> top > docs > PMC:7519301 > spans > 8672-12457 > annotations

PMC:7519301 / 8672-12457 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T30 43-50 Body_part denotes Genomes http://purl.org/sig/ont/fma/fma84116
T31 161-167 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T32 524-531 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T33 536-544 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T34 612-619 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T35 761-767 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T36 953-961 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T37 990-998 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T38 1082-1088 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T39 1457-1463 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T40 1486-1497 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T41 1813-1820 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T42 1924-1930 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T43 2757-2763 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T44 2890-2897 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T45 3016-3023 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T46 3171-3178 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T47 3265-3273 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T48 3324-3331 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T49 3766-3774 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 1208-1213 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T74 32-40 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 32-36 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T76 68-76 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T77 68-72 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T78 150-158 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T79 150-154 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T80 513-521 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T81 513-517 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T82 577-585 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T83 577-581 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T84 2360-2370 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T85 2787-2795 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 2787-2791 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T85 434-435 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 487-488 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87 551-553 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T88 622-623 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T89 696-697 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T90 1285-1292 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T91 1313-1315 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T92 1397-1400 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T93 1401-1402 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T94 1533-1534 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 1662-1664 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T96 1877-1878 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T97 1976-1981 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T98 2094-2097 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T99 2199-2200 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T100 2611-2612 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 2798-2805 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T102 3087-3088 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 3115-3116 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 3231-3232 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T105 3280-3282 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T106 3280-3282 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T107 3374-3375 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T108 3422-3423 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 3683-3684 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 3726-3727 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 3781-3783 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T112 3781-3783 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T27 533-535 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T28 953-961 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T29 990-998 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T30 1486-1497 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T31 3262-3264 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T32 3280-3282 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T33 3763-3765 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T34 3781-3783 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
179 32-42 Species denotes SARS-CoV-2 Tax:2697049
184 68-78 Species denotes SARS-CoV-2 Tax:2697049
185 150-160 Species denotes SARS-CoV-2 Tax:2697049
186 513-523 Species denotes SARS-CoV-2 Tax:2697049
187 192-200 Disease denotes infected MESH:D007239
192 1020-1021 Gene denotes M Gene:43740571
193 1030-1031 Gene denotes N Gene:43740575
194 1000-1001 Gene denotes S Gene:43740568
195 577-587 Species denotes SARS-CoV-2 Tax:2697049
199 1874-1875 Gene denotes N Gene:43740575
200 2787-2797 Species denotes SARS-CoV-2 Tax:2697049
201 2360-2370 Disease denotes infections MESH:D007239

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T56 0-51 Sentence denotes Limited Diversity across 18,514 SARS-CoV-2 Genomes.
T57 52-229 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 230-322 Sentence denotes The alignment was curated to retain independent sequences that covered over 95% of the ORFs.
T59 323-567 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 568-575 Sentence denotes Fig. 1.
T61 577-768 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 769-911 Sentence denotes Proportion of sequences that showed polymorphisms compared to the reference sequence, Wuhan-Hu-1 (GISAID: EPI_ISL_402215, GenBank: NC_045512).
T63 912-1099 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 1100-1203 Sentence denotes The tree was rooted at the reference sequence, Wuhan-Hu-1, and tips are colored by collection location.
T65 1204-1271 Sentence denotes The scale indicates the distance corresponding to one substitution.
T66 1272-1317 Sentence denotes Lineages are labeled following PANGOLIN (22).
T67 1318-1478 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 1479-1499 Sentence denotes 29,409 nucleotides).
T69 1500-1656 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 1657-1777 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 1778-1876 Sentence denotes The mean pairwise diversity across genomes was 0.025%, ranging between 0.01% for E to 0.11% for N.
T72 1877-1982 Sentence denotes A phylogenetic tree reconstructed based on all genome sequences reflected the global spread of the virus:
T73 1983-2077 Sentence denotes Samples from the first 6 wk of the outbreak were collected predominantly from China (Fig. 1C).
T74 2078-2208 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 2209-2447 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 2448-2696 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 2697-2874 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 2875-3055 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 3056-3284 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 3285-3514 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 3515-3664 Sentence denotes We identified that this bimodal distribution was driven by sequences from Washington State, possibly reflecting separate introductions in that state.
T82 3665-3785 Sentence denotes Nonetheless, such a bimodal distribution could also indicate a bias in the sampling of sequences (SI Appendix, Fig. S2).