Format

Send to

Choose Destination
PLoS Negl Trop Dis. 2019 Mar 7;13(3):e0007065. doi: 10.1371/journal.pntd.0007065. eCollection 2019 Mar.

Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon.

Author information

1
Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, FIOCRUZ, Manaus, Brazil.
2
Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
3
Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
4
Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
5
Laboratório de Patologia Experimental, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil.
6
Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil.
7
Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
8
Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom.
9
Harvard Medical School, Department of Pediatrics, Boston, MA, United States of America.
10
Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States of America.
11
Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, United States of America.
12
Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom.
13
Evandro Chagas Institute, Brazilian Ministry of Health, Ananindeua, Brazil.
14
Laboratório Central de Saúde Pública, Boa Vista, Roraima, Brazil.
15
Superintendência de Vigilância em Saúde, Secretaria Municipal de Saúde de Boa Vista, Roraima, Brazil.
16
Departamento de Virologia, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Amazonas, Brazil.
17
Laboratório Central de Saúde Pública do Amazonas, Manaus, Amazonas, Brazil.
18
Organização Pan-Americana da Saúde/Organização Mundial da Saúde-(OPAS/OMS), Brasília-DF, Brazil.
19
Secretaria de Vigilância em Saúde, Ministério da Saúde (SVS/MS), Brasília-DF, Brazil.

Abstract

BACKGROUND:

Since its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region remains poorly understood despite its importance to better understand the epidemiological spread and public health impact of CHIKV in the country.

METHODOLOGY/PRINCIPAL FINDINGS:

We report a large CHIKV outbreak (5,928 notified cases between August 2014 and August 2018) in Boa vista municipality, capital city of Roraima's state, located in the Brazilian Amazon region. We generated 20 novel CHIKV-ECSA genomes from the Brazilian Amazon region using MinION portable genome sequencing. Phylogenetic analyses revealed that despite an early introduction of the Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista was caused by an ECSA-lineage most likely introduced from northeastern Brazil. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which translates in an estimated 39 (95% CI: 36 to 45) % of Roraima's population infected with CHIKV-ECSA. Finally, we find a strong association between Google search activity and the local laboratory-confirmed CHIKV cases in Roraima.

CONCLUSIONS/SIGNIFICANCE:

This study highlights the potential of combining traditional surveillance with portable genome sequencing technologies and digital epidemiology to inform public health surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of the Asian genotype by the ECSA genotype in the Amazon region.

PMID:
30845267
PMCID:
PMC6424459
DOI:
10.1371/journal.pntd.0007065
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Public Library of Science Icon for PubMed Central
Loading ...
Support Center