Chikungunya virus (CHIKV) is considered a public health problem due to its rapid spread and high morbidity. This study aimed to determine the genetic diversity and phylogenetic relationships of CHIKVs in Colombia. A descriptive and retrospective study was carried out using sera of patients infected with Chikungunya during the outbreak in Colombia. The whole genomes of CHIKV (n = 16) were sequenced with an Illumina Hi-seq 2500 and were assembled using the Iterative Virus Assembler software. A Bayesian inference phylogenetic analysis was carried out with 157 strains of worldwide origin. The Colombian CHIKV sequences were grouped in the Asian genotype; however, three independent phylogenetic subclades were observed, probably the result of three separate introductions from Panama, Nicaragua, and St. Barts. Each subclade showed several different non-synonymous mutations (nsP2-A153V; nsp2-Y543H; nsp2-G720A; nsP3-L458P; Capside R78Q), that may have functional consequences for CHIKV biology and pathogenesis. These same mutations may affect the efficacy of potential CHIKV vaccines.

The Zika virus (ZIKV) is an emerging flavivirus transmitted primarily through arthropods, endemic in Africa, Asia, and the Americas, and is considered a global threat by the World Health Organization. Objective To evaluate a commercial Zika virus test (IgG/IgM catalog number B815C, Biocan, Canada. Methods We evaluated 30 sera of patients diagnosed with Dengue, Leptospira, Malaria, Hantavirus, and Chikungunya. To establish the sensitivity of the test, two groups of sera were analyzed, the first one was patients with Zika RT-qPCR positive, and the second were patients RT-qPCR negative but with clinical suspicion of Zika. Results The specificity was of 23.3% (7/30), the sensitivity in acute patients with positive RT-qPCR was of 63.6%, the patients with clinical suspicion of Zika the sensitivity (IgM) was of 80% (n = 8/10). Overall sensitivity (IgM) of both groups was of 71.4% (15/21). Conclusions The test showed a low specificity to be used as a serological test in an endemic area of flavivirus infection.