PMC:7443692 / 4430-6426 JSONTXT

{"project":"LitCovid-sample-MedDRA","denotations":[{"id":"T5","span":{"begin":1029,"end":1041},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"},{"id":"T6","span":{"begin":1552,"end":1574},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"},{"id":"T7","span":{"begin":1931,"end":1954},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"}],"attributes":[{"id":"A5","pred":"meddra_id","subj":"T5","obj":"http://purl.bioontology.org/ontology/MEDDRA/10062026"},{"id":"A6","pred":"meddra_id","subj":"T6","obj":"http://purl.bioontology.org/ontology/MEDDRA/10058063"},{"id":"A7","pred":"meddra_id","subj":"T7","obj":"http://purl.bioontology.org/ontology/MEDDRA/10058063"}],"text":"The SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T19","span":{"begin":21,"end":33},"obj":"Chemical"},{"id":"T20","span":{"begin":175,"end":187},"obj":"Chemical"},{"id":"T21","span":{"begin":317,"end":327},"obj":"Chemical"},{"id":"T22","span":{"begin":659,"end":672},"obj":"Chemical"},{"id":"T23","span":{"begin":876,"end":884},"obj":"Chemical"},{"id":"T24","span":{"begin":1215,"end":1222},"obj":"Chemical"},{"id":"T25","span":{"begin":1326,"end":1334},"obj":"Chemical"},{"id":"T26","span":{"begin":1345,"end":1352},"obj":"Chemical"}],"attributes":[{"id":"A24","pred":"chebi_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A21","pred":"chebi_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A19","pred":"chebi_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A22","pred":"chebi_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A26","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A20","pred":"chebi_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A23","pred":"chebi_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"}],"text":"The SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T26","span":{"begin":4,"end":14},"obj":"Species"},{"id":"T27","span":{"begin":906,"end":914},"obj":"Species"},{"id":"T28","span":{"begin":1045,"end":1055},"obj":"Species"},{"id":"T29","span":{"begin":1612,"end":1617},"obj":"Species"}],"attributes":[{"id":"A26","pred":"ncbi_taxonomy_id","subj":"T26","obj":"NCBItxid:2697049"},{"id":"A27","pred":"ncbi_taxonomy_id","subj":"T27","obj":"NCBItxid:694009"},{"id":"A28","pred":"ncbi_taxonomy_id","subj":"T28","obj":"NCBItxid:2697049"},{"id":"A29","pred":"ncbi_taxonomy_id","subj":"T29","obj":"NCBItxid:11676"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"The SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T27","span":{"begin":0,"end":164},"obj":"Sentence"},{"id":"T28","span":{"begin":165,"end":449},"obj":"Sentence"},{"id":"T29","span":{"begin":450,"end":773},"obj":"Sentence"},{"id":"T30","span":{"begin":774,"end":1079},"obj":"Sentence"},{"id":"T31","span":{"begin":1080,"end":1447},"obj":"Sentence"},{"id":"T32","span":{"begin":1448,"end":1806},"obj":"Sentence"},{"id":"T33","span":{"begin":1807,"end":1996},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T19","span":{"begin":4,"end":14},"obj":"Disease"},{"id":"T20","span":{"begin":906,"end":914},"obj":"Disease"},{"id":"T21","span":{"begin":1045,"end":1055},"obj":"Disease"},{"id":"T22","span":{"begin":1986,"end":1995},"obj":"Disease"}],"attributes":[{"id":"A19","pred":"mondo_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A20","pred":"mondo_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A21","pred":"mondo_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A22","pred":"mondo_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"The SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}

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SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T27","span":{"begin":394,"end":399},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T28","span":{"begin":479,"end":486},"obj":"http://purl.obolibrary.org/obo/IDO_0000508"},{"id":"T29","span":{"begin":1124,"end":1129},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T30","span":{"begin":1210,"end":1214},"obj":"http://purl.obolibrary.org/obo/IDO_0000531"},{"id":"T31","span":{"begin":1489,"end":1498},"obj":"http://purl.obolibrary.org/obo/BFO_0000034"},{"id":"T32","span":{"begin":1986,"end":1995},"obj":"http://purl.obolibrary.org/obo/IDO_0000586"}],"text":"The SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T21","span":{"begin":21,"end":33},"obj":"Body_part"},{"id":"T22","span":{"begin":175,"end":187},"obj":"Body_part"},{"id":"T23","span":{"begin":317,"end":327},"obj":"Body_part"},{"id":"T24","span":{"begin":500,"end":534},"obj":"Body_part"},{"id":"T25","span":{"begin":513,"end":534},"obj":"Body_part"},{"id":"T26","span":{"begin":554,"end":565},"obj":"Body_part"},{"id":"T27","span":{"begin":659,"end":672},"obj":"Body_part"},{"id":"T28","span":{"begin":876,"end":884},"obj":"Body_part"},{"id":"T29","span":{"begin":1215,"end":1222},"obj":"Body_part"},{"id":"T30","span":{"begin":1566,"end":1574},"obj":"Body_part"},{"id":"T31","span":{"begin":1612,"end":1615},"obj":"Body_part"}],"attributes":[{"id":"A22","pred":"fma_id","subj":"T22","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A23","pred":"fma_id","subj":"T23","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A30","pred":"fma_id","subj":"T30","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A25","pred":"fma_id","subj":"T25","obj":"http://purl.org/sig/ont/fma/fma63842"},{"id":"A31","pred":"fma_id","subj":"T31","obj":"http://purl.org/sig/ont/fma/fma278683"},{"id":"A24","pred":"fma_id","subj":"T24","obj":"http://purl.org/sig/ont/fma/fma84806"},{"id":"A27","pred":"fma_id","subj":"T27","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A21","pred":"fma_id","subj":"T21","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A26","pred":"fma_id","subj":"T26","obj":"http://purl.org/sig/ont/fma/fma76577"},{"id":"A28","pred":"fma_id","subj":"T28","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A29","pred":"fma_id","subj":"T29","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"The SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T12","span":{"begin":98,"end":113},"obj":"http://purl.obolibrary.org/obo/GO_0061025"},{"id":"T13","span":{"begin":278,"end":291},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T14","span":{"begin":380,"end":393},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T15","span":{"begin":932,"end":945},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T16","span":{"begin":997,"end":1004},"obj":"http://purl.obolibrary.org/obo/GO_0007114"},{"id":"T17","span":{"begin":1215,"end":1236},"obj":"http://purl.obolibrary.org/obo/GO_0006486"},{"id":"T18","span":{"begin":1223,"end":1236},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T19","span":{"begin":1285,"end":1299},"obj":"http://purl.obolibrary.org/obo/GO_0020012"},{"id":"T20","span":{"begin":1285,"end":1299},"obj":"http://purl.obolibrary.org/obo/GO_0051805"},{"id":"T21","span":{"begin":1831,"end":1844},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"The SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T11","span":{"begin":98,"end":113},"obj":"http://purl.obolibrary.org/obo/GO_0061025"},{"id":"T12","span":{"begin":278,"end":291},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T13","span":{"begin":380,"end":393},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T14","span":{"begin":932,"end":945},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T15","span":{"begin":997,"end":1004},"obj":"http://purl.obolibrary.org/obo/GO_0007114"},{"id":"T16","span":{"begin":1215,"end":1236},"obj":"http://purl.obolibrary.org/obo/GO_0006486"},{"id":"T17","span":{"begin":1223,"end":1236},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T18","span":{"begin":1285,"end":1299},"obj":"http://purl.obolibrary.org/obo/GO_0042783"},{"id":"T19","span":{"begin":1831,"end":1844},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"The SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}

{"project":"2_test","denotations":[{"id":"32841605-32007145-19659473","span":{"begin":139,"end":143},"obj":"32007145"},{"id":"32841605-32015507-19659474","span":{"begin":158,"end":162},"obj":"32015507"},{"id":"32841605-17210170-19659477","span":{"begin":742,"end":746},"obj":"17210170"},{"id":"32841605-25855243-19659478","span":{"begin":767,"end":771},"obj":"25855243"},{"id":"32841605-32363391-19659479","span":{"begin":826,"end":830},"obj":"32363391"},{"id":"32841605-20129637-19659481","span":{"begin":1073,"end":1077},"obj":"20129637"},{"id":"32841605-17210170-19659482","span":{"begin":1369,"end":1373},"obj":"17210170"},{"id":"32841605-25855243-19659483","span":{"begin":1394,"end":1398},"obj":"25855243"},{"id":"32841605-31121217-19659485","span":{"begin":1441,"end":1445},"obj":"31121217"},{"id":"32841605-30076101-19659486","span":{"begin":1632,"end":1636},"obj":"30076101"},{"id":"32841605-31142836-19659487","span":{"begin":1655,"end":1659},"obj":"31142836"},{"id":"32841605-32422645-19659488","span":{"begin":1675,"end":1679},"obj":"32422645"},{"id":"32841605-32433992-19659489","span":{"begin":1699,"end":1703},"obj":"32433992"},{"id":"32841605-31121217-19659490","span":{"begin":1722,"end":1726},"obj":"31121217"},{"id":"32841605-29677181-19659491","span":{"begin":1739,"end":1743},"obj":"29677181"}],"text":"The SARS-CoV-2 Spike glycoprotein consists of two subunits, a receptor binding subunit (S1) and a membrane fusion subunit (S2) (Lu et al., 2020; Zhou et al., 2020). The Spike glycoprotein assembles into stable homotrimers that together possess 66 canonical sequons for N-linked glycosylation (N-X-S/T, where X is any amino acid except P) as well as a number of potential O-linked glycosylation sites (Watanabe et al., 2020a; Watanabe et al., 2020b). Interestingly, coronaviruses virions bud into the lumen of the endoplasmic reticulum-Golgi intermediate compartment, ERGIC, raising unanswered questions regarding the precise mechanisms by which viral surface glycoproteins are processed as they traverse the secretory pathway (Stertz et al., 2007; Ujike and Taguchi, 2015). Although this and similar studies (Shajahan et al., 2020; Watanabe et al., 2020a) analyze recombinant proteins, a previous study on SARS-CoV-1 suggested that glycosylation of the Spike can be impacted by this intracellular budding, and this remains to be investigated in SARS-CoV-2 (Ritchie et al., 2010). Nonetheless, it has been proposed that this virus, and others, acquires a glycan coat sufficient and similar enough to endogenous host protein glycosylation that it serves as a glycan shield, facilitating immune evasion by masking non-self viral peptides with self-glycans (Stertz et al., 2007; Ujike and Taguchi, 2015; Watanabe et al., 2020b; Watanabe et al., 2019). In parallel with their potential masking functions, glycan-dependent epitopes can elicit specific, even neutralizing, antibody responses, as has been described for HIV-1 (Duan et al., 2018; Escolano et al., 2019; Pinto et al., 2020; Seabright et al., 2020; Watanabe et al., 2019; Yu et al., 2018; https://www.biorxiv.org/content/10.1101/2020.06.30.178897v1). Thus, understanding the glycosylation of the viral Spike trimer is fundamental for the development of efficacious vaccines, neutralizing antibodies, and therapeutic inhibitors of infection."}