Molecular Characterization of Herpes Simplex Virus 2 Strains by Analysis of Microsatellite Polymorphism

Abstract

The complete 154-kbp linear double-stranded genomic DNA sequence of herpes simplex virus 2 (HSV-2), consisting of two extended regions of unique sequences bounded by a pair of inverted repeat elements, was published in 1998 and since then has been widely employed in a wide range of studies. Throughout the HSV-2 genome are scattered 150 microsatellites (also referred to as short tandem repeats) of 1-to 6-nucleotide motifs, mainly distributed in noncoding regions. Microsatellites are considered reliable markers for genetic mapping to differentiate herpesvirus strains, as shown for cytomegalovirus and HSV-1. The aim of this work was to characterize 12 polymorphic microsatellites within the HSV-2 genome by use of 3 multiplex PCR assays in combination with length polymorphism analysis for the rapid genetic differentiation of 56 HSV-2 clinical isolates and 2 HSV-2 laboratory strains (gHSV-2 and MS). This new system was applied to a specific new HSV-2 variant recently identified in HIV-1-infected patients originating from West Africa. Our results confirm that microsatellite polymorphism analysis is an accurate tool for studying the epidemiology of HSV-2 infections.

Genetic Diversity within Alphaherpesviruses: Characterization of a Novel Variant of Herpes Simplex Virus 2

“…Each HSV-2 isolate was characterized by determining its microsatellite haplotypethe combination of the PCR product lengths obtained in the three multiplex assays-for rapid evaluation of the genetic profiles of the 14 HSV-2v and 8 HSV-2c isolates. As reported in a previous study (19), haplotypes were obtained for all isolates, making it possible to generate an unrooted phylogenetic tree with the NJ algorithm from microsatellite allele frequencies. Moreover, all HSV-2v haplotypes were correctly discriminated from each other, and all HSV-2v isolates other than HSV-2v isolates 4 and 9 (12/14) clustered together (Fig.…”

“…The microsatellites were given names beginning with an M, with this letter being followed by position numbers within noncoding regions of the HSV-2 genome, as previously described (Fig. 2) (19). The genetic relationships between the HSV-2v and HSV-2c isolates, based on the frequencies of particular amplicon sizes at (9).…”

“…Microsatellite markers are widely used in epidemiological studies and have already proven useful for the precise characterization of HSV-2 isolates by length polymorphism analysis (19). Haplotype, defined as the combination of the lengths of the nine PCR products obtained in three multiplex PCR assays amplifying 12 polymorphic microsatellites (corresponding to nine loci), was used to differentiate between HSV-2 isolates.…”

“…The hatched boxes represent the genes analyzed by conventional sequencing: DNA polymerase (POL) (UL30 gene), processivity factor of DNA polymerase (PF) (UL42 gene), thymidine kinase (TK) (UL23 gene), glycoprotein L (gL) (UL1 gene), gH (UL22 gene), gB (UL27 gene), gG (US4 gene), and gD (US6 gene). The labeled vertical bars represent microsatellite markers (M followed by position numbers, as previously identified [19]) analyzed by length polymorphism analysis: M20 (TRL), M28 (TRL), M37-38 (inter-UL10-UL11), M43 (inter-UL15-UL18), M50-51 (inter-UL25-UL26), M55 (inter-UL26-UL27), M63-64 (inter-UL37-UL38), M72 (inter-UL50-UL51), and M125 (inter-US4-US5). …”

Genomic, Phylogenetic, and Recombinational Characterization of Herpes Simplex Virus 2 Strains

“…Microsatellite and tandem repeats have been used in the past to characterize HSV-1 and HSV-2 strains (38)(39)(40), and genomic analysis of the multiple strains in this study may allow precise short sequence repeat targeted analysis for the rapid characterization of viral strains. Genomic distances.…”