Assessment of Genetic Diversity of Noroviruses Circulating in Temporary Accommodation Centers for Refugees in the Rostov Region in 2022 Using the NoroNetRus Online Software

Abstract

Introduction: It is obvious that effective investigation of norovirus outbreaks is impossible without the use of methods enabling differentiation of pathogen genotypes, the principal of which is the determination of the type of capsid and polymerase based on sequencing data. Yet, unstable operation of international services for assessment of norovirus genomes from a number of IP addresses located in the Russian Federation has been noted recently, which may affect the efficiency and promptness of inves- tigation of norovirus outbreaks in our country. Objective: To develop domestic software for genotyping of noroviruses and further assessment of genetic diversity of norovi- ruses identified in the year 2022 in the Rostov Region. Materials and methods: The materials for the study were stool samples from 210 patients with symptoms of gastrointestinal infec- tions from temporary accommodation centers for refugees and children’s centers. The study population included patients aged 1 month to 74 years with symptoms of acute bowel infections. Detection of the pathogen RNA was carried out using a reagent kit AmpliSens® OKI screen-FL (Moscow, Russia). Fragment sequencing was performed using a genomic analyzer SeqStudio (Thermo Fisher, USA). The authors’ software was developed in the Java and Python programming languages. Results: We developed a domestic NoroNetRus software allowing determination of the type of capsid and polymerase of noroviruses based on sequencing data. The software is free of charge and available online at http://antiplague.ru/noronetrus. The fragment analysis of VP1 gene sequences for 25 norovirus samples showed that they belonged to three different genotypes (GII.4 Sydney, GII.10, and GII.17), and the genotype GII.10, in its turn, was distributed between two different clusters. Our findings indicate the existence of at least four different sources of infection. Conclusion. The data obtained indicate the circulation of at least four different genovariants of the causative agent of norovirus infection in the Rostov Region in 2022.