Genetic diversity and molecular epidemiological characterization of group A rotaviruses in raw sewage in Jinan by next generation sequencing

To understand the genetic diversity and molecular epidemiology characteristics of group A Rotavirus (RVA) in domestic sewage through next generation sequencing (NGS), and to explore the feasibility and necessity of NGS method for RVA environmental surveillance. In this study, two sewage samples from Jinan each quarter in 2019 were selected for concentration, RNA extraction, and then RT-PCR reaction. The amplified positive products were subjected to NGS. Finally, the results were analyzed for diversity and phylogeny. A total of 9 G-genotypes and 13 P-genotypes were detected. The Simpson diversity indices in autumn and winter were relatively high. Phylogenetic analysis showed that the dominant types G9 and P[8] were closely related to human-derived sequences. This study proves that environmental surveillance as a means to understand the prevalence of RVA in the population is not only feasible but necessary. NGS based environmental surveillance greatly improves our understanding on RVA genetic diversity, and should be encouraged as a sensitive surveillance tool. •To study the molecular epidemiological characteristics of RVA in Jinan City through environmental sewage surveillance.•9 RVA G- and 13 RVA P-genotypes was detected in this study.•G9 and P[8] were the most significant genotypes, closely related to human-derived strains.•NGS based environmental surveillance greatly improves our understanding on RVA genetic diversity.•Continuous study and surveillance of environmental sewage is important for understanding the prevalence of RVA in the population.