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. 2025 Mar 18;17(3):430.
doi: 10.3390/v17030430.

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

Alessandra Lo Presti  1 , Claudio Argentini  1 , Giulia Marsili  1 , Claudia Fortuna  1 , Antonello Amendola  1 , Cristiano Fiorentini  1 , Giulietta Venturi  1
Affiliations

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

Alessandra Lo Presti et al. Viruses. .

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.

Keywords: CHIKV; early warning; evolution; genetic diversity; genomic surveillance; phylogeny.

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Conflict of interest statement

The authors declare that there are no conflicts of interest.

Figures

Figure 1
Figure 1
Bayesian phylogeographic tree of CHIKV E1 sequences. The significant statistical support for the clades or clusters subtending the branch is indicated with an asterisk along that branch (posterior probability ≥ 80%). The time of the most recent common ancestor and the credibility interval based on the 95% highest posterior density interval (95% HPD) is reported for the supported nodes. The red bar indicates the presence of the A226V mutation. Geographic locations are shown with different colours in the tree and highlighted in the legend on the left (BD: Bangladesh; CN: China; ES: Spain ex-Thailand; FI: Finland ex-Thailand; HK: Hong Kong; IL: Israel ex-Thailand; IN: India; IT: Italy and Italy ex-Thailand; KE: Kenya; KH: Cambodia; KM: Comoros; LK: Sri Lanka; LS: Laos; MG: Madagascar; MU: Mauritius; MY: Malaysia; PG: Papua New Guinea; PK: Pakistan; RE: Reunion; SC: Seychelles; SG: Singapore; AT: Austria and Austria ex-Thailand; SI: Slovenia ex-Thailand; and TH: Thailand).
Figure 2
Figure 2
Bayesian skyline plot (BSP) of the CHIKV E1 dataset. The effective number of infections is reported on the Y-axis. Time is reported in the X-axis. The colored area corresponds to the credibility interval based on 95% highest posterior density interval (HPD). The dotted vertical line is the lower 95% HPD on CHIKV E1 dataset TMRCA.
See this image and copyright information in PMC

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