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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T1","span":{"begin":828,"end":832},"obj":"Body_part"},{"id":"T2","span":{"begin":1876,"end":1880},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0001769"},{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0008915"}],"text":"The rapid identification of this novel coronavirus is attributed to recent advances in the detection of respiratory virus infection, including reverse transcription PCR (RT-PCR), real-time reverse transcription PCR (rRT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and real-time RT-LAMP as well as multiplex nucleic acid amplification and microarray-based assays [4]. These methods are useful for detecting novel coronaviruses not only in humans, but also in animals for identification of animal reservoir or intermediate host of 2019-nCoV. WHO recommended that if there is no clue about the putative pathogen from the pneumonia outbreak, a pan-coronavirus assay should be used for amplification followed by sequencing of the amplicon for characterization and confirmation (https://apps.who.int/iris/bitstream/handle/10665/330374/WHO-2019-nCoV-laboratory-2020.1-eng.pdf). By aligning 2019-nCoV S protein sequence with those of SARS-CoV and several bat-SL-CoVs, we predicted that the cleavage site for generating S1 and S2 subunits is located at R694/S695 (Figure 1). S1 subunit contains two functional domains, the N-terminal domain (NTD) and a receptor-binding domain (RBD), both of which are responsible for the binding of the virion to the receptor on the host cell. They also contain several conformational neutralizing epitopes, serving as a target for developing neutralizing antibodies and vaccines [5]. S2 subunit contains three functional domains, fusion peptide (FP), and heptad repeat (HR) 1 and 2. After binding of RBD in S1 to the receptor, the S2 subunit changes conformation by inserting the FP into the host cell membrane and association between HR1 and HR2 to form six-helical bundle (6-HB), resulting in the fusion between viral and cellular membranes. The viral genetic materials enter into the host cell through the fusion pore for replication in the cell [5]. A peptide derived from the HR2 domain of SARS-CoV S protein (SC-1) can interact with HR1 region in viral S protein to form heterologous 6-HB, resulting in the inhibition of homologous 6-HB formation between HR1 and HR2 domains in viral S protein and thus blocking the viral fusion with the host cell [6]. Since 2019-nCoV S-HR2 sequence is 100% identical to that of SARS-CoV, while there are only a few mutations of non-critical amino acids in S-HR1 region, SC-1 peptide is expected to be also effective against 2019-nCoV infection."}

LitCovid_AGAC

{"project":"LitCovid_AGAC","denotations":[{"id":"p5527s40","span":{"begin":2098,"end":2112},"obj":"MPA"}],"text":"The rapid identification of this novel coronavirus is attributed to recent advances in the detection of respiratory virus infection, including reverse transcription PCR (RT-PCR), real-time reverse transcription PCR (rRT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and real-time RT-LAMP as well as multiplex nucleic acid amplification and microarray-based assays [4]. These methods are useful for detecting novel coronaviruses not only in humans, but also in animals for identification of animal reservoir or intermediate host of 2019-nCoV. WHO recommended that if there is no clue about the putative pathogen from the pneumonia outbreak, a pan-coronavirus assay should be used for amplification followed by sequencing of the amplicon for characterization and confirmation (https://apps.who.int/iris/bitstream/handle/10665/330374/WHO-2019-nCoV-laboratory-2020.1-eng.pdf). By aligning 2019-nCoV S protein sequence with those of SARS-CoV and several bat-SL-CoVs, we predicted that the cleavage site for generating S1 and S2 subunits is located at R694/S695 (Figure 1). S1 subunit contains two functional domains, the N-terminal domain (NTD) and a receptor-binding domain (RBD), both of which are responsible for the binding of the virion to the receptor on the host cell. They also contain several conformational neutralizing epitopes, serving as a target for developing neutralizing antibodies and vaccines [5]. S2 subunit contains three functional domains, fusion peptide (FP), and heptad repeat (HR) 1 and 2. After binding of RBD in S1 to the receptor, the S2 subunit changes conformation by inserting the FP into the host cell membrane and association between HR1 and HR2 to form six-helical bundle (6-HB), resulting in the fusion between viral and cellular membranes. The viral genetic materials enter into the host cell through the fusion pore for replication in the cell [5]. A peptide derived from the HR2 domain of SARS-CoV S protein (SC-1) can interact with HR1 region in viral S protein to form heterologous 6-HB, resulting in the inhibition of homologous 6-HB formation between HR1 and HR2 domains in viral S protein and thus blocking the viral fusion with the host cell [6]. Since 2019-nCoV S-HR2 sequence is 100% identical to that of SARS-CoV, while there are only a few mutations of non-critical amino acids in S-HR1 region, SC-1 peptide is expected to be also effective against 2019-nCoV infection."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T10","span":{"begin":116,"end":131},"obj":"Disease"},{"id":"T11","span":{"begin":122,"end":131},"obj":"Disease"},{"id":"T12","span":{"begin":652,"end":661},"obj":"Disease"},{"id":"T13","span":{"begin":960,"end":968},"obj":"Disease"},{"id":"T14","span":{"begin":1167,"end":1170},"obj":"Disease"},{"id":"T16","span":{"begin":1955,"end":1963},"obj":"Disease"},{"id":"T17","span":{"begin":2279,"end":2287},"obj":"Disease"},{"id":"T18","span":{"begin":2425,"end":2444},"obj":"Disease"},{"id":"T19","span":{"begin":2435,"end":2444},"obj":"Disease"}],"attributes":[{"id":"A10","pred":"mondo_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/MONDO_0005108"},{"id":"A11","pred":"mondo_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A12","pred":"mondo_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A13","pred":"mondo_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A14","pred":"mondo_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/MONDO_0008449"},{"id":"A15","pred":"mondo_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/MONDO_0018075"},{"id":"A16","pred":"mondo_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A17","pred":"mondo_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A18","pred":"mondo_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A19","pred":"mondo_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"The rapid identification of this novel coronavirus is attributed to recent advances in the detection of respiratory virus infection, including reverse transcription PCR (RT-PCR), real-time reverse transcription PCR (rRT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and real-time RT-LAMP as well as multiplex nucleic acid amplification and microarray-based assays [4]. These methods are useful for detecting novel coronaviruses not only in humans, but also in animals for identification of animal reservoir or intermediate host of 2019-nCoV. WHO recommended that if there is no clue about the putative pathogen from the pneumonia outbreak, a pan-coronavirus assay should be used for amplification followed by sequencing of the amplicon for characterization and confirmation (https://apps.who.int/iris/bitstream/handle/10665/330374/WHO-2019-nCoV-laboratory-2020.1-eng.pdf). By aligning 2019-nCoV S protein sequence with those of SARS-CoV and several bat-SL-CoVs, we predicted that the cleavage site for generating S1 and S2 subunits is located at R694/S695 (Figure 1). S1 subunit contains two functional domains, the N-terminal domain (NTD) and a receptor-binding domain (RBD), both of which are responsible for the binding of the virion to the receptor on the host cell. They also contain several conformational neutralizing epitopes, serving as a target for developing neutralizing antibodies and vaccines [5]. S2 subunit contains three functional domains, fusion peptide (FP), and heptad repeat (HR) 1 and 2. After binding of RBD in S1 to the receptor, the S2 subunit changes conformation by inserting the FP into the host cell membrane and association between HR1 and HR2 to form six-helical bundle (6-HB), resulting in the fusion between viral and cellular membranes. The viral genetic materials enter into the host cell through the fusion pore for replication in the cell [5]. A peptide derived from the HR2 domain of SARS-CoV S protein (SC-1) can interact with HR1 region in viral S protein to form heterologous 6-HB, resulting in the inhibition of homologous 6-HB formation between HR1 and HR2 domains in viral S protein and thus blocking the viral fusion with the host cell [6]. Since 2019-nCoV S-HR2 sequence is 100% identical to that of SARS-CoV, while there are only a few mutations of non-critical amino acids in S-HR1 region, SC-1 peptide is expected to be also effective against 2019-nCoV infection."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T4","span":{"begin":652,"end":661},"obj":"Phenotype"}],"attributes":[{"id":"A4","pred":"hp_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"The rapid identification of this novel coronavirus is attributed to recent advances in the detection of respiratory virus infection, including reverse transcription PCR (RT-PCR), real-time reverse transcription PCR (rRT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and real-time RT-LAMP as well as multiplex nucleic acid amplification and microarray-based assays [4]. These methods are useful for detecting novel coronaviruses not only in humans, but also in animals for identification of animal reservoir or intermediate host of 2019-nCoV. WHO recommended that if there is no clue about the putative pathogen from the pneumonia outbreak, a pan-coronavirus assay should be used for amplification followed by sequencing of the amplicon for characterization and confirmation (https://apps.who.int/iris/bitstream/handle/10665/330374/WHO-2019-nCoV-laboratory-2020.1-eng.pdf). By aligning 2019-nCoV S protein sequence with those of SARS-CoV and several bat-SL-CoVs, we predicted that the cleavage site for generating S1 and S2 subunits is located at R694/S695 (Figure 1). S1 subunit contains two functional domains, the N-terminal domain (NTD) and a receptor-binding domain (RBD), both of which are responsible for the binding of the virion to the receptor on the host cell. They also contain several conformational neutralizing epitopes, serving as a target for developing neutralizing antibodies and vaccines [5]. S2 subunit contains three functional domains, fusion peptide (FP), and heptad repeat (HR) 1 and 2. After binding of RBD in S1 to the receptor, the S2 subunit changes conformation by inserting the FP into the host cell membrane and association between HR1 and HR2 to form six-helical bundle (6-HB), resulting in the fusion between viral and cellular membranes. The viral genetic materials enter into the host cell through the fusion pore for replication in the cell [5]. A peptide derived from the HR2 domain of SARS-CoV S protein (SC-1) can interact with HR1 region in viral S protein to form heterologous 6-HB, resulting in the inhibition of homologous 6-HB formation between HR1 and HR2 domains in viral S protein and thus blocking the viral fusion with the host cell [6]. Since 2019-nCoV S-HR2 sequence is 100% identical to that of SARS-CoV, while there are only a few mutations of non-critical amino acids in S-HR1 region, SC-1 peptide is expected to be also effective against 2019-nCoV infection."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T1","span":{"begin":143,"end":164},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T2","span":{"begin":151,"end":164},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T3","span":{"begin":189,"end":210},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T4","span":{"begin":197,"end":210},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T5","span":{"begin":226,"end":247},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T6","span":{"begin":234,"end":247},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T7","span":{"begin":2103,"end":2112},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"text":"The rapid identification of this novel coronavirus is attributed to recent advances in the detection of respiratory virus infection, including reverse transcription PCR (RT-PCR), real-time reverse transcription PCR (rRT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and real-time RT-LAMP as well as multiplex nucleic acid amplification and microarray-based assays [4]. These methods are useful for detecting novel coronaviruses not only in humans, but also in animals for identification of animal reservoir or intermediate host of 2019-nCoV. WHO recommended that if there is no clue about the putative pathogen from the pneumonia outbreak, a pan-coronavirus assay should be used for amplification followed by sequencing of the amplicon for characterization and confirmation (https://apps.who.int/iris/bitstream/handle/10665/330374/WHO-2019-nCoV-laboratory-2020.1-eng.pdf). By aligning 2019-nCoV S protein sequence with those of SARS-CoV and several bat-SL-CoVs, we predicted that the cleavage site for generating S1 and S2 subunits is located at R694/S695 (Figure 1). S1 subunit contains two functional domains, the N-terminal domain (NTD) and a receptor-binding domain (RBD), both of which are responsible for the binding of the virion to the receptor on the host cell. They also contain several conformational neutralizing epitopes, serving as a target for developing neutralizing antibodies and vaccines [5]. S2 subunit contains three functional domains, fusion peptide (FP), and heptad repeat (HR) 1 and 2. After binding of RBD in S1 to the receptor, the S2 subunit changes conformation by inserting the FP into the host cell membrane and association between HR1 and HR2 to form six-helical bundle (6-HB), resulting in the fusion between viral and cellular membranes. The viral genetic materials enter into the host cell through the fusion pore for replication in the cell [5]. A peptide derived from the HR2 domain of SARS-CoV S protein (SC-1) can interact with HR1 region in viral S protein to form heterologous 6-HB, resulting in the inhibition of homologous 6-HB formation between HR1 and HR2 domains in viral S protein and thus blocking the viral fusion with the host cell [6]. Since 2019-nCoV S-HR2 sequence is 100% identical to that of SARS-CoV, while there are only a few mutations of non-critical amino acids in S-HR1 region, SC-1 peptide is expected to be also effective against 2019-nCoV infection."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T20","span":{"begin":0,"end":400},"obj":"Sentence"},{"id":"T21","span":{"begin":401,"end":573},"obj":"Sentence"},{"id":"T22","span":{"begin":574,"end":904},"obj":"Sentence"},{"id":"T23","span":{"begin":905,"end":1099},"obj":"Sentence"},{"id":"T24","span":{"begin":1100,"end":1302},"obj":"Sentence"},{"id":"T25","span":{"begin":1303,"end":1443},"obj":"Sentence"},{"id":"T26","span":{"begin":1444,"end":1542},"obj":"Sentence"},{"id":"T27","span":{"begin":1543,"end":1803},"obj":"Sentence"},{"id":"T28","span":{"begin":1804,"end":1913},"obj":"Sentence"},{"id":"T29","span":{"begin":1914,"end":2218},"obj":"Sentence"},{"id":"T30","span":{"begin":2219,"end":2445},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The rapid identification of this novel coronavirus is attributed to recent advances in the detection of respiratory virus infection, including reverse transcription PCR (RT-PCR), real-time reverse transcription PCR (rRT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and real-time RT-LAMP as well as multiplex nucleic acid amplification and microarray-based assays [4]. These methods are useful for detecting novel coronaviruses not only in humans, but also in animals for identification of animal reservoir or intermediate host of 2019-nCoV. WHO recommended that if there is no clue about the putative pathogen from the pneumonia outbreak, a pan-coronavirus assay should be used for amplification followed by sequencing of the amplicon for characterization and confirmation (https://apps.who.int/iris/bitstream/handle/10665/330374/WHO-2019-nCoV-laboratory-2020.1-eng.pdf). By aligning 2019-nCoV S protein sequence with those of SARS-CoV and several bat-SL-CoVs, we predicted that the cleavage site for generating S1 and S2 subunits is located at R694/S695 (Figure 1). S1 subunit contains two functional domains, the N-terminal domain (NTD) and a receptor-binding domain (RBD), both of which are responsible for the binding of the virion to the receptor on the host cell. They also contain several conformational neutralizing epitopes, serving as a target for developing neutralizing antibodies and vaccines [5]. S2 subunit contains three functional domains, fusion peptide (FP), and heptad repeat (HR) 1 and 2. After binding of RBD in S1 to the receptor, the S2 subunit changes conformation by inserting the FP into the host cell membrane and association between HR1 and HR2 to form six-helical bundle (6-HB), resulting in the fusion between viral and cellular membranes. The viral genetic materials enter into the host cell through the fusion pore for replication in the cell [5]. A peptide derived from the HR2 domain of SARS-CoV S protein (SC-1) can interact with HR1 region in viral S protein to form heterologous 6-HB, resulting in the inhibition of homologous 6-HB formation between HR1 and HR2 domains in viral S protein and thus blocking the viral fusion with the host cell [6]. Since 2019-nCoV S-HR2 sequence is 100% identical to that of SARS-CoV, while there are only a few mutations of non-critical amino acids in S-HR1 region, SC-1 peptide is expected to be also effective against 2019-nCoV infection."}

PMC:7033706 / 3066-5511 JSONTXT

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PMC:7033706 / 3066-5511 JSON TXT