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T112 12453-12455 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T113 12482-12485 http://purl.obolibrary.org/obo/CLO_0051582 denotes Has
T114 12675-12676 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T115 12694-12695 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 12958-12963 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T117 12977-12978 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 13141-13142 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 13518-13523 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T120 13550-13552 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T121 13649-13650 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T122 13885-13886 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 13927-13928 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T124 14023-14025 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T125 14023-14025 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T126 14072-14073 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T127 14315-14317 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T128 14401-14402 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T129 14525-14526 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T130 14732-14733 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T131 14767-14774 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T132 14844-14845 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T133 15183-15184 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T134 15319-15320 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T135 15337-15341 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T136 15508-15509 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T137 15646-15650 http://purl.obolibrary.org/obo/CLO_0001550 denotes a 10
T138 15752-15756 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T139 15773-15777 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T140 15884-15885 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 16046-16047 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 16405-16411 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T143 16464-16466 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T144 16471-16473 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T145 16471-16473 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T146 16550-16552 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T147 16715-16717 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T148 17273-17279 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T149 17304-17305 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 17306-17312 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T151 17363-17366 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T152 17371-17374 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T153 17443-17447 http://purl.obolibrary.org/obo/CLO_0007653 denotes M, E
T154 17470-17475 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T155 17525-17526 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T156 17627-17633 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T157 18076-18077 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T158 18300-18304 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T159 18377-18378 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T160 18553-18559 http://purl.obolibrary.org/obo/CLO_0002821 denotes dS > 1
T161 18553-18559 http://purl.obolibrary.org/obo/CLO_0002822 denotes dS > 1
T162 18680-18685 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T163 18784-18789 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T164 18816-18821 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T165 18838-18842 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T166 18866-18869 http://purl.obolibrary.org/obo/CLO_0008190 denotes Per
T167 18940-18944 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T168 19023-19028 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T169 19093-19094 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T170 19486-19487 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T171 19574-19580 http://purl.obolibrary.org/obo/CLO_0002821 denotes dS > 1
T172 19574-19580 http://purl.obolibrary.org/obo/CLO_0002822 denotes dS > 1
T173 19598-19599 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T174 19623-19627 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T175 19817-19822 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T176 19869-19873 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T177 20033-20037 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T178 20904-20914 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes, the
T179 21408-21409 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T180 21709-21711 http://purl.obolibrary.org/obo/CLO_0008935 denotes S9
T181 21725-21727 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T182 21759-21761 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T183 22004-22008 http://purl.obolibrary.org/obo/CLO_0002040 denotes b(t)
T184 22269-22273 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T185 22609-22610 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T186 22721-22725 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T187 22728-22729 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T188 22909-22910 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T189 22983-22984 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T190 23060-23064 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T191 23227-23228 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T192 23292-23293 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T193 23354-23355 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T194 23413-23417 http://purl.obolibrary.org/obo/CLO_0002040 denotes b(t)
T195 23748-23752 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T196 24293-24294 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 24594-24595 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T198 24596-24599 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T199 24637-24642 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T200 24656-24661 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T201 24662-24665 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T202 24700-24705 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T203 24715-24720 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T204 24815-24817 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T205 24866-24867 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T206 24942-24947 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T207 25904-25905 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T208 26023-26024 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T209 26205-26206 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T210 26381-26382 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T211 26504-26509 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T212 26526-26529 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T213 26564-26567 http://purl.obolibrary.org/obo/CLO_0001375 denotes 455
T214 26656-26658 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T215 26656-26658 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T216 27037-27038 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T217 27061-27062 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T218 27149-27156 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus’s
T219 27224-27225 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T220 27248-27253 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T221 27432-27433 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T222 27458-27462 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T223 27491-27498 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T224 27577-27578 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T225 27634-27635 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T226 27941-27948 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T227 27994-27995 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T228 28058-28061 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T229 28328-28329 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T230 28506-28507 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T231 28570-28575 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T232 28646-28648 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T233 28773-28774 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T234 28791-28792 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T235 29226-29229 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T236 29262-29269 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T237 29339-29340 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T238 29445-29449 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T239 29648-29654 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T240 29684-29685 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T241 29754-29758 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T242 29990-29997 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T243 30033-30034 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T244 30555-30560 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T245 30664-30669 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T246 30686-30691 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T247 30776-30786 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T248 30863-30870 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T249 30897-30902 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T250 30916-30923 http://purl.obolibrary.org/obo/NCBITaxon_9443 denotes primate
T251 30932-30934 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T252 31065-31068 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T253 31272-31273 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T254 31415-31416 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T255 31521-31527 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T256 31791-31792 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T257 32080-32081 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T258 32236-32237 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T259 32433-32434 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T260 32435-32440 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T261 32602-32603 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T262 33074-33077 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T263 33094-33095 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T264 33158-33161 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T265 33169-33170 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T266 33470-33475 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T267 33487-33488 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T268 33698-33705 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T269 33748-33749 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T270 33796-33799 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T271 33849-33856 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T272 33904-33911 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T273 33928-33929 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T274 33970-33977 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T275 34115-34116 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T276 34397-34398 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T277 34669-34671 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T278 35748-35750 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T279 35941-35942 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T280 36196-36199 http://purl.obolibrary.org/obo/NCBITaxon_314295 denotes ape
T281 36214-36216 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T282 36750-36752 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T283 36755-36756 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T284 37620-37622 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T285 38188-38189 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T286 38318-38322 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T287 38355-38359 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T288 38421-38425 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T289 38569-38570 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T290 39037-39041 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T291 39043-39044 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T292 39293-39294 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T293 39507-39508 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T294 39842-39843 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T295 40639-40640 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T296 40691-40695 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T297 40916-40920 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T298 41363-41367 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T299 41634-41635 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T300 41666-41667 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T301 41743-41744 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T302 42447-42448 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T303 42493-42495 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T304 42672-42673 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T305 42733-42739 http://purl.obolibrary.org/obo/CLO_0002045 denotes b(t)=b
T306 42773-42777 http://purl.obolibrary.org/obo/CLO_0002040 denotes b(t)
T307 42788-42789 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T308 42920-42922 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T309 42936-42938 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T310 43303-43306 http://purl.obolibrary.org/obo/NCBITaxon_314295 denotes ape
T311 43887-43888 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T312 43913-43917 http://purl.obolibrary.org/obo/CLO_0002040 denotes b(t)
T313 44245-44249 http://purl.obolibrary.org/obo/CLO_0001550 denotes a 10
T314 44369-44372 http://purl.obolibrary.org/obo/NCBITaxon_314295 denotes ape
T315 44563-44564 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T316 44590-44593 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T317 44686-44695 http://purl.obolibrary.org/obo/UBERON_0001353 denotes posterior
T318 44722-44723 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T319 44761-44762 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T320 44909-44912 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T321 45010-45011 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T322 45050-45051 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T323 45136-45141 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T324 45142-45145 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T325 45150-45155 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T326 45156-45159 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T327 45199-45204 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T328 45272-45273 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T329 45299-45300 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T330 45339-45340 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T331 45422-45423 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T332 45428-45434 http://purl.obolibrary.org/obo/UBERON_0002415 denotes tailed
T333 45437-45441 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T334 45578-45581 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T335 45587-45590 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T336 45592-45598 http://purl.obolibrary.org/obo/CL_0000084 denotes T Cell
T337 45609-45612 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T338 45618-45621 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T339 45623-45629 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T340 45811-45814 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T341 45816-45822 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T342 45853-45854 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T343 45887-45895 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T344 45994-45995 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T345 45996-46003 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T346 46274-46282 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T347 46306-46313 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T348 46374-46377 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T349 46379-46385 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T350 46440-46441 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T351 46442-46449 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T352 46494-46495 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T353 46501-46502 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T354 46832-46838 http://purl.obolibrary.org/obo/CL_0000084 denotes T Cell
T355 46878-46879 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T356 47074-47075 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T357 47090-47091 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T358 47213-47214 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T359 47220-47221 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T360 47689-47697 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T361 47750-47758 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T362 47778-47783 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T363 47896-47900 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T364 48441-48442 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T365 48595-48597 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T366 48782-48787 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T367 48858-48859 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 592-599 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T2 1017-1024 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T3 1746-1756 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T4 2014-2021 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T5 2648-2653 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T6 3251-3255 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695
T7 3354-3362 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T8 3383-3391 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T9 3682-3684 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T10 3782-3793 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T11 4315-4325 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T12 4315-4320 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T13 4321-4325 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T14 4514-4525 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T15 4514-4519 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T16 4520-4525 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T17 4566-4568 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T18 4587-4594 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T19 4604-4606 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T20 4987-4989 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T21 6063-6071 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T22 6808-6818 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T23 6984-6994 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T24 8053-8060 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T25 8243-8251 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T26 8338-8346 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T27 9205-9207 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T28 9625-9633 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T29 9662-9670 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T30 10158-10169 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T31 11934-11936 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T32 11952-11954 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T33 12435-12437 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T34 12453-12455 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T35 12613-12623 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T36 12656-12666 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T37 12725-12735 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T38 14005-14007 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T39 14023-14025 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T40 15789-15791 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T41 15807-15809 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T42 16090-16100 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T43 16090-16095 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T44 16096-16100 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T45 16189-16191 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T46 16218-16220 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T47 16236-16238 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T48 16471-16473 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T49 16532-16534 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T50 16550-16552 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T51 16609-16616 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T52 17375-17382 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T53 17413-17421 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T54 17486-17493 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T55 17691-17693 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T56 17826-17828 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T57 17844-17846 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T58 18122-18129 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T59 18230-18232 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T60 18317-18319 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T61 18335-18337 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T62 18550-18552 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T63 18660-18662 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T64 19181-19189 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T65 19571-19573 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T66 19613-19615 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T67 19629-19631 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T68 19683-19685 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T69 21690-21692 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T70 22108-22110 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T71 23070-23072 Chemical denotes Ln http://purl.obolibrary.org/obo/CHEBI_33319
T72 23340-23344 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T74 24815-24817 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T76 24878-24880 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T77 25285-25287 Chemical denotes 5B http://purl.obolibrary.org/obo/CHEBI_27560
T78 25723-25733 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T79 26075-26087 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T80 26089-26096 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T81 26107-26109 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T82 26537-26547 Chemical denotes Amino acid http://purl.obolibrary.org/obo/CHEBI_33704
T83 26543-26547 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T84 26656-26658 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T85 27159-27171 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T86 27471-27480 Chemical denotes immunogen http://purl.obolibrary.org/obo/CHEBI_60816
T87 27539-27547 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T88 28339-28346 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T89 28782-28789 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T90 30600-30612 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T91 31745-31753 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T92 31775-31783 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T93 31824-31832 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T94 31958-31966 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T95 33370-33377 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T96 33979-33981 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T97 36053-36058 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212
T98 36732-36734 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T99 37325-37330 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212
T100 39112-39114 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T101 39274-39276 Chemical denotes IQ http://purl.obolibrary.org/obo/CHEBI_42725|http://purl.obolibrary.org/obo/CHEBI_74065
T103 39356-39358 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T104 39684-39691 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T105 39750-39752 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T106 39986-39988 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T107 40039-40041 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T108 44392-44399 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T109 44437-44444 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T110 44482-44492 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T111 44482-44487 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T112 44488-44492 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T113 44802-44807 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212
T114 45033-45044 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T115 45033-45038 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T116 45039-45044 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T117 45062-45072 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T118 45062-45067 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T119 45068-45072 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T120 45390-45397 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T121 45685-45693 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T122 45887-45895 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T123 45907-45915 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T124 45996-46003 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T125 46028-46030 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T126 46274-46282 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T127 46306-46313 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T128 46442-46449 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T129 46890-46897 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T130 47027-47034 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T131 47092-47099 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T132 47369-47371 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T133 49223-49225 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
1 2-12 Species denotes SARS-CoV-2 Tax:2697049
10 586-591 Gene denotes Spike Gene:43740568
11 705-709 Gene denotes ACE2 Gene:59272
12 147-157 Species denotes SARS-CoV-2 Tax:2697049
13 390-400 Species denotes SARS-CoV-2 Tax:2697049
14 547-557 Species denotes SARS-CoV-2 Tax:2697049
15 785-795 Species denotes SARS-CoV-2 Tax:2697049
16 137-145 Disease denotes COVID-19 MESH:C000657245
17 605-610 Mutation denotes D614G p.D614G
29 1011-1016 Gene denotes Spike Gene:43740568
30 1564-1569 Gene denotes Spike Gene:43740568
31 2008-2013 Gene denotes Spike Gene:43740568
32 1150-1197 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
33 1199-1209 Species denotes SARS-CoV-2 Tax:2697049
34 1439-1449 Species denotes SARS-CoV-2 Tax:2697049
35 1610-1620 Species denotes SARS-CoV-2 Tax:2697049
36 2363-2373 Species denotes SARS-CoV-2 Tax:2697049
37 898-906 Disease denotes COVID-19 MESH:C000657245
38 2224-2229 Mutation denotes D614G p.D614G
39 1546-1551 Mutation denotes D614G p.D614G
66 3422-3427 Gene denotes Spike Gene:43740568
67 3429-3430 Gene denotes S Gene:43740568
68 3433-3441 Gene denotes Membrane Gene:43740571
69 3443-3444 Gene denotes M Gene:43740571
70 3447-3455 Gene denotes Envelope Gene:43740570
71 3465-3477 Gene denotes Nucleocapsid Gene:43740575
72 3479-3480 Gene denotes N Gene:43740575
73 3782-3813 Gene denotes angiotensin-converting enzyme 2 Gene:59272
74 3815-3819 Gene denotes ACE2 Gene:59272
75 3643-3644 Gene denotes S Gene:43740568
76 3483-3484 Gene denotes S Gene:43740568
77 2503-2550 Species denotes Severe acute respiratory syndrome coronavirus 2 Tax:2697049
78 2552-2562 Species denotes SARS-CoV-2 Tax:2697049
79 2616-2629 Species denotes Coronaviridae Tax:11118
80 2707-2713 Species denotes humans Tax:9606
81 2893-2910 Species denotes betacoronaviruses Tax:694002
82 2967-2972 Species denotes human Tax:9606
83 2973-2986 Species denotes coronaviruses Tax:11118
84 2998-3008 Species denotes SARS-CoV-2 Tax:2697049
85 3058-3067 Species denotes MERS) CoV Tax:1335626
86 3072-3116 Species denotes severe acute respiratory syndrome (SARS) CoV Tax:694009
87 3118-3126 Species denotes SARS-CoV Tax:694009
88 3155-3160 Species denotes human Tax:9606
89 3170-3180 Species denotes SARS-CoV-2 Tax:2697049
90 2587-2595 Disease denotes COVID-19 MESH:C000657245
91 2768-2795 Disease denotes upper respiratory illnesses MESH:D012141
113 4439-4445 Gene denotes ORF1ab Gene:43740578
114 4478-4479 Gene denotes S Gene:43740568
115 4272-4273 Gene denotes S Gene:43740568
116 4121-4132 Species denotes coronavirus Tax:11118
117 4187-4197 Species denotes SARS-CoV-2 Tax:2697049
118 4249-4263 Species denotes horseshoe bats Tax:49442
119 4340-4350 Species denotes SARS-CoV-2 Tax:2697049
120 4416-4426 Species denotes SARS-CoV-2 Tax:2697049
121 4648-4658 Species denotes SARS-CoV-2 Tax:2697049
122 4739-4756 Species denotes Malayan pangolins Tax:9974
123 4797-4808 Species denotes coronavirus Tax:11118
124 4936-4946 Species denotes SARS-CoV-2 Tax:2697049
125 5337-5347 Species denotes SARS-CoV-2 Tax:2697049
126 5467-5477 Species denotes SARS-CoV-2 Tax:2697049
127 5504-5510 Species denotes humans Tax:9606
128 5584-5594 Species denotes SARS-CoV-2 Tax:2697049
129 5603-5609 Species denotes humans Tax:9606
130 5769-5779 Species denotes SARS-CoV-2 Tax:2697049
131 3874-3882 Disease denotes COVID-19 MESH:C000657245
132 3955-3964 Disease denotes mortality MESH:D003643
133 4070-4076 Disease denotes deaths MESH:D003643
143 5883-5893 Species denotes SARS-CoV-2 Tax:2697049
144 6464-6474 Species denotes SARS-CoV-2 Tax:2697049
145 6630-6643 Species denotes coronaviruses Tax:11118
146 6764-6774 Species denotes SARS-CoV-2 Tax:2697049
147 6880-6888 Species denotes SARS-CoV Tax:694009
148 7235-7245 Species denotes SARS-CoV-2 Tax:2697049
149 6302-6311 Species denotes influenza Tax:11309
150 6153-6161 Disease denotes infected MESH:D007239
151 6219-6227 Disease denotes COVID-19 MESH:C000657245
165 8102-8103 Gene denotes S Gene:43740568
166 7312-7318 Species denotes humans Tax:9606
167 7936-7941 Species denotes Ebola Tax:1570291
168 8077-8087 Species denotes SARS-CoV-2 Tax:2697049
169 8167-8173 Species denotes humans Tax:9606
170 8423-8433 Species denotes SARS-CoV-2 Tax:2697049
171 8452-8458 Species denotes humans Tax:9606
172 8477-8487 Species denotes SARS-CoV-2 Tax:2697049
173 7904-7913 Species denotes influenza Tax:11309
174 7438-7446 Disease denotes infected MESH:D007239
175 7497-7510 Disease denotes viral fitness
176 7527-7540 Disease denotes viral fitness
177 8130-8137 Disease denotes fitness MESH:D012640
179 8704-8714 Species denotes SARS-CoV-2 Tax:2697049
184 8740-8750 Species denotes SARS-CoV-2 Tax:2697049
185 8822-8832 Species denotes SARS-CoV-2 Tax:2697049
186 9185-9195 Species denotes SARS-CoV-2 Tax:2697049
187 8864-8872 Disease denotes infected MESH:D007239
192 9692-9693 Gene denotes M Gene:43740571
193 9702-9703 Gene denotes N Gene:43740575
194 9672-9673 Gene denotes S Gene:43740568
195 9249-9259 Species denotes SARS-CoV-2 Tax:2697049
199 10546-10547 Gene denotes N Gene:43740575
200 11459-11469 Species denotes SARS-CoV-2 Tax:2697049
201 11032-11042 Disease denotes infections MESH:D007239
204 12463-12464 Gene denotes S Gene:43740568
205 12475-12480 Mutation denotes D614G p.D614G
217 12605-12611 Gene denotes ORF1ab Gene:43740578
218 12952-12953 Gene denotes S Gene:43740568
219 12653-12654 Gene denotes S Gene:43740568
220 13985-13995 Species denotes SARS-CoV-2 Tax:2697049
221 12595-12601 Mutation denotes P4715L p.P4715L
222 14050-14055 Mutation denotes D614G p.D614G
223 13710-13715 Mutation denotes D614G p.D614G
224 13317-13322 Mutation denotes D614G p.D614G
225 13243-13248 Mutation denotes D614G p.D614G
226 13054-13059 Mutation denotes D614G p.D614G
227 12644-12649 Mutation denotes D614G p.D614G
239 14634-14640 Gene denotes ORF1ab Gene:43740578
240 14618-14619 Gene denotes S Gene:43740568
241 14362-14363 Gene denotes S Gene:43740568
242 14197-14198 Gene denotes S Gene:43740568
243 14756-14766 Species denotes SARS-CoV-2 Tax:2697049
244 15150-15155 Mutation denotes D614G p.D614G
245 15105-15110 Mutation denotes D614G p.D614G
246 14609-14614 Mutation denotes D614G p.D614G
247 14624-14630 Mutation denotes P4715L p.P4715L
248 14252-14257 Mutation denotes D614G p.D614G
249 14208-14213 Mutation denotes D614G p.D614G
266 16847-16851 Gene denotes ACE2 Gene:59272
267 16934-16938 Gene denotes ACE2 Gene:59272
268 17363-17366 Gene denotes CD8 Gene:925
269 17371-17374 Gene denotes CD4 Gene:920
270 17443-17444 Gene denotes M Gene:43740571
271 17440-17441 Gene denotes N Gene:43740575
272 17437-17438 Gene denotes S Gene:43740568
273 16640-16641 Gene denotes S Gene:43740568
274 15815-15816 Gene denotes S Gene:43740568
275 17425-17435 Species denotes SARS-CoV-2 Tax:2697049
276 17470-17475 Species denotes human Tax:9606
277 17495-17498 Gene denotes HLA Gene:3113
278 16189-16191 Chemical denotes dN MESH:C022306
279 16192-16194 Chemical denotes dS MESH:D003903
280 16657-16662 Mutation denotes D614G p.D614G
281 16351-16356 Mutation denotes D614G p.D614G
283 17868-17878 Species denotes SARS-CoV-2 Tax:2697049
290 18732-18737 Gene denotes ORF10 Gene:43740576
291 18713-18714 Gene denotes M Gene:43740571
292 18031-18032 Gene denotes N Gene:43740575
293 18019-18020 Gene denotes S Gene:43740568
294 18550-18552 Chemical denotes dN MESH:C022306
295 18553-18555 Chemical denotes dS MESH:D003903
297 19466-19476 Species denotes SARS-CoV-2 Tax:2697049
305 21796-21806 Species denotes SARS-CoV-2 Tax:2697049
306 22161-22171 Species denotes SARS-CoV-2 Tax:2697049
307 22397-22407 Species denotes SARS-CoV-2 Tax:2697049
308 22494-22504 Species denotes SARS-CoV-2 Tax:2697049
309 20517-20524 Disease denotes fitness MESH:D012640
310 21580-21593 Disease denotes viral fitness
311 22520-22533 Disease denotes viral fitness
315 23242-23252 Species denotes SARS-CoV-2 Tax:2697049
316 23519-23529 Species denotes SARS-CoV-2 Tax:2697049
317 23776-23786 Species denotes SARS-CoV-2 Tax:2697049
335 25350-25351 Gene denotes S Gene:43740568
336 24365-24366 Gene denotes S Gene:43740568
337 24354-24364 Species denotes SARS-CoV-2 Tax:2697049
338 24465-24475 Species denotes SARS-CoV-2 Tax:2697049
339 24498-24508 Species denotes SARS-CoV-2 Tax:2697049
340 24637-24642 Species denotes human Tax:9606
341 24656-24661 Species denotes human Tax:9606
342 24700-24705 Species denotes human Tax:9606
343 24715-24720 Species denotes human Tax:9606
344 24942-24947 Species denotes human Tax:9606
345 24959-24969 Species denotes SARS-CoV-2 Tax:2697049
346 23977-23985 Disease denotes infected MESH:D007239
347 25527-25535 Disease denotes infected MESH:D007239
348 25819-25824 Mutation denotes D614G p.D614G
349 25381-25386 Mutation denotes D614G p.D614G
350 25808-25814 Mutation denotes P4715L p.P4715L
351 25273-25278 Mutation denotes D614G p.D614G
362 26073-26074 Gene denotes S Gene:43740568
363 25890-25891 Gene denotes S Gene:43740568
364 25879-25889 Species denotes SARS-CoV-2 Tax:2697049
365 25920-25928 Species denotes SARS-CoV Tax:694009
366 25956-25966 Species denotes SARS-CoV-2 Tax:2697049
367 26062-26072 Species denotes SARS-CoV-2 Tax:2697049
368 26504-26509 Species denotes human Tax:9606
369 26713-26723 Species denotes SARS-CoV-2 Tax:2697049
370 26805-26815 Species denotes SARS-CoV-2 Tax:2697049
371 26393-26398 Mutation denotes D614G p.D614G
394 28038-28039 Gene denotes S Gene:43740568
395 27502-27503 Gene denotes S Gene:43740568
396 27463-27464 Gene denotes S Gene:43740568
397 27337-27338 Gene denotes S Gene:43740568
398 27157-27158 Gene denotes S Gene:43740568
399 27039-27049 Species denotes SARS-CoV-2 Tax:2697049
400 27434-27444 Species denotes SARS-CoV-2 Tax:2697049
401 27597-27607 Species denotes SARS-CoV-2 Tax:2697049
402 28197-28207 Species denotes SARS-CoV-2 Tax:2697049
403 28541-28549 Species denotes MERS-CoV Tax:1335626
404 28709-28719 Species denotes SARS-CoV-2 Tax:2697049
405 29001-29011 Species denotes SARS-CoV-2 Tax:2697049
406 28900-28909 Species denotes influenza Tax:11309
407 28495-28499 Chemical denotes D614
408 27135-27143 Disease denotes COVID-19 MESH:C000657245
409 27363-27382 Disease denotes SARS-CoV-2−infected MESH:C000657245
410 28691-28696 Mutation denotes D614G p.D614G
411 28417-28422 Mutation denotes D614G p.D614G
412 28217-28222 Mutation denotes D614G p.D614G
413 28518-28523 Mutation denotes S612L p.S612L
414 28020-28025 Mutation denotes D614G p.D614G
415 29050-29055 Mutation denotes N439K p.N439K
430 29825-29826 Gene denotes S Gene:43740568
431 29149-29159 Species denotes SARS-CoV-2 Tax:2697049
432 29630-29640 Species denotes SARS-CoV-2 Tax:2697049
433 29648-29654 Species denotes humans Tax:9606
434 29736-29744 Species denotes SARS-CoV Tax:694009
435 29787-29797 Species denotes SARS-CoV-2 Tax:2697049
436 30270-30274 Species denotes ncov Tax:2697049
437 29299-29306 Disease denotes fitness MESH:D012640
438 30155-30160 Mutation denotes D614G p.D614G
439 30011-30016 Mutation denotes D614G p.D614G
440 29819-29824 Mutation denotes D614G p.D614G
441 29479-29484 Mutation denotes D614G p.D614G
442 29275-29280 Mutation denotes D614G p.D614G
443 29195-29200 Mutation denotes D614G p.D614G
450 30626-30627 Gene denotes S Gene:43740568
451 30460-30465 Species denotes Ebola Tax:1570291
452 30632-30642 Species denotes SARS-CoV-2 Tax:2697049
453 30897-30902 Species denotes mouse Tax:10090
454 30579-30583 Mutation denotes A82V p.A82V
455 31109-31114 Mutation denotes D614G p.D614G
457 31745-31783 Disease denotes proteins versus nonstructural proteins MESH:D018455
463 32304-32314 Species denotes SARS-CoV-2 Tax:2697049
464 32625-32635 Disease denotes infections MESH:D007239
465 33000-33005 Mutation denotes D614G p.D614G
466 32454-32459 Mutation denotes D614G p.D614G
467 32229-32234 Mutation denotes D614G p.D614G
479 33063-33073 Species denotes SARS-CoV-2 Tax:2697049
480 33423-33433 Species denotes SARS-CoV-2 Tax:2697049
481 33470-33475 Species denotes human Tax:9606
482 33637-33647 Species denotes SARS-CoV-2 Tax:2697049
483 33687-33697 Species denotes SARS-CoV-2 Tax:2697049
484 33865-33870 Species denotes HIV-1 Tax:11676
485 33959-33969 Species denotes SARS-CoV-2 Tax:2697049
486 34136-34146 Species denotes SARS-CoV-2 Tax:2697049
487 34281-34291 Species denotes SARS-CoV-2 Tax:2697049
488 33872-33881 Species denotes influenza Tax:11309
489 33315-33320 Mutation denotes D614G p.D614G
493 35232-35235 Gene denotes Hu1 Gene:3215
494 34618-34628 Species denotes SARS-CoV-2 Tax:2697049
495 35683-35687 Species denotes CoV2 Tax:2697049
497 37644-37647 Species denotes cov Tax:11118
500 39750-39752 Chemical denotes dN MESH:C022306
501 39757-39759 Chemical denotes dS MESH:D003903
504 40949-40952 Gene denotes GST
505 41611-41626 Species denotes other sequences Tax:28384
507 43329-43339 Species denotes SARS-CoV-2 Tax:2697049
513 43410-43420 Species denotes SARS-CoV-2 Tax:2697049
514 43743-43753 Species denotes SARS-CoV-2 Tax:2697049
515 43806-43816 Species denotes SARS-CoV-2 Tax:2697049
516 44079-44089 Species denotes SARS-CoV-2 Tax:2697049
517 44142-44152 Species denotes SARS-CoV-2 Tax:2697049
519 44390-44391 Gene denotes S Gene:43740568
528 44435-44436 Gene denotes S Gene:43740568
529 44509-44519 Species denotes SARS-CoV-2 Tax:2697049
530 44565-44576 Species denotes coronavirus Tax:11118
531 44619-44629 Species denotes SARS-CoV-2 Tax:2697049
532 44635-44648 Species denotes coronaviruses Tax:11118
533 45136-45141 Species denotes human Tax:9606
534 45150-45155 Species denotes human Tax:9606
535 45199-45204 Species denotes human Tax:9606
538 45578-45581 Gene denotes CD4 Gene:920
539 45587-45590 Gene denotes CD8 Gene:925
561 45609-45612 Gene denotes CD4 Gene:920
562 45618-45621 Gene denotes CD8 Gene:925
563 45811-45814 Gene denotes CD4 Gene:920
564 45903-45906 Gene denotes MHC Gene:3107
565 46046-46054 Gene denotes HLA-DQB1 Gene:3119
566 46079-46087 Gene denotes HLA-DPA1 Gene:3113
567 46088-46092 Gene denotes DPB1 Gene:3115
568 46097-46105 Gene denotes HLA-DQA1 Gene:3117
569 46374-46377 Gene denotes CD8 Gene:925
570 46490-46495 Gene denotes HLA-A Gene:3105
571 46497-46502 Gene denotes HLA-B Gene:3106
572 46463-46466 Gene denotes MHC Gene:3107
573 45751-45752 Gene denotes M Gene:43740571
574 45723-45724 Gene denotes N Gene:43740575
575 45695-45696 Gene denotes S Gene:43740568
576 45663-45673 Species denotes SARS-CoV-2 Tax:2697049
577 46018-46021 Gene denotes MHC Gene:3107
578 46508-46511 Gene denotes HLA Gene:3113
579 46250-46253 Gene denotes hla Gene:3113
580 45968-45979 Chemical denotes NetMHCIIPan
581 46416-46425 Chemical denotes NetMHCPan
596 47209-47214 Gene denotes HLA-A Gene:3105
597 47216-47221 Gene denotes HLA-B Gene:3106
598 47399-47407 Gene denotes HLA-DQB1 Gene:3119
599 47409-47417 Gene denotes HLA-DPA1 Gene:3113
600 47418-47422 Gene denotes DPB1 Gene:3115
601 47428-47436 Gene denotes HLA-DQA1 Gene:3117
602 47496-47499 Gene denotes MHC Gene:3107
603 47359-47362 Gene denotes MHC Gene:3107
604 47184-47187 Gene denotes MHC Gene:3107
605 47570-47573 Gene denotes HLA Gene:3113
606 47372-47375 Gene denotes HLA Gene:3113
607 47299-47302 Gene denotes hla Gene:3113
608 47227-47230 Gene denotes HLA Gene:3113
609 47196-47199 Gene denotes HLA Gene:3113

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 2774-2795 Phenotype denotes respiratory illnesses http://purl.obolibrary.org/obo/HP_0002086

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 3563-3576 http://purl.obolibrary.org/obo/GO_0044409 denotes entry to host
T2 5624-5636 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T3 29953-29965 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T4 30225-30237 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T5 30664-30691 http://purl.obolibrary.org/obo/GO_0046718 denotes virus entry into host cells
T6 30670-30685 http://purl.obolibrary.org/obo/GO_0044409 denotes entry into host
T7 31896-31911 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-84 Sentence denotes A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants
T2 86-98 Sentence denotes Significance
T3 99-233 Sentence denotes The rapid spread of the virus causing COVID-19, SARS-CoV-2, raises questions about the possibility of a universally effective vaccine.
T4 234-343 Sentence denotes The virus can mutate in a given individual, and these variants can be propagated across populations and time.
T5 344-439 Sentence denotes To understand this process, we analyze 18,514 SARS-CoV-2 sequences sampled since December 2019.
T6 440-566 Sentence denotes We find that neutral evolution, rather than adaptive selection, can explain the rare mutations seen across SARS-CoV-2 genomes.
T7 567-719 Sentence denotes In the immunogenic Spike protein, the D614G mutation has become consensus, yet there is no evidence of mutations affecting binding to the ACE2 receptor.
T8 720-866 Sentence denotes Our results suggest that, to date, the limited diversity seen in SARS-CoV-2 should not preclude a single vaccine from providing global protection.
T9 868-876 Sentence denotes Abstract
T10 877-973 Sentence denotes The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine.
T11 974-1107 Sentence denotes Many vaccine candidates focus on the Spike protein, as it is targeted by neutralizing antibodies and plays a key role in viral entry.
T12 1108-1295 Sentence denotes Here we investigate the diversity seen in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences and compare it to the sequence on which most vaccine candidates are based.
T13 1296-1405 Sentence denotes Using 18,514 sequences, we perform phylogenetic, population genetics, and structural bioinformatics analyses.
T14 1406-1458 Sentence denotes We find limited diversity across SARS-CoV-2 genomes:
T15 1459-1601 Sentence denotes Only 11 sites show polymorphisms in >5% of sequences; yet two mutations, including the D614G mutation in Spike, have already become consensus.
T16 1602-1787 Sentence denotes Because SARS-CoV-2 is being transmitted more rapidly than it evolves, the viral population is becoming more homogeneous, with a median of seven nucleotide substitutions between genomes.
T17 1788-1956 Sentence denotes There is evidence of purifying selection but little evidence of diversifying selection, with substitution rates comparable across structural versus nonstructural genes.
T18 1957-2193 Sentence denotes Finally, the Wuhan-Hu-1 reference sequence for the Spike protein, which is the basis for different vaccine candidates, matches optimized vaccine inserts, being identical to an ancestral sequence and one mutation away from the consensus.
T19 2194-2384 Sentence denotes While the rapid spread of the D614G mutation warrants further study, our results indicate that drift and bottleneck events can explain the minimal diversity found among SARS-CoV-2 sequences.
T20 2385-2501 Sentence denotes These findings suggest that a single vaccine candidate should be efficacious against currently circulating lineages.
T21 2503-2714 Sentence denotes Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is a member of the Coronaviridae family, a diverse group of virus species, seven of which are known to infect humans.
T22 2715-2911 Sentence denotes Four are considered endemic and typically cause mild upper respiratory illnesses; two of these, NL63 and 229E, are within the alphacoronavirus genus, and two, HKU1 and OC43, are betacoronaviruses.
T23 2912-3117 Sentence denotes The latter genus comprises the three highly pathogenic human coronaviruses, including SARS-CoV-2, as well as Middle Eastern respiratory syndrome (MERS) CoV and severe acute respiratory syndrome (SARS) CoV.
T24 3118-3268 Sentence denotes SARS-CoV is the most closely related human virus to SARS-CoV-2, which is a single-stranded positive-sense RNA virus, with an ∼30,000-base pair genome.
T25 3269-3392 Sentence denotes The genome is split into 10 open reading frames (ORFs) that include 16 nonstructural proteins and four structural proteins.
T26 3393-3482 Sentence denotes The latter category includes Spike (S), Membrane (M), Envelope (E), and Nucleocapsid (N).
T27 3483-3642 Sentence denotes S is the basis for most candidate vaccines, as it mediates virus attachment and entry to host cells and is the target of neutralizing antibody responses (1–4).
T28 3643-3685 Sentence denotes S is cleaved into two subunits, S1 and S2:
T29 3686-3844 Sentence denotes The former contains the receptor binding domain (RBD), which enables the virus to attach to the angiotensin-converting enzyme 2 (ACE2) receptor on host cells.
T30 3845-3996 Sentence denotes In the span of 7 months, the COVID-19 pandemic has caused a devastating global health crisis with significant mortality and socioeconomic implications.
T31 3997-4151 Sentence denotes As of July 23, 2020, more than 15 million cases and 622,000 attributable deaths have been reported worldwide (5–8) (https://coronavirus.jhu.edu/map.html).
T32 4152-4268 Sentence denotes Phylogenetic analyses suggest that SARS-CoV-2 is likely derived from a clade of viruses found in horseshoe bats (9).
T33 4269-4355 Sentence denotes In S, the bat genome RaTG13 has more than 97% amino acid identity with SARS-CoV-2 (6).
T34 4356-4665 Sentence denotes Interestingly, the RmYN02 sequence, which is the closest to SARS-CoV-2 in the long ORF1ab but more distant than RaTG13 in S, showed the insertion of multiple amino acids at the cleavage site between the S1 and S2 subunits of the S protein (this S1/S2 insertion is a characteristic feature of SARS-CoV-2) (10).
T35 4666-4854 Sentence denotes Highly similar sequences, especially in the RBD, were also identified in Malayan pangolins (11, 12), emphasizing the plasticity of coronavirus genomes and their propensity to switch hosts.
T36 4855-5348 Sentence denotes Although the closest currently available bat sequences are fairly divergent from SARS-CoV-2, their characteristics (insertion at S1/S2 cleavage site, high diversity, and similarity between specific gene fragments and particular strains) together with their known adaptive properties (high recombination and host-switching rates and evidence of positive selection) support that these bat viruses constitute a generalist lineage where a specific virus is likely the natural origin of SARS-CoV-2.
T37 5349-5511 Sentence denotes We did not study the transmission of the virus from its animal reservoir and focused our analysis on the evolution of SARS-CoV-2 since its introduction in humans.
T38 5512-5853 Sentence denotes While the scale of the pandemic attests to the high transmissibility of SARS-CoV-2 between humans, with a basic reproduction number R0 estimated to be 2.2 (95% CI, 1.4 to 3.9) in Wuhan, China (13), we wanted to investigate evidence of further adaptation of SARS-CoV-2 to its host, as adaptive processes could interfere with vaccine efficacy.
T39 5854-5977 Sentence denotes Developing a vaccine against SARS-CoV-2 is a high priority for preventing and mitigating future waves of the pandemic (14).
T40 5978-6174 Sentence denotes Vaccine candidates typically include an insert that corresponds to one or more virus antigens, either derived computationally or from one or multiple sequence(s) sampled from infected individuals.
T41 6175-6386 Sentence denotes The first viral sequence derived during the COVID-19 outbreak, Wuhan-Hu-1 (available from the Global initiative on sharing all influenza data, GISAID, accession EPI_ISL_402125), was published on January 9, 2020.
T42 6387-6598 Sentence denotes As many vaccine programs were initiated at that time, it is likely that this SARS-CoV-2 sequence, sampled in December 2019 in Wuhan, China, is the foundation for many vaccine candidates currently in development.
T43 6599-6725 Sentence denotes Compared to other RNA viruses, coronaviruses have a more complex molecular machinery resulting in higher replication fidelity.
T44 6726-7010 Sentence denotes Early evolutionary rate estimates for SARS-CoV-2 were ∼1 × 10−3 substitutions per nucleotide per year (15), a rate comparable to that observed during the SARS-CoV-1 outbreak (16) and in the range for other RNA viruses (1 × 10−3 to 1 × 10−5 substitutions per nucleotide per year) (17).
T45 7011-7256 Sentence denotes While the evolutionary rate is likely to decrease over time (18), it is important to monitor the introduction of any mutation that may compromise the potential efficacy of vaccine candidates derived from the first available SARS-CoV-2 sequences.
T46 7257-7319 Sentence denotes New mutations will be observed as the virus spreads in humans.
T47 7320-7447 Sentence denotes The viral evolutionary dynamics can be characterized by analyzing viral sequences sampled from individuals who became infected.
T48 7448-7511 Sentence denotes The accumulation of mutations can be a marker of viral fitness:
T49 7512-7777 Sentence denotes An increase in viral fitness as the virus adapts to its host will be associated with pervasive mutations at specific sites, whereas a neutral evolution context will be associated with a minimal number of fixed mutations distributed stochastically across the genome.
T50 7778-7955 Sentence denotes Indicators of viral evolution have been shown to be robust predictors of transmission dynamics for several pathogens, such as influenza (19), Lassa (20), and Ebola (21) viruses.
T51 7956-8061 Sentence denotes Typically, the evolution of a virus is driven by genotypic and phenotypic changes in its surface protein.
T52 8062-8174 Sentence denotes In the case of SARS-CoV-2, mutations in S are most likely to confer fitness to the virus as it adapts to humans.
T53 8175-8459 Sentence denotes However, adaptive changes can occur in structural and nonstructural proteins, and these changes, as well as different patterns across structural and nonstructural proteins, may provide insights into the near- and long-term evolutionary dynamics of SARS-CoV-2, as it spreads in humans.
T54 8460-8661 Sentence denotes Here we analyzed SARS-CoV-2 sequences sampled since the beginning of the pandemic and found that mutations were rare, indicating that potential vaccine candidates should cover all circulating variants.
T55 8663-8670 Sentence denotes Results
T56 8672-8723 Sentence denotes Limited Diversity across 18,514 SARS-CoV-2 Genomes.
T57 8724-8901 Sentence denotes To characterize SARS-CoV-2 diversification since the beginning of the epidemic, we aligned 27,977 SARS-CoV-2 genome sequences isolated from infected individuals in 84 countries.
T58 8902-8994 Sentence denotes The alignment was curated to retain independent sequences that covered over 95% of the ORFs.
T59 8995-9239 Sentence denotes In addition, because sequences from the United Kingdom constituted 47% of the dataset (n = 12,157), we sampled a representative set of 5,000 UK sequences, yielding a final dataset of 18,514 SARS-CoV-2 genomes (SI Appendix, Fig. S1 and Fig. 1A).
T60 9240-9247 Sentence denotes Fig. 1.
T61 9249-9440 Sentence denotes SARS-CoV-2 diversity across 18,514 genomes. (A) Distribution representing the location and date of sample collection. (B) Location and frequency of sites with polymorphisms across the genome.
T62 9441-9583 Sentence denotes Proportion of sequences that showed polymorphisms compared to the reference sequence, Wuhan-Hu-1 (GISAID: EPI_ISL_402215, GenBank: NC_045512).
T63 9584-9771 Sentence denotes ORFs are shown in gray for nonstructural proteins and in color for structural proteins (S, purple; E, blue; M, green; N, red). (C) Global phylogeny of 18,514 independent genome sequences.
T64 9772-9875 Sentence denotes The tree was rooted at the reference sequence, Wuhan-Hu-1, and tips are colored by collection location.
T65 9876-9943 Sentence denotes The scale indicates the distance corresponding to one substitution.
T66 9944-9989 Sentence denotes Lineages are labeled following PANGOLIN (22).
T67 9990-10150 Sentence denotes There were 7,559 polymorphic sites (that is, sites where at least one sequence has a change relative to the reference sequence) across the genome (total length:
T68 10151-10171 Sentence denotes 29,409 nucleotides).
T69 10172-10328 Sentence denotes Most substitutions were found in a single sequence; only 8.41% (n = 2,474) of the polymorphic sites showed substitutions in two or more sequences (Fig. 1B).
T70 10329-10449 Sentence denotes Only 11 mutations were found in >5% of sequences, and only 7 were found in >10% of sequences (3 of which were adjacent).
T71 10450-10548 Sentence denotes The mean pairwise diversity across genomes was 0.025%, ranging between 0.01% for E to 0.11% for N.
T72 10549-10654 Sentence denotes A phylogenetic tree reconstructed based on all genome sequences reflected the global spread of the virus:
T73 10655-10749 Sentence denotes Samples from the first 6 wk of the outbreak were collected predominantly from China (Fig. 1C).
T74 10750-10880 Sentence denotes As the epidemic has progressed, samples have been increasingly obtained across Europe and from the United States (Fig. 1 A and C).
T75 10881-11119 Sentence denotes The tree shows numerous introductions of different variants across the globe, with introductions from distant locations seeding local epidemics, where infections sometimes went unrecognized for several weeks and allowed wider spread (23).
T76 11120-11368 Sentence denotes Prior to the severe travel restrictions that were seen in March 2020, intense travel patterns between China, Europe, and the United States allowed transmission of a myriad of variants, which is currently reflected by different lineages in the tree.
T77 11369-11546 Sentence denotes Yet, the tree topology shows minimal structure, even at the genome level, indicating that SARS-CoV-2 viruses have not diverged significantly since the beginning of the pandemic.
T78 11547-11727 Sentence denotes To compare how genomes differed from one another, we calculated Hamming distances (which correspond to the number of differences between two genomes) across all pairs of sequences.
T79 11728-11956 Sentence denotes These Hamming distances showed a narrow distribution, with a median of seven substitutions between two independent genomes, while linked sequences sampled in cruise ships had a median of two substitutions (SI Appendix, Fig. S2).
T80 11957-12186 Sentence denotes Surprisingly, Hamming distances across genomes sampled in the United States did not show a similar quasi-normal distribution but instead a bimodal distribution, observed despite the large number of sequences compared (n = 5,398).
T81 12187-12336 Sentence denotes We identified that this bimodal distribution was driven by sequences from Washington State, possibly reflecting separate introductions in that state.
T82 12337-12457 Sentence denotes Nonetheless, such a bimodal distribution could also indicate a bias in the sampling of sequences (SI Appendix, Fig. S2).
T83 12459-12502 Sentence denotes One S Mutation (D614G) Has Become Dominant.
T84 12503-12823 Sentence denotes Since the beginning of the pandemic, two mutations across the genome have become consensus: P4715L in ORF1ab (nucleotide 14,143, C to T) and D614G in S (nucleotide 23,403, A to G) (Fig. 1B) (a third consensus mutation, at nucleotide 3,037, is not reported as the site was masked during our sequence-filtering procedure).
T85 12824-12927 Sentence denotes These mutations were found in 69.3% and 69.4% of sequences, respectively, and are in linkage (Fig. 2B).
T86 12928-13104 Sentence denotes Given the importance of S for virus entry and as a target of the host neutralizing response, the biologic implications of the D614G mutation are under intense scrutiny (24–28).
T87 13105-13232 Sentence denotes This mutation was first observed in a sequence from China dated January 24, with seven more sequences sampled until February 8.
T88 13233-13299 Sentence denotes Then, the D614G mutation was not observed in China until March 13.
T89 13300-13554 Sentence denotes In contrast, the D614G mutation was introduced in Europe at the end of January (first sequence identified in Germany, dated January 28), and it rapidly became dominant on that continent and at every location where the virus subsequently spread (Fig. 2A).
T90 13555-13666 Sentence denotes The phylogenetic tree (Fig. 2B) and the distribution of sequences (Fig. 2C) are suggestive of a founder effect.
T91 13667-13875 Sentence denotes The rapid spread of sequences carrying the D614G mutation implies that the growing viral population should become more homogeneous, that is, the frequency of sequences with shared polymorphisms will increase.
T92 13876-14027 Sentence denotes We found a median of seven substitutions (based on a comparison of 18,514 sequences) between two independent SARS-CoV-2 genomes (SI Appendix, Fig. S2).
T93 14028-14183 Sentence denotes Yet, genomes with the D614G mutation showed a median of five substitutions, whereas those with D at position 614 differed by eight substitutions (Fig. 2D).
T94 14184-14191 Sentence denotes Fig. 2.
T95 14193-14238 Sentence denotes The S mutation D614G quickly became dominant.
T96 14239-14641 Sentence denotes The mutation D614G was found in 69% of sequences sampled globally as of May 18, 2020, the second most frequent mutation in S was only found in ∼2% of sequences. (A) Number of sequences with D (gray) or G (purple) by continent and sampling date shown cumulatively through the outbreak. (B) Phylogenetic tree reconstructed from all of the ORFs showing the linkage between D614G in S and P4715L in ORF1ab.
T97 14642-14672 Sentence denotes Tips are colored by continent.
T98 14673-14896 Sentence denotes The phylogeny suggests that these mutations were linked to a bottleneck event when SARS-CoV-2 viruses were introduced in Europe; this mutation was first seen in Europe in a sequence sampled in Germany at the end of January.
T99 14897-15292 Sentence denotes There is no evidence that the increasing predominance of this mutation was caused by convergent selection events that would have occurred in multiple individuals. (C) Overall number of sequences with D614 or D614G across continents; the predominance of D614G in Europe is suggestive of a founder event. (D) Distribution of Hamming distances between sequences with D614, G614 or discordant pairs.
T100 15293-15333 Sentence denotes The median is marked with a dashed line.
T101 15334-15609 Sentence denotes To test whether this site was under selection, we used likelihood-based, phylogenetically informed models that assume branch-specific substitution rates (29) and implemented a sampling strategy to circumvent computational limitations imposed by the large number of sequences.
T102 15610-15811 Sentence denotes Subsampled alignments (100 times at a 10% sampling fraction) had diversity estimates statistically similar to the complete alignment for each gene (Mann−Whitney U test, P > 0.09; SI Appendix, Fig. S3).
T103 15812-16240 Sentence denotes In S, only site 614 was estimated to be under diversifying selection in a majority of subsampled alignments (58%); evidence of diversifying selection indicates that genetic diversity increases in the viral population (i.e., there was a higher proportion of mutations causing an amino acid change than not at site 614, or, the nonsynonymous/synonymous substitution rates ratio, dN/dS, was over 1, P < 0.1) (SI Appendix, Fig. S4).
T104 16241-16422 Sentence denotes Because diversifying selection is often associated with the host adaptive response, we considered whether the D614G mutation coincided with targets of antibody and T cell responses.
T105 16423-16554 Sentence denotes Site 614 is at the interface between the S1 and S2 subunits and is thus not highly accessible to antibodies (SI Appendix, Fig. S5).
T106 16555-16723 Sentence denotes Therefore, we predict that antibodies to the native S protein would cross-react with S containing the D614G mutation, in agreement with recent reports (24, 25, 27, 28).
T107 16724-16993 Sentence denotes Many known neutralizing antibodies target the RBD, yet we found little evidence that mutations could affect binding to the ACE2 receptor, as only five shared mutations were identified at contact sites with the ACE2 receptor, and all were found in 10 or fewer sequences.
T108 16994-17087 Sentence denotes Of these, one mutation, at position 489, was synonymous and found in three sequences (0.02%).
T109 17088-17221 Sentence denotes The others were nonsynonymous: G476S (n = 10 sequences, 0.05%), Y453F (n = 5, 0.02%), G446V (n = 3, 0.02%), and A475V (n = 2, 0.01%).
T110 17222-17544 Sentence denotes To predict the potential immune pressure linked to T cell responses, we developed a T cell immunogenicity index which takes into account the CD8 and CD4 epitope repertoires in the structural proteins of SARS-CoV-2 (S, N, M, E) and the frequency of human leukocyte antigen (HLA) alleles or haplotypes in a given population.
T111 17545-17709 Sentence denotes We found that sites with mutations, including 614 in S, were not colocalized with T cell epitopes frequently identified in different populations (SI Appendix, Figs.
T112 17710-17848 Sentence denotes S6 and S7), and there was no significant relationship between the number of mutations and the immunogenicity index (SI Appendix, Fig. S8).
T113 17850-17917 Sentence denotes Most Sites in the SARS-CoV-2 Genome Were under Purifying Selection.
T114 17918-18112 Sentence denotes Using phylogenetically informed models (as described above), we identified two sites, residue 614 in S and 13 in N, that were under diversifying selection in a majority of subsampled alignments.
T115 18113-18428 Sentence denotes For each protein, subsampled alignments tended to have more sites under purifying selection (median = 7.34 ± 4.06% [±SD]) than under diversifying selection (3.10 ± 1.92%) (Mann−Whitney U test, P = 0.057; SI Appendix, Fig. S4) (purifying selection is indicative of a decrease in genetic diversity in the population).
T116 18429-18640 Sentence denotes Likewise, for each codon separately, the proportion of each phylogeny (i.e., the percentage of total branch length) with dN/dS > 1 was small, indicating diversifying selection was episodic and limited (Fig. 3A).
T117 18641-18865 Sentence denotes Global measures of dN/dS varied across genes, ranging from 0.35 ± 0.02 (M) to 1.43 ± 0.24 (ORF10), and were significantly lower for structural genes compared to nonstructural genes (Mann−Whitney U test, P = 0.042) (Fig. 3B).
T118 18866-19162 Sentence denotes Per-lineage nonsynonymous substitution rates were comparable (Student’s t test, P = 0.218) in structural (0.0011 ± 0.021) and nonstructural (0.0012 ± 0.028) genes, although some subsampled alignments showed rates that could be a hundred times higher than the median over all alignments (Fig. 3C).
T119 19163-19435 Sentence denotes Across structural proteins, mutations were disproportionately neutral: >70.3% of branch length evolved under neutral (or negative) selection for all sites, and over half of all branch length evolved under neutral (or negative) selection for >82.8% of sites (Fig. 3D) (29).
T120 19436-19443 Sentence denotes Fig. 3.
T121 19445-19662 Sentence denotes Evolution across the SARS-CoV-2 genome. (A) Bar plot of the average percentage of branch length under diversifying selection (dN/dS > 1) for each site. (B) Bar plot of dN/dS per gene (dN = dS is shown as dashed line).
T122 19663-19823 Sentence denotes Error bars indicate SD across subsampled alignments. (C) Box plot of nonsynonymous substitutions per lineage per site across structural and nonstructural genes.
T123 19824-20038 Sentence denotes Values across subsampled alignments for each gene are plotted. (D) Average percentage (over subsampled alignments) of branch lengths evolving under neutral (or negative) selection per site for each structural gene.
T124 20039-20079 Sentence denotes Median values are shown by dashed lines.
T125 20081-20136 Sentence denotes No Evidence of Differentiation of the Viral Population.
T126 20137-20349 Sentence denotes While there was only limited evidence of diversification at selected sites, we also assessed whether subpopulations among the globally circulating viral population had become genetically differentiated over time.
T127 20350-20568 Sentence denotes To do so, we used two measures of population differentiation, the GST and D statistics, which characterize changes in allele frequency across populations and can show fitness differences between subpopulations (30–32).
T128 20569-20698 Sentence denotes Genetic distances between two subpopulations can range between 0 and 1, indicating no and complete differentiation, respectively.
T129 20699-20870 Sentence denotes We initially compared 30 genomes sampled from the initial outbreak in Wuhan, China, with subsampled alignments of the 18,484 genomes sampled subsequently across the globe.
T130 20871-21150 Sentence denotes Although distances varied across genes, the median genetic distance between these subpopulations was small for both GST (0.0049 ± 0.0047) and D (0.0053 ± 0.0272), indicating little differentiation between the initial outbreak and its global derivatives in the pandemic (Fig. 4A).
T131 21151-21230 Sentence denotes We then compared subpopulations sampled before and after each consecutive week.
T132 21231-21417 Sentence denotes Similarly, genetic distances between subpopulations were small for both GST (0.0058 ± 0.0096) and D (0.0098 ± 0.0650) and tended to narrow over time rather than diverge (Fig. 4 B and C).
T133 21418-21512 Sentence denotes Signatures of host adaptation can also be seen in the branching patterns of viral phylogenies.
T134 21513-21708 Sentence denotes Bursts in transmissibility are emblematic of increases in relative viral fitness and are reflected in imbalances in the phylogeny, which can be estimated at each internal node (SI Appendix, Figs.
T135 21709-21729 Sentence denotes S9 and S10) (33–35).
T136 21730-22019 Sentence denotes We estimated phylogenetic η (36, 37) at each internal node of the SARS-CoV-2 phylogeny reconstructed from subsampled (10%) alignments and compared the distribution of estimates through time to phylogenies simulated under models of neutral and positive time-dependent rates (b(t) = beα(t)).
T137 22020-22131 Sentence denotes Simulation analyses demonstrated that this metric was robust against sampling fraction (SI Appendix, Fig. S10).
T138 22132-22382 Sentence denotes The distribution of η in the SARS-CoV-2 phylogenies adhered to expectations of the neutral model and deviated significantly (Student’s t test, P < 0.001) from those of positive time-dependent rates for selection coefficients α ≥ 0.2 (Fig. 4 D and E).
T139 22383-22542 Sentence denotes Together, the SARS-CoV-2 population and phylogenetic dynamics showed little evidence that the global spread of SARS-CoV-2 was related to viral fitness effects.
T140 22543-22550 Sentence denotes Fig. 4.
T141 22552-22894 Sentence denotes Limited evidence of adaptation of the viral population. (A–C) Bootstrapped global estimates of Nei’s GST and Jost’s D for population differentiation for each structural gene. (A) Estimates of Nei’s GST (closed circles) and Jost’s D (open circles) comparing sequences sampled from the Hubei province to sequences subsequently sampled globally.
T142 22895-22999 Sentence denotes Estimates of (B) Nei’s GST and (C) Jost’s D comparing sequences sampled before or after a specific date.
T143 23000-23676 Sentence denotes Lines connect the median estimates across datasets for each gene. (D) Ln-transformed phylogenetic η, indicative of the number of iterative events in the sampled subtree, for subtrees from each internal node (after the root) of a down-sampled SARS-CoV-2 whole-genome phylogeny (dark gray), of a phylogeny simulated under neutral parameters (gold), and of a phylogeny simulated under positive time-dependent rates (b(t) = 0.01e0.4t, green). (E) Box plot of ln-transformed phylogenetic η estimates across all down-sampled SARS-CoV-2 whole-genome phylogenies, phylogenies simulated under neutral parameters, and phylogenies simulated under different positive time dependencies, α.
T144 23677-23837 Sentence denotes Asterisks indicate significant differences in mean values (Student’s t test, P < 0.05) between the SARS-CoV-2 and positive time-dependent phylogenies at each α.
T145 23839-23891 Sentence denotes Sequence Identity with Potential Vaccine Candidates.
T146 23892-24165 Sentence denotes Typical vaccine design strategies rely on either 1) selecting sequences sampled from infected individuals or 2) computationally deriving sequences that cover the diversity seen across circulating sequences and are, in theory, optimal compared to an individual isolate (38).
T147 24166-24312 Sentence denotes Computationally derived sequences include consensus and ancestral sequences, such as the most recent common ancestor (MRCA) of a set of sequences.
T148 24313-24600 Sentence denotes We inferred the MRCA corresponding to 1) SARS-CoV-2 S sequences sampled from Wuhan within the first month of the epidemic, 2) all currently circulating SARS-CoV-2 sequences, and 3) all SARS-CoV-2 sequences together with closely related sequences sampled from pangolins (n = 6) and a bat.
T149 24601-24735 Sentence denotes There were 17 mutations between the human MRCA and the human−bat MRCA and 44 mutations between the human MRCA and human−pangolin MRCA.
T150 24736-24906 Sentence denotes Overall, three segments in S reflected significant variability across species (AA 439 to 445, 482 to 501, and 676 to 690) (Fig. 5 A and C and SI Appendix, Fig. S11) (39).
T151 24907-24992 Sentence denotes In contrast, when considering only human sequences, SARS-CoV-2 diversity was limited:
T152 24993-25140 Sentence denotes Both MRCAs (derived from early sequences from Wuhan or from all circulating sequences) were identical to the initial reference sequence Wuhan-Hu-1.
T153 25141-25289 Sentence denotes Comparing these sequences to the consensus sequence derived from all of the sequences sampled to date, there was only one mutation: D614G (Fig. 5B).
T154 25290-25372 Sentence denotes Fig. 5D illustrates that mutations found across circulating S sequences were rare:
T155 25373-25674 Sentence denotes Besides D614G (found in 69.4% of sequences), the next most frequent substitution is found in 1.96% of sequences (synonymous), with sequences sampled from infected individuals, on average, 0.55 mutations away from the consensus sequence (consisting of 0.12 synonymous and 0.43 nonsynonymous mutations).
T156 25675-25852 Sentence denotes Across the genome, there were, on average, 4.05 nucleotide mutations per individual genome when compared to the consensus, with only P4715L and D614G found in >50% of sequences.
T157 25853-25860 Sentence denotes Fig. 5.
T158 25862-26160 Sentence denotes Mutations across SARS-CoV-2 S sequences. (A) Structure of SARS-CoV (5 × 58) (shown instead of SARS-CoV-2 for completeness of the Receptor Binding Motif [RBM]). (B–D) The three protomers in the closed SARS-CoV-2 S glycoprotein (Protein Data Bank ID code 6VXX) are colored in yellow, cyan, and white.
T159 26161-26254 Sentence denotes Sites with mutations are shown as spheres. (B) Near-identity of potential vaccine candidates.
T160 26255-26400 Sentence denotes The MRCA and Wuhan-Hu-1 reference sequences were identical, while the consensus derived from all circulating sequences showed a mutation (D614G).
T161 26401-26536 Sentence denotes Site 614 is located at the interface between two subunits. (C) Sequence segments that differed between human and pangolin or bat hosts.
T162 26537-26746 Sentence denotes Amino acid segments 439 to 455 and 482 to 501 impact receptor binding, while the 574 to 690 segment corresponds to the S2 cleavage site. (D) Sites with shared mutations across SARS-CoV-2 circulating sequences.
T163 26747-26914 Sentence denotes The colors of the spheres correspond to the proportion of SARS-CoV-2 sequences that differed from the Wuhan-Hu-1 sequence (GISAID: EPI_ISL_402125, GenBank: NC_045512).
T164 26915-26991 Sentence denotes Mutations that were found only in one or two sequences were not represented.
T165 26993-27003 Sentence denotes Discussion
T166 27004-27144 Sentence denotes There remains an urgent need for a SARS-CoV-2 vaccine as a primary countermeasure to mitigate and eventually contain the spread of COVID-19.
T167 27145-27296 Sentence denotes The virus’s S glycoprotein makes an attractive vaccine target because it plays a key role in mediating virus entry and is known to be immunogenic (40).
T168 27297-27481 Sentence denotes Neutralizing antibody responses against S have been identified in SARS-CoV-2−infected individuals (2), and several clinical trials for a SARS-CoV-2 vaccine will test S as an immunogen.
T169 27482-27576 Sentence denotes While we focused on S, our comparative analyses of other proteins yielded similar conclusions:
T170 27577-27832 Sentence denotes A randomly selected SARS-CoV-2 sequence could be used as a vaccine candidate, given the similarity of any sequence to the computationally derived optimum vaccine candidate (as defined by the MRCAs or consensus sequence based on all circulating sequences).
T171 27833-27949 Sentence denotes Vaccines developed using any of these sequences should, theoretically, be effective against all circulating viruses.
T172 27950-28088 Sentence denotes Vaccine developers could consider designing a vaccine insert with the D614G mutation in S, as this mutation has become dominant worldwide.
T173 28089-28223 Sentence denotes While mutations that become fixed are often linked to the host immune pressure, this seems unlikely for the SARS-CoV-2 mutation D614G.
T174 28224-28388 Sentence denotes Because this residue lies at the interface between two subunits, it would not be expected to be part of a critical epitope for vaccine-mediated protection (Fig. 4).
T175 28389-28505 Sentence denotes As such, pseudoviruses with D614G were as susceptible to neutralization as those with the initial residue D614 (25).
T176 28506-28790 Sentence denotes A mutation, S612L, that emerged in MERS-CoV after passaging the virus in the presence of two antibodies (in 5/15 clones after 20 passages) (41) warrants the evaluation of the analogous D614G mutation in SARS-CoV-2 for its ability to interfere with the recognition of a distal epitope.
T177 28791-28919 Sentence denotes A more direct path to viral escape from antibody recognition would be mutations in the RBD, as described for influenza (42, 43).
T178 28920-29125 Sentence denotes Importantly, we found no mutation in the RBD that was present in more than 1% of SARS-CoV-2 sequences (highest frequency was 0.2% N439K); such rare variants are unlikely to interfere with vaccine efficacy.
T179 29126-29312 Sentence denotes In the context of rare SARS-CoV-2 mutations, the rapid spread of the D614G mutation is singular and has led authors to hypothesize that viruses with D614G may have enhanced fitness (24).
T180 29313-29493 Sentence denotes The strongest evidence of a biological effect for this mutation comes from recent reports of an increase in in vitro infectivity or cell entry for pseudoviruses with D614G (25–28).
T181 29494-29722 Sentence denotes Additional work is needed to evaluate whether the increase in infectivity in vitro translates to increased transmissibility (spread) of SARS-CoV-2 across humans, as there is not necessarily a linear relationship between the two.
T182 29723-29842 Sentence denotes For example, SARS-CoV mediates cell entry more efficiently than SARS-CoV-2 (with or without the D614G S mutation) (26).
T183 29843-30026 Sentence denotes Hence, it would be important to understand whether, controlling for epidemiological factors, there are higher reproduction numbers associated with viruses carrying the D614G mutation.
T184 30027-30373 Sentence denotes While a preliminary comparison of the lineages with either D or G in Washington State did not indicate an obvious advantage for D614G mutants, as they found similar maximal values for the effective reproduction number (https://github.com/blab/ncov-wa-phylodynamics), additional comparisons in different geographic locations should be informative.
T185 30374-30448 Sentence denotes Correlating in vitro findings with clinical phenotypes can be complicated.
T186 30449-30561 Sentence denotes During the Ebola outbreak of 2013–2016, some fixed mutations were suspected to confer an advantage to the virus.
T187 30562-30748 Sentence denotes Specifically, an A82V mutation in the glycoprotein, which, like S for SARS-CoV-2, is critical for the virus entry into host cells, was associated with an increase in infectivity (44–46).
T188 30749-31034 Sentence denotes Yet, effects varied across cell types (47), and no phenotypic differences were associated with the mutations when viruses were evaluated in vivo in mouse and nonhuman primate models (48), highlighting the difficulty in linking biological mechanisms to outcomes at the population level.
T189 31035-31141 Sentence denotes So far, no causal association has been identified between the presence of D614G and disease severity (24).
T190 31142-31376 Sentence denotes These findings, together with our results, illustrate that mutations can spread through the population without necessarily having a selective advantage, especially at the beginning of an epidemic when most individuals are susceptible.
T191 31377-31504 Sentence denotes Mutations occur more frequently after a host switch, and even slightly deleterious mutations may have an opportunity to spread.
T192 31505-31631 Sentence denotes Hence, the main signal in our study was one of purifying selection that can ultimately eliminate mildly deleterious mutations.
T193 31632-32111 Sentence denotes Our analyses showed limited evidence of diversifying selection, with comparable substitution rates in structural proteins versus nonstructural proteins (under a selection paradigm, structural proteins which are essential for viral entry and the target of the host immune response would have higher rates than the nonessential proteins), low estimates of genetic differentiation following the initial outbreak, and phylogenetic patterns adhering to a neutral process of evolution.
T194 32112-32235 Sentence denotes These data indicate that epidemiologic factors could be sufficient to explain the global spread of mutations such as D614G.
T195 32236-32402 Sentence denotes A founder effect means that these mutations were likely exported to SARS-CoV-2 naive areas early in the outbreak and therefore given the opportunity to spread widely.
T196 32403-32539 Sentence denotes As such, on January 28, 2020, a virus carrying the D614G mutation, which was rare among sequences from China, was identified in Germany.
T197 32540-32743 Sentence denotes Host and environmental factors permitted the establishment of a sustained cluster of infections that propagated this mutation until it became dominant among European sequences and then globally (Fig. 2).
T198 32744-32906 Sentence denotes We found no evidence that the frequent identification of this mutation was caused by convergent selection events that would have occurred in multiple individuals.
T199 32907-33015 Sentence denotes Further analyses are needed to characterize the biologic mechanisms behind the spread of the D614G mutation.
T200 33016-33240 Sentence denotes In summary, our results indicate that, so far, SARS-CoV-2 has evolved through a nondeterministic, noisy process and that random genetic drift has played a dominant role in disseminating unique mutations throughout the world.
T201 33241-33422 Sentence denotes Yet, it is important to note that founder effects do not exclude that the D614G can confer distinguishing properties in terms of protein stability, infectivity, or transmissibility.
T202 33423-33566 Sentence denotes SARS-CoV-2 was only recently identified in the human population—a short time frame relative to adaptive processes that can take years to occur.
T203 33567-33779 Sentence denotes Although we cannot predict whether adaptive selection will be seen in SARS-CoV-2 in the future, the key finding is that SARS-CoV-2 viruses that are currently circulating constitute a homogeneous viral population.
T204 33780-34002 Sentence denotes Viral diversity has challenged vaccine development efforts for other viruses such as HIV-1, influenza, or Dengue, but these viruses each constitute a more diverse population than SARS-CoV-2 viruses (SI Appendix, Fig. S12).
T205 34003-34292 Sentence denotes We can therefore be cautiously optimistic that viral diversity should not be an obstacle for the development of a broadly protective SARS-CoV-2 vaccine, and that vaccines in current development should elicit responses that are reactive against currently circulating variants of SARS-CoV-2.
T206 34294-34315 Sentence denotes Materials and Methods
T207 34317-34331 Sentence denotes Sequence Data.
T208 34332-34396 Sentence denotes Sequences were downloaded from GISAID (https://www.gisaid.org/).
T209 34397-34577 Sentence denotes A full list, along with the originating and submitting laboratories (GISAID_acknowledgment_table_20200518.xls), is available at https://www.hivresearch.org/publication-supplements.
T210 34579-34613 Sentence denotes Sequence Processing and Filtering.
T211 34614-34834 Sentence denotes All SARS-CoV-2 sequences available on GISAID as of May 18, 2020 (n = 27,989) were downloaded and deduplicated where possible, and those missing accurate dates (that is, only recording the month and/or year) were removed.
T212 34835-34916 Sentence denotes Sequences were processed using the Biostrings package (version 2.48.0) in R (49).
T213 34917-35112 Sentence denotes Sequences known to be linked through direct transmission were removed, and only the sample with the earliest date (chosen at random when multiple samples were taken on the same day) was retained.
T214 35113-35275 Sentence denotes Sequences were then aligned with Mafft v7.467 using the -addfragments option to align to the reference sequence (Wuhan-Hu1, GISAID accession EPI_ISL_402125) (50).
T215 35276-35451 Sentence denotes Insertions relative to Wuhan-Hu-1 were removed, and the 5′ and 3′ ends of sequences (where coverage was low) were excised, resulting in an alignment consisting of the 10 ORFs.
T216 35452-35756 Sentence denotes Any sequences with less than 95% coverage of the ORFs (i.e., >5% gaps) were removed, and 30 homoplasic sites likely due to sequencing artifacts identified by de Maio et al. were masked (https://github.com/W-L/ProblematicSites_SARS-CoV2/blob/master/archived_vcf/problematic_sites_sarsCov2.2020-05-27.vcf).
T217 35757-36078 Sentence denotes To identify individual sequences that were much more divergent than expected, given their sampling date, which likely reflected sequencing artifacts rather than evolution, we obtained a tree using FastTree v2.10.1 compiled with double precision under the general time reversible (GTR) model with gamma heterogeneity (51).
T218 36079-36222 Sentence denotes This tree was rooted at the reference sequence, and root-to-tip regression was performed following TempEst using the ape package in R (52, 53).
T219 36223-36322 Sentence denotes Outliers were defined as sequences that had studentized residuals greater than 3, and were removed.
T220 36323-36452 Sentence denotes Sequences from the United Kingdom corresponded to nearly half of the sequences (n = 12,157/25,671, 47%) of this filtered dataset.
T221 36453-36754 Sentence denotes To avoid overrepresentation of the UK sequences and bias in subsequent analyses, we investigated the effect of downsampling sequences on the mean Hamming distance and identified the minimum number of sequences required to recover the mean corresponding to the full distribution (SI Appendix, Fig. S1).
T222 36755-36954 Sentence denotes A subsample of 5,000 sequences satisfied these criteria, and also ensured that there were fewer sequences from the United Kingdom than from the United States (n = 5,398), reflecting the epidemiology.
T223 36955-37077 Sentence denotes These 5,000 sequences were sampled randomly, with weight proportional to the number of UK sequences collected on that day.
T224 37078-37176 Sentence denotes After these filtering steps, the alignment used for subsequent analyses included 18,514 sequences.
T225 37178-37209 Sentence denotes Global Phylogeny and Evolution.
T226 37210-37388 Sentence denotes The global phylogeny was reconstructed in FastTree v2.10.1 compiled with double precision under the GTR model with gamma heterogeneity (51), and rooted at the reference sequence.
T227 37389-37436 Sentence denotes The tree was visualized using ggtree in R (54).
T228 37437-37667 Sentence denotes Lineages were defined using PANGOLIN (Phylogenetic Assignment of Named Global Outbreak LINeages), with lineages with >200 taxa as of the May 19 summary being highlighted in the tree (22) (https://github.com/cov-lineages/lineages).
T229 37668-37848 Sentence denotes The number of polymorphic sites was calculated as the number of sites which had at least one mutation relative to the reference sequence, Wuhan-Hu-1, ignoring gaps and ambiguities.
T230 37850-37880 Sentence denotes Pairwise Distance Comparisons.
T231 37881-38036 Sentence denotes For each pair of sequences, we calculated the Hamming distance as the number of sites that are different after removing sites with ambiguities and/or gaps.
T232 38037-38203 Sentence denotes For computational efficiency, given the size of the alignment, this was implemented in parallel in C++, using Bazel (https://bazel.build/) to build on a Linux system.
T233 38204-38304 Sentence denotes This implementation is available to download at https://www.hivresearch.org/publication-supplements.
T234 38306-38334 Sentence denotes Subsampling Gene Alignments.
T235 38335-38415 Sentence denotes Alignments for each gene were subsampled for sequence and phylogenetic analyses.
T236 38416-38520 Sentence denotes Each gene alignment was randomly subsampled 100 times per collection date at 5%, 10%, 20%, 30%, and 40%.
T237 38521-38613 Sentence denotes When fewer than 10 sequences were available for a collection date, all sequences were taken.
T238 38614-38691 Sentence denotes Median Hamming distances were computed for each set of subsampled alignments.
T239 38692-38834 Sentence denotes These were bootstrapped 100,000 times, and 95% CIs were estimated and compared to the median Hamming distance for the fully sampled alignment.
T240 38836-38909 Sentence denotes Global and Site-Specific Nonsynonymous and Synonymous Substitution Rates.
T241 38910-38990 Sentence denotes Alignments subsampled at 10% 100 times were used to estimate substitution rates.
T242 38991-39187 Sentence denotes For the set of subsampled alignments for each gene, a mixed-effect likelihood method was used to estimate nonsynonymous (dN) and synonymous (dS) substitution rates globally and at each codon (29).
T243 39188-39410 Sentence denotes Maximum-likelihood phylogenies were constructed for each alignment using the software IQ-TREE (55) under a best-fit model determined with ModelFinder (56) to prime the dN and dS estimates before branch length optimization.
T244 39411-39465 Sentence denotes This step serves to expedite the optimization process.
T245 39466-39579 Sentence denotes Branch length optimization was done with a MG94 model [which is the only model available for this analysis (29)].
T246 39580-39783 Sentence denotes The proportion of each phylogeny evolving under neutral (or negative) selection was determined from the mixture density across lineages for each site, assuming different dN and dS along each branch (57).
T247 39784-39997 Sentence denotes On the same set of subsampled alignments and phylogenies, a fixed-effects likelihood method was used on internal branches to identify sites under pervasive diversifying selection and to estimate global dN/dS (58).
T248 39998-40307 Sentence denotes Known biases associated with calculating dN/dS on exponentially growing populations (59) were counterbalanced by subsampling phylogenies, as the typical approach to address this bias, which is to ignore terminal branches, would considerably diminish the power of the analysis to detect any significant result.
T249 40308-40678 Sentence denotes As P values from the fixed-effect likelihood method are uncorrected, results were not averaged over P values; rather, given that P value calculations are conservative for this analysis (58), sites were considered to be under pervasive diversifying selection if their P value was <0.1 in ≥50% of alignments, which would account for a typical 5% false discovery rate (58).
T250 40680-40732 Sentence denotes Global and Gene-Specific Population Differentiation.
T251 40733-40821 Sentence denotes Alignments subsampled at 10% 100 times were used to estimate population differentiation.
T252 40822-40953 Sentence denotes The genetic differentiation of subpopulations within sampled sequences was calculated on each gene separately using Nei’s (30) GST.
T253 40954-41281 Sentence denotes Because comparisons between subpopulations of different sizes can bias genetic differentiation estimates (60), genetic differentiation was also calculated using Jost’s (31) D, which accounts for differences in genetic heterogeneity between subpopulations and is intended to correct for biases in the size of the subpopulations.
T254 41282-41353 Sentence denotes Both statistics were computed with the mmod package (32) in R (v3.6.1).
T255 41354-41456 Sentence denotes For each gene, statistics were calculated over 100 bootstrapped samples for each subsampled alignment.
T256 41457-41497 Sentence denotes Subpopulations were defined in two ways.
T257 41498-41657 Sentence denotes First, sequences originating from the initial outbreak in the Hubei province (30 sequences) were compared to all other sequences within a subsampled alignment.
T258 41658-41853 Sentence denotes Second, a 1-wk sliding window was designed to compare all sequences sampled prior to a collection date (subpopulation 1) to all sequences sampled after the same collection date (subpopulation 2).
T259 41854-42102 Sentence denotes The first collection date for subpopulation 1 was February 14, 2020, the week after the last sequence from the Hubei province was sampled (February 8, 2020), The window was designed to terminate when <30 sequences were available in subpopulation 2.
T260 42104-42161 Sentence denotes Time-Dependent Estimates of Phylogenetic Diversification.
T261 42162-42501 Sentence denotes Time-dependent estimates of phylogenetic diversification were measured by extracting the branches descending from each internal node (above the root) of each phylogeny and calculating the peak height (η) of the spectral density profile of the graph Laplacian of each subtree, which is a measure of the density of branching events (36, 37).
T262 42502-42616 Sentence denotes The code to perform the analysis is available for download at https://www.hivresearch.org/publication-supplements.
T263 42618-42638 Sentence denotes Simulation analyses.
T264 42639-42950 Sentence denotes Phylogenies were simulated using a time-forward branching process under constant birth rates (b(t)=b) and time-dependent birth rates (b(t)=beαt) for b = 0.01, 0.03, 0.05, 0.07, and 0.09 and α = ±0.01, ±0.11, ±0.21, ±0.31, and ±0.41, for 20, 220, 420, 620, and 820 tips, and for 1, 11, 21, 31, and 41 time units.
T265 42951-43020 Sentence denotes Simulated phylogenies were downsampled at 0%, 10%, 30%, 50%, and 70%.
T266 43021-43071 Sentence denotes For each scenario, 100 phylogenies were simulated.
T267 43072-43193 Sentence denotes Time-dependent diversification (i.e., η across subtrees) was calculated for each phylogeny simulated under each scenario.
T268 43194-43312 Sentence denotes Simulations were conducted using the R packages RPANDA (R Phylogenetic ANalyses of DiversificAtion) (61) and ape (53).
T269 43314-43350 Sentence denotes Comparisons to SARS-CoV-2 phylogeny.
T270 43351-43598 Sentence denotes Phylogenies downsampled at 10% from the full (18,514 tips) SARS-CoV-2 genome phylogeny (following the subsampling strategy described above) were used to calculate the phylogenetic η for each subtree (above the root) for each downsampled phylogeny.
T271 43599-43764 Sentence denotes Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny.
T272 43765-43829 Sentence denotes This was iterated across all downsampled SARS-CoV-2 phylogenies.
T273 43830-44100 Sentence denotes Positive time-dependent phylogenies were simulated using a time-dependent process (b(t)=0.01eαt) for α = 0.001, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, and 1, with branch lengths restricted to the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny.
T274 44101-44176 Sentence denotes This was iterated across all downsampled SARS-CoV-2 phylogenies for each α.
T275 44177-44269 Sentence denotes Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction.
T276 44270-44304 Sentence denotes Polytomies were randomly resolved.
T277 44305-44378 Sentence denotes Simulations were conducted using the R packages RPANDA (61) and ape (53).
T278 44380-44424 Sentence denotes Ancestral S Protein Sequence Reconstruction.
T279 44425-44827 Sentence denotes Ancestral S protein sequences were reconstructed from an amino acid alignment of 30 SARS-CoV-2 sequences sampled from the Hubei province, a coronavirus sampled from bat (Yunnan RaTG13), and six SARS-CoV-2-like coronaviruses sampled from pangolins using maximum posterior probability and returning a unique residue at each site assuming a Jones-Taylor-Thornton (JTT) model with gamma heterogeneity (62).
T280 44828-44904 Sentence denotes The JTT model was the most appropriate model available in the software (62).
T281 44905-45009 Sentence denotes The bat sequence was retrieved from GenBank, and the pangolin sequences were retrieved from GISAID (63).
T282 45010-45224 Sentence denotes A sliding window of 10 amino acids (and a step of 1 amino acid) was used to compare the cumulative number of mutations in the human−bat and human−bat−pangolin ancestors with respect to the human ancestral sequence.
T283 45225-45442 Sentence denotes Median values for each window were compared to a null window (computed as a normal distribution of 10 values with a mean equal to the mean value across the entire S protein, 0.046 mutations) using a one-tailed t test.
T284 45443-45562 Sentence denotes An alignment including the reconstructed sequences is available at https://www.hivresearch.org/publication-supplements.
T285 45564-45608 Sentence denotes Prediction of CD4+ and CD8+ T Cell Epitopes.
T286 45609-45694 Sentence denotes CD4+ and CD8+ T cell epitopes were predicted for four SARS-CoV-2 structural proteins:
T287 45695-45810 Sentence denotes S (accession YP_009724390), N (accession YP_009724397), M (accession YP_009724393), and E (accession YP_009724392).
T288 45811-46017 Sentence denotes CD4+ T cell epitopes were predicted using a server that predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks, NetMHCIIPan 4.0 (64) with a peptide length of 15.
T289 46018-46261 Sentence denotes MHC class II HLA alleles of HLA-DQB1, plus the haplotypes of HLA-DPA1-DPB1 and HLA-DQA1-DPB, were selected for predictions if they had frequencies of >1/1,000 in known allele/haplotype distributions (http://17ihiw.org/17th-ihiw-ngs-hla-data/).
T290 46262-46373 Sentence denotes If multiple peptides had the same core, the peptide with the strongest binding score was selected for analysis.
T291 46374-46462 Sentence denotes CD8+ T cell epitopes were predicted using NetMHCPan 4.1 (64) with a peptide length of 9.
T292 46463-46717 Sentence denotes MHC class I HLA alleles of HLA-A, HLA-B, and HLA-C were selected if they were classified as common (frequency ≥ 1/10,000) in any of the populations in the database CIWD 3.0 (Common, Intermediate and Well-Documented HLA Alleles in World Populations) (65).
T293 46718-46830 Sentence denotes Epitopes predicted as strong binders (with predicted binding affinities below 50 nM) were selected for analyses.
T294 46832-46860 Sentence denotes T Cell Immunogenicity Index.
T295 46861-47101 Sentence denotes For each site in a predicted epitope, the immunogenicity index was defined as the sum of the frequency of the HLA alleles or haplotypes restricting the corresponding epitope (multiple epitopes can be predicted at a given site in a protein).
T296 47102-47442 Sentence denotes Total frequencies from CIWD 3.0 were used as the frequencies of the corresponding MHC class I HLA alleles (HLA-A, HLA-B, and HLA-C), and the global frequencies from http://17ihiw.org/17th-ihiw-ngs-hla-data/ were used as the frequencies of the corresponding MHC class II HLA alleles or haplotypes (HLA-DQB1, HLA-DPA1-DPB1, and HLA-DQA1-DPB).
T297 47443-47592 Sentence denotes This procedure was repeated using the frequencies of MHC alleles or haplotypes in different subpopulations listed in the above HLA frequency dataset.
T298 47594-47615 Sentence denotes Statistical Analyses.
T299 47616-47703 Sentence denotes For comparisons of mean values in normally distributed data, Student’s t test was used.
T300 47704-47764 Sentence denotes When data were not normal, the Mann−Whitney U test was used.
T301 47765-47817 Sentence denotes Shapiro−Wilk tests were used to determine normality.
T302 47818-47901 Sentence denotes Differences in data distributions were estimated using the Kolmogorov−Smirnov test.
T303 47903-47925 Sentence denotes Supplementary Material
T304 47926-47944 Sentence denotes Supplementary File
T305 47946-48107 Sentence denotes We gratefully acknowledge the authors and originating and submitting laboratories of the sequences from GISAID’s EpiCov Database on which this research is based.
T306 48108-48257 Sentence denotes We thank Lionel Condé, Robert Gramzinski, Joshua Herbeck, Mélanie Merbah, Thembi Mdluli, Lydie Trautmann, Douglas Whalin, and Suzanne Wollen-Roberts.
T307 48258-48339 Sentence denotes We also thank two reviewers for critical improvements of the original manuscript.
T308 48340-48485 Sentence denotes This work was funded by US Department of Defense Health Agency and the US Department of the Army and a cooperative agreement between The Henry M.
T309 48486-48606 Sentence denotes Jackson Foundation for the Advancement of Military Medicine, Inc., and the US Department of the Army (W81XWH-18-2-0040).
T310 48607-48797 Sentence denotes The views expressed are those of the authors and should not be construed to represent the positions of the US Army, the Department of Defense, or the Department of Health and Human Services.
T311 48798-48841 Sentence denotes The authors declare no competing interests.
T312 48842-48883 Sentence denotes This article is a PNAS Direct Submission.
T313 48884-48936 Sentence denotes See online for related content such as Commentaries.
T314 48937-49071 Sentence denotes This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2008281117/-/DCSupplemental.
T315 49073-49091 Sentence denotes Data Availability.
T316 49092-49175 Sentence denotes Data and code are available at https://www.hivresearch.org/publication-supplements.
T317 49176-49235 Sentence denotes All study data are included in the article and SI Appendix.

2_test

Id Subject Object Predicate Lexical cue
32868447-32697968-132542393 13097-13099 32697968 denotes 24
32868447-22807683-132542394 15488-15490 22807683 denotes 29
32868447-32697968-132542395 16707-16709 32697968 denotes 24
32868447-22807683-132542396 19431-19433 22807683 denotes 29
32868447-4519626-132542397 20561-20563 4519626 denotes 30
32868447-19238703-132542397 20561-20563 19238703 denotes 30
32868447-22883857-132542397 20561-20563 22883857 denotes 30
32868447-26147205-132542398 21722-21724 26147205 denotes 33
32868447-28472435-132542398 21722-21724 28472435 denotes 33
32868447-26658901-132542399 21759-21761 26658901 denotes 36
32868447-31700680-132542400 21763-21765 31700680 denotes 37
32868447-12089434-132542401 24161-24163 12089434 denotes 38
32868447-32155444-132542402 24902-24904 32155444 denotes 39
32868447-19538115-132542403 27292-27294 19538115 denotes 40
32868447-29514901-132542404 28646-28648 29514901 denotes 41
32868447-25414313-132542405 28911-28913 25414313 denotes 42
32868447-31452511-132542406 28915-28917 31452511 denotes 43
32868447-32697968-132542407 29308-29310 32697968 denotes 24
32868447-28238624-132542408 30741-30743 28238624 denotes 44
32868447-28084671-132542408 30741-30743 28084671 denotes 44
32868447-27847361-132542408 30741-30743 27847361 denotes 44
32868447-30333174-132542409 30788-30790 30333174 denotes 47
32868447-29742435-132542410 30932-30934 29742435 denotes 48
32868447-32697968-132542411 31137-31139 32697968 denotes 24
32868447-23329690-132542412 35271-35273 23329690 denotes 50
32868447-20224823-132542413 36074-36076 20224823 denotes 51
32868447-27774300-132542414 36214-36216 27774300 denotes 52
32868447-30016406-132542415 36218-36220 30016406 denotes 53
32868447-20224823-132542416 37346-37348 20224823 denotes 51
32868447-30351396-132542417 37432-37434 30351396 denotes 54
32868447-22807683-132542418 39183-39185 22807683 denotes 29
32868447-25371430-132542419 39283-39285 25371430 denotes 55
32868447-28481363-132542420 39339-39341 28481363 denotes 56
32868447-22807683-132542421 39574-39576 22807683 denotes 29
32868447-21670087-132542422 39779-39781 21670087 denotes 57
32868447-15703242-132542423 39993-39995 15703242 denotes 58
32868447-19081788-132542424 40083-40085 19081788 denotes 59
32868447-15703242-132542425 40494-40496 15703242 denotes 58
32868447-15703242-132542426 40674-40676 15703242 denotes 58
32868447-4519626-132542427 40945-40947 4519626 denotes 30
32868447-21375616-132542428 41060-41062 21375616 denotes 60
32868447-19238703-132542429 41123-41125 19238703 denotes 31
32868447-22883857-132542430 41335-41337 22883857 denotes 32
32868447-26658901-132542431 42493-42495 26658901 denotes 36
32868447-31700680-132542432 42497-42499 31700680 denotes 37
32868447-30016406-132542433 43308-43310 30016406 denotes 53
32868447-30016406-132542434 44374-44376 30016406 denotes 53
32868447-10833195-132542435 44823-44825 10833195 denotes 62
32868447-10833195-132542436 44900-44902 10833195 denotes 62
32868447-31565258-132542437 45005-45007 31565258 denotes 63
32868447-32406916-132542438 45985-45987 32406916 denotes 64
32868447-32406916-132542439 46431-46433 32406916 denotes 64
32868447-31970929-132542440 46713-46715 31970929 denotes 65