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Nucleotide sequence polymorphism in circoviruses.

Austin L Hughes1, Helen Piontkivska

  • 1Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States. austin@biol.sc.edu

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
|December 21, 2007
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Summary
This summary is machine-generated.

Circovirus rep genes face strong purifying selection, indicating functional constraints. Porcine circovirus 2 (PCV2) shows unique patterns suggesting a population bottleneck and expansion, aligning with its global spread.

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Area of Science:

  • * Virology
  • * Molecular Evolution
  • * Population Genetics

Background:

  • * Circoviruses are small, single-stranded DNA viruses with significant impact on animal health.
  • * Understanding selective pressures on viral genes is crucial for predicting evolution and spread.

Purpose of the Study:

  • * To analyze nucleotide diversity and selective pressures on the rep and cap genes across six circovirus species.
  • * To investigate the population genetics of porcine circovirus 2 (PCV2) and its evolutionary history.

Main Methods:

  • * Comparative analysis of nucleotide diversity at synonymous and nonsynonymous sites in the rep and cap genes.
  • * Assessment of AT-skew and selection at polymorphic sites.
  • * Inference of population demographic history for PCV2.

Main Results:

  • * Stronger purifying selection observed at nonsynonymous sites in the rep gene compared to the cap gene across all species.
  • * Lower synonymous nucleotide diversity in the rep gene suggests functional constraint, associated with negative AT-skew.
  • * Porcine circovirus 2 (PCV2) exhibited an excess of rare nonsynonymous polymorphisms, indicative of a population bottleneck followed by expansion.

Conclusions:

  • * The rep gene of circoviruses is under significant functional constraint, impacting both coding and non-coding sites.
  • * PCV2's unique population genetics align with its recent global dissemination and suggest a history of demographic shifts.