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bioRxiv · 10.1101/2020.05.19.097410

The impact of super-spreaders in COVID-19: mapping genome variation worldwide

Gomez-Carballa, A.·Bello, X.·Pardo-Seco, J.·Martinon-Torres, F.·Salas, A.
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Abstract

The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the 21st century. We analyzed >4,700 SARS-CoV-2 genomes and associated meta-data retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and >160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a uniform mutation occurrence along branches that could complicate the design of future vaccines. The root of SARS-CoV-2 genomes locates at the Chinese haplogroup B1, with a TMRCA dating to 12 November 2019 - thus matching epidemiological records. Sub-haplogroup A2a originates in China and represents the major non-Asian outbreak. Multiple founder effect episodes, most likely associated with super-spreader hosts, explain COVID-19 pandemic to a large extent.

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Gomez-Carballa, A., Bello, X., Pardo-Seco, J., Martinon-Torres, F., Salas, A.. 2020-05-19. The impact of super-spreaders in COVID-19: mapping genome variation worldwide. https://doi.org/10.1101/2020.05.19.097410

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