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Size and Structure of Viral Genomes

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Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns.

Irene Hoxie1,2, John J Dennehy1,2

  • 1Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA.

Viruses
|August 28, 2021
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Summary

Rotavirus A genome reassortment creates new strains, impacting host range and immune evasion. Segment evolution varies, with VP7 showing the weakest host association and NSP5 adapting best to hosts.

Keywords:
codon biasgenetic diversitygenome constellationsphylogenyreassortmentvirus evolution

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Area of Science:

  • Virology
  • Molecular Evolution
  • Genomics

Background:

  • Rotavirus A (RVA) reassortment can generate novel genome constellations, influencing host range and immune evasion.
  • Genomic segment co-evolution can be obscured by reassortment, complicating the study of epistasis and substitution rates.

Purpose of the Study:

  • To investigate the co-segregation patterns of RVA genome segments.
  • To analyze segment-specific evolutionary histories and host associations.
  • To assess the impact of RVA vaccines on genetic diversity and host adaptation.

Main Methods:

  • Construction of time-scaled phylogenetic trees for 789 complete RVA genomes from mammalian hosts.
  • Comparison of geodesic distances between segments to determine co-segregation.
  • Generation of Bayesian Skyride plots to track genetic diversity over time.
  • Calculation of codon adaptation indices to assess host-specific selection pressures.

Main Results:

  • Segments 4 (VP4) and 9 (VP7) exhibited distinct phylogenetic spaces, while segments 10 (NSP4) and 11 (NSP5/6) showed strong co-segregation.
  • Segment 9 (VP7) displayed the weakest association with host species.
  • A significant decrease in genetic diversity across all segments was observed around 2007, coinciding with RVA vaccine introduction.
  • Segment 11 (NSP5) demonstrated the highest codon usage adaptation to host genomes, with RVA appearing optimized for human and bird expression.

Conclusions:

  • RVA genome segments exhibit varying degrees of co-segregation and host association.
  • RVA vaccine introduction led to a marked decline in viral genetic diversity.
  • Translational efficiency in humans and birds does not appear to be a limiting factor for RVA zoonosis.