Differentiation of Cucumber mosaic virus isolates by hybridization to oligonucleotides in a microarray format

A system for microarrays was developed to detect and differentiate Cucumber mosaic virus (CMV) serogroups and subgroups. The coat protein genes of 14 different isolates were amplified using cy3-labelled generic but species–specific primers. These amplicons were hybridized against a set of five diffe...

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Bibliographic Details
Published in:Journal of virological methods 2005, Vol.123 (1), p.101-108
Main Authors: Deyong, Zhang, Willingmann, Peter, Heinze, Cornelia, Adam, Günter, Pfunder, Monica, Frey, Beatrice, Frey, Jürg E.
Format: Article
Language:English
Subjects:
Biological and medical sciences
Capsid Proteins - genetics
Capture probes
Cucumber mosaic virus
Cucumovirus - classification
Cucumovirus - genetics
Cucumovirus - isolation & purification
Detection
Differentiation
Fundamental and applied biological sciences. Psychology
Microbiology
NA-arrays
Nucleic Acid Hybridization
Oligonucleotide Array Sequence Analysis - methods
Oligonucleotide Probes
Oligonucleotides
RNA, Viral - genetics
Techniques used in virology
Virology
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Summary:A system for microarrays was developed to detect and differentiate Cucumber mosaic virus (CMV) serogroups and subgroups. The coat protein genes of 14 different isolates were amplified using cy3-labelled generic but species–specific primers. These amplicons were hybridized against a set of five different serotype and subgroup specific 24-mer oligonucleotides bound to an aldehyde-coated glass slide via an aminolinker. The results of the hybridization revealed that the method allowed a clear differentiation of the 14 different CMV isolates into the serogroupes 1 and 2, and in addition was able to assign 9 out of 10 different serogroup 1 isolates correctly into subgroups 1a and 1b. This differentiation was not possible by RFLP analysis with the restriction enzyme MspI. The use of amplicons larger than 700 base pairs and their successful differentiation by hybridization to specific oligonucleotides opens avenues to highly parallel, yet sensitive assays for plant viruses.
ISSN:0166-0934
1879-0984
DOI:10.1016/j.jviromet.2004.09.021