ArticleZoological research2021
Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics.
Article in Zoological research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review.European journal of medical research · 2021Pooled it
- A Timeframe for SARS-CoV-2 Genomes: A Proof of Concept for Postmortem Interval Estimations.International journal of molecular sciences · 2022Article
- Mapping Data to Deep Understanding: Making the Most of the Deluge of SARS-CoV-2 Genome Sequences.mSystems · 2022Article
- CovidPhy: A tool for phylogeographic analysis of SARS-CoV-2 variation.Environmental research · 2022Article
- Superspreading in the emergence of COVID-19 variants.Trends in genetics : TIG · 2021Review
- Generation of restriction endonucleases barcode map to trace SARS-CoV-2 origin and evolution.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of SARS-CoV-2 genome variation using a minimal number of selected informative sites conforming a genetic barcode presents several drawbacks. We show that purely mathematical procedures for site selection should be supervised by known phylogeny (i) to ensure that solid tree branches are represented instead of mutational hotspots with poor phylogeographic proprieties, and (ii) to avoid phylogenetic redundancy. We propose a procedure that prevents information redundancy in site selection by considering the cumulative informativeness of previously selected sites (as a proxy for phylogenetic-based criteria). This procedure demonstrates that, for short barcodes (e.g., 11 sites), there are thousands of informative site combinations that improve previous proposals. We also show that barcodes based on worldwide databases inevitably prioritize variants located at the basal nodes of the phylogeny, such that most representative genomes in these ancestral nodes are no longer in circulation. Consequently, coronavirus phylodynamics cannot be properly captured by universal genomic barcodes because most SARS-CoV-2 variation is generated in geographically restricted areas by the continuous introduction of domestic variants.
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Registered trials
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