# Phylogenetic Analysis of Chikungunya Virus Eastern/Central/South African-Indian Ocean Epidemic Strains, 2004–2019

## TL;DR

This study analyzes the genetic evolution and spread of the Chikungunya virus in Italy and other regions, highlighting the importance of genomic surveillance for public health.

## Contribution

The study provides new insights into the phylogenetic and phylogeographic patterns of ECSA-IOL CHIKV strains in Italy.

## Key findings

- The 2017 Italian CHIKV outbreak strains originated from a sub-clade linked to India, dating back to 2015.
- The estimated evolutionary rate of CHIKV E1 is 1.313 × 10−3 substitutions per site per year.
- Genomic surveillance and phylogeographic analysis can aid in public health risk assessment and early warning systems.

## Abstract

CHIKV infection is transmitted by Aedes mosquitoes spp., with Ae. aegypti considered as the primary vector and Ae. Albopictus playing an important role in sustaining outbreaks in Europe. The ECSA-Indian Ocean Lineage (IOL) strain emerged in Reunion, subsequently spreading to areas such as India, the Indian Ocean, and Southeast Asia, also causing outbreaks in naive countries, including more temperate regions, which originated from infected travelers. In Italy, two authocthounous outbreaks occurred in 2007 (Emilia Romagna region) and 2017 (Lazio and Calabria regions), caused by two different ECSA-IOL strains. The phylogenetics, evolution, and phylogeography of ECSA-IOL-CHIKV strains causing the 2007 and 2017 outbreaks in Italy were investigated. The mean evolutionary rate and time-scaled phylogeny were performed through BEAST. Specific adaptive vector mutations or key signature substitutions were also investigated. The estimated mean value of the CHIKV E1 evolutionary rate was 1.313 × 10−3 substitution/site/year (95% HPD: 8.709 × 10−4–1.827 × 10−3). The 2017 CHIKV Italian sequences of the outbreak in Lazio and of the secondary outbreak in Calabria were located inside a sub-clade dating back to 2015 (95% HPD: 2014–2015), showing an origin in India. Continued genomic surveillance combined with phylogeographic analysis could be useful in public health, as a starting point for future risk assessment models and early warning.