Pitfalls of barcodes in the study of worldwide SARSCoV-2 variation and phylodynamics  

作　　者：Jacobo Pardo-Seco Alberto Gómez-Carballa Xabier Bello Federico Martinón-Torres Antonio Salas 

机构地区：[1]Unidade de Xenética,Instituto de Ciencias Forenses(INCIFOR),Facultade de Medicina,Universidade de Santiago de Compostela,and GenPoB Research Group,Instituto de Investigación Sanitaria(IDIS),Hospital Clínico Universitario de Santiago(SERGAS),Galicia 15706,Spain [2]Genetics,Vaccines and Pediatric Infectious Diseases Research Group(GENVIP),Instituto de Investigación Sanitaria de Santiago(IDIS)and Universidad de Santiago de Compostela(USC),Galicia 15706,Spain [3]Translational Pediatrics and Infectious Diseases,Department of Pediatrics,Hospital Clínico Universitario de Santiago de Compostela(SERGAS),Galicia 15706,Spain

出　　处：《Zoological Research》2021年第1期87-93,共7页动物学研究（英文）

基　　金：This study was supported by the GePEM(Instituto de Salud Carlos III(ISCIII)/PI16/01478/Cofinanciado FEDER);DIAVIR(Instituto de Salud Carlos III(ISCIII)/DTS19/00049/Cofinanciado FEDER;Proyecto de Desarrollo Tecnológico en Salud),Resvi-Omics(Instituto de Salud Carlos III(ISCIII)/PI19/01039/Cofinanciado FEDER),BI-BACVIR(PRIS-3;Agencia de Conocimiento en Salud(ACIS)-Servicio Gallego de Salud(SERGAS)-Xunta de Galicia;Spain),Programa Traslaciona Covid-19(ACIS-Servicio Gallego de Salud(SERGAS)-Xunta de Galicia;Spain)and Axencia Galega de Innovación(GAIN;IN607B 2020/08-Xunta de Galicia;Spain)to A.S.;and ReSVinext(Instituto de Salud Carlos III(ISCIII)/PI16/01569/Cofinanciado FEDER),and Enterogen(Instituto de Salud Carlos III(ISCIII)/PI19/01090/Cofinanciado FEDER)to F.M.-T;We gratefully acknowledge GISAID and contributing laboratories(Supplementary Table S1)for giving us access to the SAR-CoV-2 genomes used in the present study.

摘　　要：DEAR EDITOR,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.

关 键 词：dynamics PROPERLY purely 

分 类 号：R373[医药卫生—病原生物学]