Figure 1. New genomic tests for chikungunya (CHIKV) infection in blood donors. A) Epidemic curve of reported cases in Puerto Rico, April 2014–February 2015. For 2014, 30,983 presumptive cases and 4,275 laboratory-confirmed cases were reported to the Secretary of Health in Puerto Rico. Three CHIKV-positive case-patients (asterisks) of 557 tested were identified by transcription-mediated amplification (TMA) screening of plasma samples during the study period. B) Heat map (cluster analysis) of 6 ViroChip (University of California San Francisco, San Francisco, CA, USA) microarrays corresponding to 6 donor plasma samples, 3 CHIKV positive and 3 CHIKV negative. Only microarray probes derived from CHIKV are plotted because signatures for other bloodborne viral pathogens were absent (data not shown). A sample is called ViroChip positive for CHIKV if at least 10% of the CHIKV probes on the heat map have a normalized probe intensity of >10% by cluster analysis (5) and/or if >1 probe is detected within the top 50 by z score analysis (6). Red bar denotes the magnitude of hybridization intensity normalized across the 45 CHIKV probes on the microarray. ViroChip microarray data have been submitted to the Gene Expression Omnibus database repository (accession no. GSE67234). C) Reverse transcription PCR (RT-PCR) testing for CHIKV and visualization of the PCR amplicon by 2% agarose gel electrophoresis confirm the transcription-mediated and ViroChip microarray results (7). D) Metagenomic next-generation sequencing (NGS) of the 3 CHIKV-positive plasma samples enables recovery of the viral genome. For each sample, coverage plots of mapped NGS reads to the “best hit” viral genome (accession no. KJ451624), identified by using the automated sequence-based ultrarapid pathogen identification pipeline, are shown (8). The read coverage (y axis, log scale) is plotted as a function of nucleotide position along the genome (x axis). The consensus whole-genome sequences obtained from the coverage plots are used for the subsequent phylogenetic and molecular clock analyses (Figure 2). NGS reads with human sequences removed have been deposited in the Sequence Read Archive (BioProject accession no. PRJNA282046; SRP accession no. SRP057614). The 3 CHIKV genome sequences have been deposited in GenBank (accession nos. KR264949–KR264951).