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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T2","span":{"begin":511,"end":517},"obj":"Body_part"},{"id":"T3","span":{"begin":1161,"end":1166},"obj":"Body_part"},{"id":"T4","span":{"begin":1360,"end":1364},"obj":"Body_part"},{"id":"T5","span":{"begin":1392,"end":1397},"obj":"Body_part"},{"id":"T6","span":{"begin":1767,"end":1773},"obj":"Body_part"},{"id":"T7","span":{"begin":1777,"end":1782},"obj":"Body_part"},{"id":"T8","span":{"begin":1824,"end":1828},"obj":"Body_part"},{"id":"T9","span":{"begin":2208,"end":2214},"obj":"Body_part"}],"attributes":[{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0000341"},{"id":"A3","pred":"uberon_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A5","pred":"uberon_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_0007311"},{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"id":"A8","pred":"uberon_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/UBERON_3010752"},{"id":"A9","pred":"uberon_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/UBERON_0007311"}],"text":"A 54-year-old Korean man living in Wuhan, China entered Korea on January 20, 2020 and felt the first symptoms of chills and muscle pain on January 22. After contacting a public health center on January 25, he was isolated in a negative pressure room at Myongji Hospital and confirmed to have COVID-19 on January 26.\nAt that time the initial confirmation of COVID-19 was made by pan-coronavirus conventional polymerase chain reaction assay and sequencing of the polymerase chain reaction (PCR) amplicons using a throat swab.\nThe index patient transmitted the virus to his friend (patient A) at a restaurant on the 1st day of the symptoms. And then patient A (confirmed on January 30, 2020) transmitted COVID-19 to his spouse and son (confirmed on January 31, 2020), and a church colleague (confirmed on February 6, 2020). Those were the first cases of tertiary transmission of COVID-19 outside China.\nThe index patient was a clothing worker at the Wuhan Fashion Center, with a height of 193 cm and weight of 96 kg (body mass index, 25.7), and had no major illness. He denied any smoking and drinking history. On admission day, he had no respiratory symptoms and blood pressure of 152/93 mmHg, pulse rate of 73 beats per minute, respiratory rate of 20 breaths per minute, and a body temperature of 37.0°C. On physical examination, no pharyngeal injection, clear lung sounds, and no haziness on chest X-ray were observed. Tests for Leptospira, Hantan virus, Tsutsugamushi, Malaria, M tuberculosis, human immunodeficiency virus (HIV) Ag/Ab, and venereal disease research laboratory (VDRL) test were all negative.\nHe developed fever and dry cough on days 5 and 7 of illness, respectively, but he had no serious respiratory symptoms such as shortness of breath, productive sputum or chest pain. Small consolidation in right upper lobe and ground-glass opacities in both lower lobes were observed on high-resolution computed tomography scan (Figs. 1 and 2, Table 1).\nThe initial viral load could not be measured because real-time PCR was not available when the patient was diagnosed. So we measured viral loads using quantitative reverse transcription (RT)-PCR since Jan. 31, 2020. Viral RNA was extracted from the sputum using QIAamp viral RNA mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. All quantitative real-time PCR amplifications were performed using Quantstudio 1 (Applied Biosystems, Foster City, CA, USA) and PowerCheck™ SARS-CoV-2 Real-Time PCR kit (KogeneBiotech, Seoul, Korea).\nThere were some reports about lopinavir/ritonavir (Kaletra, AbbVie) for the treatment of COVID-19.1 Lopinavir/ritonavir was started from the hospital day 8 (day 10 of illness); 2 tablets (lopinavir 200 mg/ritonavir 50 mg) were given per oral bid. Interestingly, from the next day of lopinavir/ritonavir administration, β-coronavirus viral load started to decrease and no detectable or little coronavirus titers have been observed since then (Fig. 2 and Supplementary Fig. 1).\nIt is possible that the decreased load of SARS-CoV-2 resulted from the natural course of the healing process rather than administration of lopinavir/ritonavir, or both. Therefore, more data need to be collected to figure out the direct effect of lopinavir/ritonavir on treatment with COVID-19.\nThe patient also complained of psychiatric symptoms such as depression, insomnia and suicidal thoughts after isolation. The patient experienced stress regarding people's reactions from the media reports about the COVID-19 patients. In addition, despite mild symptoms of COVID-19 in his case, isolation in the negative pressure room during treatment might be one of the reasons provoking psychological symptoms. Counseling and related medications were provided under the consult of a psychiatrist.2\nThis case shows that the COVID-19 may induce relatively mild symptoms and a patient can recover when early diagnosis of pneumonia was made.345 When lopinavir/ritonavir was used, we found reduced viral loads and improved clinical symptoms during the treatment. So lopinavir/ritonavir can be recommended to relatively high-risk groups of COVID-19 pneumonia (elderly patients or patients with underlying diseases) from the early stage. But we need more evidence to prove the clinical efficacy of lopinavir/ritonavir based on well controlled clinical trials.\nThe images are published under agreement of the patient.\n\nEthics statement\nMyongji Hospital Institutional Review Board (IRB) approved this study (No. IRB 2020-01-027) and written informed consent was given by the patient."}

LitCovid_AGAC

{"project":"LitCovid_AGAC","denotations":[{"id":"p3240s19","span":{"begin":2874,"end":2882},"obj":"NegReg"},{"id":"p3248s9","span":{"begin":3974,"end":3981},"obj":"NegReg"}],"text":"A 54-year-old Korean man living in Wuhan, China entered Korea on January 20, 2020 and felt the first symptoms of chills and muscle pain on January 22. After contacting a public health center on January 25, he was isolated in a negative pressure room at Myongji Hospital and confirmed to have COVID-19 on January 26.\nAt that time the initial confirmation of COVID-19 was made by pan-coronavirus conventional polymerase chain reaction assay and sequencing of the polymerase chain reaction (PCR) amplicons using a throat swab.\nThe index patient transmitted the virus to his friend (patient A) at a restaurant on the 1st day of the symptoms. And then patient A (confirmed on January 30, 2020) transmitted COVID-19 to his spouse and son (confirmed on January 31, 2020), and a church colleague (confirmed on February 6, 2020). Those were the first cases of tertiary transmission of COVID-19 outside China.\nThe index patient was a clothing worker at the Wuhan Fashion Center, with a height of 193 cm and weight of 96 kg (body mass index, 25.7), and had no major illness. He denied any smoking and drinking history. On admission day, he had no respiratory symptoms and blood pressure of 152/93 mmHg, pulse rate of 73 beats per minute, respiratory rate of 20 breaths per minute, and a body temperature of 37.0°C. On physical examination, no pharyngeal injection, clear lung sounds, and no haziness on chest X-ray were observed. Tests for Leptospira, Hantan virus, Tsutsugamushi, Malaria, M tuberculosis, human immunodeficiency virus (HIV) Ag/Ab, and venereal disease research laboratory (VDRL) test were all negative.\nHe developed fever and dry cough on days 5 and 7 of illness, respectively, but he had no serious respiratory symptoms such as shortness of breath, productive sputum or chest pain. Small consolidation in right upper lobe and ground-glass opacities in both lower lobes were observed on high-resolution computed tomography scan (Figs. 1 and 2, Table 1).\nThe initial viral load could not be measured because real-time PCR was not available when the patient was diagnosed. So we measured viral loads using quantitative reverse transcription (RT)-PCR since Jan. 31, 2020. Viral RNA was extracted from the sputum using QIAamp viral RNA mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. All quantitative real-time PCR amplifications were performed using Quantstudio 1 (Applied Biosystems, Foster City, CA, USA) and PowerCheck™ SARS-CoV-2 Real-Time PCR kit (KogeneBiotech, Seoul, Korea).\nThere were some reports about lopinavir/ritonavir (Kaletra, AbbVie) for the treatment of COVID-19.1 Lopinavir/ritonavir was started from the hospital day 8 (day 10 of illness); 2 tablets (lopinavir 200 mg/ritonavir 50 mg) were given per oral bid. Interestingly, from the next day of lopinavir/ritonavir administration, β-coronavirus viral load started to decrease and no detectable or little coronavirus titers have been observed since then (Fig. 2 and Supplementary Fig. 1).\nIt is possible that the decreased load of SARS-CoV-2 resulted from the natural course of the healing process rather than administration of lopinavir/ritonavir, or both. Therefore, more data need to be collected to figure out the direct effect of lopinavir/ritonavir on treatment with COVID-19.\nThe patient also complained of psychiatric symptoms such as depression, insomnia and suicidal thoughts after isolation. The patient experienced stress regarding people's reactions from the media reports about the COVID-19 patients. In addition, despite mild symptoms of COVID-19 in his case, isolation in the negative pressure room during treatment might be one of the reasons provoking psychological symptoms. Counseling and related medications were provided under the consult of a psychiatrist.2\nThis case shows that the COVID-19 may induce relatively mild symptoms and a patient can recover when early diagnosis of pneumonia was made.345 When lopinavir/ritonavir was used, we found reduced viral loads and improved clinical symptoms during the treatment. So lopinavir/ritonavir can be recommended to relatively high-risk groups of COVID-19 pneumonia (elderly patients or patients with underlying diseases) from the early stage. But we need more evidence to prove the clinical efficacy of lopinavir/ritonavir based on well controlled clinical trials.\nThe images are published under agreement of the patient.\n\nEthics statement\nMyongji Hospital Institutional Review Board (IRB) approved this study (No. IRB 2020-01-027) and written informed consent was given by the patient."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T2","span":{"begin":2123,"end":2144},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T3","span":{"begin":2131,"end":2144},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T4","span":{"begin":2146,"end":2148},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"A 54-year-old Korean man living in Wuhan, China entered Korea on January 20, 2020 and felt the first symptoms of chills and muscle pain on January 22. After contacting a public health center on January 25, he was isolated in a negative pressure room at Myongji Hospital and confirmed to have COVID-19 on January 26.\nAt that time the initial confirmation of COVID-19 was made by pan-coronavirus conventional polymerase chain reaction assay and sequencing of the polymerase chain reaction (PCR) amplicons using a throat swab.\nThe index patient transmitted the virus to his friend (patient A) at a restaurant on the 1st day of the symptoms. And then patient A (confirmed on January 30, 2020) transmitted COVID-19 to his spouse and son (confirmed on January 31, 2020), and a church colleague (confirmed on February 6, 2020). Those were the first cases of tertiary transmission of COVID-19 outside China.\nThe index patient was a clothing worker at the Wuhan Fashion Center, with a height of 193 cm and weight of 96 kg (body mass index, 25.7), and had no major illness. He denied any smoking and drinking history. On admission day, he had no respiratory symptoms and blood pressure of 152/93 mmHg, pulse rate of 73 beats per minute, respiratory rate of 20 breaths per minute, and a body temperature of 37.0°C. On physical examination, no pharyngeal injection, clear lung sounds, and no haziness on chest X-ray were observed. Tests for Leptospira, Hantan virus, Tsutsugamushi, Malaria, M tuberculosis, human immunodeficiency virus (HIV) Ag/Ab, and venereal disease research laboratory (VDRL) test were all negative.\nHe developed fever and dry cough on days 5 and 7 of illness, respectively, but he had no serious respiratory symptoms such as shortness of breath, productive sputum or chest pain. Small consolidation in right upper lobe and ground-glass opacities in both lower lobes were observed on high-resolution computed tomography scan (Figs. 1 and 2, Table 1).\nThe initial viral load could not be measured because real-time PCR was not available when the patient was diagnosed. So we measured viral loads using quantitative reverse transcription (RT)-PCR since Jan. 31, 2020. Viral RNA was extracted from the sputum using QIAamp viral RNA mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. All quantitative real-time PCR amplifications were performed using Quantstudio 1 (Applied Biosystems, Foster City, CA, USA) and PowerCheck™ SARS-CoV-2 Real-Time PCR kit (KogeneBiotech, Seoul, Korea).\nThere were some reports about lopinavir/ritonavir (Kaletra, AbbVie) for the treatment of COVID-19.1 Lopinavir/ritonavir was started from the hospital day 8 (day 10 of illness); 2 tablets (lopinavir 200 mg/ritonavir 50 mg) were given per oral bid. Interestingly, from the next day of lopinavir/ritonavir administration, β-coronavirus viral load started to decrease and no detectable or little coronavirus titers have been observed since then (Fig. 2 and Supplementary Fig. 1).\nIt is possible that the decreased load of SARS-CoV-2 resulted from the natural course of the healing process rather than administration of lopinavir/ritonavir, or both. Therefore, more data need to be collected to figure out the direct effect of lopinavir/ritonavir on treatment with COVID-19.\nThe patient also complained of psychiatric symptoms such as depression, insomnia and suicidal thoughts after isolation. The patient experienced stress regarding people's reactions from the media reports about the COVID-19 patients. In addition, despite mild symptoms of COVID-19 in his case, isolation in the negative pressure room during treatment might be one of the reasons provoking psychological symptoms. Counseling and related medications were provided under the consult of a psychiatrist.2\nThis case shows that the COVID-19 may induce relatively mild symptoms and a patient can recover when early diagnosis of pneumonia was made.345 When lopinavir/ritonavir was used, we found reduced viral loads and improved clinical symptoms during the treatment. So lopinavir/ritonavir can be recommended to relatively high-risk groups of COVID-19 pneumonia (elderly patients or patients with underlying diseases) from the early stage. But we need more evidence to prove the clinical efficacy of lopinavir/ritonavir based on well controlled clinical trials.\nThe images are published under agreement of the patient.\n\nEthics statement\nMyongji Hospital Institutional Review Board (IRB) approved this study (No. IRB 2020-01-027) and written informed consent was given by the patient."}

LitCovid-sentences

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T4","span":{"begin":113,"end":119},"obj":"Phenotype"},{"id":"T5","span":{"begin":124,"end":135},"obj":"Phenotype"},{"id":"T6","span":{"begin":1501,"end":1517},"obj":"Phenotype"},{"id":"T7","span":{"begin":1622,"end":1627},"obj":"Phenotype"},{"id":"T8","span":{"begin":1632,"end":1641},"obj":"Phenotype"},{"id":"T9","span":{"begin":1735,"end":1754},"obj":"Phenotype"},{"id":"T10","span":{"begin":1777,"end":1787},"obj":"Phenotype"},{"id":"T11","span":{"begin":3349,"end":3359},"obj":"Phenotype"},{"id":"T12","span":{"begin":3361,"end":3369},"obj":"Phenotype"},{"id":"T13","span":{"begin":3907,"end":3916},"obj":"Phenotype"},{"id":"T14","span":{"begin":4132,"end":4141},"obj":"Phenotype"}],"attributes":[{"id":"A4","pred":"hp_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/HP_0025143"},{"id":"A5","pred":"hp_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/HP_0003326"},{"id":"A6","pred":"hp_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/HP_0002721"},{"id":"A7","pred":"hp_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/HP_0001945"},{"id":"A8","pred":"hp_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/HP_0031246"},{"id":"A9","pred":"hp_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/HP_0002098"},{"id":"A10","pred":"hp_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/HP_0100749"},{"id":"A11","pred":"hp_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/HP_0000716"},{"id":"A12","pred":"hp_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/HP_0100785"},{"id":"A13","pred":"hp_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A14","pred":"hp_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"A 54-year-old Korean man living in Wuhan, China entered Korea on January 20, 2020 and felt the first symptoms of chills and muscle pain on January 22. After contacting a public health center on January 25, he was isolated in a negative pressure room at Myongji Hospital and confirmed to have COVID-19 on January 26.\nAt that time the initial confirmation of COVID-19 was made by pan-coronavirus conventional polymerase chain reaction assay and sequencing of the polymerase chain reaction (PCR) amplicons using a throat swab.\nThe index patient transmitted the virus to his friend (patient A) at a restaurant on the 1st day of the symptoms. And then patient A (confirmed on January 30, 2020) transmitted COVID-19 to his spouse and son (confirmed on January 31, 2020), and a church colleague (confirmed on February 6, 2020). Those were the first cases of tertiary transmission of COVID-19 outside China.\nThe index patient was a clothing worker at the Wuhan Fashion Center, with a height of 193 cm and weight of 96 kg (body mass index, 25.7), and had no major illness. He denied any smoking and drinking history. On admission day, he had no respiratory symptoms and blood pressure of 152/93 mmHg, pulse rate of 73 beats per minute, respiratory rate of 20 breaths per minute, and a body temperature of 37.0°C. On physical examination, no pharyngeal injection, clear lung sounds, and no haziness on chest X-ray were observed. Tests for Leptospira, Hantan virus, Tsutsugamushi, Malaria, M tuberculosis, human immunodeficiency virus (HIV) Ag/Ab, and venereal disease research laboratory (VDRL) test were all negative.\nHe developed fever and dry cough on days 5 and 7 of illness, respectively, but he had no serious respiratory symptoms such as shortness of breath, productive sputum or chest pain. Small consolidation in right upper lobe and ground-glass opacities in both lower lobes were observed on high-resolution computed tomography scan (Figs. 1 and 2, Table 1).\nThe initial viral load could not be measured because real-time PCR was not available when the patient was diagnosed. So we measured viral loads using quantitative reverse transcription (RT)-PCR since Jan. 31, 2020. Viral RNA was extracted from the sputum using QIAamp viral RNA mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. All quantitative real-time PCR amplifications were performed using Quantstudio 1 (Applied Biosystems, Foster City, CA, USA) and PowerCheck™ SARS-CoV-2 Real-Time PCR kit (KogeneBiotech, Seoul, Korea).\nThere were some reports about lopinavir/ritonavir (Kaletra, AbbVie) for the treatment of COVID-19.1 Lopinavir/ritonavir was started from the hospital day 8 (day 10 of illness); 2 tablets (lopinavir 200 mg/ritonavir 50 mg) were given per oral bid. Interestingly, from the next day of lopinavir/ritonavir administration, β-coronavirus viral load started to decrease and no detectable or little coronavirus titers have been observed since then (Fig. 2 and Supplementary Fig. 1).\nIt is possible that the decreased load of SARS-CoV-2 resulted from the natural course of the healing process rather than administration of lopinavir/ritonavir, or both. Therefore, more data need to be collected to figure out the direct effect of lopinavir/ritonavir on treatment with COVID-19.\nThe patient also complained of psychiatric symptoms such as depression, insomnia and suicidal thoughts after isolation. The patient experienced stress regarding people's reactions from the media reports about the COVID-19 patients. In addition, despite mild symptoms of COVID-19 in his case, isolation in the negative pressure room during treatment might be one of the reasons provoking psychological symptoms. Counseling and related medications were provided under the consult of a psychiatrist.2\nThis case shows that the COVID-19 may induce relatively mild symptoms and a patient can recover when early diagnosis of pneumonia was made.345 When lopinavir/ritonavir was used, we found reduced viral loads and improved clinical symptoms during the treatment. So lopinavir/ritonavir can be recommended to relatively high-risk groups of COVID-19 pneumonia (elderly patients or patients with underlying diseases) from the early stage. But we need more evidence to prove the clinical efficacy of lopinavir/ritonavir based on well controlled clinical trials.\nThe images are published under agreement of the patient.\n\nEthics statement\nMyongji Hospital Institutional Review Board (IRB) approved this study (No. IRB 2020-01-027) and written informed consent was given by the patient."}

PMC:7025910 / 1266-5829 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7025910 / 1266-5829 JSON TXT