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LitCovid-PubTator

LitCovid-PMC-OGER-BB

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T203","span":{"begin":121,"end":130},"obj":"SP_7"},{"id":"T202","span":{"begin":380,"end":385},"obj":"SP_6;NCBITaxon:9606"},{"id":"T201","span":{"begin":389,"end":394},"obj":"SP_6;NCBITaxon:9606"},{"id":"T200","span":{"begin":617,"end":622},"obj":"SP_6;NCBITaxon:9606"},{"id":"T199","span":{"begin":626,"end":631},"obj":"SP_6;NCBITaxon:9606"},{"id":"T198","span":{"begin":750,"end":755},"obj":"SP_6;NCBITaxon:9606"},{"id":"T197","span":{"begin":759,"end":764},"obj":"SP_6;NCBITaxon:9606"},{"id":"T196","span":{"begin":1109,"end":1115},"obj":"NCBITaxon:33208"},{"id":"T195","span":{"begin":1334,"end":1339},"obj":"GO:0016265"},{"id":"T194","span":{"begin":1400,"end":1408},"obj":"SP_10"},{"id":"T193","span":{"begin":1413,"end":1421},"obj":"SP_9"},{"id":"T192","span":{"begin":1653,"end":1658},"obj":"GO:0016265"},{"id":"T191","span":{"begin":1705,"end":1709},"obj":"SP_10"},{"id":"T190","span":{"begin":1757,"end":1762},"obj":"GO:0016265"},{"id":"T189","span":{"begin":2040,"end":2044},"obj":"GO:0016265"},{"id":"T188","span":{"begin":2475,"end":2481},"obj":"SO:0000417"}],"text":"Discussion\nIn this article, we describe a preliminary assessment of the outbreak of infections with the newly identified 2019-nCoV. This assessment is based on the cases of infection reported over time by health authorities in Wuhan and then at the national level, as well as the media in China and other countries. One of the most urgent priorities is to determine the degree of human-to-human transmissibility of the novel pathogen, and accordingly, this is where information is most urgently needed. We outline two possible scenarios in the Table and find that the early evidence was most consistent with limited human-to-human transmissibility, however more recent data seem to be increasingly more compatible with scenario 2 in which sustained human-to-human transmission has been occurring. Determining the exposure profile among the recently confirmed cases would directly contribute to this assessment. Additional information on approaches to case identification and laboratory testing protocols in Wuhan and in other cities in China would also be informative. A separate priority is to identify the animal reservoir of this novel pathogen and any intermediary hosts, including potential supply chains of wild or game meat.\nIt is challenging to judge severity from the information available to date. We estimated the risk of death among hospitalised cases of around 14% (Figure 2). For both SARS-CoV and MERS-CoV infections, the risk of severe disease increases substantially with age and with the presence of underlying conditions [23-25]. One other caveat with estimating severity is that there can be long delays between hospitalisation and death for infections that are ultimately fatal. For SARS in Hong Kong, the average time from illness to death for fatal cases was 24 days [26]. This means that early estimates of the case fatality risk that ignore the potential outcomes of cases still in hospital are typically underestimates of the final severity profile [27]. We accounted for that by only including cases that either died or recovered in our estimate of the hospital fatality risk. Given that the cases reported outside Wuhan have mostly not been severe, it would be reasonable to infer that there might be a large number of undetected relatively mild infections in Wuhan and that the infection fatality risk is below 1% or even below 0.1%.\nThere are a number of limitations to our analyses. Most importantly, they are only based on data in the public domain to date. Detailed information has not yet been released by authoritative sources on the most recently reported cases. In our analysis in the Table, support for scenario 2 might increase if contact tracing or medical surveillance was incomplete, if there was incomplete ascertainment of clusters or if there was an early focus in testing cases linked to the Southern China Seafood Wholesale Market that led to a selection bias in the prevalence of market exposures among the early cases."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T54","span":{"begin":84,"end":94},"obj":"Disease"},{"id":"T55","span":{"begin":173,"end":182},"obj":"Disease"},{"id":"T56","span":{"begin":1400,"end":1408},"obj":"Disease"},{"id":"T57","span":{"begin":1422,"end":1432},"obj":"Disease"},{"id":"T58","span":{"begin":1663,"end":1673},"obj":"Disease"},{"id":"T59","span":{"begin":1705,"end":1709},"obj":"Disease"},{"id":"T60","span":{"begin":2275,"end":2288},"obj":"Disease"},{"id":"T61","span":{"begin":2308,"end":2317},"obj":"Disease"}],"attributes":[{"id":"A54","pred":"mondo_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A56","pred":"mondo_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A57","pred":"mondo_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A58","pred":"mondo_id","subj":"T58","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A59","pred":"mondo_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A60","pred":"mondo_id","subj":"T60","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A61","pred":"mondo_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"Discussion\nIn this article, we describe a preliminary assessment of the outbreak of infections with the newly identified 2019-nCoV. This assessment is based on the cases of infection reported over time by health authorities in Wuhan and then at the national level, as well as the media in China and other countries. One of the most urgent priorities is to determine the degree of human-to-human transmissibility of the novel pathogen, and accordingly, this is where information is most urgently needed. We outline two possible scenarios in the Table and find that the early evidence was most consistent with limited human-to-human transmissibility, however more recent data seem to be increasingly more compatible with scenario 2 in which sustained human-to-human transmission has been occurring. Determining the exposure profile among the recently confirmed cases would directly contribute to this assessment. Additional information on approaches to case identification and laboratory testing protocols in Wuhan and in other cities in China would also be informative. A separate priority is to identify the animal reservoir of this novel pathogen and any intermediary hosts, including potential supply chains of wild or game meat.\nIt is challenging to judge severity from the information available to date. We estimated the risk of death among hospitalised cases of around 14% (Figure 2). For both SARS-CoV and MERS-CoV infections, the risk of severe disease increases substantially with age and with the presence of underlying conditions [23-25]. One other caveat with estimating severity is that there can be long delays between hospitalisation and death for infections that are ultimately fatal. For SARS in Hong Kong, the average time from illness to death for fatal cases was 24 days [26]. This means that early estimates of the case fatality risk that ignore the potential outcomes of cases still in hospital are typically underestimates of the final severity profile [27]. We accounted for that by only including cases that either died or recovered in our estimate of the hospital fatality risk. Given that the cases reported outside Wuhan have mostly not been severe, it would be reasonable to infer that there might be a large number of undetected relatively mild infections in Wuhan and that the infection fatality risk is below 1% or even below 0.1%.\nThere are a number of limitations to our analyses. Most importantly, they are only based on data in the public domain to date. Detailed information has not yet been released by authoritative sources on the most recently reported cases. In our analysis in the Table, support for scenario 2 might increase if contact tracing or medical surveillance was incomplete, if there was incomplete ascertainment of clusters or if there was an early focus in testing cases linked to the Southern China Seafood Wholesale Market that led to a selection bias in the prevalence of market exposures among the early cases."}

LitCovid-PD-CLO

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T98","span":{"begin":0,"end":10},"obj":"Sentence"},{"id":"T99","span":{"begin":11,"end":131},"obj":"Sentence"},{"id":"T100","span":{"begin":132,"end":315},"obj":"Sentence"},{"id":"T101","span":{"begin":316,"end":502},"obj":"Sentence"},{"id":"T102","span":{"begin":503,"end":797},"obj":"Sentence"},{"id":"T103","span":{"begin":798,"end":911},"obj":"Sentence"},{"id":"T104","span":{"begin":912,"end":1069},"obj":"Sentence"},{"id":"T105","span":{"begin":1070,"end":1232},"obj":"Sentence"},{"id":"T106","span":{"begin":1233,"end":1308},"obj":"Sentence"},{"id":"T107","span":{"begin":1309,"end":1390},"obj":"Sentence"},{"id":"T108","span":{"begin":1391,"end":1549},"obj":"Sentence"},{"id":"T109","span":{"begin":1550,"end":1700},"obj":"Sentence"},{"id":"T110","span":{"begin":1701,"end":1796},"obj":"Sentence"},{"id":"T111","span":{"begin":1797,"end":1981},"obj":"Sentence"},{"id":"T112","span":{"begin":1982,"end":2104},"obj":"Sentence"},{"id":"T113","span":{"begin":2105,"end":2363},"obj":"Sentence"},{"id":"T114","span":{"begin":2364,"end":2414},"obj":"Sentence"},{"id":"T115","span":{"begin":2415,"end":2490},"obj":"Sentence"},{"id":"T116","span":{"begin":2491,"end":2599},"obj":"Sentence"},{"id":"T117","span":{"begin":2600,"end":2968},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Discussion\nIn this article, we describe a preliminary assessment of the outbreak of infections with the newly identified 2019-nCoV. This assessment is based on the cases of infection reported over time by health authorities in Wuhan and then at the national level, as well as the media in China and other countries. One of the most urgent priorities is to determine the degree of human-to-human transmissibility of the novel pathogen, and accordingly, this is where information is most urgently needed. We outline two possible scenarios in the Table and find that the early evidence was most consistent with limited human-to-human transmissibility, however more recent data seem to be increasingly more compatible with scenario 2 in which sustained human-to-human transmission has been occurring. Determining the exposure profile among the recently confirmed cases would directly contribute to this assessment. Additional information on approaches to case identification and laboratory testing protocols in Wuhan and in other cities in China would also be informative. A separate priority is to identify the animal reservoir of this novel pathogen and any intermediary hosts, including potential supply chains of wild or game meat.\nIt is challenging to judge severity from the information available to date. We estimated the risk of death among hospitalised cases of around 14% (Figure 2). For both SARS-CoV and MERS-CoV infections, the risk of severe disease increases substantially with age and with the presence of underlying conditions [23-25]. One other caveat with estimating severity is that there can be long delays between hospitalisation and death for infections that are ultimately fatal. For SARS in Hong Kong, the average time from illness to death for fatal cases was 24 days [26]. This means that early estimates of the case fatality risk that ignore the potential outcomes of cases still in hospital are typically underestimates of the final severity profile [27]. We accounted for that by only including cases that either died or recovered in our estimate of the hospital fatality risk. Given that the cases reported outside Wuhan have mostly not been severe, it would be reasonable to infer that there might be a large number of undetected relatively mild infections in Wuhan and that the infection fatality risk is below 1% or even below 0.1%.\nThere are a number of limitations to our analyses. Most importantly, they are only based on data in the public domain to date. Detailed information has not yet been released by authoritative sources on the most recently reported cases. In our analysis in the Table, support for scenario 2 might increase if contact tracing or medical surveillance was incomplete, if there was incomplete ascertainment of clusters or if there was an early focus in testing cases linked to the Southern China Seafood Wholesale Market that led to a selection bias in the prevalence of market exposures among the early cases."}

MyTest

{"project":"MyTest","denotations":[{"id":"31992388-16864761-29332093","span":{"begin":1542,"end":1544},"obj":"16864761"},{"id":"31992388-20205928-29332093","span":{"begin":1542,"end":1544},"obj":"20205928"},{"id":"31992388-29680581-29332093","span":{"begin":1542,"end":1544},"obj":"29680581"},{"id":"31992388-15520422-29332094","span":{"begin":1792,"end":1794},"obj":"15520422"},{"id":"31992388-16981181-29332095","span":{"begin":1977,"end":1979},"obj":"16981181"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Discussion\nIn this article, we describe a preliminary assessment of the outbreak of infections with the newly identified 2019-nCoV. This assessment is based on the cases of infection reported over time by health authorities in Wuhan and then at the national level, as well as the media in China and other countries. One of the most urgent priorities is to determine the degree of human-to-human transmissibility of the novel pathogen, and accordingly, this is where information is most urgently needed. We outline two possible scenarios in the Table and find that the early evidence was most consistent with limited human-to-human transmissibility, however more recent data seem to be increasingly more compatible with scenario 2 in which sustained human-to-human transmission has been occurring. Determining the exposure profile among the recently confirmed cases would directly contribute to this assessment. Additional information on approaches to case identification and laboratory testing protocols in Wuhan and in other cities in China would also be informative. A separate priority is to identify the animal reservoir of this novel pathogen and any intermediary hosts, including potential supply chains of wild or game meat.\nIt is challenging to judge severity from the information available to date. We estimated the risk of death among hospitalised cases of around 14% (Figure 2). For both SARS-CoV and MERS-CoV infections, the risk of severe disease increases substantially with age and with the presence of underlying conditions [23-25]. One other caveat with estimating severity is that there can be long delays between hospitalisation and death for infections that are ultimately fatal. For SARS in Hong Kong, the average time from illness to death for fatal cases was 24 days [26]. This means that early estimates of the case fatality risk that ignore the potential outcomes of cases still in hospital are typically underestimates of the final severity profile [27]. We accounted for that by only including cases that either died or recovered in our estimate of the hospital fatality risk. Given that the cases reported outside Wuhan have mostly not been severe, it would be reasonable to infer that there might be a large number of undetected relatively mild infections in Wuhan and that the infection fatality risk is below 1% or even below 0.1%.\nThere are a number of limitations to our analyses. Most importantly, they are only based on data in the public domain to date. Detailed information has not yet been released by authoritative sources on the most recently reported cases. In our analysis in the Table, support for scenario 2 might increase if contact tracing or medical surveillance was incomplete, if there was incomplete ascertainment of clusters or if there was an early focus in testing cases linked to the Southern China Seafood Wholesale Market that led to a selection bias in the prevalence of market exposures among the early cases."}

2_test

{"project":"2_test","denotations":[{"id":"31992388-16864761-29332093","span":{"begin":1542,"end":1544},"obj":"16864761"},{"id":"31992388-20205928-29332093","span":{"begin":1542,"end":1544},"obj":"20205928"},{"id":"31992388-29680581-29332093","span":{"begin":1542,"end":1544},"obj":"29680581"},{"id":"31992388-15520422-29332094","span":{"begin":1792,"end":1794},"obj":"15520422"},{"id":"31992388-16981181-29332095","span":{"begin":1977,"end":1979},"obj":"16981181"}],"text":"Discussion\nIn this article, we describe a preliminary assessment of the outbreak of infections with the newly identified 2019-nCoV. This assessment is based on the cases of infection reported over time by health authorities in Wuhan and then at the national level, as well as the media in China and other countries. One of the most urgent priorities is to determine the degree of human-to-human transmissibility of the novel pathogen, and accordingly, this is where information is most urgently needed. We outline two possible scenarios in the Table and find that the early evidence was most consistent with limited human-to-human transmissibility, however more recent data seem to be increasingly more compatible with scenario 2 in which sustained human-to-human transmission has been occurring. Determining the exposure profile among the recently confirmed cases would directly contribute to this assessment. Additional information on approaches to case identification and laboratory testing protocols in Wuhan and in other cities in China would also be informative. A separate priority is to identify the animal reservoir of this novel pathogen and any intermediary hosts, including potential supply chains of wild or game meat.\nIt is challenging to judge severity from the information available to date. We estimated the risk of death among hospitalised cases of around 14% (Figure 2). For both SARS-CoV and MERS-CoV infections, the risk of severe disease increases substantially with age and with the presence of underlying conditions [23-25]. One other caveat with estimating severity is that there can be long delays between hospitalisation and death for infections that are ultimately fatal. For SARS in Hong Kong, the average time from illness to death for fatal cases was 24 days [26]. This means that early estimates of the case fatality risk that ignore the potential outcomes of cases still in hospital are typically underestimates of the final severity profile [27]. We accounted for that by only including cases that either died or recovered in our estimate of the hospital fatality risk. Given that the cases reported outside Wuhan have mostly not been severe, it would be reasonable to infer that there might be a large number of undetected relatively mild infections in Wuhan and that the infection fatality risk is below 1% or even below 0.1%.\nThere are a number of limitations to our analyses. Most importantly, they are only based on data in the public domain to date. Detailed information has not yet been released by authoritative sources on the most recently reported cases. In our analysis in the Table, support for scenario 2 might increase if contact tracing or medical surveillance was incomplete, if there was incomplete ascertainment of clusters or if there was an early focus in testing cases linked to the Southern China Seafood Wholesale Market that led to a selection bias in the prevalence of market exposures among the early cases."}