Background
The Chikungunya virus (CHIKV) is a re-emerging mosquito-borne alphavirus posing a significant public health problem in tropical and subtropical regions [
1]. CHIKV infection is usually characterized by an acute onset of fever, rash, and arthralgias, and is often accompanied by headache, joint swelling, and conjunctivitis. Unlike dengue virus (DENV), CHIKV infection is associated with recurrent polyarthralgias and high rates of symptomatic infections. CHIKV is typically transmitted between humans by the anthropophilic vectors
Aedes aegypti and
Ae. albopictus [
2].
Four CHIKV genotypes have been identified since its discovery in 1952 [
3]. The East-Central-South-African (ECSA) and West African genotypes are endemic and cause epidemics in sub-Saharan Africa, whereas the Asian genotype circulates in
Ae. aegypti-human urban transmission cycles in Southeast Asia. The Indian Ocean lineage (IOL) caused explosive epidemics in Indian Ocean islands and Asia between 2005 and 2011. Several IOL strains harbour mutations that augment infectivity and transmissibility in
Ae. albopictus [
4]. Imported cases caused limited outbreaks in temperate regions where only
Ae. albopictus is present [
5]. On December 5, 2013, Asian genotype CHIKV infections were reported in the Caribbean island of Saint Martin [
6]. For the first time in recorded history, CHIKV had established a mosquito-human cycle in the Americas. As of October 31, 2014, >1,222,000 suspected CHIKV cases have been reported in the Americas and autochthonous infections have been confirmed in 50 territories in the region [
7].
The first autochthonous cases of CHIKV in Brazil were confirmed in Oiapoque, Amapa State, on September 13, 2014. Seven days later, autochthonous cases were also confirmed in Feira de Santana, Bahia state. By October 18, 2014, 682 confirmed autochthonous cases had been notified to the Brazilian Ministry of Health [
8]. Yet, the source of the ongoing outbreaks in these municipalities and the potential for virus establishment in the country remain unknown. We performed serological and virological analysis on 68 samples collected from June to September 2014 and full-length viral genome sequencing on six isolates. CHIKV and DENV have similar transmission cycles [
9], and DENV is hyperendemic in Brazil [
10]. Herein, we describe the epidemiological and genetic characteristics of CHIKV emergence in Brazil and provide a prediction of the risk of CHIKV importation and establishment in each Brazilian municipality for the coming year, using data on human mobility, vector distribution, and retrospective DENV incidence.
Discussion
This study reports the emergence of both Asian and ECSA CHIKV genotypes in Brazil. This is the first time that an outbreak of the ECSA genotype has been reported in the Americas. Genetic and epidemiological data suggest that the ECSA genotype was introduced from Angola to Feira de Santana in June 2014, where epidemiological investigation is ongoing. CHIKV appears to be endemic in Angola [
32], where thousands of Brazilians, mostly from Northeast and Southeast areas [
33], work in the petroleum and mining industries. Genetic data suggests multiple introductions of the Asian genotype to Brazil from ongoing epidemics in the Caribbean and South America. Surveillance data suggests autochthonous transmission in Oiapoque began by early September 2014 [
8], and we posit that the strain circulating there was imported from French Guiana, a country bordering Oiapoque that has reported a steady increase in autochthonous cases since January 2014 [
8].
The clinical picture of patients with confirmed CHIKV infection included fever, arthralgia, rash, myalgia, and headache, symptoms similar to DENV infection, which is endemic in Brazil. The fact that we observe two different strains is sufficient to demonstrate that the epidemics in Oiapoque and Feira de Santana resulted from separate introductions and this result is robust to the number of sequences obtained. Our genetic estimate of the date of introduction of the ECSA genotype to Feira de Santana has an upper bound of 15 August, 2014, suggesting that the CHIKV surveillance network in Brazil was able to detect early cases of this introduction. Moreover, the confirmation of ~7 (3 to 13) importations of CHIKV to Brazil per month implies that Brazil is at risk of additional importations from endemic regions and that CHIKV may be exported from Brazil to other locations.
It is possible that the sustained transmission described here in results from the introduction of CHIKV strains into a location with appropriate vector abundance and during a period with appropriate climate conditions [
34], particularly during monsoon rainfall period and high temperatures [
35]. Some additional observations deserve further investigation. Prediction of future transmission of CHIKV within Brazil indicates that the geographic ranges of the current Asian and ECSA lineages will likely overlap and that nearly 99% of the population in Brazil may be at risk for CHIKV infection. There is no population immunity to CHIKV in Brazil, so incidence is expected to increase [
36]. Training health care workers for differential diagnosis of DENV and CHIKV, increased availability of diagnostic tests for patient sera and mosquitoes, as well as educational programs and a national active surveillance system are needed to control CHIKV spread [
3]. A small percentage of those living in rural northern and western areas of the country have antibodies to Mayaro virus (MAYV), a related alphavirus associated with Haemagogus mosquitoes [
34]. Cross-reactivity between the antigenically-related MAYV and CHIKV [
37] has been reported [
38] but it is unknown if prior exposure to MAYV provides protection against CHIKV. As CHIKV genotypes are more similar to each other than to MAYV it seems probable that immunity against one CHIKV genotype will provide at least partial protection against another [
39].
We follow international guidance and evaluate CHIKV importation risk using data on past DENV transmission [
2]. The similarity of DENV and CHIKV transmission cycles [
9] suggests that CHIKV may become endemic in several Brazilian municipalities, with transmission peaks occurring between January and April (Figure
4). Risk of CHIKV transmission is driven by a range of factors, including the presence and local abundance of suitable vector species, environmental variables such as ambient temperature, and socioeconomic factors. Whilst few of these factors are well understood or quantified for Brazil, many are likely to be shared with DENV, and it is known that the CHIKV-competent
Ae. aegypti and
Ae. albopictus vectors [
40] are widespread in Brazil. More specifically,
Ae. aegypti is more dispersed in Brazil with higher incidence in northern, north-eastern, central-eastern regions and less frequent in southern Brazil, due to a cooler climate [
41]. In contrast,
Ae. albopictus has high incidence in subtropical areas, more specifically in southern areas of the country [
28]. Although our index of introduction risk (Figure
3) indicates the municipalities in Brazil at greatest risk for CHIKV transmission, and can be used to prioritise disease surveillance, we cannot estimate the absolute number of importations expected in each location over a given time frame because the relevant data on human mobility within Brazil are currently unavailable. This could be obtained from, for example, anonymised cell phone call records [
42] or through collating existing microcensus data.
The ECSA outbreak in Feira de Santana persists and is disseminating to other regions in Brazil – and potentially to locations outside the country. Therefore, continued genetic surveillance will be necessary to investigate whether the ECSA genotype will acquire the A226V mutation in the viral E1 protein that can increase viral transmission in
Ae. albopictus and which was associated with explosive CHIKV outbreaks in the Indian Ocean nations and Indian subcontinent [
4]. Other scenarios are also possible: the Asian CHIKV genotype may become dominant in tropical regions of Brazil, where
Ae. aegypti is well established, and the ECSA genotype in subtropical and more temperate regions, where
Ae. albopictus is more abundant. The ECSA genotype has acquired mutations that increase transmissibility and persistence in
Ae. albopictus on multiple independent occasions [
3], whereas the Asian genotype appears less able to accrue such adaptations. In the long term, both genotypes could potentially disappear from the region if levels of human population immunity increase sufficiently. Alternatively, CHIKV could establish an enzootic cycle in the region with sporadic human epidemics. This pattern has been seen in Africa [
31] and potentially in Southeast Asia [
43], where there is some evidence of a sylvatic CHIKV transmission cycle involving non-human primates and forest-dwelling mosquitoes, similar to that observed for sylvatic yellow fever virus, which was introduced into tropical Americas from Africa with the slave trade and is still endemic in the Amazon and Orinoco River basins [
44]. DENV serotypes also exhibit sylvatic cycles in some areas of Southeast Asia and Africa, but this has not been yet observed in the Americas.
Competing interests
The authors declare that they have no competing interests.
Authors’ contributions
MRTN and NRF designed the research study, performed the evolutionary analyses, analysed data, and wrote the manuscript. JMV collected data, performed genome sequencing, and edited the manuscript. NG and MUGK conceived the statistical analysis, evaluated results, and edited the manuscript. LFO, DEAS, and SPS performed genome sequencing. RSSA contributed with clinical data. EVPS and VLC carried out the cell culture analysis. SPS and JFC participated in sequence alignment. GEC collected epidemiological data. ACRC performed the molecular biology diagnostic tests. SGR performed serological tests. JLSGVJr participated in sequence alignment and edited the manuscript. BTDN performed the qPCR analyses. RBT and SIH analysed data and revised the manuscript. OGP and PFCV helped design the study and interpret results, contributed epidemiological information, and helped draft the manuscript. All authors read and approved the final manuscript.