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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 47-54 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T2 103-111 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T3 630-637 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T4 836-844 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T5 1393-1400 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T6 2638-2645 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T7 2707-2719 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T8 2767-2783 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T9 2778-2783 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T10 2804-2816 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T11 2804-2808 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T12 2897-2907 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T13 2970-2977 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T14 3698-3706 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T15 4207-4215 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T16 4563-4571 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T17 4737-4744 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T18 4921-4933 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T19 4943-4950 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T20 5230-5237 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T21 6004-6011 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T22 6463-6468 Body_part denotes helix http://purl.org/sig/ont/fma/fma60992
T23 6568-6576 Body_part denotes arginine http://purl.org/sig/ont/fma/fma82763
T24 6787-6793 Body_part denotes lysine http://purl.org/sig/ont/fma/fma82758
T25 6833-6839 Body_part denotes valine http://purl.org/sig/ont/fma/fma82766
T26 6992-6999 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T27 7379-7386 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 7544-7551 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T29 7830-7838 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T30 8154-8162 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T31 8210-8218 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T32 8538-8546 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T33 8802-8810 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T34 8829-8834 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T35 8895-8903 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T36 8940-8947 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T37 9308-9316 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T38 10036-10043 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T39 10203-10211 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 6463-6468 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T2 8829-8834 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p8111s23 6647-6656 NegReg denotes abolished
p8111s25 6661-6667 MPA denotes strong
p8111s26 6668-6686 MPA denotes polar interactions
p8111s33 6707-6715 NegReg denotes decrease
p8111s36 6723-6747 Interaction denotes binding affinity between
p8112s39 6937-6952 MPA denotes binding ability

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 60-64 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T2 288-298 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T3 527-535 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T4 589-593 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T5 801-809 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 1193-1213 Disease denotes 2019-nCoV infections http://purl.obolibrary.org/obo/MONDO_0100096
T7 1254-1262 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 1353-1361 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 1445-1453 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T10 1884-1897 Disease denotes infections in http://purl.obolibrary.org/obo/MONDO_0005550
T11 2140-2159 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T12 2150-2159 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T13 2346-2379 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T14 2432-2436 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T15 2548-2552 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T16 2566-2574 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 2653-2661 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 3103-3111 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 3184-3192 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 3468-3476 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 3583-3591 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 3640-3648 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 3840-3848 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 3909-3911 Disease denotes VL http://purl.obolibrary.org/obo/MONDO_0024555
T25 4047-4049 Disease denotes VL http://purl.obolibrary.org/obo/MONDO_0024555
T26 4085-4093 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 4343-4351 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 4379-4387 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 4477-4485 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 4696-4704 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 5168-5176 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 5274-5282 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 5366-5374 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 5444-5452 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 5461-5469 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 5551-5559 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 6189-6197 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 6472-6480 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 6586-6594 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 6849-6857 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 7057-7065 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 7364-7372 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 7626-7634 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 8520-8528 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 8853-8857 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T46 9460-9468 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 9616-9624 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 9893-9901 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 9996-10004 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 10261-10269 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 10456-10464 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 10727-10747 Disease denotes 2019-nCoV infections http://purl.obolibrary.org/obo/MONDO_0100096
T53 10812-10820 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 58-59 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 86-91 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T3 233-236 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T4 282-287 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T5 329-330 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 349-354 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T7 799-800 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 819-824 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T9 1468-1471 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T10 1472-1473 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 1676-1677 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1823-1826 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T13 1839-1840 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 1878-1883 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T15 1931-1934 http://purl.obolibrary.org/obo/CLO_0054061 denotes 132
T16 2268-2269 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T17 2333-2336 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T18 2340-2345 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T19 2428-2431 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T20 2473-2474 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 2499-2500 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 2684-2685 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 2749-2754 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T24 2767-2777 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T25 2778-2783 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T26 2804-2808 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T27 3217-3222 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T28 3226-3227 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 3498-3499 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T30 3683-3684 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 3878-3879 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 4224-4226 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T33 4877-4878 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 5025-5031 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T35 5117-5118 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T36 5874-5875 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 5876-5879 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1
T38 6110-6115 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T39 6492-6493 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 6520-6521 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 6705-6706 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 6785-6786 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 7035-7036 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 7128-7133 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T45 7295-7300 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T46 7392-7397 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T47 7726-7736 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T48 7793-7794 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 7813-7818 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T50 8175-8176 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 8662-8663 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 8673-8676 http://purl.obolibrary.org/obo/CLO_0009946 denotes kon
T53 8691-8695 http://purl.obolibrary.org/obo/CLO_0007875 denotes Ms−1
T54 8691-8695 http://purl.obolibrary.org/obo/CLO_0050048 denotes Ms−1
T55 8691-8695 http://purl.obolibrary.org/obo/CLO_0052410 denotes Ms−1
T56 8731-8734 http://purl.obolibrary.org/obo/CLO_0050050 denotes s−1
T57 8767-8771 http://purl.obolibrary.org/obo/CLO_0001692 denotes a KD
T58 8829-8834 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T59 8829-8834 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T60 8838-8839 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 9048-9053 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T62 9121-9129 http://purl.obolibrary.org/obo/CLO_0007225 denotes labelled
T63 9182-9187 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T64 9238-9242 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T65 9697-9698 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 9799-9800 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 10292-10299 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T68 10303-10304 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 10468-10469 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 10570-10573 http://purl.obolibrary.org/obo/CLO_0051582 denotes has

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 47-54 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T2 404-413 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T3 630-637 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T4 894-896 Chemical denotes KD http://purl.obolibrary.org/obo/CHEBI_73601
T5 913-920 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T6 1393-1400 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T7 2112-2121 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T8 2455-2457 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T9 2638-2645 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T10 2666-2668 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T11 2707-2719 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T12 2826-2837 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T13 2897-2907 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T14 2897-2902 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T15 2903-2907 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T16 2970-2977 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T17 3880-3884 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T19 3909-3911 Chemical denotes VL http://purl.obolibrary.org/obo/CHEBI_75013
T20 4047-4049 Chemical denotes VL http://purl.obolibrary.org/obo/CHEBI_75013
T21 4308-4312 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T23 4371-4375 Chemical denotes R162 http://purl.obolibrary.org/obo/CHEBI_85885
T24 4737-4744 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T25 4921-4933 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T26 4943-4950 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T27 5017-5021 Chemical denotes MEGA http://purl.obolibrary.org/obo/CHEBI_6617
T28 5230-5237 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T29 6004-6011 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T30 6399-6407 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T31 6494-6498 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T33 6522-6530 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T34 6568-6576 Chemical denotes arginine http://purl.obolibrary.org/obo/CHEBI_16467|http://purl.obolibrary.org/obo/CHEBI_29016|http://purl.obolibrary.org/obo/CHEBI_32696
T37 6603-6613 Chemical denotes asparagine http://purl.obolibrary.org/obo/CHEBI_22653
T38 6787-6793 Chemical denotes lysine http://purl.obolibrary.org/obo/CHEBI_18019|http://purl.obolibrary.org/obo/CHEBI_25094
T40 6833-6839 Chemical denotes valine http://purl.obolibrary.org/obo/CHEBI_27266
T41 6885-6889 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T43 6992-6999 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T44 7269-7271 Chemical denotes KD http://purl.obolibrary.org/obo/CHEBI_73601
T45 7379-7386 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T46 7544-7551 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T47 8769-8771 Chemical denotes KD http://purl.obolibrary.org/obo/CHEBI_73601
T48 8940-8947 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T49 9196-9204 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T50 9495-9502 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T51 10036-10043 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T52 10415-10422 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T53 10909-10918 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-111 Sentence denotes Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody
T2 112-142 Sentence denotes Emerging Microbes & Infections
T3 143-145 Sentence denotes X.
T4 146-157 Sentence denotes Tian et al.
T5 159-167 Sentence denotes Abstract
T6 168-176 Sentence denotes ABSTRACT
T7 177-362 Sentence denotes The newly identified 2019 novel coronavirus (2019-nCoV) has caused more than 11,900 laboratory-confirmed human infections, including 259 deaths, posing a serious threat to human health.
T8 363-435 Sentence denotes Currently, however, there is no specific antiviral treatment or vaccine.
T9 436-758 Sentence denotes Considering the relatively high identity of receptor-binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV.
T10 759-908 Sentence denotes Here, we report for the first time that a SARS-CoV-specific human monoclonal antibody, CR3022, could bind potently with 2019-nCoV RBD (KD of 6.3 nM).
T11 909-996 Sentence denotes The epitope of CR3022 does not overlap with the ACE2 binding site within 2019-nCoV RBD.
T12 997-1214 Sentence denotes These results suggest that CR3022 may have the potential to be developed as candidate therapeutics, alone or in combination with other neutralizing antibodies, for the prevention and treatment of 2019-nCoV infections.
T13 1215-1659 Sentence denotes Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g. m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, implying that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD.
T14 1661-1789 Sentence denotes Very recently, a novel coronavirus which was temporarily named “2019 novel coronavirus (2019-nCoV)” emerged in Wuhan, China [1].
T15 1790-2067 Sentence denotes As of 1 February 2020, 2019-nCoV has resulted in a total of 11,821 laboratory-confirmed human infections in China, including 259 deaths, and 132 exported cases in 23 countries outside of China (https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports).
T16 2068-2160 Sentence denotes Currently, there is no vaccine or effective antiviral treatment against 2019-nCoV infection.
T17 2161-2217 Sentence denotes Based on the phylogenetic analysis (GISAID accession no.
T18 2218-2477 Sentence denotes EPI_ISL_402124) [2], 2019-nCoV belongs to lineage B betacoronavirus and shares high sequence identity with that of bat or human severe acute respiratory syndrome coronavirus-related coronavirus (SARSr-CoV) and bat SARS-like coronavirus (SL-CoV) (Figure 1(a)).
T19 2478-2603 Sentence denotes In previous studies, a number of potent monoclonal antibodies against SARS coronavirus (SARS-CoV) have been identified [3–7].
T20 2604-2869 Sentence denotes These antibodies target the spike protein (S) of SARS-CoV and SL-CoVs, which is a type I transmembrane glycoprotein and mediates the entrance to human respiratory epithelial cells by interacting with cell surface receptor angiotensin-converting enzyme 2 (ACE2) [8].
T21 2870-3033 Sentence denotes More specifically, the 193 amino acid length (N318-V510) receptor binding domain (RBD) within the S protein is the critical target for neutralizing antibodies [9].
T22 3034-3252 Sentence denotes Some of the antibodies recognize different epitopes on RBD; e.g. the SARS-CoV neutralizing antibodies CR3014 and CR3022 bound noncompetitively to the SARS-CoV RBD and neutralized the virus in a synergistic fashion [5].
T23 3253-3502 Sentence denotes We predicted the conformation of 2019-nCoV RBD as well as its complex structures with several neutralizing antibodies, and found that the modelling results support the interactions between 2019-nCoV RBD and certain SARS-CoV antibodies (Figure 1(b)).
T24 3503-3606 Sentence denotes This could be due to the relatively high identity (73%) of RBD in 2019-nCoV and SARS-CoV (Figure 1(c)).
T25 3607-3819 Sentence denotes For instance, residues in RBD of SARS-CoV that make polar interactions with a neutralizing antibody m396 as indicated by the complex crystal structure [10] are invariably conserved in 2019-nCoV RBD (Figure 1(d)).
T26 3820-3912 Sentence denotes In the structure of SARS-CoV-RBD-m396, R395 in RBD formed a salt bridge with D95 of m396-VL.
T27 3913-4051 Sentence denotes Concordantly, the electrostatic interaction was also observed in the model of 2019-nCoV-RBD-m396, forming by R408 (RBD) and D95 (m396-VL).
T28 4052-4168 Sentence denotes This analysis suggests that some SARS-CoV-specific monoclonal antibodies may be effective in neutralizing 2019-nCoV.
T29 4169-4410 Sentence denotes In contrast, the interactions between antibody F26G19 [11] or 80R [12] and the RBD in 2019-nCoV decreased significantly due to the lack of salt bridges formed by R426-D56 in SARS-CoV-RBD-F26G19 or D480-R162 in SARS-CoV-RBD-80R, respectively.
T30 4411-4614 Sentence denotes Furthermore, while most of the 80R-binding residues on the RBD of SARS-CoV are not conserved on RBD of 2019-nCoV (Figure 1(c)), it is unlikely that the antibody 80R could effectively recognize 2019-nCoV.
T31 4615-4865 Sentence denotes Therefore, it is urgent to experimentally determine the cross-reactivity of anti-SARS-CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV.
T32 4866-4967 Sentence denotes Figure 1. (a) Phylogenetic analysis of 2019-nCoV spike glycoprotein from its protein BLAST sequences.
T33 4968-5836 Sentence denotes The neighbour-joining tree was constructed using MEGA X, tested by bootstrap method of 2000 replicates, and edited by the online tool of iTOL (v5). (b) The simulated model of 2019-nCoV RBD binding to SARS-CoV-RBD-specific antibodies (m396, 80R, and F26G19). (c) Protein sequence alignment of 2019-nCoV and SARS-CoV RBD, showing the predominant residues that contribute to interactions with ACE2 or SARS-CoV-specific antibodies. (d) The comparison of the complex structures of SARS-CoV-RBD and SARS-CoV-RBD-specific antibodies (shown in the first row) and models of 2019-nCoV-RBD and SARS-CoV-RBD-specific antibodies (shown in the second row). (e) Binding of monoclonal antibodies to 2019-nCoV RBD determined by ELISA. (f) Binding profiles of 2019-nCoV RBD to ACE2 and antibodies, and (g) competition of CR3022 and ACE2 with 2019-nCoV RBD measured by BLI in OctetRED96.
T34 5837-5942 Sentence denotes Binding kinetics was evaluated using a 1:1 Langmuir binding model by ForteBio Data Analysis 7.0 software.
T35 5943-6012 Sentence denotes In this study, we first expressed and purified 2019-nCoV RBD protein.
T36 6013-6121 Sentence denotes We also predicted the conformations of 2019-nCoV RBD and its complex with the putative receptor, human ACE2.
T37 6122-6295 Sentence denotes Comparison of the interaction between the complex of ACE2 [13] and SARS-CoV RBD and homology model of ACE2 and 2019-nCoV RBD revealed similar binding modes (data not shown).
T38 6296-6433 Sentence denotes In both complexes, β5–β6 loop and β6–β7 loop form extensive contact, including at least seven pairs of hydrogen bonds, with the receptor.
T39 6434-6554 Sentence denotes Notably, R426 on the forth α helix in SARS-CoV RBD builds a salt bridge with E329 and a hydrogen bond with Q325 on ACE2.
T40 6555-6769 Sentence denotes However, the arginine (R426 in SARS-CoV RBD) to asparagine (N439) mutation in 2019-nCoV RBD abolished the strong polar interactions, which may induce a decrease in the binding affinity between RBD and the receptor.
T41 6770-6953 Sentence denotes Interestingly, a lysine (K417 in 2019-nCoV RBD) replacement of valine (V404 in SARS-CoV RBD) on β6 formed an extra salt bridge with D30 on ACE2, which may recover the binding ability.
T42 6954-7075 Sentence denotes These data indicate that the RBD in S protein of 2019-nCoV may bind to ACE2 with a similar affinity as SARS-CoV RBD does.
T43 7076-7243 Sentence denotes Indeed, we measured the binding of 2019-nCoV RBD to human ACE2 by the biolayer interferometry binding (BLI) assay, and found that 2019-nCoV RBD bound potently to ACE2.
T44 7244-7416 Sentence denotes The calculated affinity (KD) of 2019-nCoV RBD with human ACE2 was 15.2 nM (Figure 1(f)), which is comparable to that of SARS-CoV spike protein with human ACE2 (15 nM) [14].
T45 7417-7570 Sentence denotes These results indicate that ACE2 could be the potential receptor for the new coronavirus, and that the expressed 2019-nCoV RBD protein is functional [2].
T46 7571-7953 Sentence denotes Next, we expressed and purified several representative SARS-CoV-specific antibodies which have been reported to target RBD and possess potent neutralizing activities, including m396 [3], CR3014 [4], CR3022 [5], as well as a MERS-CoV-specific human monoclonal antibody m336 developed by our laboratory [15], and measured their binding ability to 2019-nCoV RBD by ELISA (Figure 1(e)).
T47 7954-8053 Sentence denotes Surprisingly, we found that most of these antibodies did not show evident binding to 2019-nCoV RBD.
T48 8054-8129 Sentence denotes To confirm this result, we further measured the binding kinetics using BLI.
T49 8130-8194 Sentence denotes An irrelevant anti-CD40 antibody was used as a negative control.
T50 8195-8356 Sentence denotes Similarly, the antibody m396, which was predicted to bind 2019-nCoV RBD (Figure 1(d)), only showed slight binding at the highest measured concentration (2.0 µM).
T51 8357-8506 Sentence denotes Further studies are needed to solve the high-resolution structure of 2019-nCoV RBD and understand why it could not be recognized by these antibodies.
T52 8507-8649 Sentence denotes Notably, one SARS-CoV-specific antibody, CR3022, was found to bind potently with 2019-nCoV RBD as determined by ELISA and BLI (Figure 1(e,f)).
T53 8650-8796 Sentence denotes It followed a fast-on (kon of 1.84 × 105 Ms−1) and slow-off (koff of 1.16 × 10−3 s−1) binding kinetics, resulting in a KD of 6.3 nM (Figure 1(f)).
T54 8797-8952 Sentence denotes This antibody was isolated from blood of a convalescent SARS patient and did not compete with the antibody CR3014 for binding to recombinant S protein [5].
T55 8953-9092 Sentence denotes To further elucidate the binding epitopes of CR3022, we measured the competition of CR3022 and human ACE2 for the binding to 2019-nCoV RBD.
T56 9093-9278 Sentence denotes The streptavidin biosensors labelled with biotinylated 2019-nCoV RBD were saturated with human ACE2 in solution, followed by the addition of the test antibodies in the presence of ACE2.
T57 9279-9396 Sentence denotes As shown in Figure 1(g), the antibody CR3022 did not show any competition with ACE2 for the binding to 2019-nCoV RBD.
T58 9397-9569 Sentence denotes These results suggest that CR3022, distinct from the other two SARS-CoV antibodies, recognizes an epitope that does not overlap with the ACE2 binding site of 2019-nCoV RBD.
T59 9570-9666 Sentence denotes The RBD of 2019-nCoV differs largely from the SARS-CoV at the C-terminus residues (Figure 1(c)).
T60 9667-9868 Sentence denotes Our results implied that such a difference did not result in drastic changes in the capability to engage the ACE2 receptor, but had a critical impact on the cross-reactivity of neutralizing antibodies.
T61 9869-10162 Sentence denotes Some of the most potent SARS-CoV-specific neutralizing antibodies (e.g. m396, CR3014) that target the receptor binding site of SARS-CoV failed to bind 2019-nCoV spike protein, indicating that it is necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD.
T62 10163-10397 Sentence denotes Interestingly, it was reported that the antibody CR3022 completely neutralized both the wild-type SARS-CoV and the CR3014 escape viruses at a concentration of 23.5 μg/ml, and that no escape variants could be generated with CR3022 [5].
T63 10398-10535 Sentence denotes Furthermore, the mixture of CR3022 and CR3014 neutralized SARS-CoV in a synergistic fashion by recognizing different epitopes on RBD [5].
T64 10536-10748 Sentence denotes These results suggest that CR3022 has the potential to be developed as candidate therapeutics, alone or in combination with other neutralizing antibodies, for the prevention and treatment of 2019-nCoV infections.
T65 10749-10945 Sentence denotes We expect more cross-reactive antibodies against 2019-nCoV and SARS-CoV or other coronaviruses to be identified soon, facilitating the development of effective antiviral therapeutics and vaccines.
T66 10947-10969 Sentence denotes Supplementary Material
T67 10970-10991 Sentence denotes Supplemental Material
T68 10993-11013 Sentence denotes Disclosure statement
T69 11014-11078 Sentence denotes No potential conflict of interest was reported by the author(s).
T70 11080-11085 Sentence denotes ORCID
T71 11086-11134 Sentence denotes Zhengli Shi http://orcid.org/0000-0001-8089-163X
T72 11135-11183 Sentence denotes Shibo Jiang http://orcid.org/0000-0001-8283-7135
T73 11184-11233 Sentence denotes Tianlei Ying http://orcid.org/0000-0002-9597-2843

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
3 18-40 Species denotes 2019 novel coronavirus Tax:2697049
4 60-76 Species denotes SARS coronavirus Tax:694009
5 86-91 Species denotes human Tax:9606
34 957-961 Gene denotes ACE2 Gene:59272
35 1332-1336 Gene denotes ACE2 Gene:59272
36 198-220 Species denotes 2019 novel coronavirus Tax:2697049
37 222-231 Species denotes 2019-nCoV Tax:2697049
38 282-287 Species denotes human Tax:9606
39 349-354 Species denotes human Tax:9606
40 513-522 Species denotes 2019-nCoV Tax:2697049
41 527-535 Species denotes SARS-CoV Tax:694009
42 614-623 Species denotes 2019-nCoV Tax:2697049
43 748-757 Species denotes 2019-nCoV Tax:2697049
44 801-809 Species denotes SARS-CoV Tax:694009
45 879-888 Species denotes 2019-nCoV Tax:2697049
46 982-991 Species denotes 2019-nCoV Tax:2697049
47 1254-1262 Species denotes SARS-CoV Tax:694009
48 1353-1361 Species denotes SARS-CoV Tax:694009
49 1377-1386 Species denotes 2019-nCoV Tax:2697049
50 1445-1453 Species denotes SARS-CoV Tax:694009
51 1458-1467 Species denotes 2019-nCoV Tax:2697049
52 1645-1654 Species denotes 2019-nCoV Tax:2697049
53 589-597 Species denotes SARS CoV Tax:694009
54 819-824 Species denotes human Tax:9606
55 846-852 Chemical denotes CR3022
56 924-930 Chemical denotes CR3022
57 1024-1030 Chemical denotes CR3022
58 1308-1314 Chemical denotes CR3014
59 288-298 Disease denotes infections MESH:D007239
60 314-320 Disease denotes deaths MESH:D003643
61 1193-1213 Disease denotes 2019-nCoV infections MESH:C000657245
71 1678-1695 Species denotes novel coronavirus Tax:2697049
72 1725-1747 Species denotes 2019 novel coronavirus Tax:2697049
73 1749-1758 Species denotes 2019-nCoV Tax:2697049
74 1813-1822 Species denotes 2019-nCoV Tax:2697049
75 1878-1883 Species denotes human Tax:9606
76 1884-1894 Disease denotes infections MESH:D007239
77 1919-1925 Disease denotes deaths MESH:D003643
78 2031-2047 Disease denotes coronavirus-2019 MESH:C000657245
79 2140-2159 Disease denotes 2019-nCoV infection MESH:C000657245
97 5358-5362 Gene denotes ACE2 Gene:59272
98 5727-5731 Gene denotes ACE2 Gene:59272
99 5782-5786 Gene denotes ACE2 Gene:59272
100 4905-4914 Species denotes 2019-nCoV Tax:2697049
101 5143-5152 Species denotes 2019-nCoV Tax:2697049
102 5168-5176 Species denotes SARS-CoV Tax:694009
103 5260-5269 Species denotes 2019-nCoV Tax:2697049
104 5274-5282 Species denotes SARS-CoV Tax:694009
105 5444-5452 Species denotes SARS-CoV Tax:694009
106 5461-5469 Species denotes SARS-CoV Tax:694009
107 5533-5542 Species denotes 2019-nCoV Tax:2697049
108 5551-5559 Species denotes SARS-CoV Tax:694009
109 5651-5660 Species denotes 2019-nCoV Tax:2697049
110 5710-5719 Species denotes 2019-nCoV Tax:2697049
111 5792-5801 Species denotes 2019-nCoV Tax:2697049
112 5366-5374 Species denotes SARS-CoV Tax:694009
113 5771-5777 Chemical denotes CR3022
153 2826-2857 Gene denotes angiotensin-converting enzyme 2 Gene:59272
154 2859-2863 Gene denotes ACE2 Gene:59272
155 2239-2248 Species denotes 2019-nCoV Tax:2697049
156 2270-2285 Species denotes betacoronavirus Tax:694002
157 2340-2345 Species denotes human Tax:9606
158 2346-2391 Species denotes severe acute respiratory syndrome coronavirus Tax:694009
159 2400-2411 Species denotes coronavirus Tax:11118
160 2413-2422 Species denotes SARSr-CoV Tax:694009
161 2428-2453 Species denotes bat SARS-like coronavirus Tax:1508227
162 2458-2461 Species denotes CoV Tax:11118
163 2548-2564 Species denotes SARS coronavirus Tax:694009
164 2566-2574 Species denotes SARS-CoV Tax:694009
165 2653-2661 Species denotes SARS-CoV Tax:694009
166 2669-2673 Species denotes CoVs Tax:11118
167 2749-2754 Species denotes human Tax:9606
168 3184-3192 Species denotes SARS-CoV Tax:694009
169 3286-3295 Species denotes 2019-nCoV Tax:2697049
170 3442-3451 Species denotes 2019-nCoV Tax:2697049
171 3569-3578 Species denotes 2019-nCoV Tax:2697049
172 3583-3591 Species denotes SARS-CoV Tax:694009
173 3640-3648 Species denotes SARS-CoV Tax:694009
174 3791-3800 Species denotes 2019-nCoV Tax:2697049
175 3840-3848 Species denotes SARS-CoV Tax:694009
176 3991-4000 Species denotes 2019-nCoV Tax:2697049
177 4158-4167 Species denotes 2019-nCoV Tax:2697049
178 4255-4264 Species denotes 2019-nCoV Tax:2697049
179 4343-4351 Species denotes SARS-CoV Tax:694009
180 4379-4387 Species denotes SARS-CoV Tax:694009
181 4477-4485 Species denotes SARS-CoV Tax:694009
182 4514-4523 Species denotes 2019-nCoV Tax:2697049
183 4604-4613 Species denotes 2019-nCoV Tax:2697049
184 4721-4730 Species denotes 2019-nCoV Tax:2697049
185 4855-4864 Species denotes 2019-nCoV Tax:2697049
186 3103-3111 Species denotes SARS-CoV Tax:694009
187 3468-3476 Species denotes SARS-CoV Tax:694009
188 4085-4093 Species denotes SARS-CoV Tax:694009
189 4696-4704 Species denotes SARS-CoV Tax:694009
190 3136-3142 Chemical denotes CR3014
191 3147-3153 Chemical denotes CR3022
234 6116-6120 Gene denotes ACE2 Gene:59272
235 6175-6179 Gene denotes ACE2 Gene:59272
236 6224-6228 Gene denotes ACE2 Gene:59272
237 6549-6553 Gene denotes ACE2 Gene:59272
238 6909-6913 Gene denotes ACE2 Gene:59272
239 7025-7029 Gene denotes ACE2 Gene:59272
240 7134-7138 Gene denotes ACE2 Gene:59272
241 7238-7242 Gene denotes ACE2 Gene:59272
242 7301-7305 Gene denotes ACE2 Gene:59272
243 7398-7402 Gene denotes ACE2 Gene:59272
244 7445-7449 Gene denotes ACE2 Gene:59272
245 5990-5999 Species denotes 2019-nCoV Tax:2697049
246 6052-6061 Species denotes 2019-nCoV Tax:2697049
247 6110-6115 Species denotes human Tax:9606
248 6189-6197 Species denotes SARS-CoV Tax:694009
249 6233-6242 Species denotes 2019-nCoV Tax:2697049
250 6472-6480 Species denotes SARS-CoV Tax:694009
251 6586-6594 Species denotes SARS-CoV Tax:694009
252 6633-6642 Species denotes 2019-nCoV Tax:2697049
253 6803-6812 Species denotes 2019-nCoV Tax:2697049
254 6849-6857 Species denotes SARS-CoV Tax:694009
255 7003-7012 Species denotes 2019-nCoV Tax:2697049
256 7057-7065 Species denotes SARS-CoV Tax:694009
257 7111-7120 Species denotes 2019-nCoV Tax:2697049
258 7128-7133 Species denotes human Tax:9606
259 7206-7215 Species denotes 2019-nCoV Tax:2697049
260 7276-7285 Species denotes 2019-nCoV Tax:2697049
261 7295-7300 Species denotes human Tax:9606
262 7364-7372 Species denotes SARS-CoV Tax:694009
263 7392-7397 Species denotes human Tax:9606
264 7490-7505 Species denotes new coronavirus Tax:2697049
265 7530-7539 Species denotes 2019-nCoV Tax:2697049
266 6399-6407 Chemical denotes hydrogen MESH:D006859
267 6511-6515 Chemical denotes E329
268 6522-6530 Chemical denotes hydrogen MESH:D006859
269 6541-6545 Chemical denotes Q325
270 6568-6576 Chemical denotes arginine MESH:D001120
271 6603-6613 Chemical denotes asparagine MESH:D001216
272 6787-6793 Chemical denotes lysine MESH:D008239
273 6795-6799 Chemical denotes K417
274 6833-6839 Chemical denotes valine MESH:D014633
275 6902-6905 Chemical denotes D30 MESH:C005496
286 8149-8153 Gene denotes CD40 Gene:958
287 7795-7803 Species denotes MERS-CoV Tax:1335626
288 7916-7925 Species denotes 2019-nCoV Tax:2697049
289 8039-8048 Species denotes 2019-nCoV Tax:2697049
290 8253-8262 Species denotes 2019-nCoV Tax:2697049
291 8426-8435 Species denotes 2019-nCoV Tax:2697049
292 7626-7634 Species denotes SARS-CoV Tax:694009
293 7813-7818 Species denotes human Tax:9606
294 7758-7764 Chemical denotes CR3014
295 7770-7776 Chemical denotes CR3022
317 9054-9058 Gene denotes ACE2 Gene:59272
318 9188-9192 Gene denotes ACE2 Gene:59272
319 9273-9277 Gene denotes ACE2 Gene:59272
320 9358-9362 Gene denotes ACE2 Gene:59272
321 9534-9538 Gene denotes ACE2 Gene:59272
322 8588-8597 Species denotes 2019-nCoV Tax:2697049
323 8858-8865 Species denotes patient Tax:9606
324 9048-9053 Species denotes human Tax:9606
325 9078-9087 Species denotes 2019-nCoV Tax:2697049
326 9148-9157 Species denotes 2019-nCoV Tax:2697049
327 9182-9187 Species denotes human Tax:9606
328 9382-9391 Species denotes 2019-nCoV Tax:2697049
329 9555-9564 Species denotes 2019-nCoV Tax:2697049
330 8520-8528 Species denotes SARS-CoV Tax:694009
331 9460-9468 Species denotes SARS-CoV Tax:694009
332 8548-8554 Chemical denotes CR3022
333 8904-8910 Chemical denotes CR3014
334 8998-9004 Chemical denotes CR3022
335 9037-9043 Chemical denotes CR3022
336 9317-9323 Chemical denotes CR3022
337 9424-9430 Chemical denotes CR3022
357 9776-9780 Gene denotes ACE2 Gene:59272
358 9581-9590 Species denotes 2019-nCoV Tax:2697049
359 9616-9624 Species denotes SARS-CoV Tax:694009
360 9893-9901 Species denotes SARS-CoV Tax:694009
361 9996-10004 Species denotes SARS-CoV Tax:694009
362 10020-10029 Species denotes 2019-nCoV Tax:2697049
363 10148-10157 Species denotes 2019-nCoV Tax:2697049
364 10261-10269 Species denotes SARS-CoV Tax:694009
365 10456-10464 Species denotes SARS-CoV Tax:694009
366 10798-10807 Species denotes 2019-nCoV Tax:2697049
367 10812-10820 Species denotes SARS-CoV Tax:694009
368 10830-10843 Species denotes coronaviruses Tax:11118
369 10212-10218 Chemical denotes CR3022
370 10278-10284 Chemical denotes CR3014
371 10386-10392 Chemical denotes CR3022
372 10426-10432 Chemical denotes CR3022
373 10437-10443 Chemical denotes CR3014
374 10563-10569 Chemical denotes CR3022
375 10727-10747 Disease denotes 2019-nCoV infections MESH:C000657245