Novel coronaviruses and mammarenaviruses of hedgehogs from Russia including the comparison of viral communities of hibernating and active specimens.

Introduction: Small mammals, especially rodents and bats, are known reservoirs of zoonotic viruses, but little is known about the viromes of insectivorous species including hedgehogs (order Eulipotyphla), which often live near human settlements and come into contact with humans.

Methods: We used high-throughput sequencing and metaviromic analysis to describe the viromes of 21 hedgehogs (Erinaceus sp.) sampled from summer 2022 to spring 2023.

Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotype.

Antimicrobial resistance poses a serious threat to global public health. The COVID-19 pandemic underscored the need to monitor the dissemination of antimicrobial resistance genes and understand the mechanisms driving this process. In this study, we analyzed changes to the oropharyngeal and fecal resistomes of patients with COVID-19 undergoing therapy in a hospital setting.

Association of Low Protein-to-Carbohydrate Energy Ratio with Cognitive Impairment in Elderly Type 2 Diabetes Patients.

Background/objectives: The relationship between macronutrient intake and cognitive decline in older adults with type 2 diabetes mellitus (T2DM) remains underexplored.

Methods: This cross-sectional study aimed to evaluate the association between the protein-to-carbohydrate energy ratio (%E:P) and cognitive impairment among 192 elderly T2DM patients. Cognitive function was assessed using the Montreal Cognitive Assessment (MoCA) and the Self-Administered Gerocognitive Exam (SAGE), while dietary intake data, including (%E:P), was gathered using a validated semi-quantitative food frequency questionnaire.

A Novel Mastadenovirus from Which Represents a Distinct Evolutionary Branch of Viruses from Bats in Europe.

Bats are natural hosts of a wide variety of viruses, including adenoviruses. European bats are known to carry mastadenoviruses categorized as species B (widespread in European Vespertilionidae bats) and whose taxonomy has not been clarified. We examined fecal samples from Vespertilionidae bats (five species) captured in central Russia and found that 2/12 (16%) were positive for mastadenoviruses.

Spectrum of , , , , and Gene Variants in Chronic Pancreatitis Patients in Russia.

Unlabelled: was to define the spectrum of genetic risk factors of chronic pancreatitis (CP) development in patients living in the European part of the Russian Federation.

Materials And Methods: The study group included 105 patients with CP, with the age of the disease onset under 40 years old (the average age of onset was 26.9 years).

Multilocus Analysis of Phylogenetic Relationships in the Crocidura suaveolens Sensu Lato Species Complex: A Comparison with Mitochondrial Data.

Multilocus analysis was for the first time used to study the phylogeny of the Crocidura suaveolens s. l. species complex.

[Progressive fibrosing lung disease. Discussion aspects of the problem: A review].

The authors of the article prove the need to include a new name for the disease - "Progressive Fibrosing Lung Disease" into clinical practice. Recognition of the fact that some lung diseases end in a fibrosing process, which does not have any significant differences depending on the initial disease that led to fibrosis, will expand the indications for earlier prescription of antifibrotic drugs, which will undoubtedly improve the prognosis in this extremely severe category of patients.

Identification and Genetic Characterization of MERS-Related Coronavirus Isolated from Nathusius' Pipistrelle () near Zvenigorod (Moscow Region, Russia).

Being diverse and widely distributed globally, bats are a known reservoir of a series of emerging zoonotic viruses. We studied fecal viromes of twenty-six bats captured in 2015 in the Moscow Region and found 13 of 26 (50%) samples to be coronavirus positive. Of (the Nathusius' pipistrelle), 3 of 6 samples were carriers of a novel MERS-related betacoronavirus.

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.

Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples.

According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes.

[Monitoring the spread of the SARS-CoV-2 (Coronaviridae: Coronavirinae: Betacoronavirus; Sarbecovirus) variants in the Moscow region using targeted high-throughput sequencing].

Introduction: Since the outbreak of the COVID-19 pandemic caused by SARS-CoV-2 novel coronavirus, the international community has been concerned about the emergence of mutations altering some biological properties of the pathogen like increasing its infectivity or virulence. Particularly, since the end of 2020, several variants of concern have been identified around the world, including Alpha (B.1.

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.

Gene Loss, Pseudogenization in Plastomes of Genus (), and Putative Selection for Adaptation to Environmental Conditions.

is a large family with more than 1,600 species, belonging to 75 genera. The largest genus--is vast, comprising about a thousand species. species (as well as other members of the ) are widespread and diversified, they are adapted to a wide range of habitats from shady forests to open habitats like meadows, steppes, and deserts.

Association of , and Genes Polymorphisms With the Calcium Urolithiasis Development in Russian Population.

Kidney stone disease is an urgent medical and social problem. Genetic factors play an important role in the disease development. This study aims to establish an association between polymorphisms in genes coding for proteins involved in calcium metabolism and the development of calcium urolithiasis in Russian population.

Isolation and characterization of Wad Medani virus obtained in the tuva Republic of Russia.

Wad Medani virus (WMV) belongs to the genus Orbivirus and is a poorly studied arbovirus with unclear medical significance. Presently, a limited number of WMV strains are characterized and available in NCBI GenBank, some isolated many years ago. A new WMV strain was isolated in 2012 from Dermacentor nuttalli ticks collected from sheep in the Tuva Republic, Russia, and sequenced using high-throughput methods.

sensu lato (Asteraceae, Cichorieae) - taxonomic reassessment in the light of new molecular phylogenetic and carpological analyses.

comprises 180-190 species and belongs to the subtribe Scorzonerinae. Its circumscription has long been the subject of debate and available molecular phylogenetic analyses affirmed the polyphyly of in its wide sense. We provide a re-evaluation of and other related genera, based on carpological (including anatomical) and extended molecular phylogenetic analyses.

Genetic diversity of Kemerovo virus and phylogenetic relationships within the Great Island virus genetic group.

Kemerovo virus (KEMV) is a member of the Great Island virus genetic group, belonging to the tick-borne arboviruses of the genus Orbivirus within the family Reoviridae. Nine strains of KEMV, which were isolated from various locations in Russia, were sequenced by high-throughput sequencing to study their intraspecific diversity and the interspecific relationships of viruses within the Great Island genetic group. For the first time, multiple reassortment within KEMV was reliably demonstrated.

Complete plastome sequencing of Allium paradoxum reveals unusual rearrangements and the loss of the ndh genes as compared to Allium ursinum and other onions.

In this work the complete chloroplast DNAs of Allium paradoxum and Allium ursinum, two edible species of Allium subg. Amerallium (the first lineage), were sequenced, assembled, annotated, and compared with complete Allium plastomes of the second and third evolutionary lines from GenBank database. The A.

Improved Protocols of ITS1-Based Metabarcoding and Their Application in the Analysis of Plant-Containing Products.

Plants are widely used for food and beverage preparation, most often in the form of complex mixtures of dried and ground parts, such as teas, spices or herbal medicines. Quality control of such products is important due to the potential health risks from the presence of unlabelled components or absence of claimed ones. A promising approach to analyse such products is DNA metabarcoding due to its high resolution and sensitivity.

Sequencing and genetic characterization of two strains Paramushir virus obtained from the Tyuleniy Island in the Okhotsk Sea (2015).

Paramushir virus belongs to Sakhalin virus genogroup within Orthonairovirus genus and is one of the poorly studied viruses with unknown pathogenicity. At the moment, only one nearly complete sequence of Paramushir virus genome, isolated in 1972, is available. Two new strains of PARV were isolated in 2015 from a sample collected at the Tyuleniy Island in the Okhotsk Sea and sequenced using a combination of high throughput sequencing and specific multiplex PCR.

The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels.

Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using rRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability.

Evaluating the accuracy and sensitivity of detecting minority HIV-1 populations by Illumina next-generation sequencing.

The accuracy and sensitivity of deep sequencing were assessed using viral standards (pNL4-3 and pLAI.2) of both DNA and RNA. The sequencing accuracy did not depend on the type of nucleic acid, but critically depended on the number of reads and threshold of sensitivity to minor viral populations.

The systematic position of Dryopteris blanfordii subsp. nigrosquamosa (Ching) Fraser-Jenkins within the genus Adans.

(C.Hope) C.Chr.

Comparative analysis of inverted repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions.

Background: Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes.

Results: We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns.