Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders.
Genome Res
; 30(10): 1434-1448, 2020 10.
Article
in English
| MEDLINE | ID: covidwho-963139
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.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Pneumonia, Viral
/
Genome, Viral
/
Coronavirus Infections
/
Betacoronavirus
Type of study:
Experimental Studies
/
Observational study
/
Randomized controlled trials
Topics:
Vaccines
Limits:
Animals
/
Humans
Country/Region as subject:
Asia
/
Europa
Language:
English
Journal:
Genome Res
Journal subject:
Molecular Biology
/
Genetics
Year:
2020
Document Type:
Article
Affiliation country:
GR.266221.120
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