Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders
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Identificadores
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Fecha de publicación
2020Título de revista
GENOME RESEARCH
Tipo de contenido
Journal Article
DeCS
homología de secuencias | animales | variación genética | mapeo cromosómico | genoma | pandemias | Chiroptera | filogeografía | secuencia de bases | neumonía | filogenia | humanos | infecciones por CoronavirusMeSH
Phylogeny | Base Sequence | Chiroptera | Pandemics | Genome | Chromosome Mapping | Coronavirus Infections | Genetic Variation | Pneumonia | Animals | Humans | Phylogeography | Sequence HomologyResumen
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.
Excepto si se señala otra cosa, la licencia del ítem se describe como Atribución-NoComercial 4.0 Internacional
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