Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil

Abstract

The emergence and reemergence of mosquito-borne diseases in Brazil such as yellow fever, zika, chikungunya, and dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus across the country since its first detection in 2014 in Northeast Brazil. In this work, we carried out on-site training activities in genomic surveillance in partnership with the National Network of Public Health Laboratories that have led to the generation of 422 chikungunya virus genomes from 12 Brazilian states over the past two years (2021–2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersal dynamics of the chikungunya virus East-Central-South-African lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C > T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving the genetic diversity of the chikungunya virus in Brazil.

A Multiplex Nanopore Sequencing Approach for the Detection of Multiple Arboviral Species

“…Once its efficacy to recover viral long reads from clinical samples had been established, the Ampli-FlaCk protocol was employed for testing in the field activities of an arbovirus genomic surveillance project carried out in Uruguay (early 2023) [ 20 ] and across Brazil in the years 2021 and 2022 [ 8 ]. The sequencing of 20 clinical samples collected during those surveillance activities resulted in the recovery and identification of reads of ZIKV, DENV-2, DENV-3, and DENV-4 ( Table S5 ).…”

“…DNA sequencing technology has been proven useful in recent efforts to control infectious disease outbreaks, by providing relevant epidemiological aspects regarding the dynamics of an epidemic [ 6 ]. The nanopore sequencing platform is a potential tool for diagnostic purposes due to its cost effectiveness, rapid turnaround time, and portability, which allow it to be employed in the investigation of several viral outbreaks [ 7 , 8 , 9 ]. Hence, in this study, we integrated nanopore sequencing and the advantages of reverse transcription polymerase chain reaction (RT-PCR) to develop a multiplex RT-PCR protocol for the detection of Chikungunya virus (CHIKV) (genus Alphavirus ) and several orthoflaviviruses in a single reaction, which provides data for sequence-based differentiation of arbovirus lineages.…”

Simultaneous Dengue and Chikungunya Coinfection in Endemic Area in Brazil: Clinical Presentation and Implications for Public Health

“…In 2014, CHIKV was first reported in the northern region of Brazil, along the border with French Guiana. Since its introduction, CHIKV, while less prevalent than dengue, has had a significant impact on public health as it spread throughout the country [ 8 ] [ 9 ]. Until 2017, the most prevalent Brazilian region was the Northeast, but since then, many cases have arisen, mainly in the Southeast region.…”

Intelligent preliminary diagnosis system for diseases with similar clinical presentation

“…For example, diseases caused by dengue, chikungunya, zika, and yellow fever viruses are closely linked to the behavior and development of the aedes aegypti mosquito [2]. Due to similarities in their clinical and epidemiological behavior, these diseases are often misdiagnosed [3], posing a serious threat to public health in tropical and subtropical areas [4]- [6].…”