Abstract
Since introduction into Brazil in 2014, chikungunya virus (CHIKV) has presented sustained transmission, although much is unknown about its circulation in the midwestern states. Here, we analyze 24 novel partial and near complete CHIKV genomes from Cuiaba, an urban metropolis located in the Brazilian midwestern state of Mato Grosso (MT).Nanopore technology was used for sequencing CHIKV complete genomes. Phylogenetic and epidemiological approaches were used to explore the recent spatio-temporal evolution and spread of the CHIKV-ECSA genotype in Midwest Brazil as well as in the Americas.Epidemiological data revealed a reduction in the number of reported cases over 2018–2020, likely as a consequence of a gradual accumulation of herd-immunity. Phylogeographic reconstructions revealed that at least two independent introductions of the ECSA lineage occurred in MT from a dispersion event originating in the northeastern region and suggest that the midwestern Brazilian region appears to have acted as a source of virus transmission towards Paraguay, a bordering South American country.Our results show a complex dynamic of transmission between epidemic seasons and suggest a possible role of Brazil as a source for international dispersion of the CHIKV-ECSA genotype to other countries in the Americas.
Highlights
After the introduction of the Asian lineage of chikungunya virus (CHIKV) into the Americas in 2013, and subsequent detection of the East/Central/South African (ECSA) lineage in 2014 in Bahia state Northeast Brazil, more than 2.9 million infections have been reported in Brazil up to 2019 [1]
Since its introduction into Brazil in 2014, chikungunya virus (CHIKV) has presented sustained transmission, much is unknown about its circulation in the midwestern states
We obtained CHIKV RT-qPCR positive clinical samples as part of the genomic surveillance project called ZIBRA 2, which aimed to perform, from a lab on wheels, genome sequencing of arboviruses circulating in Midwest Brazil, in the Mato Grosso state
Summary
After the introduction of the Asian lineage of chikungunya virus (CHIKV) into the Americas in 2013, and subsequent detection of the East/Central/South African (ECSA) lineage in 2014 in Bahia state Northeast Brazil, more than 2.9 million infections have been reported in Brazil up to 2019 [1]. The ECSA lineage seems to be the main genotype currently circulating in Brazil since its introduction in the northeastern region in 2014, despite detection of the Asian lineage in that same year in northern Brazil [4]. Despite the large number of cases, much is unknown about the genomic diversity and evolution of CHIKV lineages currently circulating in the midwestern region of Brazil, as well as their dispersion dynamics in South American countries that border this Brazilian region. To investigate the genomic diversity and evolution of CHIKV, we analyzed 24 new CHIKV genomes generated by generation sequencing, providing additional information on the introduction and spread of the ECSA lineage in Midwest Brazil as well as in the Americas
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