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PMC:7712180 / 11530-22485 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
476 38-47 Gene denotes Siaα2,3/2
477 5-14 Species denotes Influenza Tax:11520
493 382-384 Gene denotes α2 Gene:170589
494 414-416 Gene denotes α2 Gene:170589
495 289-291 Gene denotes α2 Gene:170589
496 623-628 Species denotes human Tax:9606
497 642-646 Species denotes H1N1 Tax:114727
498 780-784 Species denotes H1N1 Tax:114727
499 252-260 Species denotes domestic Tax:8839
500 676-678 Gene denotes α2 Gene:170589
501 111-118 Chemical denotes glycans MESH:D011134
502 868-875 Chemical denotes glycans MESH:D011134
503 1013-1019 Chemical denotes glycan MESH:D011134
504 1276-1283 Chemical denotes glycans MESH:D011134
505 184-199 Disease denotes virus infection MESH:D001102
506 607-612 Mutation denotes A138S p.A138S
507 702-707 Mutation denotes E190T p.E190T
556 3300-3302 Gene denotes α2 Gene:170589
557 1773-1775 Gene denotes α2 Gene:170589
558 1396-1411 Species denotes influenza virus Tax:11308
559 1456-1460 Species denotes H5N1 Tax:102793
560 1471-1475 Species denotes H9N2 Tax:102796
561 1480-1485 Species denotes swine Tax:9823
562 1495-1499 Species denotes H1N1 Tax:114727
563 1501-1505 Species denotes H1N2 Tax:114728
564 1510-1514 Species denotes H3N2 Tax:119210
565 1586-1592 Species denotes humans Tax:9606
566 1608-1613 Species denotes human Tax:9606
567 1617-1622 Species denotes human Tax:9606
568 1762-1767 Species denotes human Tax:9606
569 1808-1813 Species denotes human Tax:9606
570 1817-1822 Species denotes human Tax:9606
571 1862-1866 Species denotes H1N1 Tax:114727
572 2137-2142 Species denotes human Tax:9606
573 2303-2307 Species denotes H2N2 Tax:114729
574 2617-2622 Species denotes human Tax:9606
575 2728-2733 Species denotes human Tax:9606
576 2754-2759 Species denotes human Tax:9606
577 2898-2903 Species denotes human Tax:9606
578 2949-2953 Species denotes H3N2 Tax:119210
579 3118-3123 Species denotes human Tax:9606
580 3186-3190 Species denotes H1N1 Tax:114727
581 3191-3196 Species denotes swine Tax:9823
582 3261-3266 Species denotes swine Tax:9823
583 3289-3294 Species denotes human Tax:9606
584 3386-3391 Species denotes swine Tax:9823
585 3555-3560 Species denotes swine Tax:9823
586 3615-3620 Species denotes human Tax:9606
587 3624-3629 Species denotes human Tax:9606
588 3346-3353 Species denotes porcine Tax:1586324
589 3392-3395 Species denotes IAV Tax:11320
590 3672-3680 Chemical denotes hydrogen MESH:D006859
591 1387-1395 Disease denotes zoonotic MESH:D015047
592 2213-2218 Mutation denotes E190D p.E190D
593 2063-2068 Mutation denotes E190D p.E190D
594 2223-2228 Mutation denotes G225D p.G225D
595 3014-3019 Mutation denotes Q226L p.Q226L
596 2839-2844 Mutation denotes Q226L p.Q226L
597 3024-3029 Mutation denotes G228S p.G228S
598 2636-2641 Mutation denotes Q226L p.Q226L
599 2849-2854 Mutation denotes G228S p.G228S
600 2589-2594 Mutation denotes Q226L p.Q226L
601 2646-2651 Mutation denotes G228S p.G228S
602 3515-3520 Mutation denotes A200T c.200A>T
603 3525-3530 Mutation denotes A227E p.A227E
658 4550-4552 Gene denotes α2 Gene:170589
659 5053-5056 Gene denotes SLN Gene:6588
660 5043-5046 Gene denotes SLN Gene:6588
661 4585-4588 Gene denotes SLN Gene:6588
662 5373-5375 Gene denotes α2 Gene:170589
663 4048-4053 Species denotes human Tax:9606
664 4101-4105 Species denotes H1N1 Tax:114727
665 4120-4124 Species denotes H2N2 Tax:114729
666 4142-4146 Species denotes H1N1 Tax:114727
667 4171-4175 Species denotes H1N1 Tax:114727
668 4245-4250 Species denotes swine Tax:9823
669 4251-4255 Species denotes H1N1 Tax:114727
670 4305-4309 Species denotes H3N2 Tax:119210
671 4327-4331 Species denotes H1N1 Tax:114727
672 4353-4358 Species denotes human Tax:9606
673 4391-4396 Species denotes human Tax:9606
674 4432-4447 Species denotes influenza virus Tax:11308
675 4467-4473 Species denotes humans Tax:9606
676 4503-4507 Species denotes H3N2 Tax:119210
677 4523-4528 Species denotes human Tax:9606
678 4827-4842 Species denotes influenza virus Tax:11308
679 4894-4898 Species denotes H3N2 Tax:119210
680 4943-4948 Species denotes human Tax:9606
681 5200-5204 Species denotes H5N1 Tax:102793
682 5209-5213 Species denotes H5N3 Tax:119221
683 5466-5471 Species denotes swine Tax:9823
684 5472-5476 Species denotes H1N2 Tax:114728
685 5490-5494 Species denotes H1N1 Tax:114727
686 5614-5618 Species denotes pigs Tax:9823
687 5700-5704 Species denotes H1N1 Tax:114727
688 5780-5785 Species denotes swine Tax:9823
689 5874-5881 Species denotes chicken Tax:9031
690 5899-5904 Species denotes human Tax:9606
691 5995-6000 Species denotes swine Tax:9823
692 6009-6014 Species denotes human Tax:9606
693 6154-6159 Species denotes swine Tax:9823
694 6327-6332 Species denotes human Tax:9606
695 6351-6356 Species denotes human Tax:9606
696 6357-6361 Species denotes H3N2 Tax:119210
697 6379-6384 Species denotes human Tax:9606
698 6399-6403 Species denotes H1N1 Tax:114727
699 6460-6464 Gene denotes α2,6 Gene:170589
700 6061-6065 Gene denotes α2,6 Gene:170589
701 5547-5551 Gene denotes α2,6 Gene:170589
702 4761-4765 Gene denotes α2,6 Gene:170589
703 4590-4604 Chemical denotes polyacrylamide MESH:C016679
704 4777-4786 Chemical denotes N-glycans
705 4969-4975 Chemical denotes LacNAc
706 5563-5570 Chemical denotes glycans MESH:D011134
707 6073-6079 Chemical denotes glycan MESH:D011134
708 6209-6216 Chemical denotes glycans MESH:D011134
709 6472-6478 Chemical denotes glycan MESH:D011134
710 5793-5798 Mutation denotes A200T c.200A>T
711 5803-5808 Mutation denotes A227E p.A227E
724 7161-7166 Gene denotes Gal-2 Gene:3957
725 7522-7524 Gene denotes α2 Gene:170589
726 6520-6525 Species denotes human Tax:9606
727 6630-6635 Species denotes human Tax:9606
728 6897-6902 Species denotes human Tax:9606
729 7290-7295 Species denotes human Tax:9606
730 7431-7436 Species denotes human Tax:9606
731 7632-7637 Species denotes human Tax:9606
732 7696-7702 Species denotes humans Tax:9606
733 7487-7492 Mutation denotes L226Q p.L226Q
734 7704-7709 Mutation denotes L226V p.L226V
735 7714-7719 Mutation denotes V226I p.V226I
769 8432-8437 Gene denotes Gal-2 Gene:3957
770 10319-10321 Gene denotes α1 Gene:597
771 9439-9441 Gene denotes α2 Gene:170589
772 7854-7859 Species denotes human Tax:9606
773 7933-7938 Species denotes human Tax:9606
774 8325-8330 Species denotes human Tax:9606
775 8778-8784 Species denotes humans Tax:9606
776 8801-8806 Species denotes human Tax:9606
777 9074-9079 Species denotes human Tax:9606
778 9103-9108 Species denotes human Tax:9606
779 9400-9405 Species denotes human Tax:9606
780 9726-9731 Species denotes human Tax:9606
781 9783-9788 Species denotes human Tax:9606
782 10067-10072 Species denotes human Tax:9606
783 10135-10140 Species denotes human Tax:9606
784 10203-10208 Species denotes human Tax:9606
785 10378-10383 Species denotes human Tax:9606
786 10498-10503 Species denotes human Tax:9606
787 10563-10568 Species denotes human Tax:9606
788 10637-10642 Species denotes human Tax:9606
789 10700-10705 Species denotes human Tax:9606
790 10746-10750 Species denotes H1N1 Tax:114727
791 10902-10907 Species denotes human Tax:9606
792 9455-9462 Chemical denotes glycans MESH:D011134
793 9839-9845 Chemical denotes glycan MESH:D011134
794 10218-10227 Chemical denotes N-glycans
795 10393-10402 Chemical denotes N-glycans
796 10416-10425 Chemical denotes N-glycans
797 10685-10692 Chemical denotes glycans MESH:D011134
798 9305-9314 Disease denotes infection MESH:D007239
799 9978-9993 Disease denotes alveolar damage MESH:D055370
800 10706-10713 Disease denotes trachea MESH:C557675
801 10931-10948 Disease denotes tracheobronchitis

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T4 9970-9993 Phenotype denotes diffuse alveolar damage http://purl.obolibrary.org/obo/HP_0033006

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T76 0-4 Sentence denotes 3.1.
T77 5-62 Sentence denotes Influenza A (H1–H16) Viruses Use Siaα2,3/2,6Gal Receptors
T78 63-212 Sentence denotes HAs of H1–H16 viruses recognize specific sialyl glycans on the host epithelial cell surface, as a crucial step mediating virus infection (Figure 3a).
T79 213-306 Sentence denotes IAVs from avians, either wild birds or domestic birds, typically prefer the α2,3Sia terminal.
T80 307-472 Sentence denotes Surprisingly, a recent study showed that some gull/tern H16 viruses prefer α2,6Neu5Ac over or equal to the α2,3Neu5Ac terminal of synthetic sialylglycopolymers [23].
T81 473-826 Sentence denotes It was suggested that the particularly distinctive receptor-binding specificity of H16 viruses may be related to their HAs containing A138S (found in human 1977-derived H1N1 viruses, reducing binding to α2,3Neu5Ac receptors) and E190T (the amino acid (aa) at position 190 determining binding specificity of H1N1 viruses to the sialyl linkage type) [23].
T82 827-912 Sentence denotes Usually, viruses adapt to bind to sialyl glycans dominant in the host target tissues.
T83 913-1224 Sentence denotes Information on virus collection from oral, nasal, nasopharyngeal, cloacal or feces swabs and sialyl glycan analysis of tissues of specific wild birds shedding the virus in the sample collection may lead to a better understanding of why some H16 viruses display binding distinct from that of other avian viruses.
T84 1225-1378 Sentence denotes Binding preference for the internal part of sialyl glycans appears to differ among different viruses based on birds of isolation as indicated in Table 1.
T85 1379-1598 Sentence denotes Several zoonotic influenza virus subtypes (Table 1) including avian subtypes H5N1, H7N9 and H9N2 and swine subtypes H1N1, H1N2 and H3N2 have been occasionally reported to cross the species barrier to infect humans [57].
T86 1599-1697 Sentence denotes However, human-to-human transmission of nonhuman viruses has been limited and non-sustained [154].
T87 1698-2014 Sentence denotes Viruses in four historical pandemics acquired strong binding to human-type α2,6Neu5Ac receptors for efficient human-to-human transmission [19,155,156,157]. (i) The H1N1 Spanish pandemic in 1918–1919 was found to include at least two strains with distinct receptor-binding properties during the pandemic period [155].
T88 2015-2158 Sentence denotes First, viral HAs have a single aa substitution, E190D, in the receptor-binding site (RBS) and bind to both avian-type and human-type receptors.
T89 2159-2387 Sentence denotes Second, there are two aa substitutions in the HA RBS, E190D and G225D, that enable HA adaptation to bind only to α2,6Neu5Ac receptors. (ii) The H2N2 Asian pandemic in 1957–1958 had virus isolates from two stages of the pandemic.
T90 2388-2789 Sentence denotes In the early pandemic stage, virus isolates can be divided into three subpopulations based on receptor binding specificities: avian-like viruses with 226Q and 228G in the HA RBS, atypical viruses with Q226L and 228G, and classic human viruses with Q226L and G228S that have preferential binding to avian-type receptors, both avian-type and human-type receptors, and human-type receptors, respectively.
T91 2790-3416 Sentence denotes In the subsequent stage, all virus isolates have Q226L and G228S substitutions with preferential binding to human-type receptors [156]. (iii) The virus in the H3N2 Hong Kong pandemic in 1968–1969 had the same acquisition of Q226L and G228S substitutions in the HA RBS as that in the H2 pandemic for switching from avian-type to human-type receptor binding preference [157]. (iv) The virus in the H1N1 swine pandemic in 2009–2010 had 190D and 225D in the HA RBS as in the swine H1 HA RBS recognizing human-type α2,6Neu5Ac receptors that are abundant in the porcine lung, which is the main site of swine IAV replication [19,39].
T92 3417-3643 Sentence denotes Protein engineering by chimeragenesis and site-directed mutagenesis of H1 proteins suggested that A200T and A227E substitutions in the H1 swine pandemic were responsible for efficient and sustained human-to-human transmission.
T93 3644-3838 Sentence denotes Molecular modeling revealed hydrogen bond formation between T200 and Q191 in the 190-helix that is important for receptor binding preference of H1 HAs and between E227 and Gal next to Sia [158].
T94 3839-4066 Sentence denotes Based on historical data, after a pandemic virus continued to circulate as a seasonal strain, the preexisting seasonal virus, which donated at least three gene segments to the pandemic virus, disappeared from human circulation.
T95 4067-4371 Sentence denotes The disappearance of 1918-derived H1N1, 1957-derived H2N2 and 1977-derived H1N1 (being the 1918-derived H1N1, recurrent from a research laboratory in 1977, same as the classical swine H1N1 viruses) [159] has resulted in only 1968-derived H3N2 and 2009-derived H1N1 viruses remaining in human circulation.
T96 4372-4694 Sentence denotes Despite binding to human-type receptors being essential for influenza virus transmission among humans, the binding of 1968-derived H3N2 viruses to the human-type receptor analog α2,6 sialyl N-acetyllactosamine (6′SLN)-polyacrylamide started to decrease significantly in 2001 and seemed to be completely lost in 2010 [160].
T97 4695-4998 Sentence denotes However, after the discovery [161] and the widespread use of long α2,6 sialylated N-glycans with multiple LN repeats for studies on influenza virus binding specificity, it appeared that 1968-derived H3N2 viruses have evolved binding preference for human-type receptors with LacNAc (LN) repeats [60,162].
T98 4999-5162 Sentence denotes Based on the binding preferences to short 3′SLN and 6′SLN and long 3′SLNLNLN and 6′SLNLNLN linked to a polyglutamic acid, IAVs can be divided into two groups [19].
T99 5163-5307 Sentence denotes Group 1 are avian viruses, including H5N1 and H5N3 viruses, that preferentially bind to terminal α2,3Neu5Ac with either short or long LN chains.
T100 5308-5443 Sentence denotes Group 2 consists of viruses that preferentially bind to terminal α2,6Neu5Ac, and the viruses can be further divided into two subgroups.
T101 5444-5571 Sentence denotes Subgroup 2-1 includes swine H1N2/2008 and pdm H1N1/2009 viruses, which can bind to both short and long α2,6 sialylated glycans.
T102 5572-5682 Sentence denotes These results support the hypothesis that pigs are vessels to generate viral HAs with pandemic potential [41].
T103 5683-6026 Sentence denotes However, the pdm H1N1/2009 viruses acquired at least two amino acids that are different from the swine H1 HA, A200T and A227E, and they are responsible for the binding differences in fetuin, chicken erythrocytes and human erythrocytes and are believed to be determinants of the shift in binding specificity from swine-type to human-type [158].
T104 6027-6279 Sentence denotes Further investigation to find the α2,6 sialyl glycan structure that is able to clearly distinguish binding specificity between swine and pandemic viruses is needed since such sialyl glycans could be useful for surveillance and prevention of a pandemic.
T105 6280-6479 Sentence denotes Subgroup 2-2 consists of long-term circulating human viruses including human H3N2/2008 viruses and human H1N1/2004 and H1N1/2006 viruses, which have binding preference to the long α2,6 sialyl glycan.
T106 6480-6967 Sentence denotes Structural comparison of avian-type and human-type receptors interacting with the receptor binding sites of avian H3/1963, pandemic (pdm) H3/1968 and human H3/2007 (Figure 3b) revealed that trisaccharide Neu5Acα2,3Galβ1,3GlcNAc of lactoseries tetrasaccharide a (LSTa) interacts with the avian H3/1963 binding site in a cone-like topology (1mqm [149]), whereas 6′SLNLN interacts with pandemic H3/1968 (6tzb [150]) and human H3/2007 binding sites in an umbrella-like topology (6aov [151]).
T107 6968-7053 Sentence denotes Residues 226 and 228 are important in determining sialyl linkage binding specificity.
T108 7054-7373 Sentence denotes As shown in Figure 3b, Q226 in the avian H3/1963 binding site directly forms hydrogen bonds with Sia-1 and Gal-2 of LSTa, whereas S228 in the pdm H3/1968 binding site directly forms a hydrogen bond with Sia-1 of 6′SLNLN and S228 in the human H3/2007 binding site directly forms two hydrogen bonds with Sia-1 of 6′SLNLN.
T109 7374-7552 Sentence denotes Although no direct interaction of residue 226 in pdm and human H3 HAs was found, a previous study suggested that L226Q mutation in the HA decreases α2,6Neu5Ac binding preference.
T110 7553-7651 Sentence denotes Both G228 and S228 can be found in H3 avian HAs, whereas only S228 is found in human H3 HAs [149].
T111 7652-7792 Sentence denotes L226 is not conserved during circulation in humans; L226V and V226I substitutions were observed before 2001 and in 2004, respectively [160].
T112 7793-8172 Sentence denotes Similar to the H1 HA receptor binding site [10], two sets of human receptor binding residues provide networks to make contact with the long human-type receptor that results in an umbrella-like topology of the receptor. (i) A base region Neu5Acα2,6Galβ1- motif is governed by residues 131–138 in a 130-loop, residues 140–145 in a 140-loop and residues 219–228 in a 220-loop [163].
T113 8173-8317 Sentence denotes Figure 3b shows direct H-bond formation between Y98, G135, S136, N137, H183, E190 and S228 in the pdm H3/1968 binding site and Sia-1 of 6′SLNLN.
T114 8318-8728 Sentence denotes In the human H3/2007 binding site, Y98, T135, S136, S137, S228, R222, and N225 make direct H-bonds with Sia-1 and Gal-2, respectively, of 6′SLNLN. (ii) The extension region -4GlcNAcβ1,4Galβ1,4GlcNAc motif is governed by residues 190–196 in a 190-helix and residues 156–160 in a 150-loop [163], and S193 and K156 in the pdm H3/1968 binding site were observed to generate direct H-bonds with GlcNAc-5 of 6′SLNLN.
T115 8729-8816 Sentence denotes Amino acid change in HA during co-evolution with humans occurs to evade human immunity.
T116 8817-9117 Sentence denotes Not only is there a change in antigenicity but the number of glycosylation sites masking antigenicity also increases over time as shown in Figure 3c; the numbers of glycosylation sites/monomer are two for avian H3/1968 HA, two for pdm H3/1968 HA, seven for human H3/2007 HA and six for human H3/2014.
T117 9118-9315 Sentence denotes The limitation of increase in the number of glycosylation sites might be because the change of the virus must have a balance between mutation and selection for optimal immune evasion and infection.
T118 9316-9632 Sentence denotes Taken together, the change in receptor binding specificity of long-term circulating human IAVs from short and long to long α2,6 sialylated glycans may have resulted from aa change in the RBS (Figure 3b,d) and an increase in glycosylation sites surrounding the RBS, possibly making the shallow RBS deeper (Figure 3c).
T119 9633-9857 Sentence denotes The differences in receptor binding preferences of avian, pandemic and long-term circulating human IAVs are associated with viral pathology along the human respiratory tract containing different sialylated glycan structures.
T120 9858-10159 Sentence denotes The preferential binding of avian and pandemic viruses to both short and extended receptors can typically cause diffuse alveolar damage, resulting in greater severity than that caused by long-term circulating human viruses with preference for long receptors that rarely infect human alveoli [164,165].
T121 10160-10269 Sentence denotes This correlates well with our finding that human alveolar N-glycans consist of mainly short receptors, 22.32:
T122 10270-10275 Sentence denotes 0.17:
T123 10276-10282 Sentence denotes 16.10:
T124 10283-10307 Sentence denotes 0.15 mol% (Neu5Acα2,3LN:
T125 10308-10339 Sentence denotes Neu5Acα2,3(α1,3fucosylated LN):
T126 10340-10353 Sentence denotes Neu5Acα2,6LN:
T127 10354-10408 Sentence denotes Neu5Ac-LN-LN), of total human alveolar N-glycans [19].
T128 10409-10661 Sentence denotes Sialyl N-glycans with various numbers of LN units (up to 10 units) have been reported in human lungs (principally terminated in α2,3Neu5Ac [166]) and the human bronchus, whereas fewer extended LN profiles can be detected in the human nasopharynx [167].
T129 10662-10865 Sentence denotes Although structures of glycans in the human trachea have not be determined, the pdm H1N1/2009 virus was found at higher levels in tracheal aspirate specimens than in throat or nasopharyngeal swabs [168].
T130 10866-10955 Sentence denotes Uncomplicated long-term circulating human viruses are related to tracheobronchitis [169].