Tracking epidemic Chikungunya virus into the Indian Ocean from East Africa

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.

Genome-Scale Phylogenetic Analyses of Chikungunya Virus Reveal Independent Emergences of Recent Epidemics and Various Evolutionary Rates

“…More recent analyses indicate that the recent Indian Ocean and Indian strains form a monophyletic group within the ECSA lineage (5,12,14,27,40,51,52). However, most CHIKV phylogenetic studies (1,14,28,29,38,40,41,47,52) have utilized only partial sequences from the envelope glycoprotein E1 gene, preventing a robust assessment of some of the relationships among strains and of their evolutionary dynamics.…”

“…Epidemics in rural Africa usually occur on a much smaller scale than in Asia, likely a result of the lower human population densities, and possibly more stable herd immunity. Although the assignments of "urban" and "sylvatic/enzootic" are based on the most common mode of transmission, CHIKV strains of African origin are capable of urban transmission by A. aegypti and A. albopictus, as evidenced by outbreaks in the Democratic Republic of the Congo (41), Nigeria (36), Kenya (27), and Gabon (42). The ecological differences between the sylvatic/enzootic (henceforth called enzootic) and urban/endemic/epidemic transmission cycles (henceforth called epidemic) such as seasonality of vector larval habitats, vertebrate host abundance and herd immunity, and vector host preferences, prompted us to hypothesize that the evolutionary dynamics of CHIKV may differ between the two transmission cycles.…”

Re-emergence of Chikungunya virus in South-east Asia: virological evidence from Sri Lanka and Singapore

“…Although we could not ascertain the evolutionary position of 2004 Kenyan strains due to lack of their sequences in current databases, we assume that they could fall either on or after the hypothesized common ancestor of Indian and Indian Ocean Islands isolates (A2 in Figs 1 and 3). This was because the Kenyan strains also possessed the E1-D284E substitution (Kariuki Njenga et al, 2008). Even though the mean evolutionary rate of the E1 gene has been shown to approximate that of the full genome of CHIKV (Cherian et al, 2009), the availability of more full genome sequences could better reflect the genome-wide variability and would provide answers to current gaps of knowledge with regard to the evolution of CHIKV.…”

“…It is now clear that the emergence of CHIKV in the Indian Ocean Islands in early 2005 was due to a newer strain of the ECSA lineage (Schuffenecker et al, 2006). Current epidemiological evidence suggests that this strain could have moved to the Indian Ocean Islands following CHIKV outbreaks in Kenya in 2004(Kariuki Njenga et al, 2008. Although the molecular epidemiology of CHIKV in India has been thoroughly described (Yergolkar et al, 2006;Arankalle et al, 2007), similar data to explain the evolutionary relationships of CHIKV that spread in the rest of the Asian region after 2005 are still limited.…”

Incrimination of Aedes (Stegomyia) hensilli Farner as an Epidemic Vector of Chikungunya Virus on Yap Island, Federated States of Micronesia, 2013

“…furcifer as an epidemic vector and implicated Mansonia africana (Theobald) as a potential vector in southern Africa 8. In 2004, CHIKV spread from Kenya onto the islands of the Indian Ocean, including Reunion Island and beyond 4,5. The epidemic on Reunion Island was unusual, because the epidemic vector was Ae.…”