期刊
GENOME RESEARCH
卷 30, 期 10, 页码 1434-1448出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.266221.120
关键词
-
资金
- Instituto de Salud Carlos III [PI16/01478]
- DIAVIR (Instituto de Salud Carlos III(ISCIII)) [DTS19/00049]
- Resvi-Omics (Instituto de Salud Carlos III(ISCIII)) [PI19/01039]
- project BI-BACVIR (PRIS-3
- Agencia de Conocimiento en Salud (ACIS)-Servicio Gallego de Salud (SERGAS)-Xunta de Galicia
- Spain)
- projects ReSVinext (Instituto de Salud Carlos III(ISCIII)) [PI16/01569]
- Enterogen (Instituto de Salud Carlos III(ISCIII)) [PI19/01090]
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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据