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Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-CoV-2

View ORCID ProfileMatteo Chiara, View ORCID ProfileDavid S. Horner, View ORCID ProfileCarmela Gissi, View ORCID ProfileGraziano Pesole
doi: https://doi.org/10.1101/2020.03.30.016790
Matteo Chiara
1Department of Biosciences, University of Milan, Italy
2Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
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  • For correspondence: matteo.chiara@unimi.it
David S. Horner
1Department of Biosciences, University of Milan, Italy
2Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
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Carmela Gissi
2Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
3Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro, Italy
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Graziano Pesole
2Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
3Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro, Italy
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Abstract

Phylogenomic analysis of SARS-CoV-2 as available from publicly available repositories suggests the presence of 3 prevalent groups of viral episomes (super-clades), which are mostly associated with outbreaks in distinct geographic locations (China, USA and Europe). While levels of genomic variability between SARS-CoV-2 isolates are limited, to our knowledge, it is not clear whether the observed patterns of variability in viral super-clades reflect ongoing adaptation of SARS-CoV-2, or merely genetic drift and founder effects. Here, we analyze more than 1100 complete, high quality SARS-CoV-2 genome sequences, and provide evidence for the absence of distinct evolutionary patterns/signatures in the genomes of the currently known major clades of SARS-CoV-2. Our analyses suggest that the presence of distinct viral episomes at different geographic locations are consistent with founder effects, coupled with the rapid spread of this novel virus. We observe that while cross species adaptation of the virus is associated with hypervariability of specific protein coding regions (including the RDB domain of the spike protein), the more variable genomic regions between extant SARS-CoV-2 episomes correspond with the 3’ and 5’ UTRs, suggesting that at present viral protein coding genes should not be subjected to different adaptive evolutionary pressures in different viral strains. Although this study can not be conclusive, we believe that the evidence presented here is strongly consistent with the notion that the biased geographic distribution of SARS-CoV-2 isolates should not be associated with adaptive evolution of this novel pathogen.

Footnotes

  • Figures have been made more clear, and easy to understand. Additional comparative genomics analyses between non SARS-CoV-2 like CoVs. More detailed discussion of the results. Fixed several typos, and a couple of sentences that were too convoluted/difficult to grasp

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 04, 2020.
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Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-CoV-2
Matteo Chiara, David S. Horner, Carmela Gissi, Graziano Pesole
bioRxiv 2020.03.30.016790; doi: https://doi.org/10.1101/2020.03.30.016790
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Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-CoV-2
Matteo Chiara, David S. Horner, Carmela Gissi, Graziano Pesole
bioRxiv 2020.03.30.016790; doi: https://doi.org/10.1101/2020.03.30.016790

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