Chikungunya Virus Asian Lineage Infection in the Amazon Region Is Maintained by Asiatic and Caribbean-Introduced Variants
Geovani de Oliveira Ribeiro,
Danielle Elise Gill,
Endrya do Socorro Foro Ramos,
Fabiola Villanova,
Edcelha Soares D’Athaide Ribeiro,
Fred Julio Costa Monteiro,
Vanessa S. Morais,
Marlisson Octavio da S. Rego,
Emerson Luiz Lima Araújo,
Ramendra Pati Pandey,
V. Samuel Raj,
Xutao Deng,
Eric Delwart,
Antonio Charlys da Costa,
Élcio Leal
Affiliations
Geovani de Oliveira Ribeiro
Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil
Danielle Elise Gill
Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil
Endrya do Socorro Foro Ramos
Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil
Fabiola Villanova
Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil
Edcelha Soares D’Athaide Ribeiro
Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Brazil
Fred Julio Costa Monteiro
Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Brazil
Vanessa S. Morais
Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil
Marlisson Octavio da S. Rego
Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Brazil
Emerson Luiz Lima Araújo
General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Brazil
Ramendra Pati Pandey
Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India
V. Samuel Raj
Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India
Xutao Deng
Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA
Eric Delwart
Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India
Antonio Charlys da Costa
Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil
Élcio Leal
Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil
The simultaneous transmission of two lineages of the chikungunya virus (CHIKV) was discovered after the pathogen’s initial arrival in Brazil. In Oiapoque (Amapá state, north Brazil), the Asian lineage (CHIKV-Asian) was discovered, while in Bahia state, the East-Central-South-African lineage (CHIKV-ECSA) was discovered (northeast Brazil). Since then, the CHIKV-Asian lineage has been restricted to the Amazon region (mostly in the state of Amapá), whereas the ECSA lineage has expanded across the country. Despite the fact that the Asian lineage was already present in the Amazon region, the ECSA lineage brought from the northeast caused a large outbreak in the Amazonian state of Roraima (north Brazil) in 2017. Here, CHIKV spread in the Amazon region was studied by a Zika–Dengue–Chikungunya PCR assay in 824 serum samples collected between 2013 and 2016 from individuals with symptoms of viral infection in the Amapá state. We found 11 samples positive for CHIKV-Asian, and, from these samples, we were able to retrieve 10 full-length viral genomes. A comprehensive phylogenetic study revealed that nine CHIKV sequences came from a local transmission cluster related to Caribbean strains, whereas one sequence was related to sequences from the Philippines. These findings imply that CHIKV spread in different ways in Roraima and Amapá, despite the fact that both states had similar climatic circumstances and mosquito vector frequencies.
