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. 2015 Apr 30:13:102.
doi: 10.1186/s12916-015-0348-x.

Emergence and potential for spread of Chikungunya virus in Brazil

Marcio Roberto Teixeira Nunes  1 , Nuno Rodrigues Faria  2 , Janaina Mota de Vasconcelos  3 , Nick Golding  4 , Moritz U G Kraemer  5 , Layanna Freitas de Oliveira  6 , Raimunda do Socorro da Silva Azevedo  7 , Daisy Elaine Andrade da Silva  8 , Eliana Vieira Pinto da Silva  9 , Sandro Patroca da Silva  10 , Valéria Lima Carvalho  11 , Giovanini Evelim Coelho  12 , Ana Cecília Ribeiro Cruz  13 , Sueli Guerreiro Rodrigues  14 , Joao Lídio da Silva Gonçalves Vianez Jr  15 , Bruno Tardelli Diniz Nunes  16 , Jedson Ferreira Cardoso  17 , Robert B Tesh  18 , Simon I Hay  19   20 , Oliver G Pybus  21 , Pedro Fernando da Costa Vasconcelos  22   23
Affiliations

Emergence and potential for spread of Chikungunya virus in Brazil

Marcio Roberto Teixeira Nunes et al. BMC Med. .

Abstract

Background: In December 2013, an outbreak of Chikungunya virus (CHIKV) caused by the Asian genotype was notified in the Caribbean. The outbreak has since spread to 38 regions in the Americas. By September 2014, the first autochthonous CHIKV infections were confirmed in Oiapoque, North Brazil, and in Feira de Santana, Northeast Brazil.

Methods: We compiled epidemiological and clinical data on suspected CHIKV cases in Brazil and polymerase-chain-reaction-based diagnostic was conducted on 68 serum samples from patients with symptom onset between April and September 2014. Two imported and four autochthonous cases were selected for virus propagation, RNA isolation, full-length genome sequencing, and phylogenetic analysis. We then followed CDC/PAHO guidelines to estimate the risk of establishment of CHIKV in Brazilian municipalities.

Results: We detected 41 CHIKV importations and 27 autochthonous cases in Brazil. Epidemiological and phylogenetic analyses indicated local transmission of the Asian CHIKV genotype in Oiapoque. Unexpectedly, we also discovered that the ECSA genotype is circulating in Feira de Santana. The presumed index case of the ECSA genotype was an individual who had recently returned from Angola and developed symptoms in Feira de Santana. We estimate that, if CHIKV becomes established in Brazil, transmission could occur in 94% of municipalities in the country and provide maps of the risk of importation of each strain of CHIKV in Brazil.

Conclusions: The etiological strains associated with the early-phase CHIKV outbreaks in Brazil belong to the Asian and ECSA genotypes. Continued surveillance and vector mitigation strategies are needed to reduce the future public health impact of CHIKV in the Americas.

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Figures

Figure 1
Figure 1
Timeline of laboratory confirmed CHIKV cases in Brazil 2014. Shown are imported (black) and autochthonous (red and blue) CHIKV cases in Brazil between April and September 2014 (A). As of September, autochthonous cases had been reported in Feira de Santana, a municipality in Bahia state, north-eastern Brazil (red) and in Amapa state, north Brazil, bordering French Guiana. Also shown is the timeline of confirmed CHIKV in Amapa and Bahia state (B), along with patients’ travel history and municipality of residence. Grey circles indicate imported cases, while blue and red circles indicate localized transmission. Filled squares indicate patient samples whose viruses were sequenced. (C) Map of confirmed cases and federal states with confirmed cases.
Figure 2
Figure 2
Dated phylogenetic reconstruction of CHIKV including Brazilian genomes. The genotypes involved in autochthonous Brazilian transmission in Oiapoque and Feira de Santana are highlighted in blue (A) and red (B), respectively. On the right, isolates sampled in Feira de Santana and Oiapoque are depicted as red and blue circles, whilst isolates from the Caribbean outbreak are shown in grey circles. The inset shows the posterior density of the age of the most recent common ancestor (MRCA) of the Caribbean outbreak (A, grey) and the Feira de Santana cluster (B, red). The arrows highlight the dates of the first notifications of CHIKV cases in the Caribbean and in Feira de Santana, respectively. The index case of the ECSA genotype in Brazil arrived in Feira de Santana in June (grey bar). A ML tree with tip information can be found in Additional file 1: Figure S1.
Figure 3
Figure 3
Risk maps for CHIKV spread from Oiapoque and Feira de Santana, Brazil. Shown is the relative risk of CHIKV spread from Oiapoque (A) and Feira de Santana (B). Black circles denote the locations of these municipalities.
Figure 4
Figure 4
Retrospective analysis of dengue virus transmission to identify municipalities where CHIKV is expected to circulate. Spatial dengue virus monthly incidence (averaged between 2001 and 2013) is shown in Brazilian municipalities.
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