Sentinelles reporting of influenza-like illness
Cases of ILI and ARI are reported in real time by participating GPs (ca 600 GPs) all over France. 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. Cases of ARI include any disease with respiratory signs and are only monitored in people older than 65 years, unlike ILI. In addition, Sentinelles GPs take nasopharyngeal swabs in one ILI case and up to two ARI cases per week for viral characterisation [4]. 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. 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. 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.
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. 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. Excess cases were computed as the difference between observed cases and expected numbers. 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). 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: 447 to 108) consultations per 100,000 in excess in week 10. Four of the 11 regions displayed positive excess (CrI excluding 0) in week 9 and seven regions in week 10 (Figure).
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)
ARA: Auvergne-Rhone-Alpes; BRE: Brittany; CVL: Centre-Val de Loire; COR: Corsica; GRE: Grand-Est; HDF: Hauts de France; IDF: Ile de France; ILI: influenza-like illness; NAQ: Nouvelle Aquitaine; OCC: Occitanie; PACA: Provence-Alpes-Cote d’Azur; PDL: Pays de la Loire.
Blue: excess consultations, computed by difference between observations (squares) and expected counts. Green: expected number of consultations fitted on the first eight weeks of 2020 (circles). Confirmed COVID-19 case counts were obtained from the Santé Publique France website [7]. 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. 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: 0.55–0.86) in Grand-Est (GRE), 0.67 (95% CrI: 0.55 to 0.83) in Ile de France (IDF), 0.68 (95% CrI: 0.56 to 0.83) in Hauts de France (HDF), 0.61 (95% CrI: 0.48 to 0.75) in Occitanie (OCC) and 0.56 (95% CrI: −1.6 to 0.8) in France overall (Table).
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)
Region  Consultations in excess/100,000)  Confirmed COVID-19 cases (cumulative)  Population(in millions)
Week 9  Week 10  Week 9  Week 10
Auvergne-Rhone-Alpes (ARA)  82 (17 to147)  115 (36 to 174)  28  146  8
Brittany (BRE)  9 (−32 to 44)  40 (−7 to 73)  5  59  3.3
Centre-Val de Loire (CVL)  72 (43 to 96)  117 (97 to 130)  0  17  2.6
Corsica (COR)  35 (32 to 37)  21 (20 to 23)  0  5  0.3
Grand-Est (GRE)  −55 (−109 to −13)  107 (56 to 138)  5  259  5.5
Hauts de France (HDF)  51 (−3 to 94)  172 (111 to 208)  34  163  6.0
Ile de France (IDF)  40 (32 to 46)  107 (103 ti 110)  18  191  12.3
Nouvelle Aquitaine (NAQ)  −3 (−110 to 32)  −9 (−44 to 26)  4  28  6.0
Occitanie (OCC)  54 (30 to75)  99 (79 to 112)  4  37  5.9
Pays de la Loire (PDL)  −25 (−70 to 5)  18 (−16 to 38)  4  25  3.5
Provence-Alpes-Cote d’Azur (PACA)  36 (−4 to 80)  94 (47 to 140)  8  52  5.0
France   33 (−8 to 64)   84 (44 to 108)   110   982   64.9a
a Total population of all 13 regions of mainland France. 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. We estimated that 760 (95% CrI: 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). 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.