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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T7","span":{"begin":7,"end":12},"obj":"Body_part"},{"id":"T8","span":{"begin":714,"end":720},"obj":"Body_part"},{"id":"T9","span":{"begin":1492,"end":1496},"obj":"Body_part"},{"id":"T10","span":{"begin":1543,"end":1547},"obj":"Body_part"},{"id":"T11","span":{"begin":1708,"end":1712},"obj":"Body_part"},{"id":"T12","span":{"begin":1744,"end":1749},"obj":"Body_part"},{"id":"T13","span":{"begin":2353,"end":2358},"obj":"Body_part"}],"attributes":[{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A8","pred":"uberon_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/UBERON_0002113"},{"id":"A9","pred":"uberon_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A12","pred":"uberon_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"}],"text":"4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16]."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-sample-PD-IDO

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T55","span":{"begin":135,"end":139},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T56","span":{"begin":396,"end":400},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T57","span":{"begin":424,"end":429},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T58","span":{"begin":727,"end":731},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T59","span":{"begin":802,"end":807},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T60","span":{"begin":808,"end":818},"obj":"http://purl.obolibrary.org/obo/IDO_0000498"},{"id":"T61","span":{"begin":845,"end":850},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T62","span":{"begin":851,"end":861},"obj":"http://purl.obolibrary.org/obo/IDO_0000498"},{"id":"T63","span":{"begin":1046,"end":1051},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T64","span":{"begin":1237,"end":1242},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T65","span":{"begin":1467,"end":1472},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T66","span":{"begin":1504,"end":1508},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T67","span":{"begin":1548,"end":1553},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T68","span":{"begin":1713,"end":1722},"obj":"http://purl.obolibrary.org/obo/IDO_0000586"},{"id":"T69","span":{"begin":2180,"end":2184},"obj":"http://purl.obolibrary.org/obo/CL_0000000"}],"text":"4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16]."}

LitCovid-sample-CHEBI

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T94","span":{"begin":333,"end":343},"obj":"Chemical"},{"id":"T95","span":{"begin":364,"end":371},"obj":"Chemical"},{"id":"T96","span":{"begin":937,"end":945},"obj":"Chemical"},{"id":"T97","span":{"begin":1015,"end":1021},"obj":"Chemical"},{"id":"T98","span":{"begin":1134,"end":1151},"obj":"Chemical"},{"id":"T99","span":{"begin":1258,"end":1275},"obj":"Chemical"},{"id":"T100","span":{"begin":1321,"end":1338},"obj":"Chemical"},{"id":"T101","span":{"begin":1366,"end":1371},"obj":"Chemical"},{"id":"T102","span":{"begin":1621,"end":1638},"obj":"Chemical"}],"attributes":[{"id":"A100","pred":"chebi_id","subj":"T100","obj":"http://purl.obolibrary.org/obo/CHEBI_135632"},{"id":"A94","pred":"chebi_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A102","pred":"chebi_id","subj":"T102","obj":"http://purl.obolibrary.org/obo/CHEBI_135632"},{"id":"A99","pred":"chebi_id","subj":"T99","obj":"http://purl.obolibrary.org/obo/CHEBI_31206"},{"id":"A101","pred":"chebi_id","subj":"T101","obj":"http://purl.obolibrary.org/obo/CHEBI_101381"},{"id":"A98","pred":"chebi_id","subj":"T98","obj":"http://purl.obolibrary.org/obo/CHEBI_31206"},{"id":"A96","pred":"chebi_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/CHEBI_15356"},{"id":"A97","pred":"chebi_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/CHEBI_17822"},{"id":"A95","pred":"chebi_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16]."}

LitCovid-sample-PD-NCBITaxon

LitCovid-sample-sentences

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T115","span":{"begin":0,"end":44},"obj":"Sentence"},{"id":"T116","span":{"begin":46,"end":167},"obj":"Sentence"},{"id":"T117","span":{"begin":168,"end":530},"obj":"Sentence"},{"id":"T118","span":{"begin":531,"end":616},"obj":"Sentence"},{"id":"T119","span":{"begin":617,"end":679},"obj":"Sentence"},{"id":"T120","span":{"begin":680,"end":874},"obj":"Sentence"},{"id":"T121","span":{"begin":875,"end":1036},"obj":"Sentence"},{"id":"T122","span":{"begin":1037,"end":1216},"obj":"Sentence"},{"id":"T123","span":{"begin":1217,"end":1303},"obj":"Sentence"},{"id":"T124","span":{"begin":1304,"end":1473},"obj":"Sentence"},{"id":"T125","span":{"begin":1474,"end":1723},"obj":"Sentence"},{"id":"T126","span":{"begin":1725,"end":1743},"obj":"Sentence"},{"id":"T127","span":{"begin":1744,"end":1825},"obj":"Sentence"},{"id":"T128","span":{"begin":1826,"end":2004},"obj":"Sentence"},{"id":"T129","span":{"begin":2005,"end":2227},"obj":"Sentence"},{"id":"T130","span":{"begin":2228,"end":2340},"obj":"Sentence"},{"id":"T131","span":{"begin":2341,"end":2402},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16]."}

LitCovid-sample-PD-UBERON

{"project":"LitCovid-sample-PD-UBERON","denotations":[{"id":"T7","span":{"begin":7,"end":12},"obj":"Body_part"},{"id":"T8","span":{"begin":714,"end":720},"obj":"Body_part"},{"id":"T9","span":{"begin":1492,"end":1496},"obj":"Body_part"},{"id":"T10","span":{"begin":1543,"end":1547},"obj":"Body_part"},{"id":"T11","span":{"begin":1708,"end":1712},"obj":"Body_part"},{"id":"T12","span":{"begin":1744,"end":1749},"obj":"Body_part"},{"id":"T13","span":{"begin":2353,"end":2358},"obj":"Body_part"}],"attributes":[{"id":"A9","pred":"uberon_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A8","pred":"uberon_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/UBERON_0002113"},{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A12","pred":"uberon_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"}],"text":"4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16]."}

LitCovid-sample-Pubtator

LitCovid-sample-UniProt

LitCovid-sample-Enju

LitCovid-sample-PD-MAT

{"project":"LitCovid-sample-PD-MAT","denotations":[{"id":"T1","span":{"begin":714,"end":720},"obj":"http://purl.obolibrary.org/obo/MAT_0000119"},{"id":"T2","span":{"begin":1492,"end":1496},"obj":"http://purl.obolibrary.org/obo/MAT_0000135"},{"id":"T3","span":{"begin":1543,"end":1547},"obj":"http://purl.obolibrary.org/obo/MAT_0000135"},{"id":"T4","span":{"begin":1708,"end":1712},"obj":"http://purl.obolibrary.org/obo/MAT_0000135"}],"text":"4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16]."}

LitCovid-sample-PD-GO-BP-0

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T20","span":{"begin":2228,"end":2232},"obj":"http://purl.obolibrary.org/obo/GO_0004617"}],"text":"4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16]."}

LitCovid-sample-PD-FMA

LitCovid-sample-PD-MONDO

LitCovid-sample-PD-HP

{"project":"LitCovid-sample-PD-HP","denotations":[{"id":"T3","span":{"begin":1492,"end":1503},"obj":"Phenotype"}],"attributes":[{"id":"A3","pred":"hp_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/HP_0100526"}],"text":"4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16]."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T115","span":{"begin":0,"end":44},"obj":"Sentence"},{"id":"T116","span":{"begin":46,"end":167},"obj":"Sentence"},{"id":"T117","span":{"begin":168,"end":530},"obj":"Sentence"},{"id":"T118","span":{"begin":531,"end":616},"obj":"Sentence"},{"id":"T119","span":{"begin":617,"end":679},"obj":"Sentence"},{"id":"T120","span":{"begin":680,"end":874},"obj":"Sentence"},{"id":"T121","span":{"begin":875,"end":1036},"obj":"Sentence"},{"id":"T122","span":{"begin":1037,"end":1216},"obj":"Sentence"},{"id":"T123","span":{"begin":1217,"end":1303},"obj":"Sentence"},{"id":"T124","span":{"begin":1304,"end":1473},"obj":"Sentence"},{"id":"T125","span":{"begin":1474,"end":1723},"obj":"Sentence"},{"id":"T126","span":{"begin":1725,"end":1743},"obj":"Sentence"},{"id":"T127","span":{"begin":1744,"end":1825},"obj":"Sentence"},{"id":"T128","span":{"begin":1826,"end":2004},"obj":"Sentence"},{"id":"T129","span":{"begin":2005,"end":2227},"obj":"Sentence"},{"id":"T130","span":{"begin":2228,"end":2340},"obj":"Sentence"},{"id":"T131","span":{"begin":2341,"end":2402},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16]."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T3","span":{"begin":1492,"end":1503},"obj":"Phenotype"}],"attributes":[{"id":"A3","pred":"hp_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/HP_0100526"}],"text":"4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16]."}

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