The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic

A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of rece...

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Published inScientific reports Vol. 13; no. 1; pp. 5571 - 13
Main Authors Yang, Jialin, Skaro, Michael, Chen, Jiani, Zhan, Duna, Lyu, Leke, Gay, Skylar, Kandeil, Ahmed, Ali, Mohamed A., Kayali, Ghazi, Stoianova, Kateryna, Ji, Pensheng, Alabady, Magdy, Bahl, Justin, Liu, Liang, Arnold, Jonathan
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 05.04.2023
Nature Publishing Group
Nature Portfolio
Subjects
631/114
631/181
692/699
Animals
Chiroptera
Conserved sequence
Coronaviridae
Coronaviruses
COVID-19
Gene flow
Humanities and Social Sciences
Humans
multidisciplinary
Nucleotide sequence
Pandemics
Pangolins
Phylogeny
SARS-CoV-2 - genetics
Science
Science (multidisciplinary)
Severe acute respiratory syndrome coronavirus 2
Species
Zoonoses
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Abstract A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489–422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.
AbstractList A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489-422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.
Abstract A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489–422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.
A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489-422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489-422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.
ArticleNumber 5571
Author Ji, Pensheng
Alabady, Magdy
Zhan, Duna
Liu, Liang
Skaro, Michael
Arnold, Jonathan
Stoianova, Kateryna
Kandeil, Ahmed
Ali, Mohamed A.
Chen, Jiani
Bahl, Justin
Lyu, Leke
Yang, Jialin
Gay, Skylar
Kayali, Ghazi
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Snippet A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to...
Abstract A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic...
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Animals
Chiroptera
Conserved sequence
Coronaviridae
Coronaviruses
COVID-19
Gene flow
Humanities and Social Sciences
Humans
multidisciplinary
Nucleotide sequence
Pandemics
Pangolins
Phylogeny
SARS-CoV-2 - genetics
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Science (multidisciplinary)
Severe acute respiratory syndrome coronavirus 2
Species
Zoonoses
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Title The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic
URI https://link.springer.com/article/10.1038/s41598-023-32622-4
https://www.ncbi.nlm.nih.gov/pubmed/37019985
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https://pubmed.ncbi.nlm.nih.gov/PMC10074375
https://doaj.org/article/a8038caa39f34fefacdc198f0f32eaa8
Volume 13
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