ArticleGenome biology2020
Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
40 citing papers in PubMed, 1 synthesis or guideline pooled it, 71 citations in OpenAlex.
- Spatio-Temporal COVID-19 Modeling: A Global Systematic Review of Data Integration, Equity, and Lessons for Pandemic Preparedness.International journal of environmental research and public health · 2026Pooled it
- Bat RNA viruses employ viral RHIMs orchestrating species-specific cell death programs linked to Z-RNA sensing and ZBP1-RIPK3 signaling.iScience · 2024Article
- Associations between epidemiological and laboratory parameters and disease severity in hospitalized patients with COVID-19 during first and second epidemic waves in middle south Mato Grosso.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective.ACS omega · 2023Review
- Early warning of emerging infectious diseases based on multimodal data.Biosafety and health · 2023Review
- Article
- L-shaped distribution of the relative substitution rate (c/μ) observed for SARS-COV-2's genome, inconsistent with the selectionist theory, the neutral theory and the nearly neutral theory but a near-neutral balanced selection theory: Implication on "neutralist-selectionist" debate.Computers in biology and medicine · 2023Article
- Article
- Review
- Unique mutations in SARS-CoV-2 Omicron subvariants' non-spike proteins: Potential impacts on viral pathogenesis and host immune evasion.Microbial pathogenesis · 2022Review
- Interpretable machine learning for genomics.Human genetics · 2022Article
- Understanding the mutational frequency in SARS-CoV-2 proteome using structural features.Computers in biology and medicine · 2022Article
- Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil.Microbes and infection · 2022Article
- A Paradigm Shift in the Combination Changes of SARS-CoV-2 Variants and Increased Spread of Delta Variant (B.1.617.2) across the World.Aging and disease · 2022Article
- The status and analysis of common mutations found in the SARS-CoV-2 whole genome sequences from Bangladesh.Gene reports · 2022Article
- Phylogenetic and genome-wide mutational analysis of SARS-CoV-2 strains circulating in Nigeria: no implications for attenuated COVID-19 outcomes.Osong public health and research perspectives · 2022Article
- Epidemiology and Genetic Analysis of SARS-CoV-2 in Myanmar during the Community Outbreaks in 2020.Viruses · 2022Article
- Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing.Frontiers in immunology · 2022Article
- Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Evolutionary analysis and lineage designation of SARS-CoV-2 genomes.Science bulletin · 2021Article
Corrections and comments
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Authors and funding
15 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundA mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic.
resultsHere we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp
conclusionsThese results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.