Genetic Diversity of the Non-Polio Enteroviruses Detected in Samples of Patients with Aseptic Meningitis in the Ural Federal District and Western Siberia

Human non-polio enteroviruses (NPEV) cause a plethora of infections in humans, ranging from mild to severe neurological diseases including aseptic meningitis. NPEV are the leading cause of aseptic meningitis in both children and adults worldwide. In Russia, reports of NPEV infections have surged, especially in the post-COVID era starting in 2022, with elevated infection rates into 2023. A comprehensive examination of the complete genome is crucial for understanding the evolution of NPEV genes and for predicting potential outbreaks. The study focused on to identify the circulating NPEV strains in the Ural Federal District and Western Siberia, using Sanger sequencing and next-generation sequencing (NGS) methodologies. Biological samples were collected from (n = 225) patients diagnosed with aseptic. Bioinformatics analysis targeted the nucleotide sequences of the VP1 gene fragment, and the assembly of complete NPEV genomes. 159 NPEV were characterized, representing 70.7% of the collected samples. The main capsid variants forming the predominant genotypic profile included E30 (n = 39, 24.3%), E6 (n = 31, 19.3%), and CVA9 (n = 25, 15.6%). Using NGS sequencing, we successfully assembled 13 complete genomes for E6, E30, EV-B80, CVA9, CVB5, E11 and EV-A71. This molecular-genetic analysis provides contemporary insights into the genotypic composition, circulation patterns, and evolutionary dynamics of the dominant NPEV associated with aseptic meningitis in the Ural Federal District and Western Siberia. The laboratory-based monitoring and epidemiological surveillance for genetic changes and evolutionary studies are important for improving prevention and healthcare.