Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

A Case of Moderately Severe COVID-19 in a Healthcare Worker in Russia: Virus Isolation and Full Genome Sequencing

The coronavirus disease 2019 (COVID-19) pandemic is probably the most studied one in history from both clinical and molecular-epidemiological perspectives. Nonetheless, data on the correlation between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genotypes and COVID-19 symptoms caused by them are still scarce. In this report, we present a moderately severe COVID-19 case in a healthcare worker in Moscow, Russia, supplemented with the data on its causative agent's phenotype regarding in vitro and full-genome characterization. The 44-year-old male healthcare worker who had frequent professional contacts with COVID-19 patients was hospitalized with a viral pneumonia diagnosis and soon started to exhibit fever, dry paroxysmal cough, loss of smell, and typical ground-glass opacities found in both lungs on chest CT scans. The COVID-19 diagnosis was verified by real-time quantitative polymerase chain reaction (qRT-PCR), immunochromatography, and immunochemiluminescent assays. The patient was treated with hydroxychloroquine, azithromycin, paracetamol, and enoxaparin, leading to his recovery after two weeks from the disease onset. The virus was successfully isolated from the nasopharyngeal swab sample taken on the fifth day of the disease onset using the Vero E6 cell line and exhibited a pronounced cytopathic effect (CPE) with a viral titer reaching 106 TCID50/ml in the cell culture medium. The full genome sequence of the viral isolate was obtained and 8 nucleotide and 5 amino acid mutations compared to the Wuhan-Hu-1 reference genome were identified. Viral isolate belonged to GR / 20B / B.1.1 genetic lineage (GISAID, Nextstrain, Pangolin nomenclatures, respectively) - the most prevalent genotype found in Russia to date

Genetic and Phylogenetic Characterization of Tataguine and Witwatersrand Viruses and Other Orthobunyaviruses of the Anopheles A, Capim, Guamá, Koongol, Mapputta, Tete, and Turlock Serogroups

The family Bunyaviridae has more than 530 members that are distributed among five genera or remain to be classified. The genus Orthobunyavirus is the most diverse bunyaviral genus with more than 220 viruses that have been assigned to more than 18 serogroups based on serological cross-reactions and limited molecular-biological characterization. Sequence information for all three orthobunyaviral genome segments is only available for viruses belonging to the Bunyamwera, Bwamba/Pongola, California encephalitis, Gamboa, Group C, Mapputta, Nyando, and Simbu serogroups. Here we present coding-complete sequences for all three genome segments of 15 orthobunyaviruses belonging to the Anopheles A, Capim, Guamá, Kongool, Tete, and Turlock serogroups, and of two unclassified bunyaviruses previously not known to be orthobunyaviruses (Tataguine and Witwatersrand viruses). Using those sequence data, we established the most comprehensive phylogeny of the Orthobunyavirus genus to date, now covering 15 serogroups. Our results emphasize the high genetic diversity of orthobunyaviruses and reveal that the presence of the small nonstructural protein (NSs)-encoding open reading frame is not as common in orthobunyavirus genomes as previously thought

Microbiological Characteristics of Some Stations of Moscow Subway

The subway is one of the most actively used means of transport in the traffic infrastructure of large metropolitan areas. More than seven million passengers use the Moscow subway every day, which promotes the exchange of microorganisms between people and the surrounding subway environment. In this research, a study of the bacterial communities of two Moscow subway stations was conducted and the common subway microbiome was determined. However, there were differences in microbiological and antibiotic-resistance profiles, depending on the station. The station’s operational period since opening correlated with the taxonomic diversity and resistance of the identified bacteria. Moreover, differences between aerosol and surface bacterial communities were found at the two subway stations, indicating the importance of diversified sampling during the microbiome profiling of public areas. In this study, we also compared our data with previously published results obtained for the Moscow subway. Despite sample collection at different stations and seasons, we showed the presence of 15 common genera forming the core microbiome of the Moscow subway, which represents human commensal species, as well as widespread microorganisms from the surrounding environment

SARS-CoV-2 evolution in a patient with secondary B-cell immunodeficiency: A clinical case

The article highlights the course of long-term SARS-CoV-2 infection in a patient with a secondary immunodeficiency developed with B-cell-depleting therapy of the underlying disease. Analysis of the intrapatient virus evolution revealed an inpatient S:G75A mutation that alters the 72GTNGTKR78 motif of the S-protein, with a possible role in binding to alternative cellular receptors. Therapy with a ready-made COVID-19-globulin preparation (native human immunoglobulin G (IgG) derived from the plasma of convalescent COVID-19-patients) resulted in rapid improvement of the patient’s condition, fast, and stable elimination of the virus, and passive immunization of the patient for at least 30 days. The results suggest the use of products containing neutralizing antibodies opens new prospects for treatment algorithms for patients with persistent coronavirus infection, as well as for passive immunization schemes for patients with a presumably reduced specific response to vaccination

Influence of Synthesis Conditions on the Crystal, Local Atomic, Electronic Structure, and Catalytic Properties of (Pr_1−<i>x</i>Yb_<i>x</i>)₂Zr₂O₇ (0 ≤ <i>x</i> ≤ 1) Powders

The influence of Yb3+ cations substitution for Pr3+ on the structure and catalytic activity of (Pr1−xYbx)2Zr2O7 powders synthesized via coprecipitation followed by calcination is studied using a combination of long- (s-XRD), medium- (Raman, FT-IR, and SEM-EDS) and short-range (XAFS) sensitive methods, as well as adsorption and catalytic techniques. It is established that chemical composition and calcination temperature are the two major factors that govern the phase composition, crystallographic, and local-structure parameters of these polycrystalline materials. The crystallographic and local-structure parameters of (Pr1−xYbx)2Zr2O7 samples prepared at 1400 °C/3 h demonstrate a tight correlation with their catalytic activity towards propane cracking. The progressive replacement of Pr3+ with Yb3+ cations gives rise to an increase in the catalytic activity. A mechanism of the catalytic cracking of propane is proposed, which considers the geometrical match between the metal–oxygen (Pr–O, Yb–O, and Zr–O) bond lengths within the active sites and the size of adsorbed propane molecule to be the decisive factor governing the reaction route