> top > docs > PMC:7288610 > annotations

PMC:7288610 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 443-448 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T2 988-993 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T3 1145-1150 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T4 1333-1338 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T5 1340-1345 Body_part denotes urine http://purl.org/sig/ont/fma/fma12274
T6 2114-2119 Body_part denotes mucus http://purl.org/sig/ont/fma/fma66938
T7 2942-2945 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T8 2950-2953 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T9 3339-3344 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T10 3406-3411 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T11 3782-3786 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T12 5024-5029 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088
T13 5086-5090 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T14 5430-5434 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 443-448 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T2 988-993 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T3 1145-1150 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T4 1333-1338 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T5 1340-1345 Body_part denotes urine http://purl.obolibrary.org/obo/UBERON_0001088
T6 2114-2119 Body_part denotes mucus http://purl.obolibrary.org/obo/UBERON_0000912
T7 3339-3344 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T8 3782-3786 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T9 3842-3858 Body_part denotes pleural effusion http://purl.obolibrary.org/obo/UBERON_0000175
T10 5024-5029 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948
T11 5086-5090 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T12 5430-5434 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2 40-48 Disease denotes COVID-19 MESH:C000657245
3 49-58 Disease denotes infection MESH:D007239
11 117-164 Species denotes Severe acute respiratory syndrome coronavirus 2 Tax:2697049
12 166-176 Species denotes SARS-CoV-2 Tax:2697049
13 218-242 Disease denotes coronavirus disease 2019 MESH:C000657245
14 244-252 Disease denotes COVID-19 MESH:C000657245
15 347-355 Disease denotes COVID-19 MESH:C000657245
16 397-432 Disease denotes acute respiratory distress syndrome MESH:D012128
17 437-460 Disease denotes multi-organ dysfunction MESH:D009102
20 565-573 Species denotes patients Tax:9606
21 553-561 Disease denotes COVID-19 MESH:C000657245
29 662-709 Species denotes Severe acute respiratory syndrome coronavirus 2 Tax:2697049
30 711-721 Species denotes SARS-CoV-2 Tax:2697049
31 763-787 Disease denotes coronavirus disease 2019 MESH:C000657245
32 789-797 Disease denotes COVID-19 MESH:C000657245
33 892-900 Disease denotes COVID-19 MESH:C000657245
34 942-977 Disease denotes acute respiratory distress syndrome MESH:D012128
35 982-1005 Disease denotes multi-organ dysfunction MESH:D009102
48 1442-1446 Gene denotes RdRP Gene:43740578
49 1216-1226 Species denotes SARS-CoV-2 Tax:2697049
50 1490-1500 Species denotes SARS-CoV-2 Tax:2697049
51 1711-1719 Species denotes patients Tax:9606
52 1792-1800 Species denotes patients Tax:9606
53 2050-2058 Species denotes patients Tax:9606
54 2321-2331 Species denotes SARS-CoV-2 Tax:2697049
55 1028-1036 Disease denotes COVID-19 MESH:C000657245
56 1100-1108 Disease denotes infected MESH:D007239
57 1783-1791 Disease denotes COVID-19 MESH:C000657245
58 1944-1953 Disease denotes infection MESH:D007239
59 2202-2210 Disease denotes COVID-19 MESH:C000657245
65 2419-2427 Species denotes patients Tax:9606
66 2581-2591 Species denotes SARS-CoV-2 Tax:2697049
67 2601-2608 Species denotes patient Tax:9606
68 2703-2710 Species denotes patient Tax:9606
69 2505-2513 Disease denotes COVID-19 MESH:C000657245
73 2812-2820 Species denotes patients Tax:9606
74 2976-2986 Species denotes SARS-CoV-2 Tax:2697049
75 2772-2780 Disease denotes COVID-19 MESH:C000657245
83 3109-3117 Species denotes patients Tax:9606
84 3305-3313 Species denotes patients Tax:9606
85 3976-3984 Species denotes patients Tax:9606
86 3822-3837 Disease denotes Lymphadenopathy MESH:D008206
87 3842-3858 Disease denotes pleural effusion MESH:D010996
88 3967-3975 Disease denotes COVID-19 MESH:C000657245
89 4027-4035 Disease denotes COVID-19 MESH:C000657245
121 4083-4093 Species denotes SARS-CoV-2 Tax:2697049
122 4182-4192 Species denotes SARS-CoV-2 Tax:2697049
123 4247-4255 Species denotes patients Tax:9606
124 4312-4320 Species denotes patients Tax:9606
125 4338-4346 Species denotes patients Tax:9606
126 4381-4388 Species denotes patient Tax:9606
127 4434-4442 Species denotes patients Tax:9606
128 4488-4504 Species denotes Candida albicans Tax:5476
129 4510-4518 Species denotes patients Tax:9606
130 4537-4559 Species denotes Pneumocystis jirovecii Tax:42068
131 4565-4572 Species denotes patient Tax:9606
132 4590-4606 Species denotes Candida glabrata Tax:5478
133 4612-4619 Species denotes patient Tax:9606
134 4641-4665 Species denotes Streptococcus pneumoniae Tax:1313
135 4671-4679 Species denotes patients Tax:9606
136 4698-4724 Species denotes Staphylococcus epidermidis Tax:1282
137 4730-4737 Species denotes patient Tax:9606
138 4755-4776 Species denotes Klebsiella pneumoniae Tax:573
139 4785-4792 Species denotes patient Tax:9606
140 4810-4830 Species denotes Enterococcus faecium Tax:1352
141 4872-4880 Species denotes patients Tax:9606
142 4906-4914 Species denotes patients Tax:9606
143 4975-4983 Species denotes patients Tax:9606
144 5047-5055 Species denotes patients Tax:9606
145 5106-5114 Species denotes patients Tax:9606
146 5212-5220 Species denotes patients Tax:9606
147 5165-5172 Species denotes patient Tax:9606
148 4856-4865 Disease denotes pneumonia MESH:D011014
149 5024-5037 Disease denotes heart failure MESH:D006333
150 5073-5098 Disease denotes interstitial lung disease MESH:D017563
151 5122-5157 Disease denotes acute respiratory distress syndrome MESH:D012128
154 5346-5354 Disease denotes COVID-19 MESH:C000657245
155 5393-5402 Disease denotes infection MESH:D007239
159 5784-5792 Species denotes patients Tax:9606
160 6067-6075 Species denotes patients Tax:9606
161 5766-5774 Disease denotes COVID-19 MESH:C000657245
163 6431-6439 Species denotes patients Tax:9606
165 6727-6735 Species denotes patients Tax:9606
168 6978-6986 Species denotes patients Tax:9606
169 6944-6964 Disease denotes SARS-CoV-2 infection MESH:C000657245
171 7109-7129 Disease denotes SARS-CoV-2 infection MESH:C000657245
173 8758-8761 Gene denotes Tor Gene:6097

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 40-48 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 49-58 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T3 96-104 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 105-114 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T5 117-164 Disease denotes Severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T6 166-174 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 218-242 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T8 244-252 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 347-355 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 397-432 Disease denotes acute respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0006502
T11 403-432 Disease denotes respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0009971
T12 553-561 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 662-709 Disease denotes Severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T14 711-719 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 763-787 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T16 789-797 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 892-900 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 942-977 Disease denotes acute respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0006502
T19 948-977 Disease denotes respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0009971
T20 1028-1036 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 1216-1224 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 1490-1498 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 1783-1791 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 1944-1953 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T25 2202-2210 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 2321-2329 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 2505-2513 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T28 2581-2589 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 2772-2780 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T30 2976-2984 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 3822-3837 Disease denotes Lymphadenopathy http://purl.obolibrary.org/obo/MONDO_0005833
T32 3967-3975 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T33 4027-4035 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T34 4083-4091 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 4182-4190 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 4537-4549 Disease denotes Pneumocystis http://purl.obolibrary.org/obo/MONDO_0019121
T37 4590-4606 Disease denotes Candida glabrata http://purl.obolibrary.org/obo/MONDO_0022636
T38 4641-4665 Disease denotes Streptococcus pneumoniae http://purl.obolibrary.org/obo/MONDO_0005972
T39 4755-4776 Disease denotes Klebsiella pneumoniae http://purl.obolibrary.org/obo/MONDO_0030602
T40 4856-4865 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T41 5024-5037 Disease denotes heart failure http://purl.obolibrary.org/obo/MONDO_0005252
T42 5073-5098 Disease denotes interstitial lung disease http://purl.obolibrary.org/obo/MONDO_0015925
T43 5086-5098 Disease denotes lung disease http://purl.obolibrary.org/obo/MONDO_0005275
T44 5122-5157 Disease denotes acute respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0006502
T45 5128-5157 Disease denotes respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0009971
T46 5346-5354 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 5393-5402 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T48 5766-5774 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T49 6944-6952 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 6955-6964 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T51 7109-7117 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 7120-7129 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 268-273 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T2 443-448 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T3 813-818 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T4 988-993 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T5 1145-1150 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T6 1183-1184 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 1207-1211 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T8 1310-1312 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T9 1455-1460 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T10 1523-1525 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T11 1577-1580 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T12 2277-2279 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T13 2301-2307 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T14 2472-2473 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 2579-2580 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 2616-2617 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 2770-2771 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 2886-2888 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T19 3145-3149 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T20 3145-3149 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T21 3157-3163 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T22 3324-3325 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 3339-3344 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T24 3406-3411 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T25 3449-3450 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 3533-3534 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 3593-3594 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 3782-3786 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T29 3782-3786 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T30 3842-3858 http://purl.obolibrary.org/obo/UBERON_0000175 denotes pleural effusion
T31 4231-4236 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T32 4869-4871 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T33 4903-4905 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T34 4972-4974 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T35 5024-5029 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T36 5024-5029 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T37 5024-5029 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T38 5024-5029 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T39 5086-5090 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T40 5086-5090 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T41 5369-5370 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 5452-5455 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T43 5456-5457 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 5719-5720 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 5937-5939 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T46 5959-5964 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T47 6031-6033 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T48 6285-6292 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T49 6898-6899 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 7505-7506 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T51 7764-7765 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T52 8070-8071 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T53 8169-8172 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T54 8227-8230 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T55 8285-8288 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T56 8346-8349 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T57 8393-8394 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T58 8405-8408 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T59 8464-8467 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T60 8525-8528 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T61 8584-8587 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T62 8643-8646 http://purl.obolibrary.org/obo/CLO_0051582 denotes has

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 1194-1206 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T2 1202-1206 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T3 1310-1312 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T6 1523-1525 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T9 2277-2279 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T12 2886-2888 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T15 3015-3018 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T16 3145-3149 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T17 3292-3295 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T18 3394-3398 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695
T19 5937-5939 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T22 6031-6033 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 1402-1415 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T2 1402-1415 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T3 1442-1446 http://purl.obolibrary.org/obo/GO_0003968 denotes RdRP

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-59 Sentence denotes Does bronchoscopy help the diagnosis in COVID-19 infection?
T2 60-115 Sentence denotes Does bronchoscopy help diagnosis in COVID-19 infection?
T3 117-263 Sentence denotes Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent responsible for the recent coronavirus disease 2019 (COVID-19) pandemic.
T4 264-321 Sentence denotes The virus is predominantly spread through large droplets.
T5 322-465 Sentence denotes The clinical features of COVID-19 are varied, ranging from asymptomatic to acute respiratory distress syndrome and multi-organ dysfunction [1].
T6 467-645 Sentence denotes This study evaluates the real value of using bronchoscopy to exclude the diagnosis of COVID-19 in patients with multiple negative nasal/oropharyngeal swabs https://bit.ly/2zmSgE8
T7 647-661 Sentence denotes To the Editor:
T8 662-808 Sentence denotes Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent responsible for the recent coronavirus disease 2019 (COVID-19) pandemic.
T9 809-866 Sentence denotes The virus is predominantly spread through large droplets.
T10 867-1010 Sentence denotes The clinical features of COVID-19 are varied, ranging from asymptomatic to acute respiratory distress syndrome and multi-organ dysfunction [1].
T11 1011-1393 Sentence denotes The diagnosis of COVID-19 is mainly based on typical symptoms, history of exposure to an infected person and bilateral involvement on chest radiographs; it is confirmed by a positive nucleic acid test for SARS-CoV-2 from numerous types of specimens, including oropharyngeal (OP) and nasopharyngeal (NP) swabs, anal swabs, stool, urine and bronchoalveolar lavage fluid (BALF) [1, 2].
T12 1394-1515 Sentence denotes Reverse transcriptase (RT)-PCR that targets the RdRP, N or E genes is the most common method of SARS-CoV-2 detection [3].
T13 1516-1724 Sentence denotes OP and NP swabs are the most frequently used samples, but it has been demonstrated that their sensitivity is limited, at 32% and 63% respectively, while BALF is reported to be positive in 93% of patients [4].
T14 1725-1817 Sentence denotes However, the role of bronchoscopy in ruling out suspected COVID-19 patients is under debate.
T15 1818-2000 Sentence denotes According to several guidelines, bronchoscopy is relatively contraindicated, mainly because of its high risk of spreading the infection to the staff involved in the procedure [5, 6].
T16 2001-2232 Sentence denotes It is primarily recommended in immunocompromised patients, if there is the strong suspicion of superinfection or mucus plugging, or in life-saving conditions, and it is not strictly recommended in the COVID-19 diagnostic algorithm.
T17 2233-2371 Sentence denotes Nevertheless, some cases of negative OP and NP swabs, in which BALF tested positive for SARS-CoV-2 with RT-PCR, have been reported [7, 8].
T18 2372-2514 Sentence denotes There are two main problems with negative-swab patients who have computed tomography (CT) scans and a clinical picture suggestive of COVID-19.
T19 2515-2647 Sentence denotes First, according to the sensitivity of the swabs, misdiagnosing a SARS-CoV-2-positive patient may be a great risk for public health.
T20 2648-2733 Sentence denotes Secondly, an alternative diagnosis may be required for patient-appropriate treatment.
T21 2734-3050 Sentence denotes Here, we report our experience from a COVID-19 hospital in Rome, Italy, where patients with typical symptoms of the disease, suggestive CT scans, three NP/OP-negative swabs performed on consecutive days, and IgG and IgM serology negative for SARS-CoV-2 underwent bronchoscopy with BAL to define the diagnostic issue.
T22 3051-3296 Sentence denotes In the period between March 13th and April 30th, 2020, 28 patients (mean±sd age 65±16 yrs, 16 male and 12 female) with the described characteristics, discussed by the multidisciplinary clinical–radiological team, underwent bronchoscopy with BAL.
T23 3297-3469 Sentence denotes All the patients performed a non-enhanced chest CT scan in supine position, from the apex to the base of the lungs during inspiratory breath-hold, with a 128-slice scanner.
T24 3470-3552 Sentence denotes Two radiologists independently evaluated the axial images with a visual score [9].
T25 3553-3821 Sentence denotes CT manifestations were characterised by a predominant ground-glass pattern (68%) mixed with consolidations (32%), mainly peripheral (26%) or combined peripheral and central distributions (72%), with the bilateral (83%) and lower lung zones (93%) being mostly involved.
T26 3822-3905 Sentence denotes Lymphadenopathy and pleural effusion were rarely founded (0% and 4%, respectively).
T27 3906-4060 Sentence denotes According to several recent reports regarding CT findings in COVID-19 patients [10–12], these results were suggestive of COVID-19 in all considered cases.
T28 4061-4153 Sentence denotes BALF was analysed for SARS-CoV-2 using RT-PCR and for routinely microbiological examination.
T29 4154-4256 Sentence denotes In the BALF, the RT-PCR for SARS-CoV-2 was negative for all three detectable genes in all 28 patients.
T30 4257-4321 Sentence denotes Microbiological examination was negative in 15 (53.6%) patients.
T31 4322-4831 Sentence denotes Of the other 13 patients, six had galactomannans >0.8, one patient had galactomannans between 0.5 and 0.8, four patients were positive at microbiological culture for Candida albicans, two patients were positive for Pneumocystis jirovecii, one patient was positive for Candida glabrata, one patient was positive for for Streptococcus pneumoniae, two patients were positive for Staphylococcus epidermidis, one patient was positive for Klebsiella pneumoniae and one patient was positive for Enterococcus faecium.
T32 4832-5173 Sentence denotes The final diagnosis was pneumonia in 22 patients (no specific agent in 11 patients, five of which were immunocompromised; specific agent in 11 patients, four of which were immunocompromised), heart failure in three patients, exacerbation of interstitial lung disease in two patients and an acute respiratory distress syndrome in one patient.
T33 5174-5263 Sentence denotes Antibiotic therapy was modified in 13 patients according to the microbiological findings.
T34 5264-5416 Sentence denotes In these pandemic times, the low sensitivity of RT-PCR can miss many diagnoses of COVID-19, representing a far too high risk for infection transmission.
T35 5417-5633 Sentence denotes On the other hand, even if CT scan has a higher sensitivity (97%), its lower specificity (25%) [2] makes alternative diagnoses more likely and bronchoscopy with BALF is the recommend procedure to rule out any doubts.
T36 5634-5875 Sentence denotes Our findings suggest that three negative swabs performed on three different days and a negative serology are sufficient to rule out COVID-19, even in patients with highly suggestive CT scans and clinical features compatible with the disease.
T37 5876-6040 Sentence denotes In contrast with other reports [7, 8], we performed three OP/NP swabs and serology tests before performing the bronchoscopy, instead of just one or two OP/NP swabs.
T38 6041-6238 Sentence denotes This allowed us to detect patients who had positive results at the third swab or at serology, avoiding unnecessary procedures, and therefore reducing the risk of transmission to healthcare workers.
T39 6239-6352 Sentence denotes Bronchoscopies were performed with disposable devices and with the recommended personal protective equipment [6].
T40 6353-6663 Sentence denotes Even if our results are very reassuring about the safety of this procedure in patients with three negative swabs and negative serology, the risk to the staff still remains high and we strongly suggest that all of the recommended precautions are maintained to minimise the risk of possible disease transmission.
T41 6664-6791 Sentence denotes Interestingly, BALF was positive for other pathogens in 46% of patients, reinforcing its role in finding alternative diagnoses.
T42 6792-7052 Sentence denotes In conclusion, our findings demonstrate that three negative swabs along with negative antibodies, despite a suggestive CT scan, can safely rule out the SARS-CoV-2 infection in suspected patients, hence allowing commencement of an alternative diagnosis process.
T43 7053-7198 Sentence denotes Bronchoscopy should not be used for the confirmation of SARS-CoV-2 infection alone, but it can be very useful in resolving diagnostic complexity.
T44 7200-7213 Sentence denotes Shareable PDF
T45 7214-7260 Sentence denotes This one-page PDF can be shared freely online.
T46 7261-7299 Sentence denotes Shareable PDF ERJ-01619-2020.Shareable
T47 7301-7323 Sentence denotes Supplementary Material
T48 7324-7352 Sentence denotes ERJ-01619-2020.Shareable.pdf
T49 7354-7374 Sentence denotes Author contribution:
T50 7375-7460 Sentence denotes Drafting the article or revising it critically for important intellectual content: J.
T51 7461-7468 Sentence denotes Ora, E.
T52 7469-7480 Sentence denotes Puxeddu, F.
T53 7481-7494 Sentence denotes Cavalli, F.M.
T54 7495-7507 Sentence denotes Giorgino, A.
T55 7508-7520 Sentence denotes Girolami, M.
T56 7521-7533 Sentence denotes Chiocchi, G.
T57 7534-7548 Sentence denotes Sergiacomi, M.
T58 7549-7564 Sentence denotes Federici and P.
T59 7565-7574 Sentence denotes Rogliani.
T60 7575-7641 Sentence denotes Visual scoring was performed independently by two radiologists: G.
T61 7642-7659 Sentence denotes Sergiacomi and M.
T62 7660-7669 Sentence denotes Chiocchi.
T63 7670-7719 Sentence denotes Final approval of the version to be published: J.
T64 7720-7727 Sentence denotes Ora, E.
T65 7728-7739 Sentence denotes Puxeddu, F.
T66 7740-7753 Sentence denotes Cavalli, F.M.
T67 7754-7766 Sentence denotes Giorgino, A.
T68 7767-7779 Sentence denotes Girolami, M.
T69 7780-7792 Sentence denotes Chiocchi, G.
T70 7793-7807 Sentence denotes Sergiacomi, M.
T71 7808-7823 Sentence denotes Federici and P.
T72 7824-7833 Sentence denotes Rogliani.
T73 7834-8025 Sentence denotes Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved: J.
T74 8026-8033 Sentence denotes Ora, E.
T75 8034-8045 Sentence denotes Puxeddu, F.
T76 8046-8059 Sentence denotes Cavalli, F.M.
T77 8060-8072 Sentence denotes Giorgino, A.
T78 8073-8085 Sentence denotes Girolami, M.
T79 8086-8098 Sentence denotes Chiocchi, G.
T80 8099-8113 Sentence denotes Sergiacomi, M.
T81 8114-8129 Sentence denotes Federici and P.
T82 8130-8139 Sentence denotes Rogliani.
T83 8140-8164 Sentence denotes Conflict of interest: J.
T84 8165-8193 Sentence denotes Ora has nothing to disclose.
T85 8194-8218 Sentence denotes Conflict of interest: E.
T86 8219-8251 Sentence denotes Puxeddu has nothing to disclose.
T87 8252-8276 Sentence denotes Conflict of interest: F.
T88 8277-8309 Sentence denotes Cavalli has nothing to disclose.
T89 8310-8336 Sentence denotes Conflict of interest: F.M.
T90 8337-8370 Sentence denotes Giorgino has nothing to disclose.
T91 8371-8395 Sentence denotes Conflict of interest: A.
T92 8396-8429 Sentence denotes Girolami has nothing to disclose.
T93 8430-8454 Sentence denotes Conflict of interest: M.
T94 8455-8488 Sentence denotes Chiocchi has nothing to disclose.
T95 8489-8513 Sentence denotes Conflict of interest: G.
T96 8514-8549 Sentence denotes Sergiacomi has nothing to disclose.
T97 8550-8574 Sentence denotes Conflict of interest: M.
T98 8575-8608 Sentence denotes Federici has nothing to disclose.
T99 8609-8633 Sentence denotes Conflict of interest: P.
T100 8634-8667 Sentence denotes Rogliani has nothing to disclose.
T101 8668-8686 Sentence denotes Support statement:
T102 8687-8785 Sentence denotes This study was supported by institutional funding (University of Rome “Tor Vergata”, Rome, Italy).

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 403-423 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T2 948-968 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T3 3822-3837 Phenotype denotes Lymphadenopathy http://purl.obolibrary.org/obo/HP_0002716
T4 3842-3858 Phenotype denotes pleural effusion http://purl.obolibrary.org/obo/HP_0002202
T5 4655-4665 Phenotype denotes pneumoniae http://purl.obolibrary.org/obo/HP_0002090
T6 4766-4776 Phenotype denotes pneumoniae http://purl.obolibrary.org/obo/HP_0002090
T7 4856-4865 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T8 5024-5037 Phenotype denotes heart failure http://purl.obolibrary.org/obo/HP_0001635
T9 5073-5098 Phenotype denotes interstitial lung disease http://purl.obolibrary.org/obo/HP_0006530
T10 5128-5148 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098