TY  - JOUR
A1  - Gómez-Carballa, Alberto
A1  - Bello, Xabier
A1  - Pardo-Seco, Jacobo
A1  - Martinón-Torres, Federico
A1  - Salas, Antonio
T1  - Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders
Y1  - 2020/10/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1434 
EP  - 1448 
DO  - 10.1101/gr.266221.120 
VL  - 30 
IS  - 10 
UR  - http://genome.cshlp.org/content/30/10/1434.abstract 
N2  - 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. 
ER  -