Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases

Zuinara Pereira Gusmão Maia; Felicidade Mota Pereira; Rodrigo Fabiano do Carmo Said; Vagner Fonseca; Tiago Gräf; Fernanda de Bruycker Nogueira; Vanessa Brandão Nardy; Joilson Xavier; Maricelia Lima Maia; André L Abreu; Carlos F Campelo de Albuquerque; Wanderson Kleber Oliveira; Julio Croda; Ana Maria Bispo de Filippis; Rivaldo Venancio Cunha; Jose Lourenço; Tulio de Oliveira; Nuno Rodrigues Faria; Luiz Carlos Junior Alcantara; Marta Giovanetti

doi:10.1080/22221751.2019.1701954

Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases

Emerg Microbes Infect. 2019 Dec 27;9(1):53-57. doi: 10.1080/22221751.2019.1701954. eCollection 2020.

Authors

Zuinara Pereira Gusmão Maia¹, Felicidade Mota Pereira¹, Rodrigo Fabiano do Carmo Said², Vagner Fonseca^{3

4}, Tiago Gräf⁵, Fernanda de Bruycker Nogueira⁶, Vanessa Brandão Nardy¹, Joilson Xavier³, Maricelia Lima Maia^{7

8}, André L Abreu⁹, Carlos F Campelo de Albuquerque¹⁰, Wanderson Kleber Oliveira¹¹, Julio Croda¹², Ana Maria Bispo de Filippis⁶, Rivaldo Venancio Cunha^{13

14}, Jose Lourenço¹⁵, Tulio de Oliveira⁴, Nuno Rodrigues Faria¹⁵, Luiz Carlos Junior Alcantara^{3

6}, Marta Giovanetti^{2

6}

Affiliations

¹ Laboratório Central de Saúde Pública, Departamento de Virologia, Salvador, BH, Brazil.
² Coordenação Geral de Vigilância de Arboviroses (CGARB).
³ Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
⁴ KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
⁵ Laboratorio de Patologia Experimental, Instituto Gonçalo Moniz, Fiocruz, Salvador, BH, Brazil.
⁶ Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
⁷ Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.
⁸ Secretaria de Saúde de Feira de Santana, Feira de Santana, Brazil.
⁹ Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS) Brasília, Distrito Federal, Brazil.
¹⁰ Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil.
¹¹ Secretaria de Vigilância em Saúde, Ministério da Saúde (SVS-MS), Brasília, Distrito Federal, Brazil.
¹² Departamento de Vigilância de Doenças Transmissíveis/Secretaria de Vigilância em Saúde, Ministério da Saúde (DEVIT/SVS-MS), Brasilia, Brazil.
¹³ Federal University of Mato Grosso do Sul, Brazil.
¹⁴ Fundação Oswaldo Cruz, Coordination of Health Surveillance and Reference Laboratories, Rio de Janeiro, RJ, Brazil.
¹⁵ Department of Zoology, University of Oxford, Oxford, UK.

Abstract

Between June 2017 and August 2018, several municipalities located in Bahia state (Brazil) reported a large increase in the number of patients presenting with febrile illness similar to that of arboviral infections. Using a combination of portable whole genome sequencing, molecular clock and epidemiological analyses, we revealed the return of the CHIKV-ECSA genotype into Bahia. Our results show local persistence of lineages in some municipalities and the re-introduction of new epidemiological strains from different Brazilian regions, highlighting a complex dynamic of transmission between epidemic seasons and sampled locations. Estimated climate-driven transmission potential of CHIKV remained at similar levels throughout the years, such that large reductions in the total number of confirmed cases suggests a slow, but gradual accumulation of herd-immunity over the 4 years of the epidemic in Bahia after its introduction in 2014. Bahia remains a reservoir of the genetic diversity of CHIKV in the Americas, and genomic surveillance strategies are essential to assist in monitoring and understanding arboviral transmission and persistence both locally and over large distances.

Keywords: Chikungunya; East-Central-South-African genotype; Northeast Brazil; portable genome sequencing; surveillance.

Publication types

Letter

MeSH terms

Animals
Brazil / epidemiology
Chikungunya Fever / diagnosis
Chikungunya Fever / epidemiology*
Chikungunya Fever / virology
Chikungunya virus / classification*
Chikungunya virus / genetics*
Chikungunya virus / isolation & purification
Epidemics
Humans
Mosquito Vectors

Grants and funding

This work was supported by the ZiBRA2 project, supported by the Brazilian Ministry of Health (SVS-MS) and the Pan American Organization (OPAS) and founded by CNPq [grant number 440685/2016-8 and 440856/2016-7]; by CAPES [grant number 88887.130716/2016-00, 88881.130825/2016-00 and 88887.130823/2016-00]; by Horizon 2020 Framework Programme [grant number PRES-005-FEX-17-4-2-33]. The Flavivirus Laboratory activities were also supported by Faperj (Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro) under the [grant number E-26/2002.930/2016], by the International Development Research Centre (IDRC) Canada over the [grant number 108411-001] and EU's Horizon 2020 Framework Programme through ZikaPlan and ZikAction under the [grant number 734584 and 734857]. JL was supported by a lectureship from the Department of Zoology, University of Oxford. MG is supported by Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro - FAPERJ; Conselho Nacional de Desenvolvimento Científico e Tecnológico; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior.