Molecular detection and characterization of rotavirus A in wastewater from Morogoro, Tanzania

Rotavirus A (RVA) remains a leading cause of acute gastroenteritis in infants and young children globally. In Tanzania, RVA accounts for over 36% diarrhea related deaths and one-third hospitalizations in children. Despite the introduction of the Rotarix® vaccine in 2013, rotavirus-associated morbidity remains high particularly in areas with poor sanitation. This cross-sectional study aimed to detect and characterize rotavirus in samples collected from three wastewater treatment plants in Morogoro, Tanzania to monitor RVA circulation. A total of 189 grab samples were collected weekly between November 2024 and February 2025. Samples were pooled by site, yielding 93 pooled samples, and processed for RVA detection using reverse transcription polymerase chain reaction (RT-PCR) targeting VP4 and VP7 genes, followed by Sanger sequencing and phylogenetic analysis. RVA was detected in 8.6% (n=93) of the pooled samples: 16.1% in Mafisa, 9.7% in Mzumbe, and 0% in Magadu (p=0.074). Genotyping identified G3 and P [8] as predominant RVA genotypes, clustering within lineage III and showing ≥97.5% nucleotide identity with known RVA strains. This study confirms the presence of rotavirus A G3P [8] genotypes in wastewater influent in Morogoro, Tanzania. The study highlights the utility of wastewater surveillance as a complementary tool for monitoring rotavirus circulation.