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Journal of Clinical Microbiology, March 2009, p. 533-540, Vol. 47, No. 3
0095-1137/09/$08.00+0 doi:10.1128/JCM.01565-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Utilization of Microsatellite Polymorphism for Differentiating Herpes Simplex Virus Type 1 Strains 
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C. Deback,1,2*
D. Boutolleau,1,2
C. Depienne,3
C. E. Luyt,4
P. Bonnafous,1,2
A. Gautheret-Dejean,1,2,5
I. Garrigue,6 and
H. Agut1,2
UPMC Université Paris 06, UPRES EA 2387, Paris F-75013, France,1 Service de Virologie, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris F-75013, France,2 Département de Génétique et de Cytogénétique, Centre de Génétique Moléculaire et Chromosomique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris F-75013, France,3 Service de Réanimation Médicale, Institut de Cardiologie, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris F-75013, France,4 Laboratoire de Microbiologie, UPRES EA 4065, Université Paris Descartes, Faculté des Sciences Pharmaceutiques et Biologiques, Paris F-75006 France,5 Laboratoire de Virologie EA2968 and IFR66, Université Bordeaux 2, Bordeaux F-33076, France6
Received 12 August 2008/ Returned for modification 10 October 2008/ Accepted 17 December 2008
The herpes simplex virus type 1 (HSV-1) genome is a linear double-stranded DNA of 152 kpb. It is divided into long and short regions of unique sequences termed UL and US, respectively, and these are flanked by regions of inverted internal and terminal repeats. Microsatellites are short tandem repeats of 1- to 6-nucleotide motifs; they are often highly variable and polymorphic within the genome, which raises the question of whether they may be used as molecular markers for the precise differentiation of HSV-1 strains. In this study, 79 different microsatellites (mono-, di-, and trinucleotide repeats) in the HSV-1 complete genome were identified by in silico analysis. Among those microsatellites, 45 were found to be distributed in intergenic or noncoding inverted repeat regions, while 34 were in open reading frames. Length polymorphism analysis of the PCR products was used to investigate a set of 12 distinct HSV-1 strains and allowed the identification of 23 polymorphic and 6 monomorphic microsatellites, including two polymorphic trinucleotide repeats (CGT and GGA) within the UL46 and US4 genes, respectively. A multiplex PCR method that amplified 10 polymorphic microsatellites was then developed for the rapid and accurate genetic characterization of HSV-1 strains. Each HSV-1 strain was characterized by its own microsatellite haplotype, which proved to be stable over time in cell culture. This relevant innovative tool was successfully applied both to confirm the close relationship between sequential HSV-1 isolates collected from patients with multiple recurrent infections and to investigate putative nosocomial infections.
* Corresponding author. Mailing address: Service de Virologie, CERVI, Groupe Hospitalier Pitié-Salpêtrière AP-HP, 47-83 Boulevard de l'Hôpital, Paris 75013, France. Phone: 33 1 42 17 74 02. Fax: 33 1 42 17 74 11. E-mail: claire.deback{at}psl.aphp.fr
Published ahead of print on 24 December 2008.
Supplemental material for this article may be found at http://jcm.asm.org/.
Journal of Clinical Microbiology, March 2009, p. 533-540, Vol. 47, No. 3
0095-1137/09/$08.00+0 doi:10.1128/JCM.01565-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
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