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PMC:7081066 / 5977-10023 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
170 34-39 Gene denotes spike Gene:43740568
171 52-61 Species denotes SARS-CoVs Tax:694009
193 112-117 Gene denotes spike Gene:43740568
194 727-732 Gene denotes spike Gene:43740568
195 526-531 Gene denotes spike Gene:43740568
196 139-149 Species denotes SARS-CoV-2 Tax:2697049
197 158-162 Species denotes CoVs Tax:11118
198 164-172 Species denotes SARS-CoV Tax:694009
199 286-296 Species denotes SARS-CoV-2 Tax:2697049
200 308-311 Species denotes CoV Tax:11118
201 375-383 Species denotes SARS-CoV Tax:694009
202 399-402 Species denotes CoV Tax:11118
203 406-425 Species denotes Rhinolophus affinis Tax:59477
204 544-547 Species denotes CoV Tax:11118
205 555-565 Species denotes SARS-CoV-2 Tax:2697049
206 743-751 Species denotes SARS-CoV Tax:694009
207 760-763 Species denotes CoV Tax:11118
208 769-788 Species denotes Rhinolophus sinicus Tax:89399
209 847-857 Species denotes SARS-CoV-2 Tax:2697049
210 937-947 Species denotes SARS-CoV-2 Tax:2697049
211 964-967 Species denotes CoV Tax:11118
212 973-992 Species denotes Rhinolophus affinis Tax:59477
213 1042-1047 Species denotes CoV-2 Tax:2697049
216 1141-1146 Gene denotes Spike Gene:43740568
217 1147-1151 Gene denotes ACE2 Gene:59272
249 1192-1197 Gene denotes spike Gene:43740568
250 1384-1388 Gene denotes ACE2 Gene:59272
251 2324-2328 Gene denotes ACE2 Gene:59272
252 2697-2701 Gene denotes ACE2 Gene:59272
253 3261-3266 Gene denotes spike Gene:43740568
254 3572-3576 Gene denotes ACE2 Gene:59272
255 4032-4037 Gene denotes spike Gene:43740568
256 1209-1217 Species denotes SARS-CoV Tax:694009
257 1245-1248 Species denotes CoV Tax:11118
258 1282-1285 Species denotes CoV Tax:11118
259 1289-1308 Species denotes Rhinolophus sinicus Tax:89399
260 1314-1324 Species denotes SARS-CoV-2 Tax:2697049
261 1378-1383 Species denotes human Tax:9606
262 1748-1758 Species denotes SARS-CoV-2 Tax:2697049
263 1763-1771 Species denotes SARS-CoV Tax:694009
264 1934-1942 Species denotes SARS-CoV Tax:694009
265 2085-2095 Species denotes SARS-CoV-2 Tax:2697049
266 2173-2178 Species denotes human Tax:9606
267 2229-2237 Species denotes SARS-CoV Tax:694009
268 2318-2323 Species denotes human Tax:9606
269 2418-2423 Species denotes human Tax:9606
270 2463-2473 Species denotes SARS-CoV-2 Tax:2697049
271 2568-2578 Species denotes SARS-CoV-2 Tax:2697049
272 3075-3080 Species denotes human Tax:9606
273 3305-3313 Species denotes SARS-CoV Tax:694009
274 3466-3476 Species denotes SARS-CoV-2 Tax:2697049
275 3773-3783 Species denotes SARS-CoV-2 Tax:2697049
276 3820-3828 Species denotes SARS-CoV Tax:694009
277 1998-2007 Disease denotes infection MESH:D007239
278 2425-2430 Mutation denotes K479N p.K479N
279 2435-2440 Mutation denotes S487T p.S487T

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T35 40-48 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T36 118-125 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T37 733-741 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T38 875-885 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T39 1072-1082 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T40 1198-1205 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T41 3267-3274 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T42 3649-3656 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T43 3657-3664 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T44 4038-4045 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T26 52-56 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T27 139-147 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 164-172 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 286-294 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 375-383 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 555-563 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 743-751 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 847-855 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 937-945 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 1209-1217 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 1314-1322 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 1748-1756 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 1763-1771 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 1934-1942 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 1998-2007 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T41 2085-2093 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 2229-2237 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 2463-2471 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 2568-2576 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 3305-3313 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 3466-3474 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 3773-3781 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 3820-3828 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T34 302-303 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 460-465 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T36 485-487 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T37 535-543 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes this Bat
T38 648-650 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T39 801-809 http://purl.obolibrary.org/obo/SO_0000418 denotes signaled
T40 838-843 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T41 1038-1041 http://purl.obolibrary.org/obo/CLO_0051568 denotes SAS
T42 1378-1383 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T43 1600-1601 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 1918-1925 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T45 2173-2178 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T46 2318-2323 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T47 2384-2385 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 2418-2423 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T49 2442-2444 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T50 2442-2444 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T51 2745-2746 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 2945-2946 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 3075-3080 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T54 3091-3098 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T55 3121-3124 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T56 3125-3130 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T41 40-48 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T42 118-125 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T43 733-741 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T44 875-885 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T45 875-880 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T46 881-885 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T47 1072-1082 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T48 1072-1077 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T49 1078-1082 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T50 1198-1205 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T51 1602-1606 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T52 2052-2054 Chemical denotes Lu http://purl.obolibrary.org/obo/CHEBI_33382
T53 2339-2341 Chemical denotes Lu http://purl.obolibrary.org/obo/CHEBI_33382
T54 2442-2444 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145
T55 3267-3274 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T56 3649-3656 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T57 3657-3664 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T58 4038-4045 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T52 0-7 Sentence denotes Results
T53 9-82 Sentence denotes Homology analysis of the spike proteins of SARS-CoVs and related Bat-CoVs
T54 83-202 Sentence denotes Phylogenetic analysis of the spike protein sequences of SARS-CoV-2 and Bat-CoVs, SARS-CoV is shown in Figure 1(Fig. 1).
T55 203-490 Sentence denotes The results are in agreement with recent reports of an independent introduction of SARS-CoV-2 from a Bat-CoV, different from the spillover which led to the introduction of SARS-CoV, being the Bat-CoV of Rhinolophus affinis the probable ancestor of this new virus (Wong et al., 2020[18]).
T56 491-607 Sentence denotes Indeed, the sequences of the whole spike of this Bat-CoV and of SARS-CoV-2 share 97.7 % identity (Figure 1(Fig. 1)).
T57 608-742 Sentence denotes More divergence is found however in the S1 subunit, particularly in the Receptor Binding Domain (RBD) of the different spike proteins.
T58 743-948 Sentence denotes SARS-CoV and Bat-CoV from Rhinolophus sinicus (originally signaled as the most closely related virus to SARS-CoV-2) exhibit several amino acid substitutions and deletions in the RBD compared to SARS-CoV-2.
T59 949-1116 Sentence denotes The RBD of Bat-CoV from Rhinolophus affinis, although more closely related to the one of SAS-CoV-2, also displayed several amino acid substitutions (Figure 2(Fig. 2)).
T60 1118-1161 Sentence denotes Structural analysis of Spike-ACE2 complexes
T61 1162-1403 Sentence denotes The crystal structures of the spike protein of SARS-CoV and homology models of Bat-CoV (accession number MG772933), Bat-CoV of Rhinolophus sinicus, and SARS-CoV-2 interacting with the putative binding domain site in human ACE2 were analyzed.
T62 1404-1476 Sentence denotes The interaction pattern between the three viral spikes is quite similar.
T63 1477-1704 Sentence denotes The main region of interaction with the putative cellular receptor counter-part is formed by fifteen residues ordered into a beta-sheet conformation surrounded by two capping loops (Figure 3(Fig. 3) and Supplementary Figure 1).
T64 1705-1926 Sentence denotes Interestingly, sequence comparison between SARS-CoV-2 and SARS-CoV revealed that the residues present in the receptor-interacting motive are highly conserved with 70 % identity, sharing nine residues between both viruses.
T65 1927-2072 Sentence denotes In the SARS-CoV RBD are present residues that allowed the interspecies infection, known as Y442, L472, N479, D480, and T487 (Lu et al., 2015[6]).
T66 2073-2225 Sentence denotes However, in SARS-CoV-2, slight modification of some residues could improve the interaction with the human cellular receptor: L455, F486, Q493, and N501.
T67 2226-2359 Sentence denotes In SARS-CoV, two main residues (479 and 487) have been associated to the recognition of the human ACE2 receptor (Lu et al., 2015[6]).
T68 2360-2455 Sentence denotes These residues suffered a punctual mutation from civet to human, K479N and S487T (Li, 2013[5]).
T69 2456-2546 Sentence denotes In the SARS-CoV-2, the residues corresponding to N479 correspond to Q493 and T487 to N501.
T70 2547-2659 Sentence denotes These changes in the SARS-CoV-2 represent energetically favorable changes for the interaction with the receptor.
T71 2660-2821 Sentence denotes The local environment present in the ACE2 receptor allows these mutations to produce a significant number of electrostatic stabilizing interactions (Table 1(Tab.
T72 2822-2826 Sentence denotes 1)).
T73 2827-3016 Sentence denotes Furthermore, as mentioned previously, the presence of the two capping loops in the binding domain is likely producing a stabilization effect over the interaction with the cellular receptor.
T74 3017-3131 Sentence denotes Our models showed that these capping loops appear in both human-infecting viruses but are absent in the bat virus.
T75 3132-3301 Sentence denotes The data showed here strongly suggest that these capping loops produce an increase in the electrostatic interactions between the spike protein and the cellular receptor.
T76 3302-3538 Sentence denotes In SARS-CoV, the residues present in these capping loops showing direct interaction with the receptor are R426, S432, T433, Y436, P462, D463, S472, and N473 and in SARS-CoV-2 are V445, Y449, Y473, Q474, A475, E484, G485, F486, and N487.
T77 3539-3611 Sentence denotes The counter-pairs located in the ACE2 receptor are shown in Table 1(Tab.
T78 3612-3615 Sentence denotes 1).
T79 3616-3687 Sentence denotes Altogether, the higher number of protein-protein contacts (Table 2(Tab.
T80 3688-3859 Sentence denotes 2)) and the longer capping loops could explain the increase in binding affinities in SARS-CoV-2 (-15.7 Kcal/mol) in comparison with SARS-CoV (-14.1 Kcal/mol) (Table 3(Tab.
T81 3860-3864 Sentence denotes 3)).
T82 3865-4046 Sentence denotes Thus, these loops could play an important role together with the punctual mutations being an interesting clue to determine the host receptor specificity for the viral spike protein.

MyTest

Id Subject Object Predicate Lexical cue
32210742-26206723-29811235 2068-2069 26206723 denotes 6
32210742-26206723-29811236 2355-2356 26206723 denotes 6
32210742-23994189-29811237 2451-2452 23994189 denotes 5

2_test

Id Subject Object Predicate Lexical cue
32210742-26206723-29811235 2068-2069 26206723 denotes 6
32210742-26206723-29811236 2355-2356 26206723 denotes 6
32210742-23994189-29811237 2451-2452 23994189 denotes 5