A5064841121- SARS-CoV-2 and COVID-19 Research
- Mycobacterium research and diagnosis
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Escherichia coli research studies
- Bacteriophages and microbial interactions
- Animal Virus Infections Studies
- Inflammatory Bowel Disease
- Microbial Community Ecology and Physiology
- Viral gastroenteritis research and epidemiology
- Gut microbiota and health
- Virology and Viral Diseases
- Protist diversity and phylogeny
- Bacterial Genetics and Biotechnology
- Plant Virus Research Studies
- RNA and protein synthesis mechanisms
- Tardigrade Biology and Ecology
- Microbial Fuel Cells and Bioremediation
- COVID-19 epidemiological studies
- COVID-19 Clinical Research Studies
- DNA Repair Mechanisms
- Viral Infections and Immunology Research
- Fetal and Pediatric Neurological Disorders
- Glycosylation and Glycoproteins Research
- Cancer Genomics and Diagnostics
Institute for Information Transmission Problems
2013-2024
National Center for Biotechnology Information
2021-2024
National Institutes of Health
2021-2024
Skolkovo Institute of Science and Technology
2017-2022
UNSW Sydney
2019
Okinawa Institute of Science and Technology Graduate University
2015
Lomonosov Moscow State University
2009
Abstract Evolution of SARS-CoV-2 in immunocompromised hosts may result novel variants with changed properties. While escape from humoral immunity certainly contributes to intra-host evolution, cellular is poorly understood. Here, we report a case long-term COVID-19 an patient non-Hodgkin’s lymphoma who received treatment rituximab and lacked neutralizing antibodies. Over the 318 days disease, genome gained total 40 changes, 34 which were present by end study period. Among acquired mutations,...
Abstract The zoonotic origin of the COVID-19 pandemic virus highlights need to fill vast gaps in our knowledge SARS-CoV-2 ecology and evolution non-human hosts. Here, we detected that was introduced from humans into white-tailed deer more than 30 times Ohio, USA during November 2021-March 2022. Subsequently, deer-to-deer transmission persisted for 2–8 months, disseminating across hundreds kilometers. Newly developed Bayesian phylogenetic methods quantified how is not only three-times faster...
Bacterial defense against phage predation involves diverse systems acting individually and concurrently, yet their interactions remain poorly understood. We investigated >100 in 42,925 bacterial genomes identified numerous instances of non-random co-occurrence negative association. For several pairs significantly co-occurring Escherichia coli strains, we demonstrate synergistic anti-phage activity. Notably, Zorya II synergizes with Druantia III ietAS systems, while tmn exhibits synergy...
Abstract The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use phylogenetics to understand control its spread. Here, we analyze emergence in Russia March April 2020. Combining phylogeographic analysis with travel history data, estimate that sampled viral diversity has originated from at least 67 closely timed introductions into Russia, mostly late February early March. All but one these were not China, suggesting border closure China helped delay...
Delta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution led to emergence multiple sublineages, which are well-mixed between countries. By contrast, here we show that nearly entire epidemic in Russia probably descended from a single import event, or closely timed imports poorly sampled geographic location. Indeed, over 90 per cent samples characterized nsp2:K81N + ORF7a:P45L pair mutations is rare outside...
Abstract The appearance of multiple new SARS-CoV-2 variants during the COVID-19 pandemic is a matter grave concern. Some these variants, such as B.1.617.2, B.1.1.7, and B.1.351, manifest higher infectivity virulence than earlier with potential dramatic effects on course pandemic. So far, analysis focused primarily nucleotide substitutions short deletions that are readily identifiable by comparison to consensus genome sequences. In contrast, insertions have largely escaped attention...
While SARS-CoV-2 has sporadically infected a wide range of animal species worldwide1, the virus been repeatedly and frequently detected in white-tailed deer North America2â€"7. The zoonotic origins this pandemic highlight need to fill vast gaps our knowledge ecology evolution non-human hosts. Here, we was introduced from humans into more than 30 times Ohio, USA during November 2021-March 2022. Subsequently, deer-to-deer transmission persisted for 2-8 months, which disseminated across...
While mutational processes operating in the Escherichia coli genome have been revealed by multiple laboratory experiments, contribution of these to accumulation bacterial polymorphism and evolution natural environments is unknown. To address this question, we reconstruct signatures distinct from experimental data on E. hypermutators, ask how contribute differences between naturally occurring strains. We show that both mutations accumulated course wild-type strains nature lab-grown nonmutator...
In 2020, SARS-CoV-2 has spread rapidly across the globe, with most nations failing to prevent or substantially delay its introduction. While many countries have imposed some limitations on trans-border passenger traffic, effect of these measures global COVID-19 strains remains unclear. Here, we report an analysis 3206 whole-genome sequences samples from 78 regions Russia covering period before variants concern (between March and November 2020). We describe recurring imports multiple into...
While most endosymbiotic bacteria are transmitted only vertically, Holospora spp., an alphaproteobacterium from the Rickettsiales order, can desert its host and invade a new one. All genus intranuclear symbionts of ciliates Paramecium spp. with strict species nuclear specificity. Comparative metabolic reconstruction based on newly-sequenced genome curviuscula, macronuclear symbiont bursaria, known genomes other shows that even though all persist outside host, they cannot synthesize essential...
Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs essential for survival, genome analysis demonstrates absence of some RP genes in genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination had only a moderate effect on growth rate. Here, we systematically analyze evolutionary conservation prokaryotes by compiling list ribosomal missing from one or more genomes recently updated version Clusters...
ABSTRACT Potato mop-top virus (PMTV) produces a defective RNA (D RNA) encompassing the 5′-terminal 479 nucleotides (nt) and 3′-terminal 372 nt of RNA-TGB (where TGB is triple gene block). The mechanism that controls D biogenesis role in accumulation was investigated by introducing deletions, insertions, point mutations into sequences open reading frames (ORFs) TGB1 8-kilodalton (8K) protein were identified as required for efficient production RNA. Transient expression absence RNA-Rep (which...
Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny E. isolated from patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, sequenced strains CD were closely related. We performed shotgun genome sequencing 28 isolates ten compared genomes these with already published other pathogenic non-pathogenic strains. CDEC shown to belong A, B1, B2 D phylogenetic groups. plasmid several operons...
ABSTRACT Bacterial defence against phage predation involves diverse systems acting both individually and concurrently, yet their interactions remain poorly understood. We investigated >100 in 42,925 bacterial genomes identified numerous instances of non-random co-occurrence mutual exclusion. For several pairs significantly co-occurring Escherichia coli strains, we demonstrate synergistic anti-phage activity, including tmn synergising with containing sensory switch ATPase domains. Some the...
The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to incomplete set of ribosomal proteins. We analyzed 214 small bacterial genomes (<1 Mb) found that although the fairly stable, proteins may be absent, especially with dramatically reduced genomes. large subunit less than subunit. identified frequently lost demonstrated they tend positioned on surface fewer...
Holospora-like bacteria (HLB) are obligate intracellular Alphaproteobacteria, inhabiting nuclei of Paramecium and other ciliates such as “Candidatus Hafkinia” is in Frontonia. The HLB clade comprised four genera, Holospora, Preeria, Gortzia”, Hafkinia”. These have a peculiar life cycle with two morphological forms some degree specificity to the host species type nucleus they inhabit. Here we describe novel HLB—“Candidatus Gortzia yakutica” sp. nov.—a symbiont from macronucleus putrinum,...
In 2021, the COVID-19 pandemic was characterized by global spread of several lineages with evidence for increased transmissibility. Throughout pandemic, Russia has remained among countries highest number confirmed cases, making it a potential hotspot emergence novel variants. Here, we show that globally significant variants concern have late 2020, alpha (B.1.1.7), beta (B.1.351) or gamma (P.1), none been sampled in before end 2020. Instead, between summer 2020 and spring epidemic two were...
Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, microbiome composition typically remains stable across a broad range conditions. However, under fixed conditions, ecology conforms with the exclusion principle which two populations competing for same resource within niche cannot coexist because less fit population inevitably goes extinct. Therefore, long-term persistence calls an explanation.
Genomes of Methanosarcina spp. are among the largest archaeal genomes. One suggested reason for that is massive horizontal gene transfer (HGT) from bacteria. Genes bacterial origin may be involved in central metabolism and solute transport, particular sugar synthesis, sulfur metabolism, phosphate DNA repair, transport small molecules etc. Horizontally transferred (HT) genes considered to play key role ability inhabit diverse environments. At moment, genomes three have been sequenced, while...
Abstract Corals harbor complex and diverse microbial communities that strongly impact host fitness resistance to diseases, but these microbes themselves can be influenced by stresses, like those caused the presence of macroscopic symbionts. In addition directly influencing host, symbionts may transmit pathogenic communities. We analyzed two coral gall-forming copepod systems using 16S rRNA gene metagenomic sequencing: (1) sea fan Gorgonia ventalina with copepods genus Sphaerippe from...
Abstract The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use phylogenetics to understand control its spread. Here, we analyze emergence in Russia March April 2020. Combining phylogeographic analysis with travel history data, estimate that sampled viral diversity has originated from 67 closely timed introductions into Russia, mostly late February early March. All but one these came non-Chinese sources, suggesting border closure China helped delay...
In 2021, the COVID-19 pandemic is characterized by global spread of several lineages with evidence for increased transmissibility. Russia among countries highest number confirmed cases, making it a potential hotspot emergence novel variants. Here, we show that globally significant variants concern, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) or P.1 (501Y.V3), none have been sampled in before January 2021. Instead, since summer 2020, epidemic has two are rare elsewhere: B.1.1.317 and sublineage...
Summary The combined processes of microbial biodegradation accompanied by extracellular electron transfer make fuel cells (MFCs) a promising new technology for cost-effective and sustainable wastewater treatment. Although number species that build biofilms on the anode surfaces operating MFCs have been identified, studies metagenomics entire electrogenic communities are limited. Here we present results wholegenome metagenomic analysis electrochemically active robust anodic communities, their...
Abstract Evolution of SARS-CoV-2 in immunocompromised hosts may result novel variants with changed properties, but the mode selection underlying this process remains unclear. While escape from humoral immunity certainly plays a role intra-host evolution, cellular is poorly understood. Here, we report case long-term COVID-19 an patient non-Hodgkin’s lymphoma who received treatment rituximab and lacked neutralizing antibodies. Over 318 days disease, genome gained total 40 changes, 34 which...