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Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV),
with ~30,000 cases reported to date. ZIKV was first detected in Brazil in
May 2015 and cases of microcephaly potentially associated with ZIKV
infection were identified in November 2015. Using next generation
sequencing we generated seven Brazilian ZIKV genomes, sampled from four
self-limited cases, one blood donor, one fatal adult case, and one newborn
with microcephaly and congenital malformations. Phylogenetic and molecular
clock analyses show a single introduction of ZIKV into the Americas,
estimated to have occurred between May-Dec 2013, more than 12 months prior
to the detection of ZIKV in Brazil. The estimated date of origin coincides
with an increase in air passengers to Brazil from ZIKV endemic areas, and
with reported outbreaks in Pacific Islands. ZIKV genomes from Brazil are
phylogenetically interspersed with those from other South American and
Caribbean countries. Mapping mutations onto existing structural models
revealed the context of viral amino acid changes present in the outbreak
lineage; however no shared amino acid changes were found among the three
currently available virus genomes from microcephaly cases.
Municipality-level incidence data indicate that reports of suspected
microcephaly in Brazil best correlate with ZIKV incidence around week 17
of pregnancy, although this does not demonstrate causation. Our genetic
description and analysis of ZIKV isolates in Brazil provide a baseline for
future studies of the evolution and molecular epidemiology in the Americas
of this emerging virus.
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