@article{Gómez-Carballa01102020,
author = {Gómez-Carballa, Alberto and Bello, Xabier and Pardo-Seco, Jacobo and Martinón-Torres, Federico and Salas, Antonio}, 
title = {Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders},
volume = {30}, 
number = {10}, 
pages = {1434-1448}, 
year = {2020}, 
doi = {10.1101/gr.266221.120}, 
abstract ={The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the twenty-first century. We analyzed more than 4700 SARS-CoV-2 genomes and associated metadata retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus genome. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and more than 160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a rather uniform mutation occurrence along branches that could have implications for diagnostics and the design of future vaccines. Identification of the root of SARS-CoV-2 genomes is not without problems, owing to conflicting interpretations derived from either using the bat coronavirus genomes as an outgroup or relying on the sampling chronology of the SARS-CoV-2 genomes and TMRCA estimates; however, the overall scenario favors haplogroup A as the ancestral node. Phylogenetic analysis indicates a TMRCA for SARS-CoV-2 genomes dating to November 12, 2019, thus matching epidemiological records. Sub-haplogroup A2 most likely originated in Europe from an Asian ancestor and gave rise to subclade A2a, which represents the major non-Asian outbreak, especially in Africa and Europe. Multiple founder effect episodes, most likely associated with super-spreader hosts, might explain COVID-19 pandemic to a large extent.}, 
URL = {http://genome.cshlp.org/content/30/10/1434.abstract}, 
eprint = {http://genome.cshlp.org/content/30/10/1434.full.pdf+html}, 
journal = {Genome Research} 
}