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Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T73","span":{"begin":861,"end":868},"obj":"Body_part"},{"id":"T70","span":{"begin":482,"end":488},"obj":"Body_part"},{"id":"T71","span":{"begin":622,"end":625},"obj":"Body_part"},{"id":"T72","span":{"begin":716,"end":720},"obj":"Body_part"}],"attributes":[{"id":"A72","pred":"fma_id","subj":"T72","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A70","pred":"fma_id","subj":"T70","obj":"http://purl.org/sig/ont/fma/fma82790"},{"id":"A71","pred":"fma_id","subj":"T71","obj":"http://purl.org/sig/ont/fma/fma278683"},{"id":"A73","pred":"fma_id","subj":"T73","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T102","span":{"begin":45,"end":52},"obj":"Chemical"},{"id":"T103","span":{"begin":218,"end":225},"obj":"Chemical"},{"id":"T104","span":{"begin":319,"end":326},"obj":"Chemical"},{"id":"T105","span":{"begin":348,"end":359},"obj":"Chemical"},{"id":"T106","span":{"begin":466,"end":473},"obj":"Chemical"},{"id":"T107","span":{"begin":482,"end":488},"obj":"Chemical"},{"id":"T108","span":{"begin":499,"end":505},"obj":"Chemical"},{"id":"T109","span":{"begin":682,"end":689},"obj":"Chemical"},{"id":"T110","span":{"begin":762,"end":769},"obj":"Chemical"},{"id":"T111","span":{"begin":861,"end":868},"obj":"Chemical"}],"attributes":[{"id":"A106","pred":"chebi_id","subj":"T106","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A105","pred":"chebi_id","subj":"T105","obj":"http://purl.obolibrary.org/obo/CHEBI_26667"},{"id":"A110","pred":"chebi_id","subj":"T110","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A103","pred":"chebi_id","subj":"T103","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A109","pred":"chebi_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A111","pred":"chebi_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A104","pred":"chebi_id","subj":"T104","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A107","pred":"chebi_id","subj":"T107","obj":"http://purl.obolibrary.org/obo/CHEBI_33984"},{"id":"A108","pred":"chebi_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A102","pred":"chebi_id","subj":"T102","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T53","span":{"begin":181,"end":191},"obj":"Species"},{"id":"T54","span":{"begin":622,"end":627},"obj":"Species"}],"attributes":[{"id":"A54","pred":"ncbi_taxonomy_id","subj":"T54","obj":"NCBItxid:11676"},{"id":"A53","pred":"ncbi_taxonomy_id","subj":"T53","obj":"NCBItxid:2697049"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T88","span":{"begin":0,"end":239},"obj":"Sentence"},{"id":"T89","span":{"begin":240,"end":391},"obj":"Sentence"},{"id":"T90","span":{"begin":392,"end":498},"obj":"Sentence"},{"id":"T91","span":{"begin":499,"end":585},"obj":"Sentence"},{"id":"T92","span":{"begin":586,"end":903},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T43","span":{"begin":181,"end":191},"obj":"Disease"}],"attributes":[{"id":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-sample-Pubtator","denotations":[{"id":"454","span":{"begin":192,"end":193},"obj":"Gene"},{"id":"455","span":{"begin":181,"end":191},"obj":"Species"},{"id":"456","span":{"begin":45,"end":52},"obj":"Chemical"},{"id":"457","span":{"begin":218,"end":225},"obj":"Chemical"},{"id":"458","span":{"begin":254,"end":255},"obj":"Chemical"},{"id":"459","span":{"begin":319,"end":326},"obj":"Chemical"},{"id":"460","span":{"begin":348,"end":359},"obj":"Chemical"},{"id":"461","span":{"begin":418,"end":422},"obj":"Chemical"},{"id":"462","span":{"begin":466,"end":473},"obj":"Chemical"},{"id":"463","span":{"begin":482,"end":488},"obj":"Chemical"},{"id":"464","span":{"begin":499,"end":505},"obj":"Chemical"},{"id":"465","span":{"begin":682,"end":689},"obj":"Chemical"},{"id":"466","span":{"begin":744,"end":756},"obj":"Chemical"},{"id":"467","span":{"begin":762,"end":769},"obj":"Chemical"},{"id":"468","span":{"begin":883,"end":889},"obj":"Chemical"},{"id":"469","span":{"begin":622,"end":645},"obj":"Disease"}],"attributes":[{"id":"A459","pred":"pubann:denotes","subj":"459","obj":"MESH:D011134"},{"id":"A468","pred":"pubann:denotes","subj":"468","obj":"MESH:D011134"},{"id":"A465","pred":"pubann:denotes","subj":"465","obj":"MESH:D011134"},{"id":"A469","pred":"pubann:denotes","subj":"469","obj":"MESH:D015658"},{"id":"A467","pred":"pubann:denotes","subj":"467","obj":"MESH:D011134"},{"id":"A455","pred":"pubann:denotes","subj":"455","obj":"Tax:2697049"},{"id":"A458","pred":"pubann:denotes","subj":"458","obj":"MESH:D009584"},{"id":"A463","pred":"pubann:denotes","subj":"463","obj":"MESH:D005643"},{"id":"A454","pred":"pubann:denotes","subj":"454","obj":"Gene:43740568"},{"id":"A464","pred":"pubann:denotes","subj":"464","obj":"MESH:D011134"},{"id":"A460","pred":"pubann:denotes","subj":"460","obj":"MESH:D019158"},{"id":"A456","pred":"pubann:denotes","subj":"456","obj":"MESH:D011134"},{"id":"A457","pred":"pubann:denotes","subj":"457","obj":"MESH:D011134"},{"id":"A462","pred":"pubann:denotes","subj":"462","obj":"MESH:D011134"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-sample-UniProt","denotations":[{"id":"T2323","span":{"begin":628,"end":631},"obj":"Protein"}],"attributes":[{"id":"A2323","pred":"uniprot_id","subj":"T2323","obj":"https://www.uniprot.org/uniprot/C1JJY3"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T35","span":{"begin":263,"end":276},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T36","span":{"begin":632,"end":645},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T33","span":{"begin":263,"end":276},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T34","span":{"begin":632,"end":645},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T38","span":{"begin":254,"end":276},"obj":"http://purl.obolibrary.org/obo/GO_0006487"},{"id":"T39","span":{"begin":263,"end":276},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T40","span":{"begin":632,"end":645},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T88","span":{"begin":0,"end":239},"obj":"Sentence"},{"id":"T89","span":{"begin":240,"end":391},"obj":"Sentence"},{"id":"T90","span":{"begin":392,"end":498},"obj":"Sentence"},{"id":"T91","span":{"begin":499,"end":585},"obj":"Sentence"},{"id":"T92","span":{"begin":586,"end":903},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"454","span":{"begin":192,"end":193},"obj":"Gene"},{"id":"455","span":{"begin":181,"end":191},"obj":"Species"},{"id":"456","span":{"begin":45,"end":52},"obj":"Chemical"},{"id":"457","span":{"begin":218,"end":225},"obj":"Chemical"},{"id":"458","span":{"begin":254,"end":255},"obj":"Chemical"},{"id":"459","span":{"begin":319,"end":326},"obj":"Chemical"},{"id":"460","span":{"begin":348,"end":359},"obj":"Chemical"},{"id":"461","span":{"begin":418,"end":422},"obj":"Chemical"},{"id":"462","span":{"begin":466,"end":473},"obj":"Chemical"},{"id":"463","span":{"begin":482,"end":488},"obj":"Chemical"},{"id":"464","span":{"begin":499,"end":505},"obj":"Chemical"},{"id":"465","span":{"begin":682,"end":689},"obj":"Chemical"},{"id":"466","span":{"begin":744,"end":756},"obj":"Chemical"},{"id":"467","span":{"begin":762,"end":769},"obj":"Chemical"},{"id":"468","span":{"begin":883,"end":889},"obj":"Chemical"},{"id":"469","span":{"begin":622,"end":645},"obj":"Disease"}],"attributes":[{"id":"A454","pred":"tao:has_database_id","subj":"454","obj":"Gene:43740568"},{"id":"A455","pred":"tao:has_database_id","subj":"455","obj":"Tax:2697049"},{"id":"A456","pred":"tao:has_database_id","subj":"456","obj":"MESH:D011134"},{"id":"A457","pred":"tao:has_database_id","subj":"457","obj":"MESH:D011134"},{"id":"A458","pred":"tao:has_database_id","subj":"458","obj":"MESH:D009584"},{"id":"A459","pred":"tao:has_database_id","subj":"459","obj":"MESH:D011134"},{"id":"A460","pred":"tao:has_database_id","subj":"460","obj":"MESH:D019158"},{"id":"A462","pred":"tao:has_database_id","subj":"462","obj":"MESH:D011134"},{"id":"A463","pred":"tao:has_database_id","subj":"463","obj":"MESH:D005643"},{"id":"A464","pred":"tao:has_database_id","subj":"464","obj":"MESH:D011134"},{"id":"A465","pred":"tao:has_database_id","subj":"465","obj":"MESH:D011134"},{"id":"A467","pred":"tao:has_database_id","subj":"467","obj":"MESH:D011134"},{"id":"A468","pred":"tao:has_database_id","subj":"468","obj":"MESH:D011134"},{"id":"A469","pred":"tao:has_database_id","subj":"469","obj":"MESH:D015658"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35). Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3). Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues. Glycan modifications can be heavily influenced by the cellular expression system used. We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36)."}