Phylogenetic analysis of chikungunya virus in travellers returning from La Reunion Island

Abstract

Highlights: Here, we present molecular detection and clinical metagenomic sequencing in seven travellers returning from La Reunion and presenting with chikungunya. The viral load and the genomic signature of the novel lineage involved raise significant concerns for the risk of local circulation of the virus in more temperate regions such as Europe.

Figure 1

Maximum-Likelihood Phylogeny of Representative Full-Length Chikungunya Virus Genomes. Viruses are identified by GenBank accession number. Also included are the names of the countries in which the sample was obtained, and the collection year. Major lineages are indicated, and tips are coloured accordingly. The presence of the A226V mutation in the E1 surface protein, the 210Q/211 T mutations in the E2 surface protein, or the 81 nt deletion in the 3’UTR are highlighted. Horizontal branch lengths are scaled to the number of nucleotide substitutions per site, and the tree is rooted at the midpoint for the sake of clarity. Bootstrap values are shown for key nodes. The Maximum-likelihood tree was inferred with the use of IQ-TREE (version 2.2.0).