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PMC:7096774 / 11725-17625 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
238 466-469 Gene denotes THL Gene:7062
239 37-45 Disease denotes COVID-19 MESH:C000657245
240 276-285 Disease denotes pneumonia MESH:D011014
241 299-305 Disease denotes nausea MESH:D009325
242 307-317 Disease denotes high fever MESH:D005334
243 319-324 Disease denotes cough MESH:D003371
244 326-343 Disease denotes muscular weakness MESH:D018908
245 348-355 Disease denotes fatigue MESH:D005221
249 537-545 Disease denotes COVID-19 MESH:C000657245
250 776-784 Disease denotes COVID-19 MESH:C000657245
251 785-794 Disease denotes infection MESH:D007239
254 1006-1013 Species denotes patient Tax:9606
255 1241-1245 Species denotes ncov Tax:2697049
260 1398-1406 Species denotes patients Tax:9606
261 1531-1541 Species denotes SARS-CoV-2 Tax:2697049
262 1318-1326 Disease denotes COVID-19 MESH:C000657245
263 1734-1754 Disease denotes SARS-CoV-2 infection MESH:C000657245
266 2294-2302 Species denotes patients Tax:9606
267 2370-2378 Species denotes SARS-CoV Tax:694009
272 2862-2863 Gene denotes S Gene:43740568
273 2575-2576 Gene denotes N Gene:43740575
274 2581-2582 Gene denotes S Gene:43740568
275 2684-2691 Species denotes patient Tax:9606
289 3132-3141 Species denotes hCoV OC43 Tax:31631
290 3185-3193 Species denotes SARS-CoV Tax:694009
291 3218-3228 Species denotes SARS-CoV-2 Tax:2697049
292 3764-3774 Species denotes SARS-CoV-2 Tax:2697049
293 3916-3924 Species denotes patients Tax:9606
294 4209-4217 Species denotes patients Tax:9606
295 4334-4342 Species denotes patients Tax:9606
296 3146-3150 Species denotes 229E Tax:11137
297 3619-3629 Species denotes SARS-CoV-2 Tax:2697049
298 4036-4044 Species denotes patients Tax:9606
299 3087-3116 Disease denotes coronavirus (hCoV) infections MESH:D018352
300 3930-3948 Disease denotes SARS-CoV infection MESH:C000657245
301 4379-4399 Disease denotes SARS-CoV-2 infection MESH:C000657245
313 4715-4759 Species denotes Middle East respiratory syndrome coronavirus Tax:1335626
314 4851-4859 Species denotes SARS-CoV Tax:694009
315 4876-4881 Species denotes human Tax:9606
316 5049-5057 Species denotes patients Tax:9606
317 5227-5236 Species denotes HCoV-229E Tax:11137
318 5241-5250 Species denotes HCoV-OC43 Tax:31631
319 5294-5302 Species denotes children Tax:9606
320 5383-5392 Species denotes HCoV-NL63 Tax:277944
321 5397-5406 Species denotes HCoV-229E Tax:11137
322 4538-4548 Species denotes SARS-CoV-2 Tax:2697049
323 5089-5093 Species denotes HCoV Tax:694448
327 5483-5491 Species denotes patients Tax:9606
328 5646-5666 Disease denotes SARS CoV-2 infection MESH:C000657245
329 5878-5899 Disease denotes SARS-CoV-2 infections MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T93 293-297 Body_part denotes nose http://purl.org/sig/ont/fma/fma46472
T94 992-998 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T95 1379-1384 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T96 1593-1598 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T97 1637-1642 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T98 1708-1716 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T99 2006-2009 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T100 2014-2017 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T101 2438-2441 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T102 2446-2449 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T103 2495-2500 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T104 2583-2590 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T105 2655-2663 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T106 2692-2697 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T107 2731-2738 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T108 2767-2775 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T109 2832-2840 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T110 2864-2871 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T111 3513-3521 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T112 4049-4052 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T113 4085-4088 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T114 4093-4096 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T115 5175-5180 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T30 293-297 Body_part denotes nose http://purl.obolibrary.org/obo/UBERON_0000004
T31 1379-1384 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T32 1593-1598 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T33 1637-1642 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T34 2495-2500 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T35 2692-2697 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T36 5175-5180 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T60 37-45 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T61 276-285 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T62 287-297 Disease denotes runny nose http://purl.obolibrary.org/obo/MONDO_0003014
T63 537-545 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T64 776-784 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T65 785-794 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T66 1318-1326 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T67 1531-1539 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 1734-1742 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T69 1745-1754 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T70 2370-2378 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T71 3106-3116 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T72 3185-3193 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T73 3218-3226 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T74 3619-3627 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 3764-3772 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T76 3930-3948 Disease denotes SARS-CoV infection http://purl.obolibrary.org/obo/MONDO_0005091
T77 3939-3948 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T78 4379-4387 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T79 4390-4399 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T80 4538-4546 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T81 4851-4859 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 5044-5048 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T83 5478-5482 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T84 5576-5580 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T85 5646-5650 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T86 5657-5666 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T87 5878-5886 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T88 5889-5899 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T74 293-297 http://www.ebi.ac.uk/efo/EFO_0000828 denotes nose
T75 412-418 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T76 1293-1305 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T77 1310-1317 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T78 1423-1430 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T79 1495-1496 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T80 1555-1558 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T81 1593-1598 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T82 1593-1598 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T83 1600-1602 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T84 1865-1872 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T85 1982-1984 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T86 2275-2276 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87 2390-2393 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T88 2542-2543 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T89 2664-2669 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T90 2757-2759 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T91 2764-2766 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T92 2764-2766 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T93 2978-2979 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T94 3081-3086 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T95 3200-3207 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T96 3242-3246 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T97 3258-3263 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T98 3331-3332 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T99 3424-3425 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 3710-3715 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T101 4065-4070 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T102 4306-4307 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 4462-4464 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T104 4517-4519 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T105 4668-4669 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T106 4814-4815 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T107 4876-4881 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T108 5408-5410 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T109 5422-5425 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T110 5599-5609 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing is
T111 5644-5645 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 5668-5670 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T113 5788-5795 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T114 5842-5843 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T68 1542-1554 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T69 1550-1554 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T70 1858-1864 Chemical denotes corona http://purl.obolibrary.org/obo/CHEBI_37409
T71 2239-2247 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T72 2583-2590 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T73 2731-2738 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T74 2764-2766 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T75 2767-2775 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T76 2864-2871 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T77 2912-2914 Chemical denotes MN http://purl.obolibrary.org/obo/CHEBI_141442
T78 3239-3241 Chemical denotes MN http://purl.obolibrary.org/obo/CHEBI_141442
T79 3583-3585 Chemical denotes MN http://purl.obolibrary.org/obo/CHEBI_141442
T80 5314-5319 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T5 1476-1491 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T104 0-10 Sentence denotes Discussion
T105 11-139 Sentence denotes In the early phase of the COVID-19 outbreak, confirmed cases outside China were mostly imported among travellers from Wuhan [7].
T106 140-234 Sentence denotes The first case in Finland was detected on 29 January among the first imported cases in Europe.
T107 235-356 Sentence denotes The case presented mild symptoms without pneumonia: runny nose, nausea, high fever, cough, muscular weakness and fatigue.
T108 357-470 Sentence denotes No secondary transmission events were detected despite active follow-up by the Lapland Hospital district and THL.
T109 471-576 Sentence denotes As at 17 March 2020, 358 additional laboratory-confirmed cases of COVID-19 have been detected in Finland.
T110 577-717 Sentence denotes Many of them are travel-related (mostly from northern Italy and Austria) but there is also local transmission from the travel-related cases.
T111 718-965 Sentence denotes The risk of widespread national community transmission of COVID-19 infection in the European Union, European Economic Area and the United Kingdom in the coming weeks is considered high by the European Centre for Disease Prevention and Control [8].
T112 966-1114 Sentence denotes The sequence of the viral genome of the patient was nearly identical to the reference strain from Wuhan, reflecting an early importation from China.
T113 1115-1251 Sentence denotes Later sequence information in Finland (up to 2 March) showed clustering with strains circulating in Italy (see nextstrain.org/ncov) [9].
T114 1252-1526 Sentence denotes Current guidelines from the World Health Organization for testing COVID-19 recommend collection of both acute and convalescent serum samples from patients for serological testing, which can support the identification of the immune response to a specific viral pathogen [10].
T115 1527-1664 Sentence denotes The SARS-CoV-2 nucleic acid has been found also in anal swabs and blood [11], however we did not detect it in serum samples in this case.
T116 1665-1763 Sentence denotes As yet, only limited data are available on antibody responses during SARS-CoV-2 infection [11,12].
T117 1764-1944 Sentence denotes Further studies are needed to better understand the seroprevalence of antibodies to different corona viruses in populations and the role of these antibodies in the risk of disease.
T118 1945-2174 Sentence denotes In accordance with earlier findings [11], we found that both IgM and IgG titres were low or undetectable at on Day 4 (the second day after admission to hospital) yet increasing on Day 9–10, i.e. 5–6 days after the first sampling.
T119 2175-2332 Sentence denotes Using other detection methods beyond IFA as well as recombinant antigens and analysing samples from a larger number of patients will shed more light on this.
T120 2333-2480 Sentence denotes The time of first appearance of anti-SARS-CoV antibodies has ranged from Day 3 to 42 and Day 5 to 47 for IgM and IgG antibodies, respectively [13].
T121 2481-2670 Sentence denotes The WB of the serum sample collected at convalescence showed a prominent response against the N and S protein, confirming their role as main candidate diagnostic targets for antibody tests.
T122 2671-2776 Sentence denotes However, the patient serum appeared to recognise also the E protein and the processed S1 and S2 proteins.
T123 2777-2921 Sentence denotes Although WB detects mainly linear epitopes, the strong antibody response against the S protein correlated well with the results of the MN assay.
T124 2922-3122 Sentence denotes Monitoring of the binding antibodies is suggested to be a more sensitive method than measuring functional neutralising antibodies for serological detection of human coronavirus (hCoV) infections [14].
T125 3123-3213 Sentence denotes However, hCoV OC43 and 229E samples can also cross-react with SARS-CoV ELISA testing [15].
T126 3214-3350 Sentence denotes The SARS-CoV-2 CPE-based MN test using live virus appeared to be very specific, while laborious to conduct requiring a BSL-3 laboratory.
T127 3351-3551 Sentence denotes An increase of at least 4-fold in the neutralising antibodies indicating a positive response was detected at Day 9–10 after the first symptoms and at Day 20, the antibody levels were still increasing.
T128 3552-3716 Sentence denotes Our findings indicate that the MN assay is specific for functional SARS-CoV-2 antibodies and could be applied in surveillance of population immunity for this virus.
T129 3717-3895 Sentence denotes The assay can be used as confirmatory tool for SARS-CoV-2 specificity in the development of more accessible diagnostic tools such as assays based on detecting binding antibodies.
T130 3896-4079 Sentence denotes Previous studies on patients with SARS-CoV infection indicated that the median time for seroconversion was 20 days, by which time 60–75% of patients had IgG against the virus [13,16].
T131 4080-4273 Sentence denotes That IgM and IgG antibodies were present within 2 weeks from the onset of symptoms in our study suggests that early convalescent patients may be suitable sources of therapeutic antibodies [17].
T132 4274-4521 Sentence denotes In accordance with our finding, a recent preprint report on patients admitted to hospital with confirmed SARS-CoV-2 infection in China indicated that the median time to seroconversion was 11–14 days, depending on the immunological assay used [18].
T133 4522-4667 Sentence denotes No neutralising SARS-CoV-2 antibodies were detected in the close contacts nor in the control population samples collected during 2019 in Finland.
T134 4668-4813 Sentence denotes A low prevalence (0.21%) of antibodies against Middle East respiratory syndrome coronavirus was reported in the general population of Qatar [19].
T135 4814-5063 Sentence denotes A meta-analysis of seroprevalence to SARS-CoV among different human populations yielded an overall low seroprevalence (0.10%), although it was slightly higher (0.23%) among healthcare workers and others who had close contact with SARS patients [20].
T136 5064-5150 Sentence denotes Binding and neutralising HCoV antibodies were found to be higher in older adults [14].
T137 5151-5412 Sentence denotes In total 97% and 99% of serum samples from healthy adults had antibodies to HCoV-229E and HCoV-OC43, respectively [21], and 75% and 65% of the children in the age group 2.5–3.5 years were found to be seropositive for, respectively, HCoV-NL63 and HCoV-229E [22].
T138 5413-5672 Sentence denotes While it has been suggested that the late seroconversion in most SARS patients reduces the value of serological assays during the incubation and initial phases of SARS [13], serological testing is suggested for the confirmation of a SARS CoV-2 infection [11].
T139 5673-5900 Sentence denotes After understanding better the kinetics, specificity and sensitivity of the assays in development, the serological testing may help contact tracing of clusters and have a role in diagnosing acute and past SARS-CoV-2 infections.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T6 276-285 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T7 287-297 Phenotype denotes runny nose http://purl.obolibrary.org/obo/HP_0031417
T8 299-305 Phenotype denotes nausea http://purl.obolibrary.org/obo/HP_0002018
T9 312-317 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T10 319-324 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T11 326-343 Phenotype denotes muscular weakness http://purl.obolibrary.org/obo/HP_0001324
T12 348-355 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378

2_test

Id Subject Object Predicate Lexical cue
32209163-32046819-29337502 136-137 32046819 denotes 7
32209163-29790939-29337503 1248-1249 29790939 denotes 9
32209163-32065057-29337504 1600-1602 32065057 denotes 11
32209163-32065057-29337505 1756-1758 32065057 denotes 11
32209163-32064855-29337506 1759-1761 32064855 denotes 12
32209163-32065057-29337507 1982-1984 32065057 denotes 11
32209163-15031782-29337508 2476-2478 15031782 denotes 13
32209163-32073157-29337509 3118-3120 32073157 denotes 14
32209163-15583332-29337510 3209-3211 15583332 denotes 15
32209163-15031782-29337511 4072-4074 15031782 denotes 13
32209163-12781535-29337512 4075-4077 12781535 denotes 16
32209163-30906787-29337513 4809-4811 30906787 denotes 19
32209163-16490123-29337514 5059-5061 16490123 denotes 20
32209163-32073157-29337515 5146-5148 32073157 denotes 14
32209163-15897988-29337516 5266-5268 15897988 denotes 21
32209163-18495857-29337517 5408-5410 18495857 denotes 22
32209163-15031782-29337518 5582-5584 15031782 denotes 13
32209163-32065057-29337519 5668-5670 32065057 denotes 11

MyTest

Id Subject Object Predicate Lexical cue
32209163-32046819-29337502 136-137 32046819 denotes 7
32209163-29790939-29337503 1248-1249 29790939 denotes 9
32209163-32065057-29337504 1600-1602 32065057 denotes 11
32209163-32065057-29337505 1756-1758 32065057 denotes 11
32209163-32064855-29337506 1759-1761 32064855 denotes 12
32209163-32065057-29337507 1982-1984 32065057 denotes 11
32209163-15031782-29337508 2476-2478 15031782 denotes 13
32209163-32073157-29337509 3118-3120 32073157 denotes 14
32209163-15583332-29337510 3209-3211 15583332 denotes 15
32209163-15031782-29337511 4072-4074 15031782 denotes 13
32209163-12781535-29337512 4075-4077 12781535 denotes 16
32209163-30906787-29337513 4809-4811 30906787 denotes 19
32209163-16490123-29337514 5059-5061 16490123 denotes 20
32209163-32073157-29337515 5146-5148 32073157 denotes 14
32209163-15897988-29337516 5266-5268 15897988 denotes 21
32209163-18495857-29337517 5408-5410 18495857 denotes 22
32209163-15031782-29337518 5582-5584 15031782 denotes 13
32209163-32065057-29337519 5668-5670 32065057 denotes 11