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Moreira FRR, de Menezes MT, Salgado-Benvindo C, Whittaker C, Cox V, Chandradeva N, de Paula HHS, Martins AF, Chagas RRD, Brasil RDV, Cândido DDS, Herlinger AL, Ribeiro MDO, Arruda MB, Alvarez P, Tôrres MCDP, Dorigatti I, Brady O, Voloch CM, Tanuri A, Iani F, de Souza WM, Cardozo SV, Faria NR, Aguiar RS. Epidemiological and genomic investigation of chikungunya virus in Rio de Janeiro state, Brazil, between 2015 and 2018. PLoS Negl Trop Dis 2023; 17:e0011536. [PMID: 37769008 PMCID: PMC10564160 DOI: 10.1371/journal.pntd.0011536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 10/10/2023] [Accepted: 07/17/2023] [Indexed: 09/30/2023] Open
Abstract
Since 2014, Brazil has experienced an unprecedented epidemic caused by chikungunya virus (CHIKV), with several waves of East-Central-South-African (ECSA) lineage transmission reported across the country. In 2018, Rio de Janeiro state, the third most populous state in Brazil, reported 41% of all chikungunya cases in the country. Here we use evolutionary and epidemiological analysis to estimate the timescale of CHIKV-ECSA-American lineage and its epidemiological patterns in Rio de Janeiro. We show that the CHIKV-ECSA outbreak in Rio de Janeiro derived from two distinct clades introduced from the Northeast region in mid-2015 (clade RJ1, n = 63/67 genomes from Rio de Janeiro) and mid-2017 (clade RJ2, n = 4/67). We detected evidence for positive selection in non-structural proteins linked with viral replication in the RJ1 clade (clade-defining: nsP4-A481D) and the RJ2 clade (nsP1-D531G). Finally, we estimate the CHIKV-ECSA's basic reproduction number (R0) to be between 1.2 to 1.6 and show that its instantaneous reproduction number (Rt) displays a strong seasonal pattern with peaks in transmission coinciding with periods of high Aedes aegypti transmission potential. Our results highlight the need for continued genomic and epidemiological surveillance of CHIKV in Brazil, particularly during periods of high ecological suitability, and show that selective pressures underline the emergence and evolution of the large urban CHIKV-ECSA outbreak in Rio de Janeiro.
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Affiliation(s)
- Filipe Romero Rebello Moreira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
| | - Mariane Talon de Menezes
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clarisse Salgado-Benvindo
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
| | - Victoria Cox
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
| | - Nilani Chandradeva
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
| | - Hury Hellen Souza de Paula
- Departamento de Saúde, Programa de Pós-graduação em Biomedicina Translacional, Universidade do Grande Rio (UNIGRANRIO), Duque de Caxias, Rio de Janeiro, Brazil
| | - André Frederico Martins
- Departamento de Saúde, Programa de Pós-graduação em Biomedicina Translacional, Universidade do Grande Rio (UNIGRANRIO), Duque de Caxias, Rio de Janeiro, Brazil
| | - Raphael Rangel das Chagas
- Departamento de Saúde, Programa de Pós-graduação em Biomedicina Translacional, Universidade do Grande Rio (UNIGRANRIO), Duque de Caxias, Rio de Janeiro, Brazil
| | - Rodrigo Decembrino Vargas Brasil
- Departamento de Saúde, Programa de Pós-graduação em Biomedicina Translacional, Universidade do Grande Rio (UNIGRANRIO), Duque de Caxias, Rio de Janeiro, Brazil
| | - Darlan da Silva Cândido
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alice Laschuk Herlinger
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marisa de Oliveira Ribeiro
- Institute of Technology in Immunobiology Bio-Manguinhos, Oswaldo Cruz Foundation/ Fiocruz, Rio de Janeiro, Brazil
| | - Monica Barcellos Arruda
- Institute of Technology in Immunobiology Bio-Manguinhos, Oswaldo Cruz Foundation/ Fiocruz, Rio de Janeiro, Brazil
| | - Patricia Alvarez
- Institute of Technology in Immunobiology Bio-Manguinhos, Oswaldo Cruz Foundation/ Fiocruz, Rio de Janeiro, Brazil
| | | | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
| | - Oliver Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Carolina Moreira Voloch
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Felipe Iani
- Fundação Ezequiel Dias (FUNED), Belo Horizonte, Minas Gerais, Brazil
| | - William Marciel de Souza
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sergian Vianna Cardozo
- Departamento de Saúde, Programa de Pós-graduação em Biomedicina Translacional, Universidade do Grande Rio (UNIGRANRIO), Duque de Caxias, Rio de Janeiro, Brazil
| | - Nuno Rodrigues Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Renato Santana Aguiar
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Instituto D’or, Rio de Janeiro, Rio de Janeiro, Brazil
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