A team of scientists in Brazil, along with collaborators in the U.S. and Europe, used diagnostics and metagenomic sequencing to reconstruct the transmission path of a recent outbreak of chikungunya virus in Maceió. We were honored to donate some lab equipment to help make this valuable project possible.
In their report in Emerging Infectious Diseases, “Spread of Chikungunya Virus East/Central/South African Genotype in Northeast Brazil,” lead author Antonio Charlys da Costa and collaborators note that diagnosis is particularly challenging in this country because of the prevalence of viruses with similar symptoms: dengue, Zika, and chikungunya. Brazil is also host to a number of different strains of chikungunya.
For this project, scientists randomly selected 273 samples from the 12,000 patients who visited two hospitals in Alagoas state in northeast Brazil during a 2016 outbreak consistent with one of these viruses. Results from diagnostic tests indicated that 208 of the patients had chikungunya virus, while 66 had Zika virus and a total of 36 patients were co-infected with both viruses. No dengue virus was detected in the samples.
The team then turned to NGS-based methods for metagenomics, analyzing 38 of the chikungunya-positive samples. Pippin Prep was used for size selection in the workflow, which was used to generate 23 new genome assemblies. Based on a phylogenetic analysis, the scientists determined that “the outbreak most likely originated from transmission cycles not previously identified in northeast Brazil and not from a separate introduction into the Americas,” they report. “Molecular dating analysis indicates that the outbreak was caused by a single founder strain that is estimated to have arrived in Alagoas around late April 2015.” The lineage appears to have come from neighboring Bahia, where a chikungunya epidemic occurred in the first half of 2015.
The evidence suggests “that this lineage has persisted since mid-2014 in Brazil and may spread in the Americas and beyond,” the scientists conclude.