A dramatic increase of influenza activity in Russia since week 3 of 2016 significantly differs from previous seasons in terms of the incidence of influenza and acute respiratory infection (ARI) and in number of lethal cases. We performed antigenic analysis of 108 and whole‐genome sequencing of 77 influenza A(H1N1)pdm09 viruses from Moscow and Saint Petersburg. Most of the viruses were antigenically related to the vaccine strain. Whole‐genome analysis revealed a composition of specific mutations in the internal genes (D2E and M83I in NEP, E125D in NS1, M105T in NP, Q208K in M1, and N204S in PA‐X) that probably emerged before the beginning of 2015/2016 epidemic season.

Survey data from autopsy specimens from patients who died from pneumonia caused by the influenza A(H1N1) pdm09 in 2012-2014 and mutant forms of influenza virus in these patients (position 222 in the receptor-binding region of hemagglutinin) were presented. In total, according to aggregate data, obtained with three different methods (sequencing, next-generation sequencing (NGS), virus isolation) mutant viruses were detected in 17 (41%) from 41 patients. The proportion of the mutant forms in viral populations ranged from 1% to 69.2%. The most frequent mixture was the wild type (D222) and mutant (D222G), with proportion of mutant type ranged from 3.3% to 69.2% in the viral population. Mutation D222N (from 1.1% to 5.5%) was found rarely. Composition of the viral population from one patient is extremely heterogeneous: in left lung there was only wild type D222, meantime in right lung - mixture of mutant forms 222D/N/G (65.4/32.5/1.1%), in trachea - mixture 222D/G/Y/A (61.8/35.6/1.2/1.4%, respectively), and in bronchi compound of 222D/G/N/A (64.3/33.7/1/1%, respectively) were detected. The obtained data indicate that the process of adaptation of the virus in the lower respiratory tract is coupled with the appearance of different virus variants with mutations in the receptor-binding region. Mutant forms of the virus are observed in the lower respiratory tract of the majority of patients with lethal viral pneumonia. However, if they are a minor part of the population, they cannot be detected by the method of conventional sequencing. They can be identified using the NGS methods.

Background To better understand the impact of seasonal influenza in pregnant women we analyzed data collected during four seasons at a hospital for acute respiratory infection that specializes in treating pregnant women. Methods This was a single-center active surveillance study of women 15–44 years of age hospitalized for acute respiratory diseases between 2012/2013 and 2015/2016 in Moscow, Russian Federation. Women had to have been hospitalized within 7 days of the onset of symptoms. Swabs were taken within 48 h of admission, and influenza was detected by reverse transcription-polymerase chain reaction. Results During the four seasons, of the 1992 hospitalized women 1748 were pregnant. Laboratory-confirmed influenza was detected more frequently in pregnant women (825/1748; 47.2%) than non-pregnant women (58/244; 23.8%) (OR for influenza = 2.87 [95% CI, 2.10–3.92]; p <  0.001). This pattern was homogenous across seasons ( p = 0.112 by test of homogeneity of equal odds). Influenza A(H1N1)pdm09 was the dominant strain in 2012/2013, A(H3N2) in 2013/2014, B/Yamagata lineage and A(H3N2) in 2014/2015, and A(H1N1)pdm09 in 2015/2016. Influenza-positive pregnant admissions went to the hospital sooner than influenza-negative pregnant admissions ( p <  0.001). The risk of influenza increased by 2% with each year of age and was higher in women with underlying conditions (OR = 1.52 [95% CI, 1.16 to 1.99]). Pregnant women positive for influenza were homogeneously distributed by trimester ( p = 0.37 for homogeneity; p = 0.49 for trend). Frequencies of stillbirth, delivery, preterm delivery, and caesarean delivery did not significantly differ between influenza-positive and influenza-negative hospitalized pregnant women or between subtypes/lineages. Conclusions Pregnant women are at increased risk for hospitalization due to influenza irrespective of season, circulating viruses, or trimester. Electronic supplementary material The online version of this article (10.1186/s12884-019-2192-z) contains supplementary material, which is available to authorized users.

In the 2015-2016 epidemic season, there were dominant influenza A(H1N1)pdm09 strains (over 90%) among the circulating influenza viruses in most countries of the Northern Hemisphere and in Russia. A study of the antigenic properties of influenza A(H1N1)pdm09 strains revealed no differences in those of vaccine virus. Sequencing showed that there were amino acid substitutions in hemagglutinin (receptor binding and Sa sites) and in the genes encoding internal proteins (PA, NP, M1, and NS1). The rise in the incidence in the Russian Federation, which was etiologically associated with influenza viruses, was registered in January-February 2016 with its maximum being observed at 4-5 weeks of 2016. Within the framework of the epidemiological surveillance of circulating influenza viruses in the Russian Federation, which was conducted by the WHO European Office, the D.I. Ivanovsky Institute of Virology, Honorary Academician N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of Russia, and the Research Institute of Influenza, Ministry of Health of Russia, monitored at the Infectious Diseases Hospital One (IDH-1), Moscow Healthcare Department. Among 1491 examinees, influenza was verified in 104 (21.3%) adults, 208 (42.5%) pregnant women, and 177 (36.2%) children. Influenza A(H1N1)pdm09 was more often diagnosed in the age group of 15-40 years (63.7%); the proportion of influenza patients aged over 50 years increased (22.1%). Most adult patients had moderate influenza; pneumonia complicated the disease in 27.4%. Influenza in the pregnant women was complicated by pneumonia in 4.8% of cases. Influenza was more frequently diagnosed in infants and preschool children aged 0 to 3 years (42.9%), 4 to 6 years (41.2%), and older (15.9%), namely: 7-9 years (10%) and 10-12 years (5.9%). Influenza in the children was complicated by acute tonsillitis (19.4%) and varying degrees of laryngeal stenosis (12.4%). Bronchial obstructive syndrome developed in 2.5%, the rate of pneumonia was 6.2%. Antiviral therapy (AVT) in the early stages of the disease reduces the risk of its severity, the frequency of secondary complications, and the duration and degree of clinical symptoms of influenza. AVT with oseltamivir, zanamivir, imidazolyl ethanamide pentandioic acid (ingavirin), and interferon-a2b (viferon) has been performed in the patients hospitalized at Moscow IDH-1 in the 2015-2016 epidemic season.

Институт вирусологии им. Д. И. Ивановского, ФГБУ «НИЦ эпидемиологии и микробиологии имени почетного академика Н. Ф. Гамалеи» Минздрава России, Москва 2 «Инфекционная клиническая больница №1» Департамента Здравоохранения г. Москвы Активность вирусов гриппа в сезон 2017-2018 гг. в России и странах Северного полушария: конфликт по В-вирусному компоненту вакцин Резюме Актуальность. Вирусы гриппа, обладая чрезвычайно высокой изменчивостью генома и существенной экологической пластичностью, продолжают сохранять потенциальную угрозу биологической безопасности человечества. Цель работы-анализ особенностей эпидемического сезона 2017-2018 гг. Материалы и методы. Сбор данных по заболеваемости и лабораторной диагностике гриппа и ОРВИ осуществлялся в рамках эпидемиологического надзора за циркуляцией вирусов гриппа в РФ. Период наблюдения составил с 40 недели (октябрь) 2017 г. по 25 неделю (июнь) 2018 г. Типирование изолятов проводили в реакции торможения гемагглютинирующей активности (РТГА) по общепринятой методике с диагностическими сыворотками к эталонным и эпидемическим вирусам гриппа. Результаты и обсуждение. Представлены особенности циркуляции вирусов гриппа с октября 2017 г. по май 2018 г. на отдельных территориях России, сотрудничающих с Институтом вирусологии им. Д. И. Ивановского. Эпидемический сезон имел свои особенности: отсроченная и длительная активность трех вирусов гриппа, долевое участие которых было практически равнозначным, с некоторым доминированием к концу сезона вируса гриппа A(H1N1)pdm09. Показатели заболеваемости по совокупному населению были сравнимы с прошлым эпидемическим сезоном в тоже время заболеваемость у школьников была значительно выше. Число госпитализаций и летальных случаев было меньше и в основном их регистрировали в возрастной группе 65 лет и старше. У пациентов с тяжелой острой респираторной инфекцией (ТОРИ) более часто детектировали грипп A(H1N1)pdm09 (58%). Вирусы гриппа A(H1N1)pdm09 и A(H3N2) имели близкое родство со штаммами, входившими в состав гриппозных вакцин, в тоже время, 96% выделенных штаммов вируса гриппа В принадлежали другой эволюционной линии. Эпидемические штаммы проявили чувствительность к препаратам с антинейраминидазной активностью, за исключением 5 штаммов вируса гриппа A(H1N1)pdm09, выделенных от беременных. Выводы. Долевое участие возбудителей ОРВИ не гриппозной этиологии было сравнимо с предыдущими эпидемическими сезонами. Представлены рекомендации экспертов