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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T30","span":{"begin":1526,"end":1534},"obj":"Body_part"},{"id":"T31","span":{"begin":1845,"end":1852},"obj":"Body_part"},{"id":"T32","span":{"begin":1967,"end":1972},"obj":"Body_part"},{"id":"T33","span":{"begin":2074,"end":2086},"obj":"Body_part"}],"attributes":[{"id":"A30","pred":"fma_id","subj":"T30","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A31","pred":"fma_id","subj":"T31","obj":"http://purl.org/sig/ont/fma/fma82749"},{"id":"A32","pred":"fma_id","subj":"T32","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma62925"}],"text":"The sequence alignment between SARS-COV in human, SARS civet, Bat RaTG13 coronavirus, and nCOV-2019 in the RBM is shown in Figure 2. There is a 50% sequence similarity between the RBM of nCOV-2019 and SARS-COV. RBM mutations played an important role in the SARS epidemic in 2002.3,12 Two mutations in the RBM of SARS-2002 from SARS-Civet were observed from strains of these viruses. These two mutations were K479N and S487T. These two residues are close to the virus binding hotspots in ACE2 including hotspot-31 and hotspot-353. Hotspot-31 centers on the salt-bridge between K31-E35 and hotspot-353 are centered on the salt-bridge between K353-E358 on ACE2. Residues K479 and S487 in SARS-Civet are in close proximity with these hotspots and mutations at these residues caused SARS to bind ACE2 with significantly higher affinity than SARS-civet and played a major role in civet-to-human and human-to-human transmission of SARS coronavirus in 2002.3,13−15 Numerous mutations in the interface of SARS-COV RBD and ACE2 from different strains of SARS isolated from humans in 2002 have been identified and the effect of these mutations on binding ACE2 has been investigated by SPR.14,16 Two identified RBD mutations (Y442F and L472F) increased the binding affinity of SARS-COV to ACE2 and two mutations (N479K, T487S) decreased the binding affinity. It was demonstrated that these mutations were viral adaptations to either human or civet ACE2.14,16 A pseudotyped viral infection assay of the interaction between different spike proteins and ACE2 confirmed the correlation between high affinity mutants and their high infection.16 Further investigation of RBD residues in binding of SARS-COV and ACE2 was performed through ala-scanning mutagenesis, which resulted in identification of residues that reduce binding affinity to ACE2 upon mutation to alanine.17 RBD mutations have also been identified in MERS-COV, which affected their affinity to receptor (DPP4) on human cells.14 Multiple monoclonal antibodies have been developed for SARS since 2002 that neutralized the spike glycoprotein on the SARS-COV surface.18−22 However, multiple escape mutations exist in the RBD of SARS-COV that affect neutralization with antibodies, which led to the use of a cocktail of antibodies as a robust treatment.23"}

LitCovid-PD-MONDO

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T57","span":{"begin":43,"end":48},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T58","span":{"begin":142,"end":143},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T59","span":{"begin":374,"end":381},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T60","span":{"begin":461,"end":466},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T61","span":{"begin":858,"end":859},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T62","span":{"begin":883,"end":888},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T63","span":{"begin":893,"end":898},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T64","span":{"begin":902,"end":907},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T65","span":{"begin":1063,"end":1069},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T66","span":{"begin":1149,"end":1152},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T67","span":{"begin":1421,"end":1429},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T68","span":{"begin":1447,"end":1448},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T69","span":{"begin":1961,"end":1972},"obj":"http://purl.obolibrary.org/obo/CLO_0053065"},{"id":"T70","span":{"begin":2111,"end":2113},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T71","span":{"begin":2114,"end":2116},"obj":"http://purl.obolibrary.org/obo/CLO_0050507"},{"id":"T72","span":{"begin":2249,"end":2250},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T73","span":{"begin":2277,"end":2278},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"The sequence alignment between SARS-COV in human, SARS civet, Bat RaTG13 coronavirus, and nCOV-2019 in the RBM is shown in Figure 2. There is a 50% sequence similarity between the RBM of nCOV-2019 and SARS-COV. RBM mutations played an important role in the SARS epidemic in 2002.3,12 Two mutations in the RBM of SARS-2002 from SARS-Civet were observed from strains of these viruses. These two mutations were K479N and S487T. These two residues are close to the virus binding hotspots in ACE2 including hotspot-31 and hotspot-353. Hotspot-31 centers on the salt-bridge between K31-E35 and hotspot-353 are centered on the salt-bridge between K353-E358 on ACE2. Residues K479 and S487 in SARS-Civet are in close proximity with these hotspots and mutations at these residues caused SARS to bind ACE2 with significantly higher affinity than SARS-civet and played a major role in civet-to-human and human-to-human transmission of SARS coronavirus in 2002.3,13−15 Numerous mutations in the interface of SARS-COV RBD and ACE2 from different strains of SARS isolated from humans in 2002 have been identified and the effect of these mutations on binding ACE2 has been investigated by SPR.14,16 Two identified RBD mutations (Y442F and L472F) increased the binding affinity of SARS-COV to ACE2 and two mutations (N479K, T487S) decreased the binding affinity. It was demonstrated that these mutations were viral adaptations to either human or civet ACE2.14,16 A pseudotyped viral infection assay of the interaction between different spike proteins and ACE2 confirmed the correlation between high affinity mutants and their high infection.16 Further investigation of RBD residues in binding of SARS-COV and ACE2 was performed through ala-scanning mutagenesis, which resulted in identification of residues that reduce binding affinity to ACE2 upon mutation to alanine.17 RBD mutations have also been identified in MERS-COV, which affected their affinity to receptor (DPP4) on human cells.14 Multiple monoclonal antibodies have been developed for SARS since 2002 that neutralized the spike glycoprotein on the SARS-COV surface.18−22 However, multiple escape mutations exist in the RBD of SARS-COV that affect neutralization with antibodies, which led to the use of a cocktail of antibodies as a robust treatment.23"}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T25","span":{"begin":556,"end":560},"obj":"Chemical"},{"id":"T27","span":{"begin":620,"end":624},"obj":"Chemical"},{"id":"T29","span":{"begin":1526,"end":1534},"obj":"Chemical"},{"id":"T30","span":{"begin":1845,"end":1852},"obj":"Chemical"},{"id":"T31","span":{"begin":2074,"end":2086},"obj":"Chemical"}],"attributes":[{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_24866"},{"id":"A26","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_26710"},{"id":"A27","pred":"chebi_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/CHEBI_24866"},{"id":"A28","pred":"chebi_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/CHEBI_26710"},{"id":"A29","pred":"chebi_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A30","pred":"chebi_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/CHEBI_16449"},{"id":"A31","pred":"chebi_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"}],"text":"The sequence alignment between SARS-COV in human, SARS civet, Bat RaTG13 coronavirus, and nCOV-2019 in the RBM is shown in Figure 2. There is a 50% sequence similarity between the RBM of nCOV-2019 and SARS-COV. RBM mutations played an important role in the SARS epidemic in 2002.3,12 Two mutations in the RBM of SARS-2002 from SARS-Civet were observed from strains of these viruses. These two mutations were K479N and S487T. These two residues are close to the virus binding hotspots in ACE2 including hotspot-31 and hotspot-353. Hotspot-31 centers on the salt-bridge between K31-E35 and hotspot-353 are centered on the salt-bridge between K353-E358 on ACE2. Residues K479 and S487 in SARS-Civet are in close proximity with these hotspots and mutations at these residues caused SARS to bind ACE2 with significantly higher affinity than SARS-civet and played a major role in civet-to-human and human-to-human transmission of SARS coronavirus in 2002.3,13−15 Numerous mutations in the interface of SARS-COV RBD and ACE2 from different strains of SARS isolated from humans in 2002 have been identified and the effect of these mutations on binding ACE2 has been investigated by SPR.14,16 Two identified RBD mutations (Y442F and L472F) increased the binding affinity of SARS-COV to ACE2 and two mutations (N479K, T487S) decreased the binding affinity. It was demonstrated that these mutations were viral adaptations to either human or civet ACE2.14,16 A pseudotyped viral infection assay of the interaction between different spike proteins and ACE2 confirmed the correlation between high affinity mutants and their high infection.16 Further investigation of RBD residues in binding of SARS-COV and ACE2 was performed through ala-scanning mutagenesis, which resulted in identification of residues that reduce binding affinity to ACE2 upon mutation to alanine.17 RBD mutations have also been identified in MERS-COV, which affected their affinity to receptor (DPP4) on human cells.14 Multiple monoclonal antibodies have been developed for SARS since 2002 that neutralized the spike glycoprotein on the SARS-COV surface.18−22 However, multiple escape mutations exist in the RBD of SARS-COV that affect neutralization with antibodies, which led to the use of a cocktail of antibodies as a robust treatment.23"}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T3","span":{"begin":1461,"end":1476},"obj":"http://purl.obolibrary.org/obo/GO_0016032"}],"text":"The sequence alignment between SARS-COV in human, SARS civet, Bat RaTG13 coronavirus, and nCOV-2019 in the RBM is shown in Figure 2. There is a 50% sequence similarity between the RBM of nCOV-2019 and SARS-COV. RBM mutations played an important role in the SARS epidemic in 2002.3,12 Two mutations in the RBM of SARS-2002 from SARS-Civet were observed from strains of these viruses. These two mutations were K479N and S487T. These two residues are close to the virus binding hotspots in ACE2 including hotspot-31 and hotspot-353. Hotspot-31 centers on the salt-bridge between K31-E35 and hotspot-353 are centered on the salt-bridge between K353-E358 on ACE2. Residues K479 and S487 in SARS-Civet are in close proximity with these hotspots and mutations at these residues caused SARS to bind ACE2 with significantly higher affinity than SARS-civet and played a major role in civet-to-human and human-to-human transmission of SARS coronavirus in 2002.3,13−15 Numerous mutations in the interface of SARS-COV RBD and ACE2 from different strains of SARS isolated from humans in 2002 have been identified and the effect of these mutations on binding ACE2 has been investigated by SPR.14,16 Two identified RBD mutations (Y442F and L472F) increased the binding affinity of SARS-COV to ACE2 and two mutations (N479K, T487S) decreased the binding affinity. It was demonstrated that these mutations were viral adaptations to either human or civet ACE2.14,16 A pseudotyped viral infection assay of the interaction between different spike proteins and ACE2 confirmed the correlation between high affinity mutants and their high infection.16 Further investigation of RBD residues in binding of SARS-COV and ACE2 was performed through ala-scanning mutagenesis, which resulted in identification of residues that reduce binding affinity to ACE2 upon mutation to alanine.17 RBD mutations have also been identified in MERS-COV, which affected their affinity to receptor (DPP4) on human cells.14 Multiple monoclonal antibodies have been developed for SARS since 2002 that neutralized the spike glycoprotein on the SARS-COV surface.18−22 However, multiple escape mutations exist in the RBD of SARS-COV that affect neutralization with antibodies, which led to the use of a cocktail of antibodies as a robust treatment.23"}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T31","span":{"begin":0,"end":132},"obj":"Sentence"},{"id":"T32","span":{"begin":133,"end":210},"obj":"Sentence"},{"id":"T33","span":{"begin":211,"end":382},"obj":"Sentence"},{"id":"T34","span":{"begin":383,"end":424},"obj":"Sentence"},{"id":"T35","span":{"begin":425,"end":529},"obj":"Sentence"},{"id":"T36","span":{"begin":530,"end":658},"obj":"Sentence"},{"id":"T37","span":{"begin":659,"end":1346},"obj":"Sentence"},{"id":"T38","span":{"begin":1347,"end":2298},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The sequence alignment between SARS-COV in human, SARS civet, Bat RaTG13 coronavirus, and nCOV-2019 in the RBM is shown in Figure 2. There is a 50% sequence similarity between the RBM of nCOV-2019 and SARS-COV. RBM mutations played an important role in the SARS epidemic in 2002.3,12 Two mutations in the RBM of SARS-2002 from SARS-Civet were observed from strains of these viruses. These two mutations were K479N and S487T. These two residues are close to the virus binding hotspots in ACE2 including hotspot-31 and hotspot-353. Hotspot-31 centers on the salt-bridge between K31-E35 and hotspot-353 are centered on the salt-bridge between K353-E358 on ACE2. Residues K479 and S487 in SARS-Civet are in close proximity with these hotspots and mutations at these residues caused SARS to bind ACE2 with significantly higher affinity than SARS-civet and played a major role in civet-to-human and human-to-human transmission of SARS coronavirus in 2002.3,13−15 Numerous mutations in the interface of SARS-COV RBD and ACE2 from different strains of SARS isolated from humans in 2002 have been identified and the effect of these mutations on binding ACE2 has been investigated by SPR.14,16 Two identified RBD mutations (Y442F and L472F) increased the binding affinity of SARS-COV to ACE2 and two mutations (N479K, T487S) decreased the binding affinity. It was demonstrated that these mutations were viral adaptations to either human or civet ACE2.14,16 A pseudotyped viral infection assay of the interaction between different spike proteins and ACE2 confirmed the correlation between high affinity mutants and their high infection.16 Further investigation of RBD residues in binding of SARS-COV and ACE2 was performed through ala-scanning mutagenesis, which resulted in identification of residues that reduce binding affinity to ACE2 upon mutation to alanine.17 RBD mutations have also been identified in MERS-COV, which affected their affinity to receptor (DPP4) on human cells.14 Multiple monoclonal antibodies have been developed for SARS since 2002 that neutralized the spike glycoprotein on the SARS-COV surface.18−22 However, multiple escape mutations exist in the RBD of SARS-COV that affect neutralization with antibodies, which led to the use of a cocktail of antibodies as a robust treatment.23"}

LitCovid-PubTator