Academic Bibliography

 Search 200 years of publications by Ghent University researchers.
Advanced search
1 file | 638.41 KB
Add to list
  1. Search results
  2. The neighborhood of the Spike gene is...

The neighborhood of the Spike gene is a hotspot for modular intertypic homologous and nonhomologous recombination in Coronavirus genomes

Marios Nikolaidis, Panayotis Markoulatos, Yves Van de Peer (UGent) , Stephen G Oliver and Grigorios D Amoutzias
(2022) MOLECULAR BIOLOGY AND EVOLUTION. 39(1).
Author
Organization
Abstract
Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and nonhomologous recombination, because such events may affect the emergence of novel CoV strains, alter their host range, infection rate, tissue tropism pathogenicity, and their ability to escape vaccination programs. Intratypic recombination among closely related CoVs of the same subgenus has often been reported; however, the patterns and limits of genomic exchange between more distantly related CoV lineages (intertypic recombination) need further investigation. Here, we report computational/evolutionary analyses that clearly demonstrate a substantial ability for CoVs of different subgenera to recombine. Furthermore, we show that CoVs can obtain—through nonhomologous recombination—accessory ORFs from core ORFs, exchange accessory ORFs with different CoV genera, with other viruses (i.e., toroviruses, influenza C/D, reoviruses, rotaviruses, astroviruses) and even with hosts. Intriguingly, most of these radical events result from double crossovers surrounding the Spike ORF, thus highlighting both the instability and mobile nature of this genomic region. Although many such events have often occurred during the evolution of various CoVs, the genomic architecture of the relatively young SARS-CoV/SARS-CoV-2 lineage so far appears to be stable.
Keywords
Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, coronavirus, recombination, genome evolution, horizontal gene transfer, bioinformatics, molecular evolution, RESPIRATORY SYNDROME CORONAVIRUS, EPIDEMIC DIARRHEA VIRUS, RNA-RNA, FELINE CORONAVIRUS, POLIOVIRUS STRAINS, SEQUENCE ALIGNMENT, BAT CORONAVIRUSES, SARS-COV, PROTEIN, REVEALS

Downloads

  • Download
    Nikolaidis et al. 2022 Molecular Biology and Evolution 39 msab292.pdf
    • full text (Published version)
    • |
    • open access
    • |
    • PDF
    • |
    • 638.41 KB

Citation

Please use this url to cite or link to this publication:

MLA
Nikolaidis, Marios, et al. “The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes.” MOLECULAR BIOLOGY AND EVOLUTION, edited by Crystal Hepp, vol. 39, no. 1, 2022, doi:10.1093/molbev/msab292.
APA
Nikolaidis, M., Markoulatos, P., Van de Peer, Y., Oliver, S. G., & Amoutzias, G. D. (2022). The neighborhood of the Spike gene is a hotspot for modular intertypic homologous and nonhomologous recombination in Coronavirus genomes. MOLECULAR BIOLOGY AND EVOLUTION, 39(1). https://doi.org/10.1093/molbev/msab292
Chicago author-date
Nikolaidis, Marios, Panayotis Markoulatos, Yves Van de Peer, Stephen G Oliver, and Grigorios D Amoutzias. 2022. “The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes.” Edited by Crystal Hepp. MOLECULAR BIOLOGY AND EVOLUTION 39 (1). https://doi.org/10.1093/molbev/msab292.
Chicago author-date (all authors)
Nikolaidis, Marios, Panayotis Markoulatos, Yves Van de Peer, Stephen G Oliver, and Grigorios D Amoutzias. 2022. “The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes.” Ed by. Crystal Hepp. MOLECULAR BIOLOGY AND EVOLUTION 39 (1). doi:10.1093/molbev/msab292.
Vancouver
1.
Nikolaidis M, Markoulatos P, Van de Peer Y, Oliver SG, Amoutzias GD. The neighborhood of the Spike gene is a hotspot for modular intertypic homologous and nonhomologous recombination in Coronavirus genomes. Hepp C, editor. MOLECULAR BIOLOGY AND EVOLUTION. 2022;39(1).
IEEE
[1]
M. Nikolaidis, P. Markoulatos, Y. Van de Peer, S. G. Oliver, and G. D. Amoutzias, “The neighborhood of the Spike gene is a hotspot for modular intertypic homologous and nonhomologous recombination in Coronavirus genomes,” MOLECULAR BIOLOGY AND EVOLUTION, vol. 39, no. 1, 2022.
@article{8724465,
  abstract     = {{Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and nonhomologous recombination, because such events may affect the emergence of novel CoV strains, alter their host range, infection rate, tissue tropism pathogenicity, and their ability to escape vaccination programs. Intratypic recombination among closely related CoVs of the same subgenus has often been reported; however, the patterns and limits of genomic exchange between more distantly related CoV lineages (intertypic recombination) need further investigation. Here, we report computational/evolutionary analyses that clearly demonstrate a substantial ability for CoVs of different subgenera to recombine. Furthermore, we show that CoVs can obtain—through nonhomologous recombination—accessory ORFs from core ORFs, exchange accessory ORFs with different CoV genera, with other viruses (i.e., toroviruses, influenza C/D, reoviruses, rotaviruses, astroviruses) and even with hosts. Intriguingly, most of these radical events result from double crossovers surrounding the Spike ORF, thus highlighting both the instability and mobile nature of this genomic region. Although many such events have often occurred during the evolution of various CoVs, the genomic architecture of the relatively young SARS-CoV/SARS-CoV-2 lineage so far appears to be stable.}},
  articleno    = {{msab292}},
  author       = {{Nikolaidis, Marios and Markoulatos, Panayotis and Van de Peer, Yves and Oliver, Stephen G and Amoutzias, Grigorios D}},
  editor       = {{Hepp, Crystal}},
  issn         = {{0737-4038}},
  journal      = {{MOLECULAR BIOLOGY AND EVOLUTION}},
  keywords     = {{Genetics,Molecular Biology,Ecology,Evolution,Behavior and Systematics,coronavirus,recombination,genome evolution,horizontal gene transfer,bioinformatics,molecular evolution,RESPIRATORY SYNDROME CORONAVIRUS,EPIDEMIC DIARRHEA VIRUS,RNA-RNA,FELINE CORONAVIRUS,POLIOVIRUS STRAINS,SEQUENCE ALIGNMENT,BAT CORONAVIRUSES,SARS-COV,PROTEIN,REVEALS}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{14}},
  title        = {{The neighborhood of the Spike gene is a hotspot for modular intertypic homologous and nonhomologous recombination in Coronavirus genomes}},
  url          = {{http://doi.org/10.1093/molbev/msab292}},
  volume       = {{39}},
  year         = {{2022}},
}
Altmetric
View in Altmetric
Web of Science
Times cited: