DOI: 10.5061/dryad.95x69p8x3
title: Standardized incidence ratio dataset of human West Nile Virus in Italy (2012-2024)

description: West Nile virus (WNV) is primarily transmitted by Culex pipiens mosquitoes
 feeding on infected birds, while humans and other mammals serve as
 dead-end hosts. Although first detected in horses in Italy in 1998, human
 cases only emerged after the implementation of a multispecies surveillance
 program in 2001, with a major outbreak occurring in 2008 in northern
 regions. In this dataset, we computed the Standardized Incidence Ratio
 (SIR) for human West Nile virus (WNV) cases at the provincial level in
 Italy over the period 2012–2024. The data are provided in a CSV file,
 where each row corresponds to a province that reported at least one
 confirmed case during the study period, and each column contains annual
 SIR values. Provinces with no reported cases in a given year are marked as
 NA. Additionally, for each province, we calculated summary statistics
 including the temporal gradient, mean, standard deviation, maximum, and
 minimum SIR values, based on the available data.
description: # Standardized incidence Ratio dataset of Human West Nile Virus in Italy
 (2012-2024) Dataset DOI:
 [10.5061/dryad.95x69p8x3](10.5061/dryad.95x69p8x3) We have computed the
 Standardized Incidence Ratio (SIR) of West Nile Virus (WNV) on humans, at
 Italian provincial level, covering the period (2012-2024). The SIR is an
 epidemiological metric used to compare the observed number of cases in a
 study population to the number expected based on a reference population.
 It accounts for differences in population size and structure, and is
 calculated as the ratio between observed and expected cases. An SIR
 greater than 1 indicates a higher-than-expected incidence, while a value
 below 1 indicates a lower-than-expected incidence. Since the WNV is not
 present or recorded in several provinces, We considered as reference
 population the set of all provinces which recorded at least one positive
 case, in order to avoid huge variation of the SIR. #### Computation of
 Standardized Incidence Ratio (SIR) of West Nile Virus (WNV) on humans, at
 Italian provincial level (2012-2024). SIR = Oₚ / Eₚ where: * Oₚ is the
 observed number of positive cases in the study population; * Eₚ is the
 expected number of cases, estimated using age-specific incidence rates
 from a reference population. Calculation of Eₚ: Eₚ = ∑ (Rᵢʳ * nᵢ), for i =
 1, ..., k where: * Rᵢʳ is the age-specific incidence rate in the reference
 population for age group *i*; * nᵢ is the size of the study population in
 age group *i*; * k is the total number of age groups considered. The
 age-specific incidence rate Rᵢʳ is computed as: Rᵢʳ = Pᵢ / Nᵢ where: * Pᵢ
 is the number of observed positive cases in age group *i* in the reference
 population; * Nᵢ is the population size in age group *i* in the reference
 population. Commonly used age groups (may vary depending on available
 data): * 0–4 years * 5–14 years * 15–24 years * 25–44 years * 45–64 years
 * 65–74 years * 75+ years Interpretation: * SIR &gt; 1:
 Higher-than-expected incidence in the study population; * SIR &lt; 1:
 Lower-than-expected incidence; * SIR = 1: Observed incidence matches
 expected levels. #### File: DryadWNV.zip We created a .zip folder named
 "DryadWNV.zip", which contains 2 different objects: a folder
 named "Auxiliary_data", in which there are all the variables
 used to compute the SIR values, and the final dataset obtained, in .csv
 format, named "sir_tot.csv". #### File: sir\_tot.csv This file
 contains the SIR values computed using the Auxiliary data the R code. *
 *Province*: Name of all the Italian provinces, as presented on the ISTAT
 website. * *sir_20** *: SIR values for the specific Province and specific
 year. * *Gradient*: Slope of the interpolation line of all available SIR
 values for each Province. * *Mean*: Average SIR values for a specific
 Province, across all available years. * *Sd*: Standard deviation of SIR
 values for a specific Province, across all available years. * *Max*: Max
 SIR values for a specific Province, across all available years. * *Min*:
 Min SIR values for a specific Province, across all available years. ####
 Folder: Auxiliary\_data This folder contains a file called
 "Ni.xlsx" and thirteen .csv file, each one starting with
 "wn-ita-provinces-human-surveillance-20**.csv", covering all the
 years mentioned above. #### File: Ni.xlsx This dataset contains the
 resident population at provincial level at specific age, for all the year
 considered. The file is organized in sheets, each one regarding a specific
 year. The data of each year can be found on the ISTAT (Istituto Nazionale
 di Statistica) website [1]. * *Province*: Name of all the Italian
 provinces, as presented on the ISTAT website. * * *-year *: Population at
 the specific age, from 0 to 100+ year. * *total*: Total number of the
 resident population in he specific province. #### Files:
 wn-ita-provinces-human-surveillance-20\*\*.csv These datasets contains the
 information provided by the ISS (Istituto Superiore di Sanità) regarding
 the WNV cases, organized by Mingione, Marco, et al. [3] and available on
 the GitHub page [2]. Each file contains the same columns. *
 *url_bulletins*: Web link that points to the specific bulletin published
 by ISS. * *data*: the date of the reference latest bulletin of that year.
 * *code_region*: ID code for each Italian region, compliant with ISTAT
 system. * *name_region*: Full name of each italian region. *
 *code_province*: ID code for each Italian province, compliant with ISTAT
 system. * *name_province*: Full name of each italian province. *
 *abbreviation_province*: Abbreviation of each Italian province, compliant
 with ISTAT system. * *lat*: Centroid latitude of the province. * *long*:
 Centroid longitude of the province. * *age*: Age group of the infected
 people. * *new_cases*: New cases recorded for that specific province and
 specific year. * *total_cases*: Cumulative distribution of positive
 population for that specific province. * *type_infection*: Type of
 infection, neuroinvasive or fever. #### Code/software The software is R,
 version 4.3.1, and the packages used are "readxl" and
 "dplyr".  Initially, a function called *calculate_sir* is
 developed, which requires the paths to the auxiliary data stored in the
 Dryad file. Once the function is executed for each year, the resulting
 data are merged into a single dataframe. Subsequently, statistical metrics
 such as gradient, mean, standard deviation, minimum, and maximum are
 computed and appended to the dataframe. Finally, the dataset is saved in
 CSV format. #### Data was derived from the following sources: \[1] ISTAT
 data: [http://dati.istat.it/](http://dati.istat.it/) \[2] Auxiliary
 data: [https://github.com/fbranda/west-nile/tree/main](https://github.com/fbranda/west-nile/tree/main) #### References: \[3] Mingione, Marco, et al. "Monitoring the West Nile virus outbreaks in Italy using open access data." Scientific Data 10.1 (2023): 777.