ArticleMolecular biology and evolution2021
Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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106 citing papers in PubMed.
- Lassa virus live tracking and lineage assignment: how nextstrain can enhance surveillance and public health in Africa and beyond.Emerging microbes & infections · 2026Article
- Rapid Phylogeographic Inference of Regional Epidemic Dynamics for Routine Genomic Surveillance.Research square · 2026Article
- HPV16 genetic variation provides evidence of positive natural selection driven by HLA class I.Nature communications · 2026Article
- Rate variation and recurrent sequence errors in pandemic-scale phylogenetics.Nature methods · 2026Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A data-driven sliding-window pairwise comparative approach for the estimation of transmission fitness of SARS-CoV-2 variants and construction of the evolution fitness landscape.Quantitative biology (Beijing, China) · 2025Article
- Article
- Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning.Molecular biology and evolution · 2025Article
- Whole-genome sequencing of 1,083 HPV45 cases and controls identifies genetic variants associated with glandular cervical lesions.International journal of cancer · 2025Article
- Heterogeneous Evolution Among SARS-CoV-2 Genes and Variants of Concern.Journal of medical virology · 2025Article
- Tracing SARS-CoV-2 clusters across local scales using genomic data.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.bioRxiv : the preprint server for biology · 2025Article
- The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree.Molecular biology and evolution · 2025Article
- Viral Network Analyzer (VirNA): A Novel Minimum Spanning Networks Algorithm for Investigating Viral Evolution.International journal of molecular sciences · 2025Article
- Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data.Nature communications · 2025Article
- Article
- Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies.Bioinformatics and biology insights · 2025Article
- Phylogenetic meta-analysis of persistent SARS-CoV-2 infections in immunocompromised individuals highlights the challenges of robust evolutionary rate estimation caused by low genetic diversity.Virus evolution · 2025Article
- Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders.Virus research · 2025Article
- Comparative Evolutionary Epidemiology of SARS-CoV-2 Delta and Omicron Variants in Kuwait.Viruses · 2024Article
46 more citing papers are in PubMed but not listed here.
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13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.
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