Back to Search
Start Over
Global Patterns of Recombination across Human Viruses
- Source :
- Molecular Biology and Evolution
- Publication Year :
- 2021
- Publisher :
- Oxford University Press, 2021.
-
Abstract
- Viral recombination is a major evolutionary mechanism driving adaptation processes, such as the ability of host-switching. Understanding global patterns of recombination could help to identify underlying mechanisms and to evaluate the potential risks of rapid adaptation. Conventional approaches (e.g., those based on linkage disequilibrium) are computationally demanding or even intractable when sequence alignments include hundreds of sequences, common in viral data sets. We present a comprehensive analysis of recombination across 30 genomic alignments from viruses infecting humans. In order to scale the analysis and avoid the computational limitations of conventional approaches, we apply newly developed topological data analysis methods able to infer recombination rates for large data sets. We show that viruses, such as ZEBOV and MARV, consistently displayed low levels of recombination, whereas high levels of recombination were observed in Sarbecoviruses, HBV, HEV, Rhinovirus A, and HIV. We observe that recombination is more common in positive single-stranded RNA viruses than in negatively single-stranded RNA ones. Interestingly, the comparison across multiple viruses suggests an inverse correlation between genome length and recombination rate. Positional analyses of recombination breakpoints along viral genomes, combined with our approach, detected at least 39 nonuniform patterns of recombination (i.e., cold or hotspots) in 18 viral groups. Among these, noteworthy hotspots are found in MERS-CoV and Sarbecoviruses (at spike, Nucleocapsid and ORF8). In summary, we have developed a fast pipeline to measure recombination that, combined with other approaches, has allowed us to find both common and lineage-specific patterns of recombination among viruses with potential relevance in viral adaptation.
- Subjects :
- Linkage disequilibrium
viruses
Computational biology
Genome, Viral
Biology
AcademicSubjects/SCI01180
Genome
Evolution, Molecular
03 medical and health sciences
Genetics
Humans
Molecular Biology
Ecology, Evolution, Behavior and Systematics
Discoveries
Phylogeny
030304 developmental biology
virus evolution
Recombination, Genetic
0303 health sciences
030306 microbiology
Breakpoint
AcademicSubjects/SCI01130
RNA
Genetic Variation
recombination
statistical learning
Viral evolution
Viruses
Topological data analysis
Adaptation
Recombination
Subjects
Details
- Language :
- English
- ISSN :
- 15371719 and 07374038
- Volume :
- 38
- Issue :
- 6
- Database :
- OpenAIRE
- Journal :
- Molecular Biology and Evolution
- Accession number :
- edsair.doi.dedup.....45fe1f7439920bdf6fc33fbc48500b67