Genomic Bootstrap Barcodes and Their Application to Study the Evolution of Sarbecoviruses
Alexandre Hassanin1, Opale Rambaud1, Dylan Klein1
1Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, Centre National de la Recherche Scientifique, École Pratique des Hautes Études, Muséum National d'Histoire Naturelle, Université des Antilles, 75231 Paris, France.
Viruses
|February 26, 2022
Summary
Recombination creates complex viral genomes. A new sliding window bootstrap method reveals mosaic structures in SARS-CoV-2, highlighting ancestral origins and recombination events in bat coronaviruses.
Area of Science:
- Virology
- Evolutionary Biology
- Genomics
Background:
- Viral genomes evolve through recombination, leading to mosaic structures with mixed ancestry.
- Understanding these complex evolutionary patterns is crucial for inferring viral relationships and origins.
Purpose of the Study:
- To develop a novel method for identifying genomic regions supporting phylogenetic relationships.
- To analyze the evolutionary history and recombination patterns of sarbecoviruses, including SARS-CoV and SARS-CoV-2.
Main Methods:
- Development of a sliding window bootstrap (SWB) method to generate genomic bootstrap (GB) barcodes.
- Application of SWB to an alignment of 56 sarbecoviruses.
- Construction of a consensus phylogenetic tree to interpret hidden phylogenetic signals.
Main Results:
- Identification of three divergent sarbecovirus lineages in bats from Yunnan: SCoVrC, SCoV2rC, and YunSar.
- Evidence of ancient and recent recombination events between these lineages.
- SARS-CoV-2 identified as a mosaic genome with mixed ancestry from Yunnan bat coronaviruses and older ancestors.
Conclusions:
- The SWB method effectively highlights regions supporting phylogenetic relationships and aids in interpreting complex evolutionary signals.
- Recombination patterns suggest host-dependent selection on viral RNA-dependent RNA polymerase.
- Viral circular RNAs may play a significant role in viral recombination mechanisms.
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