Extracting circumstances of Covid-19 transmission from free text with large language models

Gaston Bizel-Bizellot, Simon Galmiche, Benoît Lelandais, Tiffany Charmet, Laurent Coudeville, Arnaud Fontanet () and Christophe Zimmer ()
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Gaston Bizel-Bizellot: Imaging and Modeling Unit
Simon Galmiche: Epidemiology of Emerging Diseases Unit
Benoît Lelandais: Imaging and Modeling Unit
Tiffany Charmet: Epidemiology of Emerging Diseases Unit
Laurent Coudeville: Global Medical
Arnaud Fontanet: Epidemiology of Emerging Diseases Unit
Christophe Zimmer: Imaging and Modeling Unit

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Identifying the circumstances of transmission of an emerging infectious disease rapidly is central for mitigation efforts. Here, we explore how large language models (LLMs) can automatically extract such circumstances from free-text descriptions in online surveys, in the context of Covid-19. In a nationwide study conducted online in France, we enrolled 545,958 adults with recent SARS-CoV-2 infection and inquired about the circumstances of transmission in both closed-ended and open-ended questions. First, we trained a classification model based on a pretrained LLM to predict one of seven predefined infection contexts (Work, Family, Friends, Sports, Cultural, Religious, Other) from the free text in answers to open-ended questions. We achieved an unbalanced accuracy of 75%, which increased to 91% when eliminating the 43% highest entropy responses. Second, we used topic modeling to define clusters of transmission circumstances agnostically. This led to 23 clusters, which agreed with the seven predefined infection contexts, but also provided finer details on previously undefined circumstances of transmission. Our study suggests that LLM-based analysis of free text may alleviate the need for closed-ended questions in epidemiological surveys and enable insights into previously unsuspected circumstances of transmission. This approach is poised to accelerate and enrich the acquisition of epidemiological insights in future pandemics.

Date: 2025
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DOI: 10.1038/s41467-025-60762-w

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