Objective: comparative study of the etiological structure of community-acquired pneumonia in SARSCoV-2 “+”and SARS-CoV-2 “-“ patients who sought help from medical organizations in the Rostov Region.Materials and methods. Biological material from 508 patients diagnosed with community-acquired pneumonia who were on outpatient treatment or in hospitals in Rostov-on-Don was studied. Verification of respiratory viruses, including SARS-CoV-2 RNA, as well as M. pneumoniae, C. pneumoniae, and L. pneumophila was performed by polymerase chain reaction in nasopharyngeal smears. Bacteriological analysis of sputum was carried out using differential diagnostic media, identification of isolated pathogens was carried out using time-of-flight mass spectrometry on Autoflex (Bruker Daltonics) with BioTyper 3.0 software.Results and discussion. During the spread of a new coronavirus infection in the Rostov Region, the main etiological agent of community-acquired pneumonia is the new SARS-CoV-2 coronavirus. Specific character of pneumonia in patients with laboratory-confirmed COVID-19 is a higher incidence of mixed infection of both viral and bacterial etiology. Against the background of detection of a new coronavirus infection in patients with pneumonia, cases of detection of other types of coronaviruses have been registered (HKU-1,OC43, HL-63 and 229Е). The most common etiological agent of bacterial pneumonia in patients was Streptococcus spp., both in patients with COVID-19-associated pneumonia and in patients who tested negative for SARS-CoV-2. Coronavirus patients represent a high risk group for the development of mycotic lung lesions.

Введение. Пандемия COVID-19 в 2020 году внесла свой вклад в эпидемиологию респираторных инфекций. Важным является своевременное проведение дифференциальной диагностики COVID-19 и сезонных острых респираторных заболеваний. У пациентов с новой коронавирусной инфекцией возрастает риск развития госпитальной пневмонии. Актуальным является анализ особенностей циркуляции резистентных к антибактериальным химиопрепаратам штаммов возбудителей внутрибольничных инфекций. Цель – изучение этиологической структуры внебольничных пневмоний в период эпидемического распространения COVID-19, оценка рисков присоединения возбудителей пневмоний, связанных с оказанием медицинской помощи. Материалы и методы: Исследовали биологический материал от 446 пациентов с диагнозом «внебольничная пневмония», находившихся на амбулаторном лечении или в стационарах г. Ростова-на-Дону. Верификация респираторных вирусов, включая РНК SARS-CoV-2, а также M. pneumoniae, C. pneumoniae, L. pneumophila выполнена методом полимеразной цепной реакции в мазках носоглотки. Бактериологический анализ мокроты проводили с использованием дифференциально-диагностических сред, идентификацию выделенных патогенов осуществляли с помощью времяпролетной масс-спектрометрии на приборе Autoflex (Bruker Daltonics) c программным обеспечением BioTyper 3,0. Результаты и обсуждение. В период распространения новой коронавирусной инфекции в Ростовской области доля положительных результатов на SARS-CoV-2 среди пациентов с диагнозом внебольничная пневмония составляет 35,6 %. Частота микстинфекций вирусной природы достоверно не отличалась среди пациентов с лабораторно подтвержденным диагнозом COVID-19 и пациентов с отрицательным результатом на SARS-CoV-2 (25,9 % и 26,2 %, соответственно). В структуре микробиоты превалировали грибы рода Candida и плазмокоагулирущие стафилококки. Достоверно чаще от пациентов с лабораторно подтвержденным COVID-19 изолировали культуры неферментирующих грамотрицательных бактерий. У 51,6% пациентов, проходивших лечение в стационаре, отмечено вторичное коинфицирование, вероятно связанное с объектами внешней среды или с передачей инфекции от персонала. Передача ИСМП между пациентами не установлена.

By August 2020, more than 850000 cases of new coronavirus infection (COVID-19) caused by SARSCoV-2 were confirmed in the Russian Federation, with the Rostov Region as one of the ten most affected regions in Russia. The spread of the disease is largely determined by the state of population immunity in a certain area. Our research focuses on specific humoral immune response and estimates the level of herd immunity to SARS-CoV-2 virus among the population of the Rostov Region.Materials and methods. The study involved 3,048 people; the volunteers participating in the study were divided into seven age groups. The content of antibodies to SARS-CoV-2 was determined applying ELISA using a kit for the analysis of human serum or blood plasma for the presence of specific IgG to the nucleocapsid of the SARS-CoV-2 virus, manufactured by the State Scientific Center of Applied Microbiology and Biotechnology (Obolensk) in accordance with the instructions for use.Results and discussion. The assessment of seroprevalence to SARS-CoV-2 in the Rostov Region showed that the proportion of people positive for IgG to the new coronavirus was 16.5 %, the range of seropositive individuals in the general population was between 13.9 % and 19.1 % (p<0.05). There were no significant gender differences in the degree of seroprevalence with a positive result registered in 16.6 % of women and 16.5 % of men. A high level of humoral immunity to SARS-CoV-2 was established in individuals aged 1–17 against the background of low incidence rates, which may indicate the dominance of asymptomatic forms of the disease in this age group. The highest level of seropositivity was found in preschool children (33.6 %), students (29.3 %), employees (17.3 %), and education professionals (15.3 %).

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.

Objective: To compare the genomic diversity of SARS-CoV-2 strains that were spread in the Rostov region and the Republic of Crimea in the period from March to June 2021.Materials and Methods: A total of 194 samples were sequenced and 186 genovariants were recognized among them using the Pangolin program. Multiple alignment was performed and dendrograms were constructed for the samples belonging to the alpha and delta genovariants.Results: Changes of the predominant genovariants were revealed for territories of the Rostov Region and the Republic of Crimea from March to June. An increasing percent of the alpha variant was observed in both regions during the spring followed by the rapid emergence of the delta variant, which became predominant in June.Conclusion: It was shown that alpha variant samples from the Rostov region share a pool of common mutations, while in contrast, alpha variant samples from the Republic of Crimea are closer to those sampled from Moscow and Moscow region. At the end of May, the delta gene variant begins to be revealed, which is rapidly replacing other lines in all the territories considered in this study.