Source of the COVID-19 pandemic: Ecology and genetics of coronaviruses (Betacoronavirus: Coronaviridae) SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS-CoV (subgenus Merbecovirus) [Истоки пандемии COVID-19: экология и генетика коронавирусов (Betacoronavirus: Coronaviridae) SARS-CoV, SARS-CoV-2 (подрод Sarbecovirus), MERS-CoV (подрод Merbecovirus)]

Since the early 2000s, three novel zooanthroponous coronaviruses (Betacoronavirus) have emerged. The first outbreak of infection (SARS) caused by SARS-CoV virus occurred in the fall of 2002 in China (Guangdong Province). A second outbreak (MERS) associated with the new MERS-CoV virus appeared in Saudi Arabia in autumn 2012. The third epidemic, which turned into a COVID-19 pandemic caused by SARS-CoV-2 virus, emerged in China (Hubei Province) in the autumn 2019. This review focuses on ecological and genetic aspects that lead to the emergence of new human zoanthroponous coronaviruses. The main mechanism of adaptation of zoonotic betacoronaviruses to humans is to changes in the receptor-binding domain of surface protein (S), as a result of which it gains the ability to bind human cellular receptors of epithelial cells in respiratory and gastrointestinal tract. This process is caused by the high genetic diversity and variability combined with frequent recombination, during virus circulation in their natural reservoir – bats (Microchiroptera, Chiroptera). Appearance of SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS (subgenus Merbecovirus) viruses is a result of evolutionary events occurring in bat populations with further transfer of viruses to the human directly or through the intermediate vertebrate hosts, ecologically connected with bats. This review is based on the report at the meeting «Coronavirus – a global challenge to science» of the Scientific Council «Life Science» of the Russian Academy of Science: Lvov D.K., Alkhovsky S.V., Burtseva E.I. COVID-19 pandemic sources: origin, biology and genetics of coronaviruses of SARS-CoV, SARS-CoV-2, MERS-CoV (Conference hall of Presidium of RAS, 14 Leninsky Prospect, Moscow, Russia. April 16, 2020) © 2020 Izdatel'stvo Meditsina. All rights reserved

The 2015-2016 epidemic season in Russia and the world: Circulation of influenza viruses, trendsin incidence, clinical aspects, and treatment algorithm

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 wascomplicated 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

Virological, epidemiological, clinic, & molecular genetic features of the influenza epidemic in 2015-2016: Prevailing of the influenza a(H1N1)09pdm virus in Russia & countries of the Northern hemisphere

Federation This work describes the specific features of the influenza virus circulating in the period from October 2015 to March 2016 in 10 cities of Russia, the basic laboratories of CEEI at the D.I. Ivanovsky Institute of Virology "Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya" of the Ministry of Health of the Russian Federation. The increase in the morbidity caused by influenza viruses was detected in January-February 2016. The duration of the morbidity peak was 4-5 weeks. The most vulnerable group included children at the age from 3 to 6; a high rate of hospitalization was also detected among people at the age of 15-64 (65%). In clinic symptoms there were middle and severe forms with high frequency of hospitalization as compared with the season of 2009-2010, but much higher in comparison with the season of 2014-2015. Some of the hospitalized patients had virus pneumonias, half of which were bilateral. Among these patients, 10% were children; 30%, adults. The mortality in the intensive care unit of the hospital was 46%. Almost all lethal cases were among unvaccinated patients in the case of late hospitalization and without early antiviral therapy. The predominance of the influenza A(H1N1)09pdm virus both in the Russian Federation and the major part of the countries in the Northern hemisphere was noted. The results of the study of the antigenic properties of influenza strains of A(H1N1)pdm09 virus did not reveal any differences with respect to the vaccine virus. The sequencing data showed the amino acid substitutions in hemagglutinin (receptor binding and Sa sites) and in genes encoding internal proteins (PA, NP, M1, NS1). Strains were sensitive to oseltamivir and zanamivir and maintained resistance to rimantadine. The participation of non-Influenza ARI viruses was comparable to that in preliminary epidemic seasons. preliminary epidemic seasons

Formation of population gene pools of zoonotic viruses, potentially threatening biosafety

The possible formation of population gene pools of zoonotic viruses with a respiratory route of transmission and a possibility of a pandemic at different stages of biosphere evolution is analyzed. Forming of Poxviruses (Entomopoxvirinae) gene pool could be the beginning of transformation from Plants to Arthropoda (Carbon – 375 million years ago) with further evolution connected with Rodentia (Pliocene – 75–70 million years ago) and further separation of genera (500–300 thousand years ago), and respiratory transmission (epidemics) between humans (10–2 thousand years BC). Smallpox comeback would be possible. Orthomyxoviruses relicts (genus Isavirus) were possibly connected with Ichthya (Silurian – 500–410 million years ago), and then close interaction with Aves (the Cretaceous, 125–110 million years ago) with the division of genera and respiratory transmission (epidemics) between humans (10–2 thousand BC). Next pandemic of influenza A could be catastrophic in terms of the number of victims and economic damage. Coronaviruses formed a gene pool by interaction with Amphibia (subfamily Letovirinae) and then with Chiroptera in Tertiary (110–75 million years ago) with transformation to Artiodactyla (Eocene – 70–60 million years ago), and only 10–2 thousand years BC acquired the ability to a respiratory transmission and became Alphaviruses, a seasonal infection of humans. A similar situation is possible in the near future with SARS-CoV-2. Pandemics associated with zoonoses even more serious than COVID-19 are likely. Constant monitoring of populational gene pools of zoonotic viruses is necessary. © LVOV D.K., GULYUKIN M. I., ZABEREZHNIY A.D., GULYUKIN F.V., 202

Evolution of pandemic influenza virus a(h1n1)pdm09 in 2009-2016: Dynamics of receptor specificity of the first hemagglutinin subunit (HA1) [ЭВОЛЮЦИЯ ПаНДЕМИЧЕСкОГО ВИРУСа ГРИППа A(H1n1)pdm09 В 2009-2016 гг.: ДИНаМИка РЕЦЕПТОРНОЙ СПЕЦИФИЧНОСТИ ПЕРВОЙ СУБЪЕДИНИЦЫ ГЕМаГГЛЮТИНИНа (На1)]

Introduction. The new reassortant of the swine flu virus A(H1N1)pdm09, which emerged in 2009, overcame the species barrier and caused the 2009-2010 pandemic. One of the key points required for the influenza virus to overcome the species barrier and adapt it to humans is its specific binding to the receptors on the epithelium of the human respiratory tract. Targets and goals. Studying the dynamics of changes in receptor specificity (RS) of the HA1 subunit of the hemagglutinin of the influenza A(H1N1)pdm09 virus strains isolated during the period 2009-2016 on the territory of the Russian Federation, and an analysis of the possible impact of these changes on the incidence rates of the population of the Russian Federation of pandemic influenza in certain epidemic seasons. Material and Methods. Standard methods of collecting clinical materials, isolation of influenza viruses, their typing and genome sequencing were used. For the study of RS of influenza A virus (H1N1)pdm09, the method of solid phase sialosidenzyme analysis was used. Results. It is shown that the change in the parameter W3/6 , which characterizes the degree of a2-3 receptor specificity (a2-3-RS) of the influenza virus A(H1N1) pdm09 over a2-6-RS, coincides with the change in the incidence rates of the Russian Federation’s pandemic flu in separate epidemic seasons. There is a tendency to increase the affinity of the virus A(H1N1)pdm09 to α2-3 analogs of the sialyl-glycan receptors of the human respiratory tract epithelium - α2-3-sialoglycopolymers (α2-3-SGP), and falls to α2-6-SGP, with the virus showing the greatest affinity for sulfated sialoglycopolymers. Discussion. Screening for RS strains of influenza A (H1N1)pdm09 virus isolated on the territory of the Russian Federation in 2009–2016 revealed a decrease in the affinity of viruses for a2-6-sialosides, especially for 6’SL-SGP, which is probably due to the presence of amino acid substitutions in the 222 and 223 positions of RBS HA1 viruses. Previous studies have shown that the presence of such substitutions correlates with an increase in the virulence of the influenza A virus (H1N1)pdm09 [16, 23]. Probably, the pandemic virus has evolved towards the selection of more virulent pneumotropic variants. Conclusion. Monitoring of the receptor specificity of a pandemic influenza virus makes it possible to identify strains with altered RS to the epithelium of the human respiratory tract and an increased ability to transfer from person to person. Change in the period 2009-2016 the W3/6 parameter characterizing the degree of α2-3-RS excess of the influenza A(H1N1)pdm09 virus over α2-6-RS, coincides with the change in the incidence rates of the pandemic influenza population of the Russian Federation in certain epidemic seasons. © 2019 Izdatel'stvo Meditsina. All rights reserved

Zoopathogenic orthobuniaviruses (orthobunyavirus, bunyaviridae)

This work deals with the systematics and taxonomy of orthobunyaviruses, little-studied dangerous and new viruses Akabane, Aino, Schmallenberg, Cache Valley diseases, Oropouche fever. The significance of the reassortment mechanism of their origin and diversification is discussed

Zoopathogenic orthobuniaviruses (orthobunyavirus, bunyaviridae)

This work deals with the systematics and taxonomy of orthobunyaviruses, little-studied dangerous and new viruses Akabane, Aino, Schmallenberg, Cache Valley diseases, Oropouche fever. The significance of the reassortment mechanism of their origin and diversification is discussed.В аналитической статье представлены систематика и таксономия ортобуньявирусов, малоизученные опасные и новые вирусы болезней Акабане, Айно, Шмалленберг, долины Кэш, лихорадки Оропуш. Обсуждается значение реассортационного механизма их возникновения и разнообразия

Influenza a virus in the western arctic

Small bays of bird bazaars of the Arctic Kola Peninsula (Barents Sea) have been studied. RNA of influenza A virus was found in the surface microlayer (SM) and aerosol samples from the bays located beneath bird colonies. The nucleotide sequencing of the PCR fragments from the SM and the sea aerosol showed their identity for each bay. Virus transfer mechanism along the "surface microlayer - sea aerosol" path has been proposed. The kinetic scheme of the virus-host-environment interaction, which allows the dependence of the viral population size on the temperature to be simulated, has been developed