Complete Genome Sequences of Chikungunya Viruses Isolated from Plasma Specimens Collected from Haitians in 2014.

Ten chikungunya virus isolates from human plasma collected in Haiti from May to August 2014, in the midst of a chikungunya fever outbreak, were fully sequenced. The resulting genomic sequences are nearly identical, and phylogenetic analyses indicate they belong to the Asian lineage of the virus.

GENOME ANNOUNCEMENT

Chikungunya virus (CHIKV) (genus Alphavirus, family Togaviridae) is a mosquito-borne virus that is the cause of chikungunya fever (CF) in humans. Although infections by CHIKV may be asymptomatic, up to 97% of those infected develop CF, which is a fever-rash-arthralgia syndrome often associated with debilitating pain that may last up to several years (1). CHIKV has been isolated in regions in Asia, Africa, and the Pacific Islands, and it emerged in the Americas for the first time in 2013 with sustained autochthonous transmission (2, 3). There is little CHIKV information from Haiti, but there is a growing body of information from other countries involved in the epidemic in the Americas and Caribbean (4).

The CHIKV genomes that were sequenced here were from viruses isolated from human plasma samples obtained from schoolchildren in Haiti during a CF outbreak, between 29 May and 13 August 2014. Plasma samples from suspected cases of CF were screened by reverse transcription (RT)-PCR; cDNA synthesis from extracted RNA was performed using a Moloney murine leukemia virus reverse transcriptase (MMLV-RT) and sequence-specific reverse primers, and PCR was performed as described by Cherabuddi et al. (5). For sequencing purposes, virus isolation in a BSL3 laboratory was accomplished by inoculation of aliquots of plasma that tested positive for CHIKV viral RNA (vRNA) by RT-PCR onto Vero E6 cells. The viruses induced rapid formation of cell-lytic cytopathic effects, usually within 4 days after inoculation of the cells. Thereafter, the viral genomes were Sanger sequenced using a high-fidelity reverse transcriptase for cDNA synthesis, followed by PCR with a high-fidelity thermal polymerase, as well as 5′ and 3′ rapid amplification of cDNA ends (RACE) performed as previously described (5).

The 10 genome sequences are nearly identical (they share 99% identity) and also have 99% identity with CHIKV strain WHCHK9, which was also collected from Haiti in May 2014 (complete genome deposited by the CDC in GenBank, accession number KR559478). Presently, three distinct CHIKV lineages have been identified: African, East/Central/South African (ECSA), and Asian (6 – 8). Phylogenetic analyses indicate that our 10 CHIKV genomes belong to the Asian lineage of the virus. All 10 virus genomes harbor an E1-A98T substitution and lack an E1-A226V substitution (they retain A at E1-226). This finding suggests they are mainly vectored by Aedes aegyptii (7, 9, 10). In support of that notion, the 10 CHIKV genomes also lack E1 and E2 Aedes albopictus-adaptive mutations that are seen in IOL strains (11), but this remains to be confirmed by field studies in Haiti.

Accession number(s).

The 10 complete CHIKV genome sequences of this study have been deposited in the GenBank database under the accession numbers KX702401, KX702402, and KY415978 to KY415985.