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Phylogenetic Network Analysis of SARS-CoV-2 Genomes

Overview
Journal Proc Natl Acad Sci U S A
Specialty Science
Date 2020 Apr 10
PMID 32269081
Citations 502
Authors
Peter Forster
Lucy Forster
Colin Renfrew
Michael Forster
Affiliations
Soon will be listed here.
Abstract

In a phylogenetic network analysis of 160 complete human severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) genomes, we find three central variants distinguished by amino acid changes, which we have named A, B, and C, with A being the ancestral type according to the bat outgroup coronavirus. The A and C types are found in significant proportions outside East Asia, that is, in Europeans and Americans. In contrast, the B type is the most common type in East Asia, and its ancestral genome appears not to have spread outside East Asia without first mutating into derived B types, pointing to founder effects or immunological or environmental resistance against this type outside Asia. The network faithfully traces routes of infections for documented coronavirus disease 2019 (COVID-19) cases, indicating that phylogenetic networks can likewise be successfully used to help trace undocumented COVID-19 infection sources, which can then be quarantined to prevent recurrent spread of the disease worldwide.

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References
1.
Zhou P, Yang X, Wang X, Hu B, Zhang L, Zhang W . A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798):270-273. PMC: 7095418. DOI: 10.1038/s41586-020-2012-7. View
2.
Bandelt H, Forster P, Rohl A . Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999; 16(1):37-48. DOI: 10.1093/oxfordjournals.molbev.a026036. View
3.
Forster P, Renfrew C . Evolution. Mother tongue and Y chromosomes. Science. 2011; 333(6048):1390-1. DOI: 10.1126/science.1205331. View
4.
Cann R, Stoneking M, Wilson A . Mitochondrial DNA and human evolution. Nature. 1987; 325(6099):31-6. DOI: 10.1038/325031a0. View
5.
Bandelt H, Forster P, Sykes B, Richards M . Mitochondrial portraits of human populations using median networks. Genetics. 1995; 141(2):743-53. PMC: 1206770. DOI: 10.1093/genetics/141.2.743. View