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. 2008 Nov;89(Pt 11):2754-2760.
doi: 10.1099/vir.0.2008/005413-0.

Tracking epidemic Chikungunya virus into the Indian Ocean from East Africa

M Kariuki Njenga  1 , L Nderitu  2 , J P Ledermann  3 , A Ndirangu  2 , C H Logue  3 , C H L Kelly  3 , R Sang  2 , K Sergon  4 , R Breiman  1 , A M Powers  3
Affiliations

Tracking epidemic Chikungunya virus into the Indian Ocean from East Africa

M Kariuki Njenga et al. J Gen Virol. 2008 Nov.

Abstract

The largest documented outbreak of Chikungunya virus (CHIKV) disease occurred in the Indian Ocean islands and India during 2004-2007. The magnitude of this outbreak led to speculation that a new variant of the virus had emerged that was either more virulent or more easily transmitted by mosquito vectors. To study this assertion, it is important to know the origin of the virus and how the particular strain circulating during the outbreak is related to other known strains. This study genetically characterized isolates of CHIKV obtained from Mombasa and Lamu Island, Kenya, during 2004, as well as strains from the 2005 outbreak recorded in Comoros. The results of these analyses demonstrated that the virus responsible for the epidemic that spread through the Indian Ocean originated in coastal Kenya during 2004 and that the closest known ancestors are members of the Central/East African clade. Genetic elements that may be responsible for the scope of the outbreak were also identified.

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Figures

Fig. 1.
Fig. 1.
Depiction of the locations of amino acid differences identified among Indian Ocean island sequences (bottom) and between early Indian Ocean isolates and older Central/East African genotype strains (top) examined in this study. Numbers indicate non-structural (ns) or structural polyprotein amino acid positions.
Fig. 2.
Fig. 2.
Distance matrix cladogram based on CHIKV E1 nucleotide sequences. The analysis included samples from the 2004 to 2007 outbreaks in Kenya, Comoros, Réunion and India, along with historical isolates from the Central/East African (lower clade) and Asian (upper clade) genotypes. Isolates are designated by country of origin, year of isolation, province or city of infection, and strain name or number (e.g. strain 1455/76 isolated from Bangkok, Thailand, in 1975 is designated TH75-BK-1455/75). Unknown data are designated by ‘??’. Isolates sequenced in this study are indicated in bold. Bootstrap values based on 1000 replicates are indicated at the nodes.
Fig. 3.
Fig. 3.
Phylogram of the full-length CHIKV genomic sequence demonstrating the extreme genetic conservation seen during the course of the outbreak. Complete nucleotide sequences of isolates from coastal Kenya, the Indian Ocean and India from 2004 to 2007 were compared using a neighbour-joining algorithm. The prototype strain (S27) was used to represent the historical Central/East African genotype. Bootstrap values are indicated at the nodes.
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