The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia.

Delta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to the emergence of multiple sublineages, most of which are well-mixed between countries. By contrast, here we show that nearly the entire Delta epidemic in Russia has probably descended from a single import event, or from multiple closely timed imports from a single poorly sampled geographic location. Indeed, over 90 per cent of Delta samples in Russia are characterized by the nsp2:K81N + ORF7a:P45L pair of mutations which is rare outside Russia, putting them in the AY.122 sublineage. The AY.122 lineage was frequent in Russia among Delta samples from the start, and has not increased in frequency in other countries where it has been observed, suggesting that its high prevalence in Russia has probably resulted from a random founder effect rather than a transmission advantage. The apartness of the genetic composition of the Delta epidemic in Russia makes Russia somewhat unusual, although not exceptional, among other countries.

Case report: change of dominant strain during dual SARS-CoV-2 infection.

BACKGROUND: The dual infection with SARS-CoV-2 is poorly described and is currently under discussion. We present a study of two strains of SARS-CoV-2 detected in the same patient during the same disease presentation. CASE PRESENTATION: A patient in their 90 s was hospitalised with fever. Oropharyngeal swab obtained on the next day (sample 1) tested positive for SARS-CoV-2. Five days later, the patient was transferred to the ICU (intensive care unit) of the hospital specialising in the treatment of COVID-19 patients, where the patient's condition progressively worsened and continuous oxygen insufflation was required. Repeated oropharyngeal swab (sample 2), which was taken eight days after the first one, also tested positive for SARS-CoV-2. After 5 days of ICU treatment, the patient died. The cause of death was a coronavirus infection, which progressed unfavourably due to premorbid status. We have performed sequencing of full SARS-CoV-2 genomes from oropharyngeal swabs obtained eight days apart. Genomic analysis revealed the presence of two genetically distant SARS-CoV-2 strains in both swabs. Detected strains belong to different phylogenetic clades (GH and GR) and differ in seven nucleotide positions. The relative abundance of strains was 70% (GH) and 30% (GR) in the first swab, and 3% (GH) and 97% (GR) in the second swab. CONCLUSIONS: Our findings suggest that the patient was infected by two genetically distinct SARS-CoV-2 strains at the same time. One of the possible explanations is that the second infection was hospital-acquired. Change of the dominant strain ratio during disease manifestation could be explained by the advantage or higher virulence of the GR clade strain.

Analysis of Google Trends queries in Russia during the coronavirus infection pandemic as a tool for epidemiological surveillance

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being, Moscow, Russia The coronavirus infection (COVID-19) pandemic has created a unique opportunity to study the activity patterns of Internet users due to the novel disease and to investigate how they are related to the real cases of SARS-CoV-2 infection. Objective. To conduct epidemiological and social studies of public awareness about the novel coronavirus infection (COVID-19) in the Russian Federation. Materials and methods. The «COVID-19» queries obtained using the Google Trends in the period from January 9, 2001 to September 24, 2020 were analyzed. Results. Search activity for the queries that may be associated with COVID-19 symptoms, such as olfaction and loss of olfaction, has a strong positive correlation with the confirmed number of cases in Russia (r = 0.81 for an olfaction query and r = 0.79 for a loss of olfaction query). There was a strong and moderate negative correlation between the queries «cough» and «sputum»: - 0.72 and - 0.53, respectively. A strong positive correlation was also found between the real cases of the infection and the queries related to the diagnosis of COVID-19, such as CT(r = 0.71) and antibodies (r = 0.79). Conclusion. The relationship between relative search volume (RSV) in the Internet and the confirmed number of cases can be of great importance for monitoring the rapidly evolving epidemic situation that requires up-to-date information on the spread of the disease. Пандемия коронавирусной инфекции (COVID-19) создала уникальную возможность исследовать закономерности активности пользователей в Интернете в связи с новым заболеванием и исследовать, как они связаны с реальными случаями заражения SARS-CoV-2. Цель исследования. Эпидемиологическое и социальное изучение осведомленности населения Российской Федерации о новой коронавирусной инфекции - COVID-19. Материалы и методы. Проведен анализ запросов по теме «COVID-19», полученных из Google Trends, за период с 09.01 по 24.09 2020 г. Результаты. Поисковая активность по запросам, которые могут быть связаны с симптомами COVID-19 «обоняние» и «потеря обоняния», имеет выраженную позитивную корреляцию с подтвержденным числом случаев заболевания в России (r = 0,81 для запроса «обоняние» и r = 0,79 для запроса «потеря обоняния»). Между запросами «кашель», «мокрота» и реальными случаями заражения была выявлена сильная и средняя отрицательная корреляция: - 0,72 и - 0,53 соответственно. Также сильная положительная корреляция выявлена между реальными случаями заражения и запросами, связанными с диагностикой COVID-19: «КТ» (компьютерная томография;r = 0,71) и «антитела» (r = 0,79). Заключение. Связь между относительным объемом поиска в Интернете и подтвержденным числом случаев может иметь важное значение для мониторинга быстро меняющейся эпидемической ситуации, когда требуется актуальная информация о распространении заболевания.