PubMed:31996437 JSONTXT

{"project":"PubMed_ArguminSci","denotations":[{"id":"T1","span":{"begin":130,"end":269},"obj":"DRI_Background"},{"id":"T2","span":{"begin":270,"end":583},"obj":"DRI_Background"},{"id":"T3","span":{"begin":584,"end":732},"obj":"DRI_Approach"},{"id":"T4","span":{"begin":733,"end":936},"obj":"DRI_Outcome"},{"id":"T5","span":{"begin":937,"end":1120},"obj":"DRI_Outcome"},{"id":"T6","span":{"begin":1121,"end":1344},"obj":"DRI_Outcome"},{"id":"T7","span":{"begin":1345,"end":1624},"obj":"DRI_Background"},{"id":"T8","span":{"begin":1625,"end":1915},"obj":"DRI_Outcome"},{"id":"T9","span":{"begin":1916,"end":1979},"obj":"DRI_Approach"},{"id":"T10","span":{"begin":1980,"end":2264},"obj":"DRI_Outcome"},{"id":"T11","span":{"begin":2265,"end":2526},"obj":"DRI_Challenge"},{"id":"T12","span":{"begin":2527,"end":2697},"obj":"DRI_Approach"},{"id":"T13","span":{"begin":2698,"end":2914},"obj":"DRI_Outcome"}],"text":"Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.\nRecently a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by SARS coronavirus (SARS-CoV). Since SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV, and may help epidemic surveillance and preventive measures against 2019-nCoV.SignificanceThe recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002-2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV."}

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EnjuParser_T437","obj":"EnjuParser_T438"},{"id":"EnjuParser_R440","pred":"arg1Of","subj":"EnjuParser_T437","obj":"EnjuParser_T439"},{"id":"EnjuParser_R441","pred":"arg2Of","subj":"EnjuParser_T440","obj":"EnjuParser_T439"},{"id":"EnjuParser_R442","pred":"arg1Of","subj":"EnjuParser_T437","obj":"EnjuParser_T440"},{"id":"EnjuParser_R443","pred":"arg2Of","subj":"EnjuParser_T442","obj":"EnjuParser_T440"},{"id":"EnjuParser_R444","pred":"arg1Of","subj":"EnjuParser_T441","obj":"EnjuParser_T442"},{"id":"EnjuParser_R445","pred":"arg2Of","subj":"EnjuParser_T443","obj":"EnjuParser_T442"},{"id":"EnjuParser_R446","pred":"arg1Of","subj":"EnjuParser_T446","obj":"EnjuParser_T444"},{"id":"EnjuParser_R447","pred":"arg1Of","subj":"EnjuParser_T446","obj":"EnjuParser_T445"},{"id":"EnjuParser_R448","pred":"arg1Of","subj":"EnjuParser_T440","obj":"EnjuParser_T446"}],"text":"Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.\nRecently a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by SARS coronavirus (SARS-CoV). Since SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV, and may help epidemic surveillance and preventive measures against 2019-nCoV.SignificanceThe recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002-2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV."}

{"project":"LitCovid-ArguminSci","denotations":[{"id":"T1","span":{"begin":0,"end":114},"obj":"DRI_Background"},{"id":"T2","span":{"begin":115,"end":269},"obj":"DRI_Background"},{"id":"T3","span":{"begin":270,"end":583},"obj":"DRI_Background"},{"id":"T4","span":{"begin":584,"end":732},"obj":"DRI_Approach"},{"id":"T5","span":{"begin":733,"end":936},"obj":"DRI_Outcome"},{"id":"T6","span":{"begin":937,"end":1120},"obj":"DRI_Outcome"},{"id":"T7","span":{"begin":1121,"end":1344},"obj":"DRI_Outcome"},{"id":"T8","span":{"begin":1345,"end":1624},"obj":"DRI_Background"},{"id":"T9","span":{"begin":1625,"end":1915},"obj":"DRI_Outcome"},{"id":"T10","span":{"begin":1916,"end":1979},"obj":"DRI_Approach"},{"id":"T11","span":{"begin":1980,"end":2264},"obj":"DRI_Outcome"},{"id":"T12","span":{"begin":2265,"end":2526},"obj":"DRI_Challenge"},{"id":"T13","span":{"begin":2527,"end":2697},"obj":"DRI_Approach"},{"id":"T14","span":{"begin":2698,"end":2914},"obj":"DRI_Outcome"}],"text":"Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.\nRecently a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by SARS coronavirus (SARS-CoV). Since SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV, and may help epidemic surveillance and preventive measures against 2019-nCoV.SignificanceThe recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002-2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV."}

{"project":"LitCovid-OGER","denotations":[{"id":"T1","span":{"begin":446,"end":450},"obj":"GO:0018995"},{"id":"T2","span":{"begin":1576,"end":1581},"obj":"GO:0018995"},{"id":"T3","span":{"begin":1694,"end":1703},"obj":"GO:0043657"},{"id":"T4","span":{"begin":2127,"end":2131},"obj":"GO:0018995"},{"id":"T5","span":{"begin":2355,"end":2360},"obj":"GO:0019012"},{"id":"T6","span":{"begin":2491,"end":2496},"obj":"GO:0018995"},{"id":"T7","span":{"begin":2673,"end":2677},"obj":"GO:0018995"},{"id":"T1","span":{"begin":109,"end":113},"obj":"PR:000014459"},{"id":"T2","span":{"begin":259,"end":263},"obj":"PR:000014459"},{"id":"T3","span":{"begin":276,"end":280},"obj":"PR:000014459"},{"id":"T4","span":{"begin":385,"end":389},"obj":"PR:000014459"},{"id":"T5","span":{"begin":460,"end":491},"obj":"PR:000003622"},{"id":"T6","span":{"begin":493,"end":497},"obj":"PR:000003622;PR:Q6NKN9"},{"id":"T7","span":{"begin":574,"end":578},"obj":"PR:000014459"},{"id":"T8","span":{"begin":678,"end":682},"obj":"PR:000014459"},{"id":"T9","span":{"begin":809,"end":812},"obj":"PR:000013814;PR:000030954;PR:O35698;PR:Q60990"},{"id":"T10","span":{"begin":837,"end":841},"obj":"PR:000003622;PR:Q6NKN9"},{"id":"T11","span":{"begin":865,"end":869},"obj":"PR:000014459"},{"id":"T12","span":{"begin":915,"end":919},"obj":"PR:000003622;PR:Q6NKN9"},{"id":"T13","span":{"begin":984,"end":987},"obj":"PR:000013814;PR:000030954;PR:O35698;PR:Q60990"},{"id":"T14","span":{"begin":1052,"end":1056},"obj":"PR:000003622;PR:Q6NKN9"},{"id":"T15","span":{"begin":1173,"end":1176},"obj":"PR:000013814;PR:000030954;PR:O35698;PR:Q60990"},{"id":"T16","span":{"begin":1253,"end":1257},"obj":"PR:000003622;PR:Q6NKN9"},{"id":"T17","span":{"begin":1345,"end":1349},"obj":"PR:000015650;PR:Q9D032"},{"id":"T18","span":{"begin":1454,"end":1458},"obj":"PR:000003622;PR:Q6NKN9"},{"id":"T19","span":{"begin":1502,"end":1506},"obj":"PR:000005054"},{"id":"T20","span":{"begin":1948,"end":1952},"obj":"PR:000014459"},{"id":"T21","span":{"begin":2046,"end":2050},"obj":"PR:000014459"},{"id":"T22","span":{"begin":2096,"end":2100},"obj":"PR:000014459"},{"id":"T23","span":{"begin":2141,"end":2172},"obj":"PR:000003622"},{"id":"T24","span":{"begin":2174,"end":2178},"obj":"PR:000003622;PR:Q6NKN9"},{"id":"T25","span":{"begin":2255,"end":2259},"obj":"PR:000014459"},{"id":"T26","span":{"begin":2285,"end":2289},"obj":"PR:000014459"},{"id":"T1","span":{"begin":1199,"end":1202},"obj":"SO:0001853"}],"namespaces":[{"prefix":"PR","uri":"http://purl.obolibrary.org/obo/PR_"},{"prefix":"UBERON","uri":"http://purl.obolibrary.org/obo/UBERON_"}],"text":"Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.\nRecently a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by SARS coronavirus (SARS-CoV). Since SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV, and may help epidemic surveillance and preventive measures against 2019-nCoV.SignificanceThe recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002-2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV."}

{"project":"LitCovid-PubTatorCentral","denotations":[{"id":"T1","span":{"begin":207,"end":213},"obj":"Species:9606"},{"id":"T2","span":{"begin":241,"end":257},"obj":"Species:227859"},{"id":"T3","span":{"begin":259,"end":267},"obj":"Species:227859"},{"id":"T4","span":{"begin":276,"end":284},"obj":"Species:227859"},{"id":"T5","span":{"begin":385,"end":393},"obj":"Species:227859"},{"id":"T6","span":{"begin":542,"end":547},"obj":"Species:9606"},{"id":"T7","span":{"begin":551,"end":556},"obj":"Species:9606"},{"id":"T8","span":{"begin":574,"end":582},"obj":"Species:227859"},{"id":"T9","span":{"begin":678,"end":686},"obj":"Species:227859"},{"id":"T10","span":{"begin":865,"end":873},"obj":"Species:227859"},{"id":"T11","span":{"begin":1046,"end":1051},"obj":"Species:9606"},{"id":"T12","span":{"begin":1099,"end":1104},"obj":"Species:9606"},{"id":"T13","span":{"begin":1247,"end":1252},"obj":"Species:9606"},{"id":"T14","span":{"begin":1316,"end":1321},"obj":"Species:9606"},{"id":"T15","span":{"begin":1325,"end":1330},"obj":"Species:9606"},{"id":"T16","span":{"begin":1502,"end":1506},"obj":"Species:10090"},{"id":"T17","span":{"begin":1511,"end":1515},"obj":"Species:10116"},{"id":"T18","span":{"begin":1948,"end":1956},"obj":"Species:227859"},{"id":"T19","span":{"begin":2046,"end":2054},"obj":"Species:227859"},{"id":"T20","span":{"begin":2096,"end":2104},"obj":"Species:227859"},{"id":"T21","span":{"begin":2223,"end":2228},"obj":"Species:9606"},{"id":"T22","span":{"begin":2232,"end":2237},"obj":"Species:9606"},{"id":"T23","span":{"begin":2255,"end":2263},"obj":"Species:227859"},{"id":"T24","span":{"begin":2285,"end":2293},"obj":"Species:227859"}],"text":"Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.\nRecently a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by SARS coronavirus (SARS-CoV). Since SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV, and may help epidemic surveillance and preventive measures against 2019-nCoV.SignificanceThe recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002-2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV."}

{"project":"LitCovid-OGER-BB","denotations":[{"id":"T19746","span":{"begin":109,"end":113},"obj":"SP_10"},{"id":"T19747","span":{"begin":145,"end":154},"obj":"SP_7"},{"id":"T19748","span":{"begin":241,"end":257},"obj":"SP_10"},{"id":"T19749","span":{"begin":259,"end":267},"obj":"SP_10"},{"id":"T19750","span":{"begin":276,"end":284},"obj":"SP_10"},{"id":"T19751","span":{"begin":351,"end":357},"obj":"CHEBI:33250"},{"id":"T19752","span":{"begin":385,"end":393},"obj":"SP_10"},{"id":"T19753","span":{"begin":460,"end":491},"obj":"PG_10"},{"id":"T19754","span":{"begin":493,"end":497},"obj":"G_3;PG_10"},{"id":"T19755","span":{"begin":542,"end":547},"obj":"SP_6"},{"id":"T19756","span":{"begin":551,"end":556},"obj":"SP_6"},{"id":"T19757","span":{"begin":574,"end":582},"obj":"SP_10"},{"id":"T19758","span":{"begin":633,"end":642},"obj":"SP_7"},{"id":"T19759","span":{"begin":678,"end":686},"obj":"SP_10"},{"id":"T19760","span":{"begin":722,"end":731},"obj":"SP_7"},{"id":"T19761","span":{"begin":756,"end":765},"obj":"SP_7"},{"id":"T19762","span":{"begin":837,"end":841},"obj":"G_3;PG_10"},{"id":"T19763","span":{"begin":865,"end":873},"obj":"SP_10"},{"id":"T19764","span":{"begin":900,"end":909},"obj":"SP_7"},{"id":"T19765","span":{"begin":915,"end":919},"obj":"G_3;PG_10"},{"id":"T19766","span":{"begin":974,"end":983},"obj":"SP_7"},{"id":"T19767","span":{"begin":1046,"end":1051},"obj":"SP_6;PG_10"},{"id":"T19768","span":{"begin":1052,"end":1056},"obj":"PG_10"},{"id":"T19769","span":{"begin":1074,"end":1083},"obj":"SP_7"},{"id":"T19770","span":{"begin":1099,"end":1104},"obj":"SP_6"},{"id":"T19771","span":{"begin":1163,"end":1172},"obj":"SP_7"},{"id":"T19772","span":{"begin":1247,"end":1252},"obj":"SP_6;PG_10"},{"id":"T19773","span":{"begin":1253,"end":1257},"obj":"PG_10"},{"id":"T19774","span":{"begin":1275,"end":1284},"obj":"SP_7"},{"id":"T19775","span":{"begin":1316,"end":1321},"obj":"SP_6"},{"id":"T19776","span":{"begin":1325,"end":1330},"obj":"SP_6"},{"id":"T19777","span":{"begin":1391,"end":1394},"obj":"SP_2"},{"id":"T19778","span":{"begin":1405,"end":1414},"obj":"SP_7"},{"id":"T19779","span":{"begin":1416,"end":1425},"obj":"SP_7"},{"id":"T19780","span":{"begin":1454,"end":1458},"obj":"G_3;PG_10"},{"id":"T19781","span":{"begin":1603,"end":1612},"obj":"SP_7"},{"id":"T19782","span":{"begin":1737,"end":1746},"obj":"SP_7"},{"id":"T19783","span":{"begin":1815,"end":1824},"obj":"SP_7"},{"id":"T19784","span":{"begin":1880,"end":1889},"obj":"SP_7"},{"id":"T19785","span":{"begin":1916,"end":1925},"obj":"SP_7"},{"id":"T19786","span":{"begin":1948,"end":1956},"obj":"SP_10"},{"id":"T19787","span":{"begin":2046,"end":2054},"obj":"SP_10"},{"id":"T19788","span":{"begin":2096,"end":2104},"obj":"SP_10"},{"id":"T19789","span":{"begin":2141,"end":2172},"obj":"PG_10"},{"id":"T19790","span":{"begin":2174,"end":2178},"obj":"G_3;PG_10"},{"id":"T19791","span":{"begin":2223,"end":2228},"obj":"SP_6"},{"id":"T19792","span":{"begin":2232,"end":2237},"obj":"SP_6"},{"id":"T19793","span":{"begin":2255,"end":2263},"obj":"SP_10"},{"id":"T19794","span":{"begin":2285,"end":2293},"obj":"SP_10"},{"id":"T19795","span":{"begin":2319,"end":2325},"obj":"CHEBI:33250"},{"id":"T19796","span":{"begin":2552,"end":2561},"obj":"SP_7"},{"id":"T19797","span":{"begin":2687,"end":2696},"obj":"SP_7"},{"id":"T19798","span":{"begin":2904,"end":2913},"obj":"SP_7"}],"namespaces":[{"prefix":"NCBITaxon","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"}],"text":"Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.\nRecently a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by SARS coronavirus (SARS-CoV). Since SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV, and may help epidemic surveillance and preventive measures against 2019-nCoV.SignificanceThe recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002-2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV."}

{"project":"LitCovid-sentences-v1","denotations":[{"id":"TextSentencer_T1","span":{"begin":0,"end":53},"obj":"Sentence"},{"id":"TextSentencer_T2","span":{"begin":54,"end":114},"obj":"Sentence"},{"id":"TextSentencer_T3","span":{"begin":115,"end":269},"obj":"Sentence"},{"id":"TextSentencer_T4","span":{"begin":270,"end":583},"obj":"Sentence"},{"id":"TextSentencer_T5","span":{"begin":584,"end":732},"obj":"Sentence"},{"id":"TextSentencer_T6","span":{"begin":733,"end":936},"obj":"Sentence"},{"id":"TextSentencer_T7","span":{"begin":937,"end":1120},"obj":"Sentence"},{"id":"TextSentencer_T8","span":{"begin":1121,"end":1344},"obj":"Sentence"},{"id":"TextSentencer_T9","span":{"begin":1345,"end":1624},"obj":"Sentence"},{"id":"TextSentencer_T10","span":{"begin":1625,"end":1915},"obj":"Sentence"},{"id":"TextSentencer_T11","span":{"begin":1916,"end":1979},"obj":"Sentence"},{"id":"TextSentencer_T12","span":{"begin":1980,"end":2264},"obj":"Sentence"},{"id":"TextSentencer_T13","span":{"begin":2265,"end":2526},"obj":"Sentence"},{"id":"TextSentencer_T14","span":{"begin":2527,"end":2697},"obj":"Sentence"},{"id":"TextSentencer_T15","span":{"begin":2698,"end":2914},"obj":"Sentence"}],"text":"Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.\nRecently a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by SARS coronavirus (SARS-CoV). Since SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV, and may help epidemic surveillance and preventive measures against 2019-nCoV.SignificanceThe recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002-2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV."}

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recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.\nRecently a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by SARS coronavirus (SARS-CoV). Since SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV, and may help epidemic surveillance and preventive measures against 2019-nCoV.SignificanceThe recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002-2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV."}

{"project":"LitCovid-PD-MONDO-v1","denotations":[{"id":"T1","span":{"begin":109,"end":113},"obj":"Disease"},{"id":"T2","span":{"begin":241,"end":245},"obj":"Disease"},{"id":"T3","span":{"begin":259,"end":267},"obj":"Disease"},{"id":"T4","span":{"begin":276,"end":284},"obj":"Disease"},{"id":"T5","span":{"begin":385,"end":393},"obj":"Disease"},{"id":"T6","span":{"begin":574,"end":582},"obj":"Disease"},{"id":"T7","span":{"begin":678,"end":686},"obj":"Disease"},{"id":"T8","span":{"begin":865,"end":873},"obj":"Disease"},{"id":"T9","span":{"begin":1110,"end":1119},"obj":"Disease"},{"id":"T10","span":{"begin":1410,"end":1420},"obj":"Disease"},{"id":"T11","span":{"begin":1603,"end":1623},"obj":"Disease"},{"id":"T12","span":{"begin":1948,"end":1956},"obj":"Disease"},{"id":"T13","span":{"begin":2046,"end":2054},"obj":"Disease"},{"id":"T14","span":{"begin":2096,"end":2104},"obj":"Disease"},{"id":"T15","span":{"begin":2255,"end":2263},"obj":"Disease"},{"id":"T16","span":{"begin":2285,"end":2293},"obj":"Disease"}],"attributes":[{"id":"A7","pred":"mondo_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A1","pred":"mondo_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A15","pred":"mondo_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A4","pred":"mondo_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A10","pred":"mondo_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A2","pred":"mondo_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A16","pred":"mondo_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A3","pred":"mondo_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A11","pred":"mondo_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A13","pred":"mondo_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A5","pred":"mondo_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A14","pred":"mondo_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A12","pred":"mondo_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A6","pred":"mondo_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.\nRecently a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by SARS coronavirus (SARS-CoV). Since SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV, and may help epidemic surveillance and preventive measures against 2019-nCoV.SignificanceThe recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002-2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV."}

{"project":"LitCovid-PD-FMA-UBERON-v1","denotations":[{"id":"T1","span":{"begin":400,"end":407},"obj":"Body_part"},{"id":"T2","span":{"begin":1105,"end":1109},"obj":"Body_part"},{"id":"T3","span":{"begin":1682,"end":1686},"obj":"Body_part"},{"id":"T4","span":{"begin":1699,"end":1703},"obj":"Body_part"},{"id":"T5","span":{"begin":2111,"end":2118},"obj":"Body_part"},{"id":"T6","span":{"begin":2568,"end":2575},"obj":"Body_part"}],"attributes":[{"id":"A2","pred":"fma_id","subj":"T2","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A4","pred":"fma_id","subj":"T4","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A6","pred":"fma_id","subj":"T6","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A1","pred":"fma_id","subj":"T1","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A3","pred":"fma_id","subj":"T3","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A5","pred":"fma_id","subj":"T5","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.\nRecently a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by SARS coronavirus (SARS-CoV). Since SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV, and may help epidemic surveillance and preventive measures against 2019-nCoV.SignificanceThe recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002-2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV."}