A36 Analysis of CHIKV evolution during the Caribbean outbreak, 2013–5, using complete genome sequences

Abstract

Chikungunya virus (CHIKV) is a re-emerging, mosquito-borne alphavirus that causes chikungunya fever, a febrile illness characterized by severe acute and persistent arthralgia. At the end of 2013, autochthonous CHIKV transmission was detected for the first time in the Americas, on the Caribbean island of Saint Martin. Subsequently, CHIKV rapidly spread through the Caribbean Islands and onto the American mainland, causing millions of cases of chikungunya fever. During the outbreak, the Dutch National Institute of Health performed diagnostics on patient samples originating from the six Caribbean islands that belong to the Kingdom of the Netherlands. Using a subset of PCR-positive patient samples, we aimed to retrospectively analyze the 2013–5 CHIKV outbreak on the Dutch Caribbean islands using whole-genome sequences. Twenty-five CHIKV-positive sera were selected for next-generation sequencing based on viral load, location, and date of sampling. Sera were subjected to high speed centrifugation, filtration, and nuclease treatment to reduce the amount of background sequences from human and bacterial origin. Total RNA was extracted, primed with random nanomers for reverse transcription, after which dsDNA was produced and purified. Libraries were created using Nextera XT library preparation kit, and samples were run on a MiSeq desktop sequencer. Reads were trimmed and mapped to a reference sequence using the CLC Genomics workbench. To date, eight full-genome sequences were obtained, originating from four different islands and dating from the start of the outbreak (December 2013) to April 2015, when the outbreak was waning. High similarity (>99%) between sequences was found; nevertheless, all genome sequences were unique with a minimum of three SNPs differentiating one sequence from another. Thirty-three unique single nucleotide polymorphisms (SNPs) were identified, of which 29 were located in the coding regions of the genome. Eight SNPs were informative, and ten SNPs led to amino acid changes. Of the amino acid changes, nine were located in the non-structural proteins (1× nsP1, 5× nsP2, and 3× nsP3), and one was located in E2. In conclusion, we report the first whole-genome sequences of CHIKV isolates from the 2013 to 2015 outbreak that originated from the Dutch Caribbean islands. Sequencing of the remaining samples is still in progress.