A5085332922- SARS-CoV-2 and COVID-19 Research
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Influenza Virus Research Studies
- COVID-19 epidemiological studies
- vaccines and immunoinformatics approaches
- COVID-19 diagnosis using AI
- Genetic diversity and population structure
- Animal Virus Infections Studies
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Photosynthetic Processes and Mechanisms
- Plant Virus Research Studies
Central Research Institute of Epidemiology
2019-2023
Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
2021
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...
SARS-CoV-2 has adapted in a stepwise manner, with multiple beneficial mutations accumulating rapid succession at origins of VOCs, and the reasons for this are unclear. Here, we searched coordinated evolution amino acid sites spike protein SARS-CoV-2. Specifically, concordantly evolving site pairs (CSPs) which changes one were rapidly followed by other same lineage. We detected 46 formed 45 CSP. Sites CSP closer to each structure than random pairs, indicating that concordant functional basis....
Significance Control of rapidly evolving pathogens requires prediction evolution. One obstacle to such predictions is the ever-changing environment, which determines strain fitness. Here, we show that fitness conferred by an amino acid variant at surface proteins influenza A virus changes systematically with time since this appeared. The direction change depends on its functional role. At antigenic regions, variants become less fit time. Conversely, internal regions more This dynamic can be...
The rate of evolution differs between protein sites and changes with time. However, the link these two phenomena remains poorly understood. Here, we design a phylogenetic approach for distinguishing pairs amino acid that evolve concordantly, i.e., such substitutions at one site trigger subsequent other; also discordantly, so impede other. We distinguish groups undergo coordinated discordantly from other groups. In mitochondrion-encoded proteins metazoans fungi, show concordantly evolving are...
Abstract Amino acid propensities at a site change in the course of protein evolution. This may happen for two reasons. Changes be triggered by substitutions epistatically interacting sites elsewhere genome. Alternatively, they arise due to environmental changes that are external Here, we design framework distinguishing between these alternatives. Using analytical modelling and simulations, show cause opposite dynamics fitness allele currently occupying site: it tends increase with time since...
Abstract Background 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, many which are well-mixed between countries. Aim Here, we aim study and spread in Russia. Methods We use a phylogeographic approach infer imports sublineages into Russia, phylodynamic models assess rate their spread. Results show that nearly entire epidemic Russia probably descended from...
Abstract The rate of evolution differs between protein sites and changes with time. However, the link these two phenomena remains poorly understood. Here, we design a phylogenetic approach for distinguishing pairs amino acid that undergo coordinated evolution, i.e., such substitutions at one site trigger subsequent other; also discordant so impede other. We distinguish groups evolve discordantly from other groups. In mitochondrially encoded proteins metazoans fungi, show concordantly...
Abstract It is currently unclear why SARS-Cov-2 has adapted in a stepwise manner, with multiple beneficial mutations accumulating rapid succession at the origins of VOCs. Here, we searched for coordinated evolution amino acid sites spike protein SARS-Cov-2. We concordantly evolving site pairs (CSP) which changes one were rapidly followed by other same lineage. detected 46 formed 45 CSP. Sites CSP closer to each structure than random pairs, indicating that concordant functional basis....