The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes.
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Authors
Nikolaidis, Marios
Markoulatos, Panayotis
Van de Peer, Yves
Publication Date
2022-01-07Journal Title
Mol Biol Evol
ISSN
0737-4038
Publisher
Oxford University Press (OUP)
Language
eng
Type
Article
This Version
AM
Physical Medium
Print-Electronic
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Nikolaidis, M., Markoulatos, P., Van de Peer, Y., Oliver, S., & Amoutzias, G. D. (2022). The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes.. Mol Biol Evol https://doi.org/10.1093/molbev/msab292
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.
Identifiers
External DOI: https://doi.org/10.1093/molbev/msab292
This record's URL: https://www.repository.cam.ac.uk/handle/1810/329931
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