Thursday, July 14, 2016

EID Journal: Distinct Zika Virus Lineage in Salvador, Bahia, Brazil

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Last week, in Emerging Microbes & Infect: Growing Genetic Diversity Of Zika Viruses In Latin America, we saw a study that found a high level of genetic diversity among Zika viruses sequenced from Brazil, and no clear sign of a dominant strain. 

Today, in much the same vein, we have an analysis of 11 ZIKV viruses collected in Bahia - Brazil's 4th most populous state - which finds a Bahia specific lineage that appears to have first arrived in mid-2014. 

Volume 22, Number 10—October 2016

Distinct Zika Virus Lineage in Salvador, Bahia, Brazil

Samia N. Naccache1, Julien Thézé1, Silvia I. Sardi, Sneha Somasekar, Alexander L. Greninger, Antonio C. Bandeira, Gubio S. Campos, Laura B. Tauro, Nuno R. Faria, Oliver G. Pybus, and Charles Y. ChiuComments to Author


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.


Previous analyses have suggested that Zika virus was introduced in the Americas at least 1 year before the virus’s initial detection in Brazil (1). The state of Bahia, Brazil, reported most (93%) suspected Zika virus infections in Brazil during 2015 (2), including cases of Zika virus–associated fetal microcephaly (6); however, except for 1 complete genome, no genetic information from the region has been available (2,7). 

We report molecular epidemiologic findings resulting from 11 new complete and partial Zika virus genomes recovered from serum samples from patients at the Hospital Aliança in the city of Salvador in Bahia, Brazil.


Our results suggest an early introduction and presence (mid-2014) of Zika virus in the Salvador region in Bahia, Brazil. Given the size of the cluster and statistical support for it, this lineage likely represents a large and sustained chain of transmission within Bahia state.
Most cases of this Zika virus lineage clustered closely to a sequence from Maranhão, and we found evidence for an additional potential introduction to Bahia from Pará state. Consequently, Zika virus in Salvador during mid-2014 was likely introduced from other regions in Brazil rather than from outside the country.
Current findings of Zika virus emergence in Bahia state during mid-2014 are consistent with first-trimester viral infection in pregnant women corresponding to the initial reported cases of fetal microcephaly, which began in January 2015 (5) and peaked in November 2015.

Broader sampling across Bahia is needed to determine whether the Salvador lineage (clade C) identified in this article comprises most Zika virus cases in the state. Brazil currently faces a major public health challenge from co-circulation of Zika, dengue, and chikungunya viruses (2–4,14,15). Additional molecular surveillance in the Americas and beyond is urgently needed to trace and predict transmission of Zika virus.

Dr. Naccache is a researcher at the University of California, San Francisco; her interests are genomic assay development for clinical infectious disease diagnosis and sequencing-based characterization of emerging viruses. Dr. Thézé is a postdoctoral researcher in computational biology at the University of Oxford, UK; he is interested in viral evolution, especially the spatiotemporal dynamics of pathogen spread.


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