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Journal of Virology, August 1999, p. 6265-6270, Vol. 73, No. 8
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Numerous Length Polymorphisms at Short Tandem Repeats in Human Cytomegalovirus

Clara L. Davis,1,* Dawn Field,1 David Metzgar,1 Robert Saiz,2 Phillip A. Morin,2 Irene L. Smith,3 Stephen A. Spector,3,4,5 and Christopher Wills1,5,*

Department of Biology,1 Department of Pediatrics,3 Center for AIDS Research,4 and Center for Molecular Genetics,5 University of California, San Diego, La Jolla, California 92093-0116, and Axys Pharmaceuticals, La Jolla, California 920372

Received 6 January 1999/Accepted 12 April 1999

We show the presence of numerous short tandem repeats in the human cytomegalovirus (HCMV) genome and assess their usefulness as molecular markers. The genome is shown to contain at least 24 microsatellite regions that exhibit length polymorphisms. Insertion-deletion polymorphisms at these short tandem repeats are common (80% of repeats examined are polymorphic among two laboratory strains and 10 clinical isolates). This is the first report of widespread microsatellite length polymorphism in a viral genome. Some regions are highly polymorphic: one was revealed by DNA sequencing to contain length variants at five closely linked sites, which combined resulted in 10 variants for this region among the 12 strains and isolates examined. This study not only provides a new molecular marker system for this virus but also extends our understanding of microsatellite polymorphism in two important ways. First, variable-length repeats in HCMV can be considerably shorter than polymorphic repeats previously found in other organisms. Second, highly variable microsatellite repeats are not confined to prokaryotes and eukaryotes, as previously assumed. This variation provides a useful marker system for distinguishing viral isolates, and similar markers are also likely to be found in other large-genome DNA viruses.

* Corresponding author. Mailing address: Department of Biology 0116, University of California, San Diego, La Jolla, CA 92093. Phone: (619) 534-4113. Fax: (619) 534-7108. E-mail: cldavis{at}ucsd.edu and cwills{at}ucsd.edu.

Journal of Virology, August 1999, p. 6265-6270, Vol. 73, No. 8
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


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