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PMC:7650537 / 20232-24156 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T134 402-407 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T135 654-657 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T136 759-762 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T137 855-858 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T138 1632-1637 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T139 1915-1918 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T140 2048-2051 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T141 2361-2364 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T142 2511-2519 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T143 2609-2612 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T144 2619-2627 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T145 3533-3536 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T11 402-407 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T12 1632-1637 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T101 38-46 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T102 480-488 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T103 525-533 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T104 920-928 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T105 1021-1030 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T106 1180-1188 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T107 1191-1200 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T108 1904-1912 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T109 2094-2103 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T110 2205-2213 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T111 2350-2358 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T112 2378-2386 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T113 2552-2560 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T114 2598-2606 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T115 3089-3097 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T116 3216-3228 Disease denotes common colds http://purl.obolibrary.org/obo/MONDO_0005709
T117 3337-3345 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T118 3449-3457 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T119 3522-3530 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T120 3807-3816 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T169 115-116 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T170 307-308 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T171 580-581 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T172 801-802 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T173 822-823 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T174 859-863 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T175 865-867 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T176 1125-1126 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T177 1156-1157 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T178 1432-1434 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T179 1786-1788 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T180 1793-1795 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T181 1793-1795 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T182 1814-1815 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 2118-2119 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T184 2628-2633 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T185 2696-2699 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T186 2794-2798 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T187 2988-2989 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T188 3153-3155 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T189 3250-3251 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T190 3619-3620 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T191 3758-3765 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T192 3783-3784 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T193 3796-3797 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T78 1793-1795 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T79 1959-1966 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T80 2166-2173 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T81 2563-2571 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T82 3400-3408 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T83 3468-3470 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T163 0-235 Sentence denotes With respect to the previous positive SARS-CoV-2 PCR result considered as the reference of first choice, following a recent suggestion [19], assay sensitivities were found to be relatively high and varied from 80.8% to 96.2% (Table 1).
T164 236-328 Sentence denotes This finding is in accordance to other studies [21,22,24,25,26] and to a meta-analysis [23].
T165 329-593 Sentence denotes Six (23.1%; five, 19.2%, if the positive retesting result of the initial serum from patient 4 is taken into account; for details, see below) of the 26 SARS-CoV-2-infected patients did not develop SARS-CoV-2-neutralizing antibodies, as demonstrated by a PRNT ≤1:10.
T166 594-786 Sentence denotes Among them were two individuals who were only recognized as IgG-positive in the Abbott and Virion-Serion assays and were partially reactive in the ViraChip® and the IgG immunoblots (Figure 1).
T167 787-869 Sentence denotes This confirms a previous report of a high sensitivity of the Abbott IgG test [27].
T168 870-1070 Sentence denotes The absence of neutralizing antibodies in several COVID-19 patients was also reported by others [28] and may be associated with the mild course of the infection mainly observed in outpatient patients.
T169 1071-1264 Sentence denotes However, since no clinical data were available to us, a severe underlying disease or a serious course of the SARS-CoV-2 infection cannot be ruled out in the individuals of our study collective.
T170 1265-1379 Sentence denotes Recently, presence of neutralizing antibodies was found to be associated with protection against reinfection [29].
T171 1380-1563 Sentence denotes If the PRNT was chosen as another reference (Figure S1), sensitivities varied from 88.9% to 96.3% (Table 1), which is largely comparable to the results obtained with the first method.
T172 1564-1797 Sentence denotes These sensitivities can be even higher, as retesting of the initial serum from patient 4 in the second part of our study revealed the presence of low-level neutralizing antibodies (1:10 vs. 1:20–1:40; Figure 5 and Figures S1 and S2).
T173 1798-1992 Sentence denotes With respect to a sample from patient 1 taken six days after the PCR, two S-based assays failed to detect SARS-CoV-2 IgG, while all assays that used the N as an epitope were reactive (Figure 1).
T174 1993-2104 Sentence denotes Thus, usage of the latter may lead to the detection of IgG/total antibodies at an earlier stage post-infection.
T175 2105-2263 Sentence denotes Furthermore, a lack of reactivity in some assays using the S antigen does not necessarily mean that SARS-CoV-2-neutralizing antibodies are missing (Figure 1).
T176 2264-2333 Sentence denotes Seroconversion was clearly demonstrated in three patients (Figure 1).
T177 2334-2466 Sentence denotes The majority of SARS-CoV-2 IgG in sera from SARS-CoV-2-infected patients were verified by both versions of an immunoblot (Figure 1).
T178 2467-2572 Sentence denotes The latter can be used to differentiate the antibody reactivities against individual SARS-CoV-2 antigens.
T179 2573-2743 Sentence denotes The specificities of the SARS-CoV-2 IgG/total antibody tests are at comparatively high levels between 96.0% and 100.0%, as has also been reported by others [21,22,24,26].
T180 2744-2952 Sentence denotes Interestingly, one sample collected in the winter 2018/2019 was found to be reactive in the Mikrogen, Roche, and Viramed assays, as well as in the prototype immunoblot, but could not be confirmed by the PRNT.
T181 2953-3157 Sentence denotes For all other 99 archived samples, a random pattern of rare, isolated reactivity was demonstrated, and none was confirmed as possessing SARS-CoV-2-neutralizing antibodies by PRNT (Figure 2 and Figure S1).
T182 3158-3266 Sentence denotes Potential cross-reactivity with the HCoVs responsible for common colds may therefore not be a major problem.
T183 3267-3472 Sentence denotes The analysis of the immunoblot results shows, however, that sera from SARS-CoV-2-infected patients may simultaneously react with the antigens from HCoVs 229E, HKU-1, NL63, OC43, and SARS-CoV-2 (Figure S3).
T184 3473-3663 Sentence denotes Due to the currently estimated low prevalence of SARS-CoV-2 IgG in the overall German population, even high specificities of 96–98% would produce a relevant number of false positive results.
T185 3664-3817 Sentence denotes Thus, such assays, which all show an accuracy over 93%, should be preferentially used for the testing of patients with a history of a probable infection.
T186 3818-3924 Sentence denotes In the case of doubt, the implementation of the labor-intensive and time-consuming PRNT may be considered.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
384 1951-1952 Gene denotes N Gene:43740575
385 2164-2165 Gene denotes S Gene:43740568
386 38-48 Species denotes SARS-CoV-2 Tax:2697049
387 413-420 Species denotes patient Tax:9606
388 500-508 Species denotes patients Tax:9606
389 929-937 Species denotes patients Tax:9606
390 1050-1060 Species denotes outpatient Tax:9606
391 1061-1069 Species denotes patients Tax:9606
392 1643-1650 Species denotes patient Tax:9606
393 1828-1835 Species denotes patient Tax:9606
394 2313-2321 Species denotes patients Tax:9606
395 2398-2406 Species denotes patients Tax:9606
396 3357-3365 Species denotes patients Tax:9606
397 3449-3459 Species denotes SARS-CoV-2 Tax:2697049
398 3769-3777 Species denotes patients Tax:9606
399 525-535 Species denotes SARS-CoV-2 Tax:2697049
400 1904-1914 Species denotes SARS-CoV-2 Tax:2697049
401 2205-2215 Species denotes SARS-CoV-2 Tax:2697049
402 2350-2360 Species denotes SARS-CoV-2 Tax:2697049
403 2552-2562 Species denotes SARS-CoV-2 Tax:2697049
404 2598-2608 Species denotes SARS-CoV-2 Tax:2697049
405 3089-3099 Species denotes SARS-CoV-2 Tax:2697049
406 3522-3532 Species denotes SARS-CoV-2 Tax:2697049
407 3194-3199 Chemical denotes HCoVs
408 480-499 Disease denotes SARS-CoV-2-infected MESH:C000657245
409 920-928 Disease denotes COVID-19 MESH:C000657245
410 1021-1030 Disease denotes infection MESH:D007239
411 1180-1200 Disease denotes SARS-CoV-2 infection MESH:C000657245
412 2094-2103 Disease denotes infection MESH:D007239
413 2378-2397 Disease denotes SARS-CoV-2-infected MESH:C000657245
414 3337-3356 Disease denotes SARS-CoV-2-infected MESH:C000657245
415 3807-3816 Disease denotes infection MESH:D007239