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Article

Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes

by 1,2
1
Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, ON K1N 9A7, Canada
2
Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
Academic Editors: Luis Martinez-Sobrido and Fernando Almazan Toral
Viruses 2021, 13(9), 1790; https://doi.org/10.3390/v13091790
Received: 18 August 2021 / Revised: 6 September 2021 / Accepted: 6 September 2021 / Published: 8 September 2021
(This article belongs to the Collection SARS-CoV-2 and COVID-19)
All dating studies involving SARS-CoV-2 are problematic. Previous studies have dated the most recent common ancestor (MRCA) between SARS-CoV-2 and its close relatives from bats and pangolins. However, the evolutionary rate thus derived is expected to differ from the rate estimated from sequence divergence of SARS-CoV-2 lineages. Here, I present dating results for the first time from a large phylogenetic tree with 86,582 high-quality full-length SARS-CoV-2 genomes. The tree contains 83,688 genomes with full specification of collection time. Such a large tree spanning a period of about 1.5 years offers an excellent opportunity for dating the MRCA of the sampled SARS-CoV-2 genomes. The MRCA is dated 16 August 2019, with the evolutionary rate estimated to be 0.05526 mutations/genome/day. The Pearson correlation coefficient (r) between the root-to-tip distance (D) and the collection time (T) is 0.86295. The NCBI tree also includes 10 SARS-CoV-2 genomes isolated from cats, collected over roughly the same time span as human COVID-19 infection. The MRCA from these cat-derived SARS-CoV-2 is dated 30 July 2019, with r = 0.98464. While the dating method is well known, I have included detailed illustrations so that anyone can repeat the analysis and obtain the same dating results. With 16 August 2019 as the date of the MRCA of sampled SARS-CoV-2 genomes, archived samples from respiratory or digestive tracts collected around or before 16 August 2019, or those that are not descendants of the existing SARS-CoV-2 lineages, should be particularly valuable for tracing the origin of SARS-CoV-2. View Full-Text
Keywords: SARS-CoV-2; tip rooting; tip dating; viral evolution; phylogeny; COVID-19; most recent common ancestor SARS-CoV-2; tip rooting; tip dating; viral evolution; phylogeny; COVID-19; most recent common ancestor
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MDPI and ACS Style

Xia, X. Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes. Viruses 2021, 13, 1790. https://doi.org/10.3390/v13091790

AMA Style

Xia X. Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes. Viruses. 2021; 13(9):1790. https://doi.org/10.3390/v13091790

Chicago/Turabian Style

Xia, Xuhua. 2021. "Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes" Viruses 13, no. 9: 1790. https://doi.org/10.3390/v13091790

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