Distinct Zika Virus Lineage in Salvador, Bahia, Brazil

Abstract

Sequencing of isolates from patients in Bahia, Brazil, where most Zika virus cases in Brazil have been reported, resulted in 11 whole and partial Zika virus genomes. Phylogenetic analyses revealed a well-supported Bahia-specific Zika virus lineage, which indicates sustained Zika virus circulation in Salvador, Bahia's capital city, since mid-2014.

Keywords: Bahia; Brazil; ZIKV; Zika virus; capture probe enrichment; flaviviruses; metagenomic next-generation sequencing; molecular clock; mosquito-borne infections; outbreak surveillance; phylogenetic analysis; vector-borne infections; viral genome assembly; viruses.

Figure

Timeframe of Zika virus outbreaks in the Americas. A molecular clock phylogeny is shown with the Zika virus outbreak lineage estimated from complete and partial (>1,500 nt) coding region sequences. For visual clarity, 5 basal Southeast Asia sequences (GenBank accession nos. HQ23499 [Malaysia, 1966]; EU545988 [Micronesia, 2007]; KU681082 [Philippines, 2012]; JN860885 [Cambodia, 2010]; and KU681081 [Thailand, 2013]) are not displayed. Blue horizontal bars represent 95% Bayesian credible intervals for divergence dates. A, B, and C denote the current American epidemic, the northeastern Brazil (Maranhão sequence and Bahia), and the Bahia clades, respectively; numbers next to the clade denote posterior probabilities and bootstrap scores in percentages. Circle sizes at each node represent the posterior probability support of that node. Taxa are labeled with the Genbank accession numbers, sampling location, and sampling date. Names of sequences generated in this study are in bold. The inset graph on the left shows the posterior probability distributions of the estimated ages (time to most recent common ancestor) for clades A, B, and C. The posterior probability density is plotted on the vertical axis as a function of time on the horizontal axis (tick marks designate 3-month intervals). Estimated ages were determined with BEAST version 1.8.2 (http://beast.bio.ed.ac.uk/) by using the best-fitting evolutionary model. The posterior probability distributions were visualized by using Tracer version 1.6 (http://tree.bio.ed.ac.uk/software/tracer/). Brazil states: BA, Bahia; CE, Ceará; MA, Maranhão; PA, Pará; PB, Paraíba; RN, Rio Grande do Norte; RJ, Rio de Janeiro; SP, São Paulo.