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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
13 0-10 Species denotes SARS-CoV-2 Tax:2697049
14 16-31 Species denotes new Coronavirus Tax:2697049
15 67-73 Species denotes humans Tax:9606
16 105-115 Species denotes SARS-CoV-2 Tax:2697049
17 422-430 Species denotes patients Tax:9606
18 44-54 Disease denotes infections MESH:D007239
19 254-288 Disease denotes upper respiratory tract infections MESH:D012141
20 299-314 Disease denotes viral pneumonia
21 343-348 Disease denotes death MESH:D003643
24 661-671 Species denotes SARS-CoV-2 Tax:2697049
25 545-553 Disease denotes COVID-19 MESH:C000657245
27 1450-1458 Species denotes patients Tax:9606
29 1741-1749 Disease denotes COVID-19 MESH:C000657245
33 2661-2669 Disease denotes COVID-19 MESH:C000657245
34 2676-2681 Disease denotes death MESH:D003643
35 2715-2721 Disease denotes deaths MESH:D003643
37 3016-3022 Disease denotes deaths MESH:D003643
39 2220-2226 Disease denotes deaths MESH:D003643
41 3647-3653 Species denotes people Tax:9606
43 3716-3724 Disease denotes COVID-19 MESH:C000657245
45 4881-4889 Disease denotes COVID-19 MESH:C000657245
47 4785-4793 Disease denotes COVID-19 MESH:C000657245
51 3980-3988 Species denotes children Tax:9606
52 4525-4535 Species denotes SARS-CoV-2 Tax:2697049
53 4250-4260 Disease denotes infections MESH:D007239
55 5142-5148 Species denotes people Tax:9606
64 6118-6126 Species denotes patients Tax:9606
65 6278-6286 Species denotes patients Tax:9606
66 6346-6354 Species denotes patients Tax:9606
67 6384-6391 Species denotes patient Tax:9606
68 6621-6628 Species denotes patient Tax:9606
69 5934-5944 Disease denotes Infections MESH:D007239
70 6331-6345 Disease denotes critically ill MESH:D016638
71 6977-6982 Disease denotes death MESH:D003643
75 7317-7325 Species denotes patients Tax:9606
76 7308-7316 Disease denotes infected MESH:D007239
77 7545-7555 Disease denotes infections MESH:D007239

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T2 0-87 Sentence denotes SARS-CoV-2 is a new Coronavirus, with first infections detected in humans late in 2019.
T3 88-206 Sentence denotes The emergence of SARS-CoV-2 has led to a large outbreak in China and is currently causing outbreaks in many countries.
T4 207-349 Sentence denotes The disease spectrum ranges from uncomplicated upper respiratory tract infections to severe viral pneumonia with multiorgan failure and death.
T5 350-489 Sentence denotes It can be transmitted by droplets from asymptomatic or oligosymptomatic patients and possibly through aerosols in health care environments.
T6 490-683 Sentence denotes The route of transmission and the spectrum of disease (COVID-19) has motivated many researchers to use models of influenza outbreaks or pandemics to forecast outbreaks of SARS-CoV-2 by analogy.
T7 684-756 Sentence denotes The epicenter of China’s outbreak has been Wuhan and the Hubei province.
T8 757-894 Sentence denotes The Chinese government has restricted travel from and to Hubei province and has implemented a number of measures to contain the outbreak.
T9 895-958 Sentence denotes Meanwhile, the number of new cases per day in China is falling.
T10 959-1027 Sentence denotes A WHO mission has visited China and Wuhan to report on the outbreak.
T11 1028-1121 Sentence denotes They corroborated the outbreak dynamic and case count reported by the Chinese government [2].
T12 1123-1205 Sentence denotes The Chinese success-estimating an upper limit to the attack rate in Hubei province
T13 1206-1329 Sentence denotes Intensive public health interventions have been employed, and some experts expect the outbreak to end as early as in April.
T14 1330-1588 Sentence denotes The bundle of public health interventions has included intensive case and contact tracking, isolation of moderately ill patients in containment centers, social distancing, and shutting down public life of a whole province and many major cities outside Hubei.
T15 1589-1665 Sentence denotes Just how effective the outbreak seems to have been contained is astonishing.
T16 1666-1768 Sentence denotes Publicly available data can be employed to estimate the attack rate of the COVID-19 outbreak in China.
T17 1769-2037 Sentence denotes There are two datasets with a very different picture of the same epidemic caused by the same virus [3].Data from Hubei (roughly 80% of the China outbreak with a focus on severe cases and high case fatality rate (CFR), currently cumulatively estimated to be around 4%).
T18 2038-2163 Sentence denotes Data from China outside Hubei province with a probably much better coverage of the whole epidemic due to active case finding.
T19 2164-2354 Sentence denotes With steadily declining case numbers and numbers of new deaths also declining in the second group, the case fatality rate in China outside Hubei province is stabilizing around 0.8% (Fig. 1).
T20 2355-2653 Sentence denotes If we put these two datasets parallelly we could cautiously (to be on the safe side for an upper limit estimate) assume, that up to 50% of cases might still be missed outside Hubei province with the consequence of a lower case fatality rate, because severe cases are unlikely to be missed (Fig. 2).
T21 2654-2698 Sentence denotes Fig. 1 COVID-19 cases/death in China by day.
T22 2699-2864 Sentence denotes Daily cases and deaths in China, case count for February 13 truncated (change of case definition, 16,119 cases in the part retrospectively reported) (adapted from 3)
T23 2865-2906 Sentence denotes Fig. 2 CFR Hubei and China outside Hubei.
T24 2907-3031 Sentence denotes CFR in Hubei (orange) and in China outside Hubei province (black), calculated from daily cumulative case and deaths numbers.
T25 3032-3089 Sentence denotes Horizontal lines indicate current status (adapted from 3)
T26 3090-3317 Sentence denotes The second cautious assumption would be that the current caseload in Hubei province represents only 2/3 of the final caseload, putting the total number to approximately 100.000 cases (with the current clinical characteristics).
T27 3318-3516 Sentence denotes To set this parallelly with the epidemic outside Hubei province, we would have to multiply this case count by 5–10 (five if the data outside Hubei reflect all cases, ten for under reporting of 50%).
T28 3517-3614 Sentence denotes Thus, the number of cases in the Hubei outbreak could be estimated as between 500.000–1.000.0000.
T29 3615-3707 Sentence denotes With a population of 57 million people in Hubei province, the attack rate would be below 2%.
T30 3709-3750 Sentence denotes How is COVID-19 different from Influenza?
T31 3751-3906 Sentence denotes This estimate of an upper limit of 2% is considerably lower than previous forecasts and estimates in analogy to influenza pandemics or outbreaks (Table 1).
T32 3907-4078 Sentence denotes Compared to influenza outbreaks the attack rate and burden of disease in children have been much lower and the secondary household attack rate has also been low (Table 1).
T33 4079-4261 Sentence denotes This is in sharp contrast to observations of a very rapid spread of the virus in confined situations as prisons or cruise ships and the high rate of healthcare-associated infections.
T34 4262-4725 Sentence denotes Several hypotheses will have to be explored to answer at least some of the questions: (1) initial estimates of R0 might have been biased by clusters of effective transmission (“super-spreaders”), (2) public health measures might be more effective to reduce Rt in SARS-CoV-2 than in influenza outbreaks and (3) whether there is a threshold of prevalent cases in the community, which if reached, the epidemic can be effectively contained only with drastic measures.
T35 4726-4818 Sentence denotes Table 1 Attack rates of pandemic or seasonal influenza and COVID-19 in Hubei province [1, 2]
T36 4819-4901 Sentence denotes Influenza 1957 Influenza 1968 Influenza 2009 Influenza 1977–8 COVID-19, Hubei 2020
T37 4902-4973 Sentence denotes Community attack rate confirmed cases 18.5–26.8% 15% 17,5 2.2–31%  < 2%
T38 4974-5042 Sentence denotes Secondary household contact attack rate 8.4–23%a 20%a 4–6% 16% 3–10%
T39 5043-5068 Sentence denotes aNot laboratory confirmed
T40 5070-5093 Sentence denotes Conclusions and lessons
T41 5094-5204 Sentence denotes First, the WHO report is very good news for the people in Hubei province and all health care workers involved.
T42 5205-5349 Sentence denotes Second, the success of the interventions demonstrates that strict and rapid response to an emerging epidemic can halt the spread of a new virus.
T43 5350-5474 Sentence denotes But there are also some sobering insights looking at the current situation outside China and the messages in the WHO report.
T44 5475-5530 Sentence denotes China’s success might not be the end of their outbreak.
T45 5531-5647 Sentence denotes An attack rate as low as 2% could cause a second wave rapidly, because the community level of immunity is still low.
T46 5648-5832 Sentence denotes Furthermore, the virus has been imported in a large number of countries, which are facing difficult choices regarding public health measures and challenges to their health care system.
T47 5833-5933 Sentence denotes The outbreak in Hubei province has shown how much harm a newly emerging respiratory virus can cause.
T48 5934-6127 Sentence denotes Infections in confined spaces, such as prisons or cruise ships, can rapidly spread, complications can be severe and health care-associated transmission poses a risk for HCWs and other patients.
T49 6128-6355 Sentence denotes Health care workers from all over China have come to Hubei to help and have been doing excellent and very trying work in treating the large number of patients with a very high number of hospitalized and critically ill patients.
T50 6356-6551 Sentence denotes Their growing experience in patient care is also reflected in the declining case fatality rate and the declining number of healthcare-associated transmission over the time course of the outbreak.
T51 6552-6711 Sentence denotes The resulting publications of clinical data will be very helpful for patient care outside Hubei province and as clinicians we will profit immensely from those.
T52 6712-6843 Sentence denotes But we do not know how the situation in Hubei might have been if the virus had spread early to other metropolitan centers in China.
T53 6844-7014 Sentence denotes The workload for healthcare workers would have been multiplied, a collapse of the healthcare system would have been possible and the death toll would have been very high.
T54 7015-7110 Sentence denotes In the light of these consequences, any public health intervention seems to be a better option.
T55 7111-7175 Sentence denotes So, despite the good news from China, the work is far from over.
T56 7176-7349 Sentence denotes Outside China, we face enormous challenges: (1) to effectively contain the current and future outbreaks worldwide, and (2) to treat infected patients effectively and safely.
T57 7350-7478 Sentence denotes Looking at the Chinese experience, we hope that public health measures outside China will be as rapid and effective as in China.
T58 7479-7556 Sentence denotes We should implement those before reaching a critical threshold of infections.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 254-288 Phenotype denotes upper respiratory tract infections http://purl.obolibrary.org/obo/HP_0002788
T2 305-314 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

2_test

Id Subject Object Predicate Lexical cue
32185635-23260039-47595282 4813-4814 23260039 denotes 1
T8644 4813-4814 23260039 denotes 1