Structure and dynamics of enterovirus genotype networks
Nathânia Dábilla1, Patrick T Dolan1
1Quantitative Virology and Evolution Unit, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA.
Science Advances
|June 19, 2024
Summary
Viral populations form complex networks of genotypes. A new single-cell sequencing method (SEARCHLIGHT) maps these networks, revealing how viruses adapt and maintain connections to beneficial mutations.
Area of Science:
- Virology
- Evolutionary Biology
- Genomics
Background:
- Viral populations adapt through mutation, forming complex genotype networks.
- Understanding these networks is key to predicting viral evolution and adaptation.
- High mutation rates in viruses facilitate rapid exploration of their mutational landscape.
Purpose of the Study:
- To develop and apply a novel single-cell sequencing method for capturing viral haplotypes and host transcriptomes.
- To reveal the intricate population structures of viruses.
- To link host cell transcriptional phenotypes with viral genetic structures driving adaptation.
Main Methods:
- Employed a single-cell sequencing technique, SEARCHLIGHT (scRNA-seq-enabled acquisition of mRNA and consensus haplotypes linking individual genotypes and host transcriptomes).
- Captured and assembled viral haplotypes from hundreds of individual infected cells.
- Obtained parallel host cell transcriptome data for each viral genotype.
Main Results:
- Revealed the complexity of viral population structures and dynamics.
- Demonstrated common evolutionary dynamics in enterovirus populations.
- Illustrated how viral populations navigate mutational landscapes via 'tunnels' to access multiple adaptive genotypes.
Conclusions:
- The SEARCHLIGHT method provides unprecedented insight into viral population structure and evolution.
- Viral adaptation is facilitated by the ability to traverse complex mutational networks.
- Understanding these dynamics is crucial for predicting viral responses to environmental changes.
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