Assessment of the covid-19 epidemiological situation in st. Petersburg

Aim. Identification of epidemiological patterns of the SARS-CoV-2 spread among the population of St. Petersburg during the one-year COVID-19 pandemic period. Materials and methods. The performed analysis focused on the dynamics of COVID-19 cases in St. Petersburg from 2/3/2020 to 4/4/2021 and on the gender-age profile of patients. The information about patients (age, gender, type of the disease, hospitalization, social, and occupational status) was obtained from the database containing the materials from statistical data form No. 058/u. Results. After one year, the dynamics of reported cases of COVID-19 in St. Petersburg shows two cycles of seasonal surge (spring and autumn-winter) and 8 epidemic periods. It has been found that there are no gender-age differences among COVID-19 patients, which can be seen from the relatively similar number of cases among men and women per 100,000 people in each age group during specific epidemic periods. The strong association between clinical manifestations of COVID-19 and the patients’ age was detected: Severe cases were more frequently diagnosed in patients over 70 years, regardless of their gender identity. Based on the social and occupational status, the people who were most exposed to the COVID-19 epidemic process were retirees and people whose occupation was associated with health and safety of St. Petersburg. Among the COVID-19 patients, retirees accounted for 13.69% (men) and 17.67% (women). The proportion of healthcare workers was 3.67% (men) and 9.41% (women). Conclusion. It has been assumed that COVID-19 tends to be a seasonal disease featuring annual autumn-winter epidemic cycles. The study addressed prospects of preventive vaccination against COVID-19 in Russia and the importance of tracking the complications pathogenetically associated with the acute phase of the disease in the system of epidemiological surveillance. © 2021, Central Research Institute for Epidemiology. All rights reserved.

Characteristics of the COVID-19 epidemiological situation in the Russian Federation in 2020

Background. The COVID-19 epidemic in the Russian Federation, which began in March 2020, caused serious damage to health of the population and led to severe economic losses. By December 28, 2020, 3 078 035 cases of COVID-19 and 55 265 lethal outcomes were registered in the country. The population of all territorial subjects of the country is involved in the epidemic process of COVID-19. The severe epidemiological situation made it necessary to conduct an analysis to identify the factors that determine the high intensity of the epidemic process, as well as the population groups with the highest risk of SARS-CoV-2 infection. Aims - to study the patterns of SARS-CoV-2 spread and the epidemiological features of the initial stage of the COVID-19 pandemic in the Russian Federation in 2020. Methods. An epidemiological analysis of the COVID-19 situation in the Russian Federation was carried out to determine the dynamics of morbidity, the gender proportion and age structure of patients, the proportion of hospitalized patients, the ratio of various forms of infection, the social and professional status of patients. Standard methods of descriptive statistics Microsoft Excel and STATISTICA 12.0 (StatSoft, USA) were used for statistical processing. The mean values were estimated with a 95% confidence interval [95% CI] (the exact Klopper - Pearson method). Results. During the observation time (2020), several periods were identified in the dynamics of the new COVID-19 cases detection: the period of importation of SARS-CoV-2 and the increase in morbidity, the period of epidemic decline, the period of autumn growth, the period of sustained high incidence of COVID-19. It was found that people over 70 years of age are the group with the highest risk of infection and a more severe course of COVID-19. The presence of target contingents among social and professional groups of the population, which should include medical workers, retired person, employees of educational institutions, law enforcement agencies, transport, who require special attention and medical and social support, was shown. Conclusions. The analysis showed that the large-scale spread of COVID-19 requires in-depth epidemiological studies and the development of additional disease control measures, taking into account the dynamics of the incidence of this socially significant infection.

Genetic variability of SARS-CoV-2 in biological samples from patients in Moscow

Currently, a lot of attention is given to SARS-CoV-2 subpopulations and their coexistence with different genomic variants within the same patient. In this study, we performed next-generation whole-genome sequencing and assembly of viruses from samples representing swabs or autopsy specimens obtained from patients diagnosed with СOVID-19, which were initially confirmed by the real-time polymerase chain reaction (Ct = 10.4-19.8). Samples were prepared for sequencing by using the SCV-2000bp protocol. The obtained data were checked for presence of more than one SARS-CoV-2 genetic variants in a sample. Variants of nucleotide substitutions, coverage for each variant, and location of the variable position in the reference genome were detected with tools incorporated in the CLC Genomics Workbench program. In our search for variable nucleotide positions, we assumed that the sample had two genetic variants (not more);the threshold value ≥ 90% was set for probability of the identified variant. Variants represented by less than 20% of the reads in the total coverage were not taken into consideration. The obtained results showed that 5 samples had variability, i.e. they had several genetic variants of SARS-CoV-2. In 4 samples, both of the detected genomic variants differed only in one nucleotide position. The fifth sample demonstrated more substantial differences: a total of 3 variable positions and one three-nucleotide deletion. Our study shows that different genetic variants of SARS-CoV-2 can coexist within the same patient. Сосуществование субпопуляций SARS-CoV-2 с различными вариантами генома внутри организма одного пациента - один из обсуждаемых в настоящее время феноменов. В данной работе мы провели высокопроизводительное секвенирование и сборку полных геномов вирусов из образцов, которые представляли собой мазки или аутопсийный материал от пациентов с диагнозом СOVID-19, предварительно подтвержденным методом полимеразной цепной реакции в реальном времени (Ct = 10,4-19,8). Подготовку образцов к секвенированию проводили с помощью протокола SCV-2000bp. Полученные данные проверяли на присутствие в образце более чем одного генетического варианта SARS-CoV-2. Варианты нуклеотидных замен, покрытие для каждого варианта, а также координаты вариабельной позиции в референсном геноме определяли с помощью инструментов программы «CLC Genomics Workbench». При поиске вариабельных нуклеотидных позиций исходили из предположения, что в образце имеются 2 генетических варианта (не более), для вероятности определяемого варианта использовали пороговое значение ≥ 90%. Также игнорировали варианты, которые были представлены менее чем 20% прочтений от общего покрытия. Полученные результаты показали, что в 5 образцах имеется вариабельность, т.е. содержится несколько генетических вариантов SARS-CoV-2. В 4 образцах оба найденных варианта геномов различались лишь в одной нуклеотидной позиции. В пятом образце были найдены более существенные различия: сразу 3 вариабельных позиции и одна делеция длиной в 3 нуклеотида. Наше исследование показывает возможность сосуществования различных генетических вариантов SARS-CoV-2 в организме пациента.

[Analysis of human coronaviruses circulation].

INTRODUCTION: The novel SARS-CoV-2 coronavirus, which emerged at the end of 2019 and caused a worldwide pandemic, triggered numerous questions about the epidemiology of the novel COVID-19 disease and  about wellknown coronavirus infections, which used to be given little attention due to their mild symptoms. THE PURPOSE: The routine screening-based multiyear retrospective observational study of prevalence and circulation patterns of epidemic-prone human coronaviruses in Moscow. MATERIAL AND METHODS: The real-time polymerase chain reaction was used to detect RNA of human coronaviruses (HCoVs) in nasal and throat swabs from 16,511 patients with an acute respiratory infection (ARI), aged 1 month to 95 years (children accounted for 58.3%) from January 2016 to March 2020, and swabs from 505 relatively healthy children in 2008, 2010 and 2011. Results. HCoVs were yearly found in 2.6-6.1% of the examined patients; the detection frequency was statistically higher in adults than in children, regardless of sex. At the height of the disease incidence in December 2019, HCoVs were detected in 13.7% of the examined, demonstrating a two-fold increase as compared to the multi-year average for that month. The statistical frequency of HCoV detection in ARI pediatric patients under 6 years was significantly higher than in their healthy peers (3.7 vs 0.7%, p = 0.008). CONCLUSION: HCoVs circulate annually, demonstrating a winter-spring seasonal activity pattern in the Moscow Region and reaching peak levels in December. Over the years of observation, the HCoV epidemic activity reached maximum levels in December 2019-February 2020 and decreased in March to the multi-year average. Amid a growing number of SARS-CoV-2 cases imported to Moscow in March 2020, the HCoV detection frequency dropped sharply, which can be explained by the competition between different coronaviruses and by the specificity of HCoV detection with the diagnostic test kit used in this study.

Gender-age distribution of patients with COVID-19 at different stages of epidemic in Moscow

The ongoing COVID-19 pandemic around the world and in Russia remains a major event of 2020. All over the world, research is being conducted to comprehensively study the patterns and manifestations of the epidemic process. The main quantitative characteristics of SARS-CoV-2 transmission dynamics among the population, based on the data of official monitoring over the current situation, play an important role in the development of the epidemiological surveillance system. The aim of this study is to explore the peculiarities of age-gender distribution of COVID-19 patients in Moscow. Material and methods. The data related to the epidemiological characteristics of age-gender structure of COVID-19 patients in Moscow between March 19, 2020 and April 15, 2020, at different stages of the epidemic were retrospectively analyzed. Results and discussion. The mean age of COVID-19 patients in Moscow was 46,41±20,58 years. The gender ratio (male/female) among the patients was 52.7/47.3 %, wherein the indicators varied depending upon the age. Male/female ratio in the age group “under 39” stood at 53.7/46.3 %, and “over 40 years of age” – at 39.3/60.7 %. The predominant age range among male cases was 19 to 39 years old – 35.4 %, while among female patients – 40–59 years (36.5 %). The age distribution of patients in Moscow is indicative of the fact that COVID-19 is a disease that primarily affects older age groups. The age structure of all COVID-19 cases during the observation period is characterized by predominance of adult patients over 19 years of age – 92,7 % (92,6–92,8 %), the share of patients aged 40–59 years is 35,7% (35,5–35,9 %). The differences in the age distribution in males and females are as follows: in the male cohort, the age groups 19–39 years old and 40–59 years old prevail – 35.4 % (35.1–35.7 %) and 34.9 % (34.6–35.2 %), respectively. The age group 40–59 years old – 36.5 % (36.3–36.8%) dominates in the female cohort. © 2020 Russian Research Anti-Plague Institute. All rights reserved.

[Patterns of the SARS-CoV-2 epidemic spread in a megacity].

The purpose of the study is to analyze patterns demonstrated by the COVID-19 epidemic process in a megacity during the increase, stabilization and reduction in the incidence, and to evaluate the effectiveness of the epidemic prevention measures. MATERIALS AND METHODS: The comprehensive study incorporating epidemiological, molecular genetic and  statistical research methods was conducted to analyze the spread of SARS-CoV-2 in Moscow during the COVID- 19 pandemic. RESULTS AND DISCUSSION: It was found that the exponential growth in COVID-19 cases was prevented due to the most stringent control and restrictive measures deployed in Moscow to break the chains of SARS-CoV-2 transmission and due to people who were very disciplined in complying with the self-isolation rules. The  analysis of the dynamics in detection of new COVID-19 cases showed that in a megacity, the impact of social distancing and self-isolation would become apparent only after 3.5 incubation periods, where the maximum length of the period is 14 days. It was discovered that the detection frequency of SARS-CoV-2 RNA in relatively healthy population and its dynamics are important monitoring parameters, especially during the increase and stabilization in the COVID-19 incidence, and are instrumental in predicting the development of the epidemic situation within a range of 1-2 incubation periods (14-28 days). In Moscow, the case fatality rate was 1.73% over the observation period (6/3/2020-23/6/2020). CONCLUSION: The epidemiological analysis of the COVID-19 situation in Moscow showed certain patterns of the SARS-CoV-2 spread and helped evaluate the effectiveness of the epidemic prevention measures aimed at  breaking the routes of transmission of the pathogen.