Genomic and epidemiologic investigation of arboviral coinfections, Espírito Santo, Brazil

Abstract

Background: In Brazil, the simultaneous circulation of arboviruses is driven by anthropological factors. In places with intense arbovirus transmission, such as Espírito Santo, it is important to investigate the epidemiology of coinfections in order to provide information to improve surveillance and management strategies.

Methods: We assessed their prevalence, clinical impact, and viral diversity in Espírito Santo, Brazil (2023-2024), testing 66,019 patients for dengue, chikungunya, Zika, Mayaro, and Oropouche viruses via RT-qPCR and genomic sequencing.

Results: Overall, 34.45% tested positive, mainly for OROV (21.93%), DENV (19.57%), and CHIKV (6.94%), while ZIKV and MAYV were undetected. Coinfections were rare (0.2%, n = 44), mostly DENV/CHIKV (75%), with 2 novel DENV-1/DENV-2/CHIKV cases and 1 OROV/DENV-2. Sequencing yielded 12 complete viral genomes, identifying distinct DENV-1, DENV-2, CHIKV, and OROV lineages.

Discussion: Genomic characterization of coinfection samples provided a comprehensive view of arboviral genetic diversity, revealing the presence of multiple cocirculating strains. Despite the hyperendemic scenario, coinfections were rare, probably due to complex interactions between viral interference, host immunity, vector behavior and diagnostic challenges.

Conclusions: We report the first triple arbovirus infection documented in Espírito Santo and coinfection with OROV outside endemic areas, emphasizing the importance of molecular diagnosis and ongoing research to understand arboviral dynamics and prepare for outbreaks.

Keywords: Arbovirus coinfection; Epidemiological surveillance; Genomic sequencing; Hyperendemic region.