Impact of non-pharmaceutical interventions, weather, vaccination, and variants on COVID-19 transmission across departments in France

Juliette Paireau (1, 2) , Marie-Laure Charpignon (3, 4, 5) , Sophie Larrieu (6) , Clémentine Calba (7) , Nathanaël Hozé (2) , Pierre-Yves Boëlle (8) , Rodolphe Thiébaut (5) , Mélanie Prague (5) , Simon Cauchemez (2)

1 Direction des maladies infectieuses - Infectious Diseases Division [Saint-Maurice]
2 Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases
3 IDSS - MIT Institute for Data, Systems, and Society [Cambridge, MA]
4 Boston Children's Hospital
5 SISTM - Statistics In System biology and Translational Medicine
6 Santé publique France Nouvelle-Aquitaine [Bordeaux]
7 Santé publique France Provence-Alpes-Côte d'azur et Corse - Provence-Alps-French Riviera and Corsica [Marseille]
8 iPLESP - Institut Pierre Louis d'Epidémiologie et de Santé Publique

Background: Multiple factors shape the temporal dynamics of the COVID-19 pandemic. Quantifying their relative contributions is key to guide future control strategies. Our objective was to disentangle the individual effects of non-pharmaceutical interventions (NPIs), weather, vaccination, and variants of concern (VOC) on local SARS-CoV-2 transmission. Methods: We developed a log-linear model for the weekly reproduction number (R) of hospital admissions in 92 French metropolitan departments. We leveraged (i) the homogeneity in data collection and NPI definitions across departments, (ii) the spatial heterogeneity in the timing of NPIs, and (iii) an extensive observation period (14 months) covering different weather conditions, VOC proportions, and vaccine coverage levels. Findings: Three lockdowns reduced R by 72.7% (95% CI 71.3–74.1), 70.4% (69.2–71.6) and 60.7% (56.4–64.5), respectively. Curfews implemented at 6/7 pm and 8/9 pm reduced R by 34.3% (27.9–40.2) and 18.9% (12.04–25.3), respectively. School closures reduced R by only 4.9% (2.0–7.8). We estimated that vaccination of the entire population would have reduced R by 71.7% (56.4–81.6), whereas the emergence of VOC (mainly Alpha during the study period) increased transmission by 44.6% (36.1–53.6) compared with the historical variant. Winter weather conditions (lower temperature and absolute humidity) increased R by 42.2% (37.3–47.3) compared to summer weather conditions. Additionally, we explored counterfactual scenarios (absence of VOC or vaccination) to assess their impact on hospital admissions. Interpretation: Our study demonstrates the strong effectiveness of NPIs and vaccination and quantifies the role of weather while adjusting for other confounders. It highlights the importance of retrospective evaluation of interventions to inform future decision-making.

Mots clés: COVID-19; SARS-CoV-2; non-pharmaceutical interventions; vaccination; variants; climate; reproduction number; multivariable regression model

Domaines: Santé publique et épidémiologie

Juliette Paireau, Marie-Laure Charpignon, Sophie Larrieu, Clémentine Calba, Nathanaël Hozé, et al.. Impact of non-pharmaceutical interventions, weather, vaccination, and variants on COVID-19 transmission across departments in France. BMC Infectious Diseases, 2023, 23 (190), ⟨10.1186/s12879-023-08106-1⟩. ⟨hal-03791761v2⟩