Uncovering DENV, CHIKV, and ZIKV in Urban Wastewater in Brazil Through Genomic and Molecular Screening

This study evaluated and compared molecular methods for the detection of arboviruses Dengue (DENV), Chikungunya (CHIKV), and Zika (ZIKV) in wastewaters collected from July 2022 to May 2023 in the region of Belo Horizonte, Brazil. Detection rates varied substantially across the methods. DENV was identified in 24% (15/63) of samples using hybrid capture method of whole-genome sequencing (WGS) and MinION sequencing, in 66.6% (20/30) using only WGS, but was not detected using the CDC Trioplex RT-PCR Assay Kit and ZDC (IBMP). CHIKV was detected in 19.0% (12/63) of the samples by WGS and MinION, in 85.7% (12/14) using only MinION sequencing, and in 4.7% (3/63) by RT-PCR. ZIKV was found in only one sample (1/63) by WGS, while RT-qPCR yielded a high false-positive rate (65.1%, 41/63). The potential of genomic wastewater surveillance for arboviruses was demonstrated and that diagnostic RT-qPCR kits used for clinical samples were not directly suitable for environmental surveillance.