ABSTRACT
The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.
Subject(s)
Disease Outbreaks/prevention & control , Epidemiological Monitoring , Genomics/methods , Yellow Fever/prevention & control , Yellow Fever/transmission , Yellow fever virus/isolation & purification , Aedes/virology , Age Factors , Animals , Brazil/epidemiology , Disease Outbreaks/statistics & numerical data , Evolution, Molecular , Humans , Phylogeny , Polymerase Chain Reaction , Risk , Sex Factors , Spatio-Temporal Analysis , Yellow Fever/epidemiology , Yellow Fever/virology , Yellow fever virus/classification , Yellow fever virus/geneticsABSTRACT
Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil. Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 2016) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 December 2016). Since the initial detection of ZIKV in Brazil, more than 45 countries in the Americas have reported local ZIKV transmission, with 24 of these reporting severe ZIKV-associated disease. However, the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this information for interpreting observed trends in reported microcephaly. Here we address this issue by generating 54 complete or partial ZIKV genomes, mostly from Brazil, and reporting data generated by a mobile genomics laboratory that travelled across northeast Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Analyses of viral genomes with ecological and epidemiological data yield an estimate that ZIKV was present in northeast Brazil by February 2014 and is likely to have disseminated from there, nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates for the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. The role of northeast Brazil in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the basic reproduction number of the virus.
Subject(s)
Zika Virus Infection/transmission , Zika Virus Infection/virology , Zika Virus/isolation & purification , Americas/epidemiology , Basic Reproduction Number , Brazil/epidemiology , Genetic Variation , Genome, Viral/genetics , Humans , Microcephaly/epidemiology , Microcephaly/virology , Molecular Epidemiology , Phylogeography , Spatio-Temporal Analysis , Zika Virus/genetics , Zika Virus Infection/epidemiologyABSTRACT
Here, we present the complete genome sequences of two Zika virus (ZIKV) strains, EcEs062_16 and EcEs089_16, isolated from the sera of febrile patients in Esmeraldas City, in the northern coastal province of Esmeraldas, Ecuador, in April 2016. These are the first complete ZIKV genomes to be reported from Ecuador.