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Phylogenetic network analysis of SARS-CoV-2 genomes
Peter Forster, Lucy Forster, Colin Renfrew, and View ORCID ProfileMichael Forster
PNAS first published April 8, 2020 https://doi.org/10.1073/pnas.2004999117
- Contributed by Colin Renfrew, March 30, 2020 (sent for review March 17, 2020; reviewed by Toomas Kivisild and Carol Stocking)
This is a phylogenetic network of SARS-CoV-2 genomes sampled from across the world. These genomes are closely related and under evolutionary selection in their human hosts, sometimes with parallel evolution events, that is, the same virus mutation emerges in two different human hosts. This makes character-based phylogenetic networks the method of choice for reconstructing their evolutionary paths and their ancestral genome in the human host. The network method has been used in around 10,000 phylogenetic studies of diverse organisms, and is mostly known for reconstructing the prehistoric population movements of humans and for ecological studies, but is less commonly employed in the field of virology.
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.
https://www.pnas.org/content/early/2.../07/2004999117
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Sars-CoV-2, the virus that causes Covid-19, originated from bats. It has been found to share 96 per cent identical genes with a coronavirus isolated by Chinese scientists from bat droppings in the southwestern province of Yunnan in 2013.
The bats were already in the Wuhan lab. Origination in South China is not needed:
"The samples were taken back to the laboratory and stored in a freezer at minus 80 ? C. Until 2011, a SARS-like coronavirus S gene closer to the SARS virus was first detected in a bat cave in Yunnan. In 2013, the Laboratory of Wuhan Institute of Virology, Chinese Academy of Sciences, isolated the first live virus of bat SARS-like coronavirus from the sample, and a more similar S gene, allowing this virus to use the same receptor as SARS virus and to Infect human cells. It was named "WIV1" by the English abbreviation of Wuhan Virus Research Institute to highlight the important value of this discovery. The results were published in the November 2013 issue of Nature. The "key" was finally found. But the secret uncovered by this small cave is far more than researchers expected."
Study from 2013:
Nature: Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor
https://flutrackers.com/forum/forum/...-ace2-receptor
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