Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 UL and US regions from genital swabs collected from 3 continents.

INTRODUCTION: Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines. METHODS: Genital lesion swabs containing ≥ 107log10 copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (UL_US) regions were identified. Phylogenetic trees were created using maximum likelihood reconstruction. RESULTS: Among 46 samples from 38 persons, 1468 intragenic base-pair substitutions were identified. The maximum nucleotide distance between strains for concatenated UL_US segments was 0.4%. Phylogeny did not reveal geographic clustering. The most variable proteins had non-synonymous mutations in < 3% of amino acids. CONCLUSIONS: Unenriched HSV-2 DNA can undergo next-generation sequencing to identify intragenic variability. The use of clinical swabs for sequencing expands the information that can be gathered directly from these specimens.

Herpesvirus: an underestimated virus.

Herpes simplex virus (HSV) infections are common and widespread; nevertheless, their outcome can be of unpredictable prognosis in neonates and in immunosuppressed patients. Anti-HSV therapy is effective, but the emergence of drug-resistant strains or the drug toxicity that hamper the treatment is of great concern. Vaccine has not yet shown relevant benefit; therefore, palliative prophylactic measures have been adopted to prevent diseases. This short review proposes to present concisely the history of HSV, its taxonomy, physical structure, and replication and to explore the pathogenesis of the infection, clinical manifestations, laboratory diagnosis, treatment, prophylaxis and epidemiology of the diseases.

Comparison of two methods of PCR followed by enzymatic restriction digestion for detection and typing of herpes simplex viruses isolated from patients with mucocutaneous or cutaneous lesions.

A multitude of different polymerase chain reactions (PCRs) have been described for detection and typing of Herpes simplex virus (HSV). This paper compares two PCRs coupled to enzymatic restriction (PCR/RFLP) to detect and type HSV. A primers set was designed to amplify a HSV DNA fragment from UL30 and UL 15 genes. Typing was done by restriction of the UL30 and UL15 amplicons with Ava II and Hpa II enzymes, respectively. This strategy was tested with two reference strains (HSV-1 McIntyre, and HSV-2 G), and 47 clinical HSV isolates. Both PCRs produced the expected amplicons (a 492 bp UL30, and 305 bp UL15). The restriction of both amplicons clearly differentiated HSV- from HSV-2, and produced equal results. Thirty one (66%) of the isolates were identified as HSV-1, and the other 16 (34%), as HSV-2. Most of the HSV-1 isolates (27/31) were from orofacial and thoracic lesions; and also, one half of the HSV-2 isolates (8/16) were from the same anatomical regions. Our results showed that either of the two PCR/RFLP could be used to detect and type HSV. Furthermore, our results of the anatomical site of HSV-1 and HSV-2 infections are consistent with previous reports which have shown changes in the classical anatomical localization of herpesvirus infections.

Herpes simplex virus genotyping: multiple optional PCR-based RFLP systems and a non-isotopic single-strand conformation polymorphism method.

Polymerase chain reaction (PCR)-based methods for herpes simplex virus (HSV) types I/II genotyping are described. These methods are based on the single-stranded conformation properties of DNA molecules obtained by PCR (PCR-SSCP) and restriction fragment analysis of PCR products (PCR-RFLP). With the aim to analyse these two genotyping techniques, genomic DNA from the standard viral strains KOS and G, and also 79 normal cervical samples were studied for HSV I/II. Sequence analysis showed 19 different RFLP possible systems for HSV typing. Five systems were used in this study and all led to the expected fragments obtained by sequence analysis. PCR-SSCP showed distinct patterns for both viral types and had 100% of concordance with PCR-RFLP results. The prevalence of herpes simplex virus in the normal cervical samples were 21.5% (17 out of 79), the most frequent viral type was HSV-2, with a prevalence of 71% (12 out of 17). Both techniques appeared suitable for HSV I/II genotyping and are easy to perform in most clinical laboratories.

Detection and direct typing of herpes simplex virus in perianal ulcers of patients with AIDS by PCR.

The presence of herpes simplex virus type 1 (HSV-1) and HSV-2 in perianal ulcerations of 41 AIDS patients was assessed by virus culture and a type-specific PCR-based assay. HSV was isolated from the lesion site in 24 of 41 (58.5%) patients, and HSV DNA was detected by PCR in all 24 (100%) of these specimens. Additionally, PCR was used to detect HSV DNA in 12 of 17 (70.5%) HSV culture-negative samples. Thus, HSV genomic sequences could be demonstrated in 36 of 41 (87.8%) perianal ulcers in this series. Full agreement in HSV typing by either immunodot assay or PCR was seen in 24 samples that were positive by both virus culture and PCR. HSV-2 was demonstrated in 35 of 36 (97.2%) HSV-positive samples.