ArticleMolecular biology and evolution2022
The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 43 citations in OpenAlex.
- Balancing Genome Plasticity and Evolutionary Constraint During the Long-Term Evolution of Feline Coronaviruses.Viruses · 2026Article
- Module-level recombination drives DBLMSP polymorphism and functional conservation in Plasmodium falciparum.Parasite (Paris, France) · 2026Article
- Coronaviruses in wild rodent and eulipotyphlan small mammals: a review of diversity, ecological implications and surveillance considerations.The Journal of general virology · 2025Review
- Patterns of Recombination in Coronaviruses.International journal of molecular sciences · 2025Article
- Coronaviruses in diarrheic pigeons and the first determination of the complete genome of a new pigeon gammacoronavirus.Scientific reports · 2025Article
- Article
- SARS-CoV-2 biology and host interactions.Nature reviews. Microbiology · 2024Review
- Bioinformatics Insights on Viral Gene Expression Transactivation: From HIV-1 to SARS-CoV-2.International journal of molecular sciences · 2024Article
- Comprehensive detection and dissection of interlineage recombination events in the SARS-CoV-2 pandemic.Virus evolution · 2024Article
- Article
- SARS-CoV-2 Recombination and Coinfection Events Identified in Clinical Samples in Russia.Viruses · 2023Article
- Enhancing SARS-CoV-2 Surveillance through Regular Genomic Sequencing in Spain: The RELECOV Network.International journal of molecular sciences · 2023Article
- Does Avian Coronavirus Co-Circulate with Avian Paramyxovirus and Avian Influenza Virus in Wild Ducks in Siberia?Viruses · 2023Article
- Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses.Virology journal · 2023Article
- Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- DNA Oligonucleotides as Antivirals and Vaccine Constituents against SARS Coronaviruses: A Prospective Tool for Immune System Tuning.International journal of molecular sciences · 2023Article
- Evolutionary plasticity of zoonotic porcine Deltacoronavirus (PDCoV): genetic characteristics and geographic distribution.BMC veterinary research · 2022Article
- Diversity of gammacoronaviruses and deltacoronaviruses in wild birds and poultry in Russia.Scientific reports · 2022Article
- The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus.Vaccines · 2022Review
- Evaluation of SARS-CoV-2 Antibody Response Post Third Dose COVID-19 mRNA Vaccination at Universitas Indonesia Hospital.Acta medica academica · 2022Observational
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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