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Journal of Clinical Microbiology, May 2003, p. 2135-2137, Vol. 41, No. 5
0095-1137/03/$08.00+0     DOI: 10.1128/JCM.41.5.2135-2137.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Failure To Genotype Herpes Simplex Virus by Real-Time PCR Assay and Melting Curve Analysis Due to Sequence Variation within Probe Binding Sites

Microbiology Unit, Canterbury Health Laboratories,¹ Department of Pathology, Christchurch School of Medicine and Health Sciences, University of Otago, Christchurch, New Zealand²

Received 1 November 2002/ Returned for modification 14 December 2002/ Accepted 10 January 2003

Real-time PCR with melting curve analysis of PCR products is a rapid procedure for detecting and genotyping herpes simplex virus (HSV). When testing mucocutaneous samples for HSV by a real-time PCR assay targeting the DNA polymerase gene, we found that some PCR products had atypical melting curves that did not conform to the expected melting temperatures for HSV type 1 or 2. Sequence analysis showed that these strains had base-pair mismatches over the probe binding sites. An alternative assay is required to type such atypical isolates.

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