2022
DOI: 10.3390/v14020440
|View full text |Cite
|
Sign up to set email alerts
|

Genomic Bootstrap Barcodes and Their Application to Study the Evolution of Sarbecoviruses

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, respectiv… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
1
1
1
1

Citation Types

0
42
0

Year Published

2022
2022
2025
2025

Publication Types

Select...
6
1

Relationship

1
6

Authors

Journals

citations
Cited by 12 publications
(42 citation statements)
references
References 47 publications
0
42
0
Order By: Relevance
“…This was later confirmed by Zhu et al in December 2020 [41]. However, more recently, using sliding window bootstrap (SWB) to highlight the regions supporting phylogenetic relationships, SARS-CoV-2 was defined as a mosaic genome composed of regions sharing recent ancestry with three bat SCoV2rCs recently discovered in the Yunnan region of China (RmYN02, RpYN06, and RaTG13) or related to more ancient ancestors in bats from Yunnan and Southeast Asia [42], with no evidence of direct recombination with pangolin viruses.…”
Section: Recombination In Sars-mentioning
confidence: 90%
“…This was later confirmed by Zhu et al in December 2020 [41]. However, more recently, using sliding window bootstrap (SWB) to highlight the regions supporting phylogenetic relationships, SARS-CoV-2 was defined as a mosaic genome composed of regions sharing recent ancestry with three bat SCoV2rCs recently discovered in the Yunnan region of China (RmYN02, RpYN06, and RaTG13) or related to more ancient ancestors in bats from Yunnan and Southeast Asia [42], with no evidence of direct recombination with pangolin viruses.…”
Section: Recombination In Sars-mentioning
confidence: 90%
“…The only exception is RecSar for which all variables show intermediate values between those found for SCoVrC and SCoV2rC . This result can be however explained by their recombinant origin between two divergent Sarbecovirus lineages, SCoV2rC and SCoVrC (see also the genomic bootstrap barcodes recently published in Hassanin et al, 2022 ). As expected, their recombinant nature was confirmed by the separate SNC analyses of the three genomic regions: the three RecSar viruses clustered with SCoV2rC in the two PCAs based on 5’ and 3’ genomic regions ( Figures 5 A and 5C ), whereas they clustered with SCoVrC in the PCA based on the central genomic region ( Figure 5 B ).…”
Section: Evidence For Eight Groups Of Snc Among Sarbecoviru...mentioning
confidence: 99%
“…Since several studies have shown evidence for multiple events of genomic recombination during the evolutionary history of sarbecoviruses ( Hon et al, 2008 , Boni et al, 2020 ), phylogenetic analyses were also conducted using the three following genomic regions of the alignment: 5’ region (positions 1-11,517; 3839 codons), central region (positions 12,970-20,289; 2440 codons), and 3’ region (positions 20,364-29,550; 3027 codons). These three genomic regions were defined after visual inspection of the translated alignment focusing on the three viruses showing evidence of recombination between SCoVrC and SCoV2rC (RpPrC31, RsVZC45, and RsVZXC21; Hu et al, 2018 , Li et al, 2021 , Hassanin et al, 2022 ).…”
Section: Phylogeny Of Sarbecovirusesmentioning
confidence: 99%
“…Furthermore, a recent study by Hassanin A et al. ( 97 ) indicated that viral circRNAs are involved in the mechanism of genome recombination, which may cause virion mutation leading to immune evasion. In addition, a study by Yang S et al.…”
Section: Potential Mechanisms Of Circrnas In Sars-cov-2 Infectionmentioning
confidence: 99%