Determining intra-host genetic diversity of Citrus tristeza virus. What is the minimal sample size?

Abstract

Intra-host populations of plant RNA viruses are genetically diverse. Due to frequent reinfections, these populations often include phylogenetically distant variants that may have different biological properties. Random selection of variants, which occurs during host-to-host virus transmission, may affect isolate pathogenicity. Accurate characterization of genetic variants in intra-host virus populations is therefore epidemiologically important. In routine molecular characterization of Citrus tristeza virus (CTV) isolates, common practice is to analyze only a few cDNA clones per isolate. In the present study, based on the characterization of CTV populations displaying different levels of genetic diversity, we evaluated if analyzing large numbers of clones increased diversity parameters. A sequential sampling approach, based on analysis of genetic richness. is proposed for determining the minimal sample size required to obtain reliable information on levels of CTV genetic diversity.

Keywords

• Cloning
• CTV
• population structure
• sequencing
• SSCP