Risk assessment and perspectives of local transmission of chikungunya and dengue in Italy, a European forerunner

This repository contains:

• a code developed in R to perform the statistical analysis on dengue and chikungunya cases presented in the article "Risk assessment and perspectives of local transmission of chikungunya and dengue in Italy, a European forerunner" by Menegale et al. (Nature Communications, 2025);
• the references to the codes used to assess i) dengue and chikungunya transmissibility from human cases surveillance and ii) risk of onward transmission from entomological and climate data as in the same article;
• model estimates of the net reproduction number (Rt) as derived from time series of human cases recorded during dengue and chikungunya outbreaks in Italy between 2007 and 2023;
• model estimates of the basic reproduction number and the likelihood of onward transmission of dengue virus and chikungunya virus computed for Italy assuming Aedes albopictus to be the main vector species responsible for the transmission, provided for the first day of each month of 2023 at a spatial scale of 100 m x 100 m. Model estimates of the duration of epidemic risk, defined as the maximum number of consecutive days with R0 > 1, are also provided for 2023 at the spatial scale of 100 m x 100 m.

The file "statistical_analysis.R" contains the code developed for the statistical analyses of the time series of imported DENV and CHIKV cases reported in Italy from 2006 to 2023. Due to the sensitive nature of the data, the input data are not included. Raw data can only be made available by the Istituto Superiore di Sanità (Italian National Institute of Health) through a data-sharing agreement directly with the user (contact mail: sorveglianza.arbovirosi@iss.it). Aggregated data are available at https://www.epicentro.iss.it/arbovirosi/dashboard and https://www.epicentro.iss.it/arbovirosi/bollettini.

The code used to estimate the net reproduction number from human cases is available at https://github.com/majelli/Rt. The code used for computing reproduction numbers and the potential risk of onward transmission is available at https://zenodo.org/records/10203374. 

The folder "Rt.zip" contains daily estimates of the net reproduction number (Rt) for historical dengue and chikungunya outbreaks. In each file, estimates are provided for every day between the dates of the first and last notified symptom onsets (column "date"). The column "avg" represents the mean estimate, while "lo" and "hi" correspond to the 25th and 97.5th percentiles of the distribution of estimates, respectively.

The folder "italy.zip" contains the mean estimates of the following quantities for dengue and chikungunya in 2023:

1. Basic reproduction number R0 (subfolders "R0_deng" and "R0_chik");
2. Likelihood of onward transmission (subfolders "lik_onward_deng" and "lik_onward_chik");
3. Duration of the epidemic risk.

Month 1 indicates estimates for January, month 12 indicates estimates for December. All estimates were obtained by assuming Ae. albopictus to be the main vector species responsible for the transmission, at a spatial scale of 100 m x 100 m.