ArticleScientific reports2020
Phylogenetic supertree reveals detailed evolution of SARS-CoV-2.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- Characteristics of an emerging canine respiratory coronavirus in China.The veterinary quarterly · 2025Article
- Article
- Phylogenetic insights into the early spread of the SARS-CoV-2 Alpha variant across Europe.Virus evolution · 2025Article
- Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders.bioRxiv : the preprint server for biology · 2024Article
- Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders.Briefings in bioinformatics · 2024Article
- NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model.Algorithms for molecular biology : AMB · 2024Article
- An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes.BMC infectious diseases · 2023Article
- The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions.Immunoinformatics (Amsterdam, Netherlands) · 2023Review
- Applying the digital data and the bioinformatics tools in SARS-CoV-2 research.Computational and structural biotechnology journal · 2023Review
- SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic.Microorganisms · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Anurans against SARS-CoV-2: A review of the potential antiviral action of anurans cutaneous peptides.Virus research · 2022Review
- Variations of SARS-CoV-2 in the Iranian population and candidate putative drug-like compounds to inhibit the mutated proteins.Heliyon · 2022Article
- Statistical modeling of SARS-CoV-2 substitution processes: predicting the next variant.Communications biology · 2022Article
- PWM2Vec: An Efficient Embedding Approach for Viral Host Specification from Coronavirus Spike Sequences.Biology · 2022Article
- Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan.Microorganisms · 2022Article
- Dynamics of SARS-CoV-2 variants of concern (VOC) in Bangladesh during the first half of 2021.Virology · 2022Article
- Human Alphacoronavirus Universal Primers for Genome Amplification and Sequencing.Frontiers in microbiology · 2022Article
- A contemporary review on the important role ofInformatics in medicine unlocked · 2022Review
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Authors and funding
8 authors.
Funding
Abstract
Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, yet limited progress was obtained, principally owing to the disability of these methods to reasonably integrate phylogenetic information from all genes of SARS-CoV-2. Supertree method based on multiple trees can produce the overall reasonable phylogenetic tree. However, the supertree method has been barely used for phylogenetic analysis of viruses. Here we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. Compared with other phylogenetic analysis methods, the supertree method showed more resolution power for phylogenetic analysis of coronaviruses. In particular, the MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences. Furthermore, the discovery of evolution and mutation in SARS-CoV-2 was achieved by MRP pseudo-sequence supertree analysis. Taken together, the MRP pseudo-sequence supertree provided more information on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.
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