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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T42865","span":{"begin":147,"end":159},"obj":"Chemical"},{"id":"T26728","span":{"begin":266,"end":273},"obj":"Chemical"},{"id":"T66150","span":{"begin":356,"end":363},"obj":"Chemical"},{"id":"T53998","span":{"begin":424,"end":431},"obj":"Chemical"},{"id":"T83174","span":{"begin":504,"end":515},"obj":"Chemical"},{"id":"T29108","span":{"begin":844,"end":851},"obj":"Chemical"},{"id":"T28218","span":{"begin":1776,"end":1783},"obj":"Chemical"},{"id":"T85504","span":{"begin":2147,"end":2149},"obj":"Chemical"}],"attributes":[{"id":"A15627","pred":"chebi_id","subj":"T42865","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A21480","pred":"chebi_id","subj":"T26728","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A4418","pred":"chebi_id","subj":"T66150","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A88738","pred":"chebi_id","subj":"T53998","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A11619","pred":"chebi_id","subj":"T83174","obj":"http://purl.obolibrary.org/obo/CHEBI_2719"},{"id":"A48731","pred":"chebi_id","subj":"T29108","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A17604","pred":"chebi_id","subj":"T28218","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A87921","pred":"chebi_id","subj":"T85504","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"}],"text":"9.2 Entry into host cell\nCell entry is an essential component of cross-species transmission, especially for the β-CoVs. All CoVs encode a surface glycoprotein, spike, which binds to the host receptor and mediates viral entry [111]. For β-CoVs, the RBD of the spike protein mediates the interaction with host receptor. Upon binding the receptor, the spike protein is cleaved by nearby host proteases and releases the signal peptide to facilitate virus entry into host cells [[112], [113], [114], [115]].\nAngiotensin converting enzyme 2 (ACE2) and dipeptidyl peptidase 4 (DPP4) are known host receptors for the β-CoVs SARS-CoV and MERS-CoV, respectively [116,117]. In similar fashion to SARS-CoV, SARS-CoV-2 also uses ACE2 to gain entry into host cells. Hoffmann et al. found that the cellular protease MPRSS2 blocks entry by cleaving the spike protein and may constitute a treatment option [118]. Zhou et al. also confirmed that SARS-CoV-2 is able to use all but mouse ACE2 as an entry receptor for ACE2-expressing cells, but not cells without ACE2, indicating that the cell receptor for SARS-CoV-2 could be ACE2, and not other coronavirus receptors such as aminopeptidase N and dipeptidyl peptidase 4 [94]. Huang also showed that the affinity of the SARS-CoV-2 S-RBD binding to ACE2 is less than that of SARS-CoV through Monte Carlo algorithm [119]. However, Wrapp et al. found that SARS-CoV-2 S binding to ACE2 has approximately 10- to 20- fold higher affinity than SARS-CoV S, which can provide one explanation why SARS-CoV-2 has more human-to human spread compared to SARS-CoV [97].\nThe combination of SARS-CoV-2 S and ACE2 of host cells is similar to the combination of SARS-CoV and ACE2, indicating that they have the same mechanism to entry into host cells [97]. The S protein of metastable prefusion conformation undergoes a series of structural rearrangements to combine with the viral membrane of host cells [111,120]. This process consists of the S1 subunit binding to the host cell receptor, triggering of the prefusion trimer's instability, and shedding of the S1 subunit, resulting in a highly stable post-fusion conformation of the S2 subunit [121]. During the binding of the subunit S1 to its cognate receptor, it is important to note that the S1 subunit exists in 2 different states, a “down” conformation and an “up” conformation state, which corresponds to a receptor-inaccessible state and an unstable receptor-accessible state, respectively [[122], [123], [124], [125]]. Unfortunately, there are significant conformational differences between SARS-CoV and SARS-CoV-2 such that the commercially available monoclonal antibodies against SARS-CoV do not react with SARS-CoV-2 [97].\nSARS-CoV-2 may directly bind to ACE2 positive cholangiocytes but not necessarily hepatocytes via specific expression of ACE2 in healthy liver tissues using cell RNA-seq data of two independent cohorts [126]. Though the respiratory systems is a primary target of SARS-CoV-2, bioinformatic analysis of single-cell transcriptomes datasets of lung, esophagus, gastric, ileum and colon reveal that the digestive system is also a potential route of entry for COVID-19, as ACE2 was not only highly expressed in lung AT2 cells, esophagus upper and stratified epithelial cells but also in absorptive enterocytes from the ileum and colon [127]."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T53","span":{"begin":5,"end":25},"obj":"http://purl.obolibrary.org/obo/GO_0044409"},{"id":"T54","span":{"begin":287,"end":308},"obj":"http://purl.obolibrary.org/obo/GO_0051701"},{"id":"T55","span":{"begin":446,"end":473},"obj":"http://purl.obolibrary.org/obo/GO_0046718"},{"id":"T56","span":{"begin":452,"end":467},"obj":"http://purl.obolibrary.org/obo/GO_0044409"},{"id":"T57","span":{"begin":730,"end":745},"obj":"http://purl.obolibrary.org/obo/GO_0044409"},{"id":"T58","span":{"begin":1742,"end":1757},"obj":"http://purl.obolibrary.org/obo/GO_0044409"}],"text":"9.2 Entry into host cell\nCell entry is an essential component of cross-species transmission, especially for the β-CoVs. All CoVs encode a surface glycoprotein, spike, which binds to the host receptor and mediates viral entry [111]. For β-CoVs, the RBD of the spike protein mediates the interaction with host receptor. Upon binding the receptor, the spike protein is cleaved by nearby host proteases and releases the signal peptide to facilitate virus entry into host cells [[112], [113], [114], [115]].\nAngiotensin converting enzyme 2 (ACE2) and dipeptidyl peptidase 4 (DPP4) are known host receptors for the β-CoVs SARS-CoV and MERS-CoV, respectively [116,117]. In similar fashion to SARS-CoV, SARS-CoV-2 also uses ACE2 to gain entry into host cells. Hoffmann et al. found that the cellular protease MPRSS2 blocks entry by cleaving the spike protein and may constitute a treatment option [118]. Zhou et al. also confirmed that SARS-CoV-2 is able to use all but mouse ACE2 as an entry receptor for ACE2-expressing cells, but not cells without ACE2, indicating that the cell receptor for SARS-CoV-2 could be ACE2, and not other coronavirus receptors such as aminopeptidase N and dipeptidyl peptidase 4 [94]. Huang also showed that the affinity of the SARS-CoV-2 S-RBD binding to ACE2 is less than that of SARS-CoV through Monte Carlo algorithm [119]. However, Wrapp et al. found that SARS-CoV-2 S binding to ACE2 has approximately 10- to 20- fold higher affinity than SARS-CoV S, which can provide one explanation why SARS-CoV-2 has more human-to human spread compared to SARS-CoV [97].\nThe combination of SARS-CoV-2 S and ACE2 of host cells is similar to the combination of SARS-CoV and ACE2, indicating that they have the same mechanism to entry into host cells [97]. The S protein of metastable prefusion conformation undergoes a series of structural rearrangements to combine with the viral membrane of host cells [111,120]. This process consists of the S1 subunit binding to the host cell receptor, triggering of the prefusion trimer's instability, and shedding of the S1 subunit, resulting in a highly stable post-fusion conformation of the S2 subunit [121]. During the binding of the subunit S1 to its cognate receptor, it is important to note that the S1 subunit exists in 2 different states, a “down” conformation and an “up” conformation state, which corresponds to a receptor-inaccessible state and an unstable receptor-accessible state, respectively [[122], [123], [124], [125]]. Unfortunately, there are significant conformational differences between SARS-CoV and SARS-CoV-2 such that the commercially available monoclonal antibodies against SARS-CoV do not react with SARS-CoV-2 [97].\nSARS-CoV-2 may directly bind to ACE2 positive cholangiocytes but not necessarily hepatocytes via specific expression of ACE2 in healthy liver tissues using cell RNA-seq data of two independent cohorts [126]. Though the respiratory systems is a primary target of SARS-CoV-2, bioinformatic analysis of single-cell transcriptomes datasets of lung, esophagus, gastric, ileum and colon reveal that the digestive system is also a potential route of entry for COVID-19, as ACE2 was not only highly expressed in lung AT2 cells, esophagus upper and stratified epithelial cells but also in absorptive enterocytes from the ileum and colon [127]."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T408","span":{"begin":0,"end":25},"obj":"Sentence"},{"id":"T409","span":{"begin":26,"end":120},"obj":"Sentence"},{"id":"T410","span":{"begin":121,"end":232},"obj":"Sentence"},{"id":"T411","span":{"begin":233,"end":318},"obj":"Sentence"},{"id":"T412","span":{"begin":319,"end":503},"obj":"Sentence"},{"id":"T413","span":{"begin":504,"end":663},"obj":"Sentence"},{"id":"T414","span":{"begin":664,"end":752},"obj":"Sentence"},{"id":"T415","span":{"begin":753,"end":896},"obj":"Sentence"},{"id":"T416","span":{"begin":897,"end":1207},"obj":"Sentence"},{"id":"T417","span":{"begin":1208,"end":1350},"obj":"Sentence"},{"id":"T418","span":{"begin":1351,"end":1586},"obj":"Sentence"},{"id":"T419","span":{"begin":1587,"end":1769},"obj":"Sentence"},{"id":"T420","span":{"begin":1770,"end":1928},"obj":"Sentence"},{"id":"T421","span":{"begin":1929,"end":2164},"obj":"Sentence"},{"id":"T422","span":{"begin":2165,"end":2491},"obj":"Sentence"},{"id":"T423","span":{"begin":2492,"end":2698},"obj":"Sentence"},{"id":"T424","span":{"begin":2699,"end":2906},"obj":"Sentence"},{"id":"T425","span":{"begin":2907,"end":3333},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"9.2 Entry into host cell\nCell entry is an essential component of cross-species transmission, especially for the β-CoVs. All CoVs encode a surface glycoprotein, spike, which binds to the host receptor and mediates viral entry [111]. For β-CoVs, the RBD of the spike protein mediates the interaction with host receptor. Upon binding the receptor, the spike protein is cleaved by nearby host proteases and releases the signal peptide to facilitate virus entry into host cells [[112], [113], [114], [115]].\nAngiotensin converting enzyme 2 (ACE2) and dipeptidyl peptidase 4 (DPP4) are known host receptors for the β-CoVs SARS-CoV and MERS-CoV, respectively [116,117]. In similar fashion to SARS-CoV, SARS-CoV-2 also uses ACE2 to gain entry into host cells. Hoffmann et al. found that the cellular protease MPRSS2 blocks entry by cleaving the spike protein and may constitute a treatment option [118]. Zhou et al. also confirmed that SARS-CoV-2 is able to use all but mouse ACE2 as an entry receptor for ACE2-expressing cells, but not cells without ACE2, indicating that the cell receptor for SARS-CoV-2 could be ACE2, and not other coronavirus receptors such as aminopeptidase N and dipeptidyl peptidase 4 [94]. Huang also showed that the affinity of the SARS-CoV-2 S-RBD binding to ACE2 is less than that of SARS-CoV through Monte Carlo algorithm [119]. However, Wrapp et al. found that SARS-CoV-2 S binding to ACE2 has approximately 10- to 20- fold higher affinity than SARS-CoV S, which can provide one explanation why SARS-CoV-2 has more human-to human spread compared to SARS-CoV [97].\nThe combination of SARS-CoV-2 S and ACE2 of host cells is similar to the combination of SARS-CoV and ACE2, indicating that they have the same mechanism to entry into host cells [97]. The S protein of metastable prefusion conformation undergoes a series of structural rearrangements to combine with the viral membrane of host cells [111,120]. This process consists of the S1 subunit binding to the host cell receptor, triggering of the prefusion trimer's instability, and shedding of the S1 subunit, resulting in a highly stable post-fusion conformation of the S2 subunit [121]. During the binding of the subunit S1 to its cognate receptor, it is important to note that the S1 subunit exists in 2 different states, a “down” conformation and an “up” conformation state, which corresponds to a receptor-inaccessible state and an unstable receptor-accessible state, respectively [[122], [123], [124], [125]]. Unfortunately, there are significant conformational differences between SARS-CoV and SARS-CoV-2 such that the commercially available monoclonal antibodies against SARS-CoV do not react with SARS-CoV-2 [97].\nSARS-CoV-2 may directly bind to ACE2 positive cholangiocytes but not necessarily hepatocytes via specific expression of ACE2 in healthy liver tissues using cell RNA-seq data of two independent cohorts [126]. Though the respiratory systems is a primary target of SARS-CoV-2, bioinformatic analysis of single-cell transcriptomes datasets of lung, esophagus, gastric, ileum and colon reveal that the digestive system is also a potential route of entry for COVID-19, as ACE2 was not only highly expressed in lung AT2 cells, esophagus upper and stratified epithelial cells but also in absorptive enterocytes from the ileum and colon [127]."}

LitCovid-PubTator

2_test

{"project":"2_test","denotations":[{"id":"32143990-27578435-55637431","span":{"begin":227,"end":230},"obj":"27578435"},{"id":"32143990-19321428-55637432","span":{"begin":476,"end":479},"obj":"19321428"},{"id":"32143990-20926566-55637433","span":{"begin":483,"end":486},"obj":"20926566"},{"id":"32143990-21994442-55637434","span":{"begin":490,"end":493},"obj":"21994442"},{"id":"32143990-24121034-55637435","span":{"begin":497,"end":500},"obj":"24121034"},{"id":"32143990-15549175-55637436","span":{"begin":654,"end":657},"obj":"15549175"},{"id":"32143990-23486063-55637437","span":{"begin":658,"end":661},"obj":"23486063"},{"id":"32143990-27578435-55637438","span":{"begin":1919,"end":1922},"obj":"27578435"},{"id":"32143990-12885899-55637439","span":{"begin":1923,"end":1926},"obj":"12885899"},{"id":"32143990-29073020-55637440","span":{"begin":2159,"end":2162},"obj":"29073020"},{"id":"32143990-28008928-55637441","span":{"begin":2464,"end":2467},"obj":"28008928"},{"id":"32143990-28807998-55637442","span":{"begin":2471,"end":2474},"obj":"28807998"}],"text":"9.2 Entry into host cell\nCell entry is an essential component of cross-species transmission, especially for the β-CoVs. All CoVs encode a surface glycoprotein, spike, which binds to the host receptor and mediates viral entry [111]. For β-CoVs, the RBD of the spike protein mediates the interaction with host receptor. Upon binding the receptor, the spike protein is cleaved by nearby host proteases and releases the signal peptide to facilitate virus entry into host cells [[112], [113], [114], [115]].\nAngiotensin converting enzyme 2 (ACE2) and dipeptidyl peptidase 4 (DPP4) are known host receptors for the β-CoVs SARS-CoV and MERS-CoV, respectively [116,117]. In similar fashion to SARS-CoV, SARS-CoV-2 also uses ACE2 to gain entry into host cells. Hoffmann et al. found that the cellular protease MPRSS2 blocks entry by cleaving the spike protein and may constitute a treatment option [118]. Zhou et al. also confirmed that SARS-CoV-2 is able to use all but mouse ACE2 as an entry receptor for ACE2-expressing cells, but not cells without ACE2, indicating that the cell receptor for SARS-CoV-2 could be ACE2, and not other coronavirus receptors such as aminopeptidase N and dipeptidyl peptidase 4 [94]. Huang also showed that the affinity of the SARS-CoV-2 S-RBD binding to ACE2 is less than that of SARS-CoV through Monte Carlo algorithm [119]. However, Wrapp et al. found that SARS-CoV-2 S binding to ACE2 has approximately 10- to 20- fold higher affinity than SARS-CoV S, which can provide one explanation why SARS-CoV-2 has more human-to human spread compared to SARS-CoV [97].\nThe combination of SARS-CoV-2 S and ACE2 of host cells is similar to the combination of SARS-CoV and ACE2, indicating that they have the same mechanism to entry into host cells [97]. The S protein of metastable prefusion conformation undergoes a series of structural rearrangements to combine with the viral membrane of host cells [111,120]. This process consists of the S1 subunit binding to the host cell receptor, triggering of the prefusion trimer's instability, and shedding of the S1 subunit, resulting in a highly stable post-fusion conformation of the S2 subunit [121]. During the binding of the subunit S1 to its cognate receptor, it is important to note that the S1 subunit exists in 2 different states, a “down” conformation and an “up” conformation state, which corresponds to a receptor-inaccessible state and an unstable receptor-accessible state, respectively [[122], [123], [124], [125]]. Unfortunately, there are significant conformational differences between SARS-CoV and SARS-CoV-2 such that the commercially available monoclonal antibodies against SARS-CoV do not react with SARS-CoV-2 [97].\nSARS-CoV-2 may directly bind to ACE2 positive cholangiocytes but not necessarily hepatocytes via specific expression of ACE2 in healthy liver tissues using cell RNA-seq data of two independent cohorts [126]. Though the respiratory systems is a primary target of SARS-CoV-2, bioinformatic analysis of single-cell transcriptomes datasets of lung, esophagus, gastric, ileum and colon reveal that the digestive system is also a potential route of entry for COVID-19, as ACE2 was not only highly expressed in lung AT2 cells, esophagus upper and stratified epithelial cells but also in absorptive enterocytes from the ileum and colon [127]."}

PMC:7126544 / 49810-53143 JSONTXT

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PMC:7126544 / 49810-53143 JSON TXT