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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
25 502-549 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
26 551-561 Species denotes SARS-CoV-2 Tax:2697049
27 33-42 Species denotes influenza Tax:11309
28 150-159 Species denotes influenza Tax:11309
29 701-710 Species denotes influenza Tax:11309
30 68-96 Disease denotes acute respiratory infections MESH:D012120
31 724-743 Disease denotes coronavirus disease MESH:D018352
32 745-753 Disease denotes COVID-19 MESH:C000657245
33 895-903 Disease denotes COVID-19 MESH:C000657245
35 931-940 Species denotes influenza Tax:11309
51 1278-1284 Species denotes people Tax:9606
52 1454-1469 Species denotes Influenza virus Tax:11309
53 1488-1515 Species denotes respiratory syncytial virus Tax:12814
54 1517-1533 Species denotes human rhinovirus Tax:169066
55 1538-1559 Species denotes human metapneumovirus Tax:162145
56 1590-1600 Species denotes SARS-CoV-2 Tax:2697049
57 1763-1773 Species denotes SARS-CoV-2 Tax:2697049
58 1859-1867 Species denotes patients Tax:9606
59 1882-1890 Species denotes patients Tax:9606
60 1941-1951 Species denotes SARS-CoV-2 Tax:2697049
61 1083-1098 Disease denotes fever of sudden MESH:D005334
62 1120-1137 Disease denotes respiratory signs MESH:D012818
63 1139-1144 Disease denotes cough MESH:D003371
64 1164-1171 Disease denotes myalgia MESH:D063806
65 1234-1251 Disease denotes respiratory signs MESH:D012818
70 2644-2647 Gene denotes CrI
71 2027-2034 Species denotes patient Tax:9606
72 2217-2226 Species denotes influenza Tax:11309
73 2513-2522 Species denotes influenza Tax:11309
75 2944-2953 Species denotes influenza Tax:11309
79 3263-3272 Species denotes influenza Tax:11309
80 3118-3121 Disease denotes ARA
81 3216-3219 Disease denotes HDF
85 3589-3597 Disease denotes COVID-19 MESH:C000657245
86 3735-3743 Disease denotes COVID-19 MESH:C000657245
87 4126-4129 Disease denotes HDF
92 5023-5068 Gene denotes Nouvelle Aquitaine (NAQ) −3 (−110 to 32) −9
93 4482-4490 Disease denotes COVID-19 MESH:C000657245
94 4590-4593 Disease denotes ARA
95 4903-4906 Disease denotes HDF
98 4324-4343 Disease denotes coronavirus disease MESH:D018352
99 4345-4353 Disease denotes COVID-19 MESH:C000657245
101 5718-5726 Disease denotes COVID-19 MESH:C000657245
105 6116-6125 Species denotes influenza Tax:11309
106 6334-6343 Species denotes influenza Tax:11309
107 6398-6406 Disease denotes COVID-19 MESH:C000657245
112 6431-6435 Species denotes H1N1 Tax:114727
113 6418-6427 Species denotes Influenza Tax:11309
114 6446-6455 Species denotes influenza Tax:11309
115 6791-6800 Species denotes influenza Tax:11309
120 6973-6981 Species denotes patients Tax:9606
121 7304-7315 Species denotes coronavirus Tax:11118
122 6906-6914 Disease denotes COVID-19 MESH:C000657245
123 7521-7529 Disease denotes COVID-19 MESH:C000657245
131 7711-7721 Species denotes SARS-CoV-2 Tax:2697049
132 7744-7752 Species denotes patients Tax:9606
133 7604-7613 Species denotes influenza Tax:11309
134 7591-7599 Disease denotes COVID-19 MESH:C000657245
135 7679-7687 Disease denotes COVID-19 MESH:C000657245
136 8109-8112 Disease denotes HDF
137 8191-8199 Disease denotes COVID-19 MESH:C000657245
142 8240-8248 Disease denotes COVID-19 MESH:C000657245
143 8441-8449 Disease denotes COVID-19 MESH:C000657245
144 8755-8758 Disease denotes HDF
145 8797-8805 Disease denotes COVID-19 MESH:C000657245
147 9065-9075 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1154-1158 Body_part denotes nose http://purl.org/sig/ont/fma/fma46472

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1154-1158 Body_part denotes nose http://purl.obolibrary.org/obo/UBERON_0000004

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T8 33-42 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T9 74-96 Disease denotes respiratory infections http://purl.obolibrary.org/obo/MONDO_0024355
T10 150-159 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T11 502-549 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T12 502-535 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T13 551-559 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 701-710 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T15 745-753 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 895-903 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 931-940 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T18 1454-1463 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T19 1590-1598 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 1763-1771 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 1941-1949 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 2217-2226 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T23 2513-2522 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T24 2944-2953 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T25 3145-3148 Disease denotes BRE http://purl.obolibrary.org/obo/MONDO_0007295
T26 3238-3241 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T27 3263-3272 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T28 3589-3597 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T29 3735-3743 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T30 4071-4074 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T31 4345-4353 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T32 4482-4490 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T33 4649-4652 Disease denotes BRE http://purl.obolibrary.org/obo/MONDO_0007295
T34 4970-4973 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T35 5718-5726 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T36 6116-6125 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T37 6334-6343 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T38 6398-6406 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T39 6418-6436 Disease denotes Influenza A (H1N1) http://purl.obolibrary.org/obo/MONDO_0005460
T40 6446-6455 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T41 6791-6800 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T42 6906-6914 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T43 7521-7529 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 7591-7599 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T45 7604-7613 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T46 7679-7687 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 7711-7719 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 8099-8102 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T49 8191-8199 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T50 8240-8248 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 8441-8449 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T52 8704-8707 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T53 8797-8805 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T54 9065-9073 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T4 336-337 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 482-488 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T6 1154-1158 http://www.ebi.ac.uk/efo/EFO_0000828 denotes nose
T7 1175-1176 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1464-1469 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T9 1510-1515 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T10 1517-1522 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T11 1538-1543 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T12 1661-1668 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T13 1743-1749 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T14 2044-2045 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 2186-2187 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 2421-2423 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T17 2458-2459 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 2504-2505 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 2804-2806 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T20 2995-2997 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T21 3172-3175 http://purl.obolibrary.org/obo/CLO_0037067 denotes Val
T22 4616-4618 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T23 4703-4706 http://purl.obolibrary.org/obo/CLO_0037067 denotes Val
T24 4781-4783 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T25 4919-4921 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T26 4942-4944 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T27 4946-4949 http://purl.obolibrary.org/obo/CLO_0001003 denotes 163
T28 5009-5011 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T29 5191-5193 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T30 5253-5255 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T31 5268-5270 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T32 5287-5289 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T33 5355-5356 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 5522-5523 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 5599-5602 http://purl.obolibrary.org/obo/CLO_0001195 denotes 219
T36 5754-5755 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 6428-6429 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T38 6456-6457 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T39 6458-6465 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T40 6542-6543 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T41 6544-6549 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T42 6574-6575 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 6604-6605 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 6821-6824 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T45 7066-7067 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 7214-7215 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 7336-7337 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 7432-7433 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 8328-8329 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 8475-8476 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 8506-8512 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T52 8631-8632 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 9026-9027 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 98-101 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T2 971-974 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T3 1205-1208 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T4 1403-1406 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T5 1878-1881 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T6 3118-3121 Chemical denotes ARA http://purl.obolibrary.org/obo/CHEBI_15843
T7 3172-3175 Chemical denotes Val http://purl.obolibrary.org/obo/CHEBI_16414|http://purl.obolibrary.org/obo/CHEBI_30015
T9 3243-3246 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T11 3362-3365 Chemical denotes PDL http://purl.obolibrary.org/obo/CHEBI_53413|http://purl.obolibrary.org/obo/CHEBI_61489
T13 4056-4059 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T15 4590-4593 Chemical denotes ARA http://purl.obolibrary.org/obo/CHEBI_15843
T16 4703-4706 Chemical denotes Val http://purl.obolibrary.org/obo/CHEBI_16414|http://purl.obolibrary.org/obo/CHEBI_30015
T18 4955-4958 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T20 5169-5172 Chemical denotes PDL http://purl.obolibrary.org/obo/CHEBI_53413|http://purl.obolibrary.org/obo/CHEBI_61489
T22 5416-5419 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T23 5610-5613 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T24 5771-5774 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T25 5829-5832 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T26 7216-7218 Chemical denotes GP http://purl.obolibrary.org/obo/CHEBI_70744
T27 8820-8823 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 3833-3839 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T2 3954-3960 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T3 5905-5915 http://purl.obolibrary.org/obo/GO_0009056 denotes break down
T4 6373-6382 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviour
T5 6960-6969 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviour
T6 7965-7971 http://purl.obolibrary.org/obo/GO_0040007 denotes growth

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T6 0-137 Sentence denotes The Sentinelles network monitors influenza-like illnesses (ILI) and acute respiratory infections (ARI) in general practice in France [1].
T7 138-281 Sentence denotes The 2019/20 influenza epidemic reached its peak in mid-February in France [2] and it was expected that ILI incidence would decrease thereafter.
T8 282-384 Sentence denotes However, in the first week of March 2020, we observed a renewed increase in ILI cases in some regions.
T9 385-563 Sentence denotes Several nasopharyngeal swabs collected in that period by Sentinelles general practitioners (GPs) tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
T10 564-720 Sentence denotes Here, we quantified the number of consultations for ILI in France in early March 2020 in excess of what was expected to be caused by the influenza epidemic.
T11 721-904 Sentence denotes As coronavirus disease (COVID-19) cases were first identified in France at the end of January 2020 [3] we examined the relationship between ILI reports and reported cases of COVID-19.
T12 906-953 Sentence denotes Sentinelles reporting of influenza-like illness
T13 954-1051 Sentence denotes Cases of ILI and ARI are reported in real time by participating GPs (ca 600 GPs) all over France.
T14 1052-1195 Sentence denotes The case definition for ILI is fever of sudden onset (> 39 °C) with respiratory signs (cough, running nose) and myalgia in a person of any age.
T15 1196-1317 Sentence denotes Cases of ARI include any disease with respiratory signs and are only monitored in people older than 65 years, unlike ILI.
T16 1318-1453 Sentence denotes In addition, Sentinelles GPs take nasopharyngeal swabs in one ILI case and up to two ARI cases per week for viral characterisation [4].
T17 1454-1639 Sentence denotes Influenza virus (see Supplement), respiratory syncytial virus, human rhinovirus and human metapneumovirus are routinely looked for, and SARS-CoV-2 was added at the end of February 2020.
T18 1640-1774 Sentence denotes In the first week of testing, week 9 (the week starting 24 February 2020), none of 119 submitted swabs tested positive for SARS-CoV-2.
T19 1775-1952 Sentence denotes In week 10 of 2020 (the week starting 2 March 2020), 93 swabs were collected in ILI patients and 23 in ARI patients, and two swabs in each category were positive for SARS-CoV-2.
T20 1953-2105 Sentence denotes For ILI, one of the two positive ILI cases had been collected because the patient reported a direct link with an existing cluster in the east of France.
T21 2106-2272 Sentence denotes We computed the expected number of ILI consultations using the superposition of a seasonal [5] and an epidemic influenza component [6], as detailed in the Supplement.
T22 2273-2362 Sentence denotes Excess cases were computed as the difference between observed cases and expected numbers.
T23 2363-2561 Sentence denotes This modelling approach allowed computing excess cases in 11 of 13 regions but did not provide a good fit in the remaining two regions where a marked influenza peak was not present (see Supplement).
T24 2562-2731 Sentence denotes The overall ILI incidence showed renewed increase with 33 (95% credible interval (CrI): −8 to 64) consultations per 100,000 in excess during week 9 and with 84 (95% CrI:
T25 2732-2791 Sentence denotes 447 to 108) consultations per 100,000 in excess in week 10.
T26 2792-2907 Sentence denotes Four of the 11 regions displayed positive excess (CrI excluding 0) in week 9 and seven regions in week 10 (Figure).
T27 2908-3117 Sentence denotes Figure Number of consultations for influenza-like illness (per 100,000) in France and 11 French regions, with expected number of consultations fitted on the first eight weeks, week 1–10, 2020 (n = 11 regions)
T28 3118-3122 Sentence denotes ARA:
T29 3123-3149 Sentence denotes Auvergne-Rhone-Alpes; BRE:
T30 3150-3164 Sentence denotes Brittany; CVL:
T31 3165-3190 Sentence denotes Centre-Val de Loire; COR:
T32 3191-3204 Sentence denotes Corsica; GRE:
T33 3205-3220 Sentence denotes Grand-Est; HDF:
T34 3221-3242 Sentence denotes Hauts de France; IDF:
T35 3243-3291 Sentence denotes Ile de France; ILI: influenza-like illness; NAQ:
T36 3292-3316 Sentence denotes Nouvelle Aquitaine; OCC:
T37 3317-3333 Sentence denotes Occitanie; PACA:
T38 3334-3366 Sentence denotes Provence-Alpes-Cote d’Azur; PDL:
T39 3367-3384 Sentence denotes Pays de la Loire.
T40 3385-3487 Sentence denotes Blue: excess consultations, computed by difference between observations (squares) and expected counts.
T41 3488-3578 Sentence denotes Green: expected number of consultations fitted on the first eight weeks of 2020 (circles).
T42 3579-3667 Sentence denotes Confirmed COVID-19 case counts were obtained from the Santé Publique France website [7].
T43 3668-3811 Sentence denotes The number of excess cases correlated with the cumulated number of COVID-19 cases reported in the same regions (r = 0.59; p < 0.05) in week 10.
T44 3812-3992 Sentence denotes Assuming exponential growth (typical of early epidemics) from week 8 to 10, 2020, we found that the excess number of cases had an exponential growth rate per week of 0.69 (95% CrI:
T45 3993-4038 Sentence denotes 0.55–0.86) in Grand-Est (GRE), 0.67 (95% CrI:
T46 4039-4091 Sentence denotes 0.55 to 0.83) in Ile de France (IDF), 0.68 (95% CrI:
T47 4092-4146 Sentence denotes 0.56 to 0.83) in Hauts de France (HDF), 0.61 (95% CrI:
T48 4147-4238 Sentence denotes 0.48 to 0.75) in Occitanie (OCC) and 0.56 (95% CrI: −1.6 to 0.8) in France overall (Table).
T49 4239-4429 Sentence denotes Table Excess consultations per 100,000 by region and cumulative number of confirmed coronavirus disease (COVID-19) cases in the corresponding weeks, France, week 9–10, 2020 (n = 11 regions)
T50 4430-4534 Sentence denotes Region Consultations in excess/100,000) Confirmed COVID-19 cases (cumulative) Population(in millions)
T51 4535-4567 Sentence denotes Week 9 Week 10 Week 9 Week 10
T52 4568-4638 Sentence denotes Auvergne-Rhone-Alpes (ARA) 82 (17 to147) 115 (36 to 174) 28 146 8
T53 4639-4695 Sentence denotes Brittany (BRE) 9 (−32 to 44) 40 (−7 to 73) 5 59 3.3
T54 4696-4765 Sentence denotes Centre-Val de Loire (CVL) 72 (43 to 96) 117 (97 to 130) 0 17 2.6
T55 4766-4820 Sentence denotes Corsica (COR) 35 (32 to 37) 21 (20 to 23) 0 5 0.3
T56 4821-4885 Sentence denotes Grand-Est (GRE) −55 (−109 to −13) 107 (56 to 138) 5 259 5.5
T57 4886-4954 Sentence denotes Hauts de France (HDF) 51 (−3 to 94) 172 (111 to 208) 34 163 6.0
T58 4955-5022 Sentence denotes Ile de France (IDF) 40 (32 to 46) 107 (103 ti 110) 18 191 12.3
T59 5023-5092 Sentence denotes Nouvelle Aquitaine (NAQ) −3 (−110 to 32) −9 (−44 to 26) 4 28 6.0
T60 5093-5150 Sentence denotes Occitanie (OCC) 54 (30 to75) 99 (79 to 112) 4 37 5.9
T61 5151-5217 Sentence denotes Pays de la Loire (PDL) −25 (−70 to 5) 18 (−16 to 38) 4 25 3.5
T62 5218-5294 Sentence denotes Provence-Alpes-Cote d’Azur (PACA) 36 (−4 to 80) 94 (47 to 140) 8 52 5.0
T63 5295-5354 Sentence denotes France 33 (−8 to 64) 84 (44 to 108) 110 982 64.9a
T64 5355-5411 Sentence denotes a Total population of all 13 regions of mainland France.
T65 5412-5566 Sentence denotes For ARI, the two positive swabs had been collected in the regions Bourgogne-Franche Comté (BFC) and GRE, from a total of seven swabs in these two regions.
T66 5567-5598 Sentence denotes We estimated that 760 (95% CrI:
T67 5599-5783 Sentence denotes 219–1,706) ARI consultations in those older than 65 years in these two regions (BFC and GRE) could have been caused by COVID-19 during week 10 (2 in 7 for a total of 2,600 ARI visits).
T68 5784-5974 Sentence denotes We did not pursue modelling excess cases for ARI as the time series (shown in the Supplement) were too noisy to properly break down the data into an expected seasonal part plus excess cases.
T69 5976-5986 Sentence denotes Discussion
T70 5987-6225 Sentence denotes This is the first time that an increase in ILI cases was observed simultaneously in several regions after the peak of the annual influenza epidemic in the last 30 seasons of routine surveillance in France with the Sentinelles network [9].
T71 6226-6417 Sentence denotes Several processes may have contributed to this observation, including, among others, characteristics of the influenza season, change in population behaviour or increase in COVID-19 incidence.
T72 6418-6523 Sentence denotes Influenza A (H1N1)pdm09 and influenza B viruses co-circulated in 2019/20 in France [10] (see Supplement).
T73 6524-6639 Sentence denotes Seasons with type B virus circulation can lead to a slow decay in incidence but a renewed increase is atypical [1].
T74 6640-6748 Sentence denotes The 2-week-long normal school holidays started between mid-February and early March depending on the region.
T75 6749-6901 Sentence denotes While holidays may change the dynamics of influenza [9], this generally has an effect in the ascending phase of the epidemic rather than after the peak.
T76 6902-7084 Sentence denotes The COVID-19 pandemic may have changed the health-seeking behaviour of patients and, to some extent, the reporting of the contributing GPs although they conform to a case definition.
T77 7085-7194 Sentence denotes In the crowdsourced surveillance system grippenet.fr [10], there was no evidence of increasing consultations:
T78 7195-7274 Sentence denotes 30% consulted with a GP in for ILI during week 10, compared with 38% in week 9.
T79 7275-7446 Sentence denotes As information regarding the coronavirus risk is widespread, a uniform increase in all regions could have been expected in this scenario rather than only in a few regions.
T80 7447-7567 Sentence denotes We however acknowledge that increased consultation rates in regions where COVID-19 is the most reported may be possible.
T81 7568-7694 Sentence denotes The similarity between COVID-19 and influenza symptoms makes it possible that the excess ILI cases were due to COVID-19 cases.
T82 7695-7779 Sentence denotes The presence of SARS-CoV-2-positive swabs in the patients supports this possibility.
T83 7780-7896 Sentence denotes The correlation between the number of confirmed cases and the computed excess is also consistent with this scenario.
T84 7897-8012 Sentence denotes In this case, the excess in cases is compatible with an exponential growth at an estimated rate of ca 0.7 per week.
T85 8013-8114 Sentence denotes Interestingly, this estimate was very similar in the four most affected regions (GRE, IDF, OCC, HDF).
T86 8115-8209 Sentence denotes It may prove useful to help calibrate models for studying the impact of the COVID-19 pandemic.
T87 8210-8364 Sentence denotes Estimating the true number of COVID-19 cases can only be tentative at this early stage of the epidemic with data from a non-dedicated surveillance system.
T88 8365-8456 Sentence denotes It is likely that the case definition of ILI does not allow identifying all COVID-19 cases.
T89 8457-8550 Sentence denotes In addition, only a few cases were virologically tested, adding uncertainty in the estimates.
T90 8551-8759 Sentence denotes Yet, the rate of excess ILI consultations applied to the French regions yielded a number of cases far in excess of confirmed cases, with 12,840 cases in IDF and around 10,000 cases in the regions GRE and HDF.
T91 8760-9013 Sentence denotes Likewise, the extrapolated number of COVID-19 presenting as ARI was 760 in those older than 65 years in the two eastern regions (GRE and BFC): this was already twice the number of reported cases in these regions at the time (n = 379), all ages combined.
T92 9014-9188 Sentence denotes As we enter a period of generalised circulation of SARS-CoV-2, surveillance based on clinical description and swabbing by GPs will prove essential in assessing the situation.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 74-96 Phenotype denotes respiratory infections http://purl.obolibrary.org/obo/HP_0011947
T2 1083-1088 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T3 1139-1144 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T4 1164-1171 Phenotype denotes myalgia http://purl.obolibrary.org/obo/HP_0003326

2_test

Id Subject Object Predicate Lexical cue
32290901-30703528-29335250 1450-1451 30703528 denotes 4
32290901-1983924-29335251 2198-2199 1983924 denotes 5
32290901-21909366-29335252 2238-2239 21909366 denotes 6
32290901-18401408-29335253 6222-6223 18401408 denotes 9
32290901-28830105-29335254 6502-6504 28830105 denotes 10
32290901-30428158-29335255 6636-6637 30428158 denotes 1
32290901-18401408-29335256 6802-6803 18401408 denotes 9
32290901-28830105-29335257 7139-7141 28830105 denotes 10

MyTest

Id Subject Object Predicate Lexical cue
32290901-30703528-29335250 1450-1451 30703528 denotes 4
32290901-1983924-29335251 2198-2199 1983924 denotes 5
32290901-21909366-29335252 2238-2239 21909366 denotes 6
32290901-18401408-29335253 6222-6223 18401408 denotes 9
32290901-28830105-29335254 6502-6504 28830105 denotes 10
32290901-30428158-29335255 6636-6637 30428158 denotes 1
32290901-18401408-29335256 6802-6803 18401408 denotes 9
32290901-28830105-29335257 7139-7141 28830105 denotes 10