Chikungunya Virus Asian Lineage Infection in the Amazon Region Is Maintained by Asiatic and Caribbean-Introduced Variants

Abstract

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.

Chikungunya virus transmission in the Southernmost state of Brazil was characterized by self-limited cases (2017–2019) and a larger 2021 outbreak

“…However, after the first years of expansion, these genotypes have been undergoing distinct transmission dynamics. While the AC genotype remained mostly restricted to the North region (13), the ECSA genotype is spreading widely and has been detected in all Brazilian states (9,12,14,15,17,17–19). A recent study showed that the most affected region of Brazil was the Northeast (16), whereas limited CHIKF cases had been detected in the South region (20,43).…”

“…Early studies characterizing these events suggested that both lineages would spread and cause outbreaks country-wide, with a higher transmission potential in the tropical region (8). This hypothesis was later corroborated with several Brazilian states in the North, Northeast, Southeast and Central-West regions experiencing large CHIKV outbreaks; whereas the South region experienced lower CHIKV incidence (12)(13)(14)(15)(16)(17)(18)(19).…”