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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T8 673-676 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T9 828-831 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T10 1390-1393 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T11 1557-1560 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 1622-1625 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T13 1837-1845 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T14 1968-1971 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 2018-2021 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T16 2048-2056 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T17 2080-2086 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T18 2144-2147 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 2384-2392 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T20 2443-2446 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T21 2621-2624 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T22 2854-2857 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T23 2866-2872 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T24 2955-2961 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T25 3117-3120 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T26 3157-3162 Body_part denotes feces http://purl.org/sig/ont/fma/fma64183
T27 3171-3177 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T28 3319-3322 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T29 3483-3486 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T30 3665-3670 Body_part denotes urine http://purl.org/sig/ont/fma/fma12274
T31 3743-3749 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T32 3804-3809 Body_part denotes urine http://purl.org/sig/ont/fma/fma12274
T33 3949-3952 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T34 3965-3971 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T35 4013-4016 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T36 4168-4173 Body_part denotes feces http://purl.org/sig/ont/fma/fma64183
T37 4181-4187 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T38 4215-4218 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T39 4271-4274 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T40 4278-4283 Body_part denotes feces http://purl.org/sig/ont/fma/fma64183
T41 4362-4365 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T42 4374-4379 Body_part denotes feces http://purl.org/sig/ont/fma/fma64183
T43 4454-4460 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T44 4555-4558 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T45 4562-4567 Body_part denotes feces http://purl.org/sig/ont/fma/fma64183
T46 4762-4767 Body_part denotes feces http://purl.org/sig/ont/fma/fma64183
T47 4828-4831 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T48 5087-5092 Body_part denotes feces http://purl.org/sig/ont/fma/fma64183
T49 5205-5208 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T50 5408-5411 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T51 5415-5421 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T52 5517-5523 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T53 5677-5683 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T54 5831-5839 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T55 5888-5891 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T4 2080-2086 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T5 2866-2872 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T6 2955-2961 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T7 3157-3162 Body_part denotes feces http://purl.obolibrary.org/obo/UBERON_0001988
T8 3171-3177 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T9 3665-3670 Body_part denotes urine http://purl.obolibrary.org/obo/UBERON_0001088
T10 3804-3809 Body_part denotes urine http://purl.obolibrary.org/obo/UBERON_0001088
T11 4168-4173 Body_part denotes feces http://purl.obolibrary.org/obo/UBERON_0001988
T12 4181-4187 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T13 4278-4283 Body_part denotes feces http://purl.obolibrary.org/obo/UBERON_0001988
T14 4374-4379 Body_part denotes feces http://purl.obolibrary.org/obo/UBERON_0001988
T15 4454-4460 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T16 4562-4567 Body_part denotes feces http://purl.obolibrary.org/obo/UBERON_0001988
T17 4762-4767 Body_part denotes feces http://purl.obolibrary.org/obo/UBERON_0001988
T18 5087-5092 Body_part denotes feces http://purl.obolibrary.org/obo/UBERON_0001988
T19 5415-5421 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T20 5517-5523 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T21 5677-5683 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T7 48-56 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T8 69-116 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T9 69-102 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T10 118-126 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 196-205 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T12 334-342 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T13 594-602 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T14 643-651 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 762-776 Disease denotes infectiousness http://purl.obolibrary.org/obo/MONDO_0005550
T16 849-857 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 907-915 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 1134-1142 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 1167-1175 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 1431-1439 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 1957-1965 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 3063-3110 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T23 3063-3096 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T24 4260-4268 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 4335-4343 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 4544-4552 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 4599-4609 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T28 5166-5174 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 5177-5186 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T30 5328-5336 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T31 5397-5405 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 5452-5461 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T33 5914-5922 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T2 231-232 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 345-349 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T4 667-672 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T5 731-732 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 784-789 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T7 1091-1093 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T8 1566-1567 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1888-1890 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T10 1937-1943 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T11 1996-1998 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T12 2100-2102 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T13 2121-2127 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T14 2303-2304 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T15 2574-2575 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T16 3029-3031 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T17 3129-3130 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T18 3154-3155 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T19 3708-3709 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 3743-3749 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T21 3838-3844 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T22 3929-3931 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T23 3965-3971 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T24 4610-4615 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T25 4642-4647 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T26 4740-4745 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T27 5024-5029 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T28 5096-5097 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 5238-5239 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 5466-5467 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 5495-5500 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T32 5527-5528 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 5597-5602 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T34 5627-5630 http://purl.obolibrary.org/obo/CLO_0051582 denotes has

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
26 69-116 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
27 118-128 Species denotes SARS-CoV-2 Tax:2697049
28 133-141 Species denotes children Tax:9606
29 334-344 Species denotes SARS-CoV-2 Tax:2697049
30 425-438 Species denotes coronaviruses Tax:11118
31 643-653 Species denotes SARS-CoV-2 Tax:2697049
32 657-665 Species denotes children Tax:9606
33 849-859 Species denotes SARS-CoV-2 Tax:2697049
34 893-901 Species denotes children Tax:9606
35 27-46 Disease denotes coronavirus disease MESH:D018352
36 48-56 Disease denotes COVID-19 MESH:C000657245
37 196-205 Disease denotes infection MESH:D007239
38 594-602 Disease denotes COVID-19 MESH:C000657245
39 907-915 Disease denotes COVID-19 MESH:C000657245
46 952-960 Species denotes patients Tax:9606
47 1081-1089 Species denotes children Tax:9606
48 1167-1177 Species denotes SARS-CoV-2 Tax:2697049
49 1431-1441 Species denotes SARS-CoV-2 Tax:2697049
50 1463-1472 Species denotes 2019-nCoV Tax:2697049
51 1134-1142 Disease denotes COVID-19 MESH:C000657245
56 1763-1771 Species denotes children Tax:9606
57 1957-1967 Species denotes SARS-CoV-2 Tax:2697049
58 1982-1990 Species denotes children Tax:9606
59 2103-2111 Species denotes children Tax:9606
64 2815-2817 Gene denotes mL Gene:21832
65 2758-2760 Gene denotes mL Gene:21832
66 2494-2496 Gene denotes mL Gene:21832
67 2241-2243 Gene denotes mL Gene:21832
74 3444-3446 Gene denotes mL Gene:21832
75 3063-3110 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
76 3217-3225 Species denotes children Tax:9606
77 3594-3602 Species denotes patients Tax:9606
78 3642-3650 Species denotes patients Tax:9606
79 3231-3250 Disease denotes coronavirus disease MESH:D018352
84 3903-3905 Gene denotes mL Gene:21832
85 3693-3701 Species denotes patients Tax:9606
86 3829-3837 Species denotes patients Tax:9606
87 3920-3927 Species denotes patient Tax:9606
91 4110-4112 Gene denotes mL Gene:21832
92 3985-3993 Species denotes children Tax:9606
93 4073-4081 Species denotes children Tax:9606
100 4260-4270 Species denotes SARS-CoV-2 Tax:2697049
101 4321-4329 Species denotes children Tax:9606
102 4517-4525 Species denotes children Tax:9606
103 4544-4554 Species denotes SARS-CoV-2 Tax:2697049
104 4918-4925 Species denotes infants Tax:9606
105 4335-4343 Disease denotes COVID-19 MESH:C000657245
110 5278-5281 Gene denotes aid Gene:57379
111 5370-5378 Species denotes children Tax:9606
112 5166-5186 Disease denotes SARS-CoV-2 infection MESH:C000657245
113 5328-5336 Disease denotes COVID-19 MESH:C000657245
118 5397-5407 Species denotes SARS-CoV-2 Tax:2697049
119 5738-5746 Species denotes children Tax:9606
120 5791-5799 Species denotes children Tax:9606
121 5452-5461 Disease denotes infection MESH:D007239

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T7 0-291 Sentence denotes In the current pandemic of coronavirus disease (COVID-19), detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in children suspected of having the disease is essential for both infection control and establishing a definite causal relationship in unprecedented cases (1,2).
T8 292-470 Sentence denotes However, efforts are hindered by negative SARS-CoV-2 test results for respiratory specimens and possible cross-reactivity with other coronaviruses among seropositive cases (2,3).
T9 471-666 Sentence denotes Little is known about the value of various samples other than nasopharyngeal or oropharyngeal swab specimens in diagnosing COVID-19 and understanding the viral dynamics of SARS-CoV-2 in children.
T10 667-805 Sentence denotes Virus RNA was persistently detected in rectal swab specimens in a previous study, although the infectiousness of the virus is unknown (4).
T11 806-916 Sentence denotes We analyzed the viral RNA load kinetics of SARS-CoV-2 in various clinical specimens in children with COVID-19.
T12 917-1048 Sentence denotes In South Korea, all confirmed case-patients, regardless of disease severity, must be isolated in hospitals or isolation facilities.
T13 1049-1376 Sentence denotes For this study, we included all children <18 years of age who were confirmed to have COVID-19 by positive results for SARS-CoV-2 in combined nasopharyngeal and oropharyngeal swab specimens and who were hospitalized in Seoul Metropolitan Government–Seoul National University Boramae Medical Center during March 8–April 28, 2020.
T14 1377-1517 Sentence denotes We extracted RNA from clinical specimens and detected SARS-CoV-2 by using the Allplex 2019-nCoV Assay kit (Seegene, http://www.seegene.com).
T15 1518-1626 Sentence denotes We performed quantitation of the viral RNA with a standard curve constructed using in vitro transcribed RNA.
T16 1627-1747 Sentence denotes This study was approved by the institutional review board at SMG-SNU Boramae Medical Center; written consent was waived.
T17 1748-1855 Sentence denotes We included 12 children in the study; 9 were mildly symptomatic and 3 were asymptomatic (Appendix Table 1).
T18 1856-1906 Sentence denotes Median age was 6.5 years (range 27 days–16 years).
T19 1907-2066 Sentence denotes Nasopharyngeal swab specimens tested positive for SARS-CoV-2 RNA in all 12 children, and 11 (92%) had positive RNA in their fecal specimens (Appendix Table 2).
T20 2067-2137 Sentence denotes We collected saliva samples from 11 children; 8 (73%) tested positive.
T21 2138-2306 Sentence denotes Viral RNA load in the nasopharyngeal swabs peaked early at median 7.56 (range 6.19–10.56) log10 copies/mL and decreased over time (p<0.001 for trend) (Figure, panel A).
T22 2307-2402 Sentence denotes The positivity of the specimens was 75% during week 2 and 55% during week 3 (Appendix Table 2).
T23 2403-2577 Sentence denotes In comparison, the median initial fecal RNA load was 7.68 (range <4.10–10.27) log10 copies/mL and remained steadily high (p = 0.148 for trend) for >3 weeks (Figure, panel B).
T24 2578-2609 Sentence denotes Fecal positivity remained >80%.
T25 2610-2830 Sentence denotes The median RNA load in fecal samples was significantly higher than that for nasopharyngeal swab specimens during week 2 (7.26 vs. 6.19 log10 copies/mL; p = 0.006) and week 3 (7.61 versus 5.49 log10 copies/mL; p = 0.006).
T26 2831-2940 Sentence denotes Except for 1 case, the RNA load in saliva declined rapidly with time (p = 0.003 for trend) (Figure, panel C).
T27 2941-3043 Sentence denotes Positivity in saliva samples was 80% in week 1 but dropped sharply to 33% in week 2 and 11% in week 3.
T28 3044-3274 Sentence denotes Figure Changes in severe acute respiratory syndrome coronavirus 2 viral RNA load in A) nasopharyngeal swabs, B) feces, and C) saliva of mildly symptomatic and asymptomatic children with coronavirus disease over time, South Korea.
T29 3275-3378 Sentence denotes The thick red line indicates trend in viral RNA load over time, and the shaded areas represent 95% CIs.
T30 3379-3448 Sentence denotes The dashed line indicates the detection limit (1.25 × 104 copies/mL).
T31 3449-3525 Sentence denotes Specimens with undetectable viral RNA loads are shown under the dashed line.
T32 3526-3651 Sentence denotes Days after onset indicates days after symptom onset for symptomatic patients, days after diagnosis for asymptomatic patients.
T33 3652-3793 Sentence denotes We collected urine specimens from the 12 patients after a median of 3 (range 0–8) days and plasma specimens at 2 (range 0–8) days from onset.
T34 3794-3907 Sentence denotes Of these, urine samples of 2 (17%) patients tested positive (median load 5.69 [range 3.82–7.55] log10 copies/mL).
T35 3908-3972 Sentence denotes Only 1 (8%) patient, 27 days of age, had RNA detected in plasma.
T36 3973-4125 Sentence denotes Symptomatic children had higher initial RNA load in nasopharyngeal swab specimens than asymptomatic children (9.01 vs. 6.32 log10 copies/mL; p = 0.048).
T37 4126-4232 Sentence denotes We observed no significant differences in feces and in saliva and no correlation between RNA load and age.
T38 4233-4344 Sentence denotes In this study, we detected SARS-CoV-2 RNA in feces of 92% of mildly ill or asymptomatic children with COVID-19.
T39 4345-4526 Sentence denotes In addition, the RNA load in feces remained steadily high, whereas that in nasopharyngeal swab specimens and saliva declined with time in both symptomatic and asymptomatic children.
T40 4527-4723 Sentence denotes The detection of SARS-CoV-2 RNA in feces does not necessarily mean that infectious virus is present; thus, lack of virus isolation in our study limits interpretation in the context of infectivity.
T41 4724-4845 Sentence denotes However, viable virus was isolated in feces in previous studies, and infectivity was dependent on viral RNA load (3,5,6).
T42 4846-5055 Sentence denotes Considering these findings, proper handwashing when changing diapers in infants and adequate hygiene measures in restrooms are recommended to prevent the potential spread of the virus among household contacts.
T43 5056-5255 Sentence denotes Our findings also suggest that feces is a promising and reliable source for detecting both current and recent SARS-CoV-2 infection because the viral RNA is present in high loads for a prolonged time.
T44 5256-5379 Sentence denotes Fecal specimens could aid in seeking the etiologic relationship between COVID-19 and unexpected manifestations in children.
T45 5380-5489 Sentence denotes We also detected SARS-CoV-2 RNA in saliva during the early phase of the infection for a short period of time.
T46 5490-5649 Sentence denotes Live virus was isolated in saliva in a previous study, and the possibility of airborne transmission of the virus through normal speaking has been raised (7,8).
T47 5650-5830 Sentence denotes Although the viral load in saliva drops rapidly, our findings suggest the necessity for children to wear masks, especially in schools, where children would talk in close proximity.
T48 5831-5839 Sentence denotes Appendix
T49 5840-5932 Sentence denotes Additional information about the study of viral RNA load in children with COVID-19 in Seoul.