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Updated: Jun 28, 2026

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
Published on: July 27, 2018
Single-strand conformation polymorphism analysis of apple stem grooving capillovirus sequence variants
Apple stem grooving capillovirus (ASGV) exists as a mixture of sequence variants within individual trees. These variants are unevenly distributed and their composition changes after passage in plants.
Area of Science:
- Plant virology
- Molecular biology
- Genetics
Background:
- Apple stem grooving capillovirus (ASGV) isolates from fruit trees exhibit significant nucleotide sequence diversity.
- Previous studies indicated the presence of 2-4 distinct sequence variants within ASGV isolates.
Purpose of the Study:
- To characterize the population of ASGV sequence variants within a single host tree.
- To investigate the distribution and dynamics of ASGV variants during host passage.
Main Methods:
- Immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) combined with single-strand conformation polymorphism (SSCP) analysis.
- Nested asymmetric PCR was used to amplify ASGV sequences for SSCP analysis.
- Serial passage of ASGV isolates in Chenopodium quinoa plants.
Main Results:
- SSCP analysis revealed 2-4 distinct bands in all ASGV-infected apple and pear trees, confirming the existence of sequence variant mixtures.
- The composition of ASGV sequence variants varied significantly between leaf samples from different branches of the same tree.
- Serial passage in C. quinoa altered the composition of ASGV sequence variants, with some variants dominating and others becoming undetectable.
Conclusions:
- ASGV exists as a complex mixture of sequence variants within individual fruit trees.
- The distribution of these variants is uneven within a single tree.
- Host passage can significantly influence the population dynamics of ASGV sequence variants.
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