. Author manuscript; available in PMC: 2017 Oct 26.

Published in final edited form as: J Infect Dis. 2016 Dec 15;214(Suppl 5):S471–S474. doi: 10.1093/infdis/jiw274

Table 1.

Chikungunya Virus (CHIKV) Oligonucleotide Primers and Probes Used in Centers for Disease Control and Prevention Real-time Reverse Transcription–Polymerase Chain Reaction Assays Designed to Detect CHIKV Asian Genotype Strains

Primer/Genome 5′ Position	Nucleotide Sequence
CHIKV3855F	GAGCATACGGTTACGCAGATAG
CHIKV3957C^a	TACTGGTGATACATGGTGGTTTC + TGCTGGTGACACATGGTGGTTTC
CHIKV3886FAM (probe)^a	ACGAGTAATCTGCGTACTGGGACGTA + ACGAGTCATCTGCGTATTGGGACGCA
CHIK856F	ACCATCGGTGTTCCATCTAAAG
CHIK962C	GCCTGGGCTCATCGTTATT
CHIK908FAM (probe)	ACAGTGGTTTCGTGTGAGGGCTAC

The 3855 primer/probe set is broadly reactive, detecting both Asian and the East/Central/South African genotypes. The 856 set is designed specifically for the Asian genotype CHIKV strain currently in the Caribbean and is slightly more sensitive for the Asian genotype than the 3855 set. The threshold of detection of both sets of primer/probes is approximately 1 RNA transcript.

Primer CHIKV3957C is produced by mixing equal volumes of the 100 µM stock solutions of the 2 individual primers; the CHIKV3886FAM probe is an equal mixture of the 25 µM individual probe stocks.