> top > docs > PMC:7519301 > spans > 12459-17848 > annotations

PMC:7519301 / 12459-17848 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T50 106-112 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T51 154-164 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T52 197-207 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T53 266-276 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T54 1537-1544 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T55 1549-1557 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T56 1574-1581 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T57 3293-3297 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T58 3333-3341 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T59 3631-3641 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T60 3762-3770 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T61 3933-3941 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T62 3948-3952 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T63 4076-4084 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T64 4150-4157 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T65 4816-4820 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T66 4849-4853 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T67 4954-4962 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T68 5017-5026 Body_part denotes leukocyte http://purl.org/sig/ont/fma/fma62852
T69 5036-5039 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T70 5170-5174 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T71 5235-5243 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T72 5370-5378 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T87 1526-1534 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T88 1526-1530 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T89 2297-2305 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T90 2297-2301 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T91 4966-4974 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T92 4966-4970 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T113 23-26 http://purl.obolibrary.org/obo/CLO_0051582 denotes Has
T114 216-217 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T115 235-236 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 499-504 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T117 518-519 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 682-683 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 1059-1064 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T120 1091-1093 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T121 1190-1191 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T122 1426-1427 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 1468-1469 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T124 1564-1566 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T125 1564-1566 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T126 1613-1614 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T127 1856-1858 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T128 1942-1943 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T129 2066-2067 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T130 2273-2274 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T131 2308-2315 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T132 2385-2386 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T133 2724-2725 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T134 2860-2861 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T135 2878-2882 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T136 3049-3050 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T137 3187-3191 http://purl.obolibrary.org/obo/CLO_0001550 denotes a 10
T138 3293-3297 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T139 3314-3318 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T140 3425-3426 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 3587-3588 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 3946-3952 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T143 4005-4007 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T144 4012-4014 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T145 4012-4014 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T146 4091-4093 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T147 4256-4258 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T148 4814-4820 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T149 4845-4846 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 4847-4853 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T151 4904-4907 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T152 4912-4915 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T153 4984-4988 http://purl.obolibrary.org/obo/CLO_0007653 denotes M, E
T154 5011-5016 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T155 5066-5067 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T156 5168-5174 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T35 154-164 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T36 197-207 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T37 266-276 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T38 1546-1548 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T39 1564-1566 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T40 3330-3332 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T41 3348-3350 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T42 3631-3641 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T43 3631-3636 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T44 3637-3641 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T45 3730-3732 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T46 3759-3761 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T47 3777-3779 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T48 4012-4014 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T49 4073-4075 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T50 4091-4093 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T51 4150-4157 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T52 4916-4923 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T53 4954-4962 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T54 5027-5034 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T55 5232-5234 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T56 5367-5369 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T57 5385-5387 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
204 4-5 Gene denotes S Gene:43740568
205 16-21 Mutation denotes D614G p.D614G
217 146-152 Gene denotes ORF1ab Gene:43740578
218 493-494 Gene denotes S Gene:43740568
219 194-195 Gene denotes S Gene:43740568
220 1526-1536 Species denotes SARS-CoV-2 Tax:2697049
221 136-142 Mutation denotes P4715L p.P4715L
222 1591-1596 Mutation denotes D614G p.D614G
223 1251-1256 Mutation denotes D614G p.D614G
224 858-863 Mutation denotes D614G p.D614G
225 784-789 Mutation denotes D614G p.D614G
226 595-600 Mutation denotes D614G p.D614G
227 185-190 Mutation denotes D614G p.D614G
239 2175-2181 Gene denotes ORF1ab Gene:43740578
240 2159-2160 Gene denotes S Gene:43740568
241 1903-1904 Gene denotes S Gene:43740568
242 1738-1739 Gene denotes S Gene:43740568
243 2297-2307 Species denotes SARS-CoV-2 Tax:2697049
244 2691-2696 Mutation denotes D614G p.D614G
245 2646-2651 Mutation denotes D614G p.D614G
246 2150-2155 Mutation denotes D614G p.D614G
247 2165-2171 Mutation denotes P4715L p.P4715L
248 1793-1798 Mutation denotes D614G p.D614G
249 1749-1754 Mutation denotes D614G p.D614G
266 4388-4392 Gene denotes ACE2 Gene:59272
267 4475-4479 Gene denotes ACE2 Gene:59272
268 4904-4907 Gene denotes CD8 Gene:925
269 4912-4915 Gene denotes CD4 Gene:920
270 4984-4985 Gene denotes M Gene:43740571
271 4981-4982 Gene denotes N Gene:43740575
272 4978-4979 Gene denotes S Gene:43740568
273 4181-4182 Gene denotes S Gene:43740568
274 3356-3357 Gene denotes S Gene:43740568
275 4966-4976 Species denotes SARS-CoV-2 Tax:2697049
276 5011-5016 Species denotes human Tax:9606
277 5036-5039 Gene denotes HLA Gene:3113
278 3730-3732 Chemical denotes dN MESH:C022306
279 3733-3735 Chemical denotes dS MESH:D003903
280 4198-4203 Mutation denotes D614G p.D614G
281 3892-3897 Mutation denotes D614G p.D614G

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T83 0-43 Sentence denotes One S Mutation (D614G) Has Become Dominant.
T84 44-364 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 365-468 Sentence denotes These mutations were found in 69.3% and 69.4% of sequences, respectively, and are in linkage (Fig. 2B).
T86 469-645 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 646-773 Sentence denotes This mutation was first observed in a sequence from China dated January 24, with seven more sequences sampled until February 8.
T88 774-840 Sentence denotes Then, the D614G mutation was not observed in China until March 13.
T89 841-1095 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 1096-1207 Sentence denotes The phylogenetic tree (Fig. 2B) and the distribution of sequences (Fig. 2C) are suggestive of a founder effect.
T91 1208-1416 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 1417-1568 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 1569-1724 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 1725-1732 Sentence denotes Fig. 2.
T95 1734-1779 Sentence denotes The S mutation D614G quickly became dominant.
T96 1780-2182 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 2183-2213 Sentence denotes Tips are colored by continent.
T98 2214-2437 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 2438-2833 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 2834-2874 Sentence denotes The median is marked with a dashed line.
T101 2875-3150 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 3151-3352 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 3353-3781 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 3782-3963 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 3964-4095 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 4096-4264 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 4265-4534 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 4535-4628 Sentence denotes Of these, one mutation, at position 489, was synonymous and found in three sequences (0.02%).
T109 4629-4762 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 4763-5085 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 5086-5250 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 5251-5389 Sentence denotes S6 and S7), and there was no significant relationship between the number of mutations and the immunogenicity index (SI Appendix, Fig. S8).

2_test

Id Subject Object Predicate Lexical cue
32868447-32697968-132542393 638-640 32697968 denotes 24
32868447-22807683-132542394 3029-3031 22807683 denotes 29
32868447-32697968-132542395 4248-4250 32697968 denotes 24