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10.24272/j.issn.2095-8137.2020.364 http://scihub22266oqcxt.onion/10.24272/j.issn.2095-8137.2020.364 33410308!7840454!33410308     free     free     free Deprecated: Implicit conversion from float 213.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 213.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 213.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 213.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Zool+Res 2021 ; 42 (1): 87-93 Nephropedia Template TP {{tp|p=33410308|t=2021. Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics |pdf=|usr=}}{{33410308}} gab.com Text Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics JO: Zool Res http://www.kidney.de/pget.php?&tw=1&pmid=33410308 #FOAvip 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. Twit Text FOAVip Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics ????Zool Res http://www.kidney.de/pget.php?&tw=1&pmid=33410308 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=33410308 #FOAvip English Wikipedia <ref>{{Cite pmid|33410308}}</ref> Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics #MMPMID33410308 Pardo-Seco J; Gomez-Carballa A; Bello X; Martinon-Torres F; Salas A Zool Res 2021[Jan]; 42 (1): 87-93 PMID33410308show ga 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. |Algorithms[MESH] |COVID-19/*virology[MESH] |DNA Barcoding, Taxonomic[MESH] |Genetic Variation[MESH] |Genome, Viral[MESH] |Humans[MESH] |Mutation[MESH] |Phylogeny[MESH] |Phylogeography[MESH]Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation an(epmc).pdf DeepDyve Pubget Overpricing