Dataset Information

Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

ABSTRACT: 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.

SUBMITTER: Faria NR

PROVIDER: S-EPMC5722632 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

Faria N R NR Quick J J Claro I M IM Thézé J J de Jesus J G JG Giovanetti M M Kraemer M U G MUG Hill S C SC Black A A da Costa A C AC Franco L C LC Silva S P SP Wu C-H CH Raghwani J J Cauchemez S S du Plessis L L Verotti M P MP de Oliveira W K WK Carmo E H EH Coelho G E GE Santelli A C F S ACFS Vinhal L C LC Henriques C M CM Simpson J T JT Loose M M Andersen K G KG Grubaugh N D ND Somasekar S S Chiu C Y CY Muñoz-Medina J E JE Gonzalez-Bonilla C R CR Arias C F CF Lewis-Ximenez L L LL Baylis S A SA Chieppe A O AO Aguiar S F SF Fernandes C A CA Lemos P S PS Nascimento B L S BLS Monteiro H A O HAO Siqueira I C IC de Queiroz M G MG de Souza T R TR Bezerra J F JF Lemos M R MR Pereira G F GF Loudal D D Moura L C LC Dhalia R R França R F RF Magalhães T T Marques E T ET Jaenisch T T Wallau G L GL de Lima M C MC Nascimento V V de Cerqueira E M EM de Lima M M MM Mascarenhas D L DL Neto J P Moura JPM Levin A S AS Tozetto-Mendoza T R TR Fonseca S N SN Mendes-Correa M C MC Milagres F P FP Segurado A A Holmes E C EC Rambaut A A Bedford T T Nunes M R T MRT Sabino E C EC Alcantara L C J LCJ Loman N J NJ Pybus O G OG

Nature 20170524 7658

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 dise ...[more]

PMID: 28538727

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Project description:BackgroundColombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to describe ZIKV dynamics in Colombia.MethodsWe sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes aegypti samples selected to cover the temporal and geographic breadth of the Colombian outbreak. We performed phylogeographic analysis of these genomes, along with other publicly-available ZIKV genomes from the Americas, to estimate the frequency and timing of ZIKV introductions to Colombia.ResultsWe attempted PCR amplification on 184 samples; 19 samples amplified sufficiently to perform sequencing. Of these, 8 samples yielded sequences with at least 50% coverage. Our phylogeographic reconstruction indicates two separate introductions of ZIKV to Colombia, one of which was previously unrecognized. We find that ZIKV was first introduced to Colombia in February 2015 (95%CI: Jan 2015 - Apr 2015), corresponding to 5 to 8 months of cryptic ZIKV transmission prior to confirmation in September 2015. Despite the presence of multiple introductions, we find that the majority of Colombian ZIKV diversity descends from a single introduction. We find evidence for movement of ZIKV from Colombia into bordering countries, including Peru, Ecuador, Panama, and Venezuela.ConclusionsSimilarly to genomic epidemiological studies of ZIKV dynamics in other countries, we find that ZIKV circulated cryptically in Colombia. More accurately dating when ZIKV was circulating refines our definition of the population at risk. Additionally, our finding that the majority of ZIKV transmission within Colombia was attributable to transmission between individuals, rather than repeated travel-related importations, indicates that improved detection and control might have succeeded in limiting the scale of the outbreak within Colombia.

Dataset Information

Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

Publications

Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

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