Abstract
Recombination creates mosaic genomes containing regions with mixed ancestry, and the accumulation of such events over time can complicate greatly many aspects of evolutionary inference. Here, we developed a sliding window bootstrap (SWB) method to generate genomic bootstrap (GB) barcodes to highlight the regions supporting phylogenetic relationships. The method was applied to an alignment of 56 sarbecoviruses, including SARS-CoV and SARS-CoV-2, responsible for the SARS epidemic and COVID-19 pandemic, respectively. The SWB analyses were also used to construct a consensus tree showing the most reliable relationships and better interpret hidden phylogenetic signals. Our results revealed that most relationships were supported by just a few genomic regions and confirmed that three divergent lineages could be found in bats from Yunnan: SCoVrC, which groups SARS-CoV related coronaviruses from China; SCoV2rC, which includes SARS-CoV-2 related coronaviruses from Southeast Asia and Yunnan; and YunSar, which contains a few highly divergent viruses recently described in Yunnan. The GB barcodes showed evidence for ancient recombination between SCoV2rC and YunSar genomes, as well as more recent recombination events between SCoVrC and SCoV2rC genomes. The recombination and phylogeographic patterns suggest a strong host-dependent selection of the viral RNA-dependent RNA polymerase. In addition, SARS-CoV-2 appears as a mosaic genome composed of regions sharing recent ancestry with three bat SCoV2rCs from Yunnan (RmYN02, RpYN06, and RaTG13) or related to more ancient ancestors in bats from Yunnan and Southeast Asia. Finally, our results suggest that viral circular RNAs may be key molecules for the mechanism of recombination.
Highlights
Many RNA viruses are known to evolve through recombination, a process resulting in mosaic genomes containing regions from different parental viruses
The dataset was bootstrapped using a window of W nucleotides (W parameter) moving in steps of 50 nt along the genome alignment in order to examine the distribution of the phylogenetic support (SWB program, Figure 1)
RecSar appeared as a monophyletic group in the tree of Figure 3, the genomic bootstrap (GB) barcode associated with this node belongs to the S3 category, meaning that the phylogenetic support was only found in the 30 region of the genome alignment (2 genomic regions containing robust phylogenetic signal (GRPS) in pos. 19,750–21,800 and 22,950–26,500)
Summary
Many RNA viruses are known to evolve through recombination, a process resulting in mosaic genomes containing regions from different parental viruses. As shown in Hassanin [17], these three divergent lineages exhibit different synonymous nucleotide compositions, suggesting that most of their evolution took place in separate Rhinolopus species assemblages, with YunSar in Yunnan, SCoVrC in China, and SCoV2rC in Southeast Asia (Cambodia, Laos, Thailand, and Vietnam) [6]. Our five main aims were: (i) to design a new tool to visualize the genomic regions supporting phylogenetic relationships; (ii) to reveal and interpret hidden phylogenetic signals; (iii) to provide a more reliable method of tree reconstruction for studying the evolutionary history of sarbecoviruses; (iv) to better characterize diversifying recombination between divergent Sarbecovirus lineages; and (v) to improve our knowledge on the mechanism of genomic recombination between RNA viruses
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