Rotavirus Outbreak Traced in Clinical, Environmental, and Food Matrices: Whole Genomic Characterization of an Equine-like G3P[8] Genotype

Abstract

The emergence of new viral strains has been frequently associated with the onset of outbreaks in different epidemiological settings. This study investigated an acute gastroenteritis (AGE) outbreak, which occurred at a university campus in southern Brazil, in 2024, affecting approximately 30–40% of undergraduate students, with over 400 reported cases. The objectives were to describe the epidemiological and molecular features of the outbreak, identify the probable transmission route, and assess the genetic relatedness of the detected strain to recently circulating rotavirus A (RVA) lineages. Clinical, environmental, and food samples were analysed for RVA and norovirus genogroup (G) I and GII. RT-qPCR detected RVA in the three specimen types with concentrations reaching 2.4 × 10 8 genome copies (GC)/g in faeces, 3.5 × 10 2 GC/g in food and 5.5 log₁₀ GC/l in water. Genotyping revealed an equine-like G3P[8] strain in clinical samples with whole genome sequencing establishing a DS-1-like backbone; G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Sequencing data of the VP6 gene of RVA detected in one of the environmental samples confirmed the same genotype (I2), consistent with the genotype found in the clinical stool samples. The detection of RVA in multiple environmental and food specimens suggests that the possible source of contamination was associated with water supply systems. Phylogenetic analyses showed that the outbreak strain clustered with equine-like G3P[8] lineages. These findings highlight the importance of integrating molecular surveillance and environmental monitoring to trace viral transmission pathways and detect the emergence of RVA strains in community outbreaks.

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