Chikungunya Virus Typing Tool

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Introduction

The definition of a Chikungunya genotype is based on the identification of well defined phylogenetic clusters that its origin has been associated to a given geographic region.

We have carefully analyses all of CHIKV whole genomes and reviewed in the literature in order to represent the diversity of each phylotype. In addition, we performed extensive testing to be sure that our reference strains accurately classify other sequences.

We include 3 phylotypes
Phylotype 1 includes sequences from Asian and Caribbean
Phylotype 2 includes sequences from East-Central-South-African
Phylotype 3 includes sequences West Africa

Chikungunya Virus phylogenetic tree — Fig. 1. Chikungunya maximum likelihood phylogenetic tree of the (A) complete genome and (B) E1 gene

Acknowledgements

Developed by: FIOCRUZ/Bahia, Brazil (Vagner Fonseca, Marta Giovanetti, Maria Inés Restovic, Murilo Freire, Luiz Alcantara), KU Leuven, Belgium (Kristof Theys, Pieter Libin, Lize Cuypers, Ana Abecasis, Anne-Mieke Vandamme), University of Oxford, U.K. (Nuno Faria and Oliver Pybus), Evandro Chagas Institute, Pará, Brazil (Marcio Roberto Teixeira Nunes), CDC/OID/NCEZID (Gilberto A. Santiago), Emweb bvba, Belgium (Koen Deforche) and Africa Centre/UKZN, South Africa (Tulio de Oliveira).

Software: Genome Detective

Contact: Vagner Fonseca, Dr. Luiz Carlos Junior Alcantara and/or Prof. Tulio de Oliveira