Genomic and Epidemiologic Investigation of Arboviral Co-infections, Espírito Santo, Brazil.

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 co-infections in order to provide information to improve surveillance and management strategies. MATERIAL AND 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. Co-infections were rare (0.2%, n=44), mostly DENV/CHIKV (75%), with two novel DENV-1/DENV-2/CHIKV cases and one OROV/DENV-2. Sequencing yielded 12 complete viral genomes, identifying distinct DENV-1, DENV-2, CHIKV, and OROV lineages. Most co-infected patients had a fever, headache, and myalgia, with only three hospitalized, all recovering. DISCUSSION: Genomic characterization of co-infection samples provided a comprehensive view of arboviral genetic diversity, revealing the presence of multiple co-circulating strains. Despite the hyperendemic scenario, co-infections 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 co-infection with OROV outside endemic areas, emphasizing the importance of molecular diagnosis and ongoing research to understand arboviral dynamics and prepare for outbreaks.