Simultaneous detection of herpes simplex virus types 1 and 2 by real-time PCR and Pyrosequencing

An atlas of the blood virome in healthy individuals

Emerging evidence indicates that gut virome plays a role in human health and disease, however, much less is known about the viral communities in blood. Here we conducted a direct metatranscriptomic sequencing of virus-like-particles in blood from 1200 healthy individuals, without prior amplification to avoid potential amplification bias and with a strictly bioinformatic and manual check for candidate viral reads to reduce false-positive matches. We identified 55 different viruses from 36 viral families, including 24 human DNA, RNA and retroviruses in 70% of the studied pools. The study showed that anelloviruses are widely distributed and dominate the blood virome in healthy individuals. Human herpesviruses and pegivirus-1 are commonly prevalent in asymptomatic humans. We identified the prevalence of RNA viruses often causing acute infection, like HEV, HPIV, RSV and HCoV-HKU1, revealing of a transmissible risk of asymptomatic infection. Several viruses possible related to transfusion safety were identified, including human Merkel cell polyomavirus, papillomavirus, parvovirus B19 and herpesvirus 8 in addition to HBV. In addition, phages in Caudovirales and Microviridae, were commonly found in pools of samples with a very low abundance; a few sequences for invertebrate, plant and giant viruses were found in some of individuals; however, the remaining 31 viruses mostly reflect extensive contamination from commercial reagents and the work environments. In conclusion, this study is the first comprehensive investigation of blood virome in healthy individuals by metatranscriptomic sequencing of VLP in China. Further investigation of potential false positives representing a major challenge for the identification of novel viruses in mNGS, will offer a systemic idea and means to reveal true viral infections of human.

HIST1H2BB and MAGI2 Methylation and Somatic Mutations as Precision Medicine Biomarkers for Diagnosis and Prognosis of High-grade Serous Ovarian Cancer

Molecular alterations that contribute to long-term (LT) and short-term (ST) survival in ovarian high-grade serous carcinoma (HGSC) may be used as precision medicine biomarkers. DNA promoter methylation is an early event in tumorigenesis, which can be detected in blood and urine, making it a feasible companion biomarker to somatic mutations for early detection and targeted treatment workflows. We compared the methylation profile in 12 HGSC tissue samples to 30 fallopian tube epithelium samples, using the Infinium Human Methylation 450K Array. We also used 450K methylation arrays to compare methylation among HGSCs long-term survivors (more than 5 years) and short-term survivors (less than 3 years). We verified the array results using bisulfite sequencing and methylation-specific PCR (qMSP). in another cohort of HGSC patient samples (n = 35). Immunoblot and clonogenic assays after pharmacologic unmasking show that HIST1H2BB and MAGI2 promoter methylation downregulates mRNA expression levels in ovarian cancer cells. We then used qMSP in paired tissue, ascites, plasma/serum, vaginal swabs, and urine from a third cohort of patients with HGSC cancer (n = 85) to test the clinical potential of HIST1H2BB and MAGI2 in precision medicine workflows. We also performed next-generation exome sequencing of 50 frequently mutated in human cancer genes, using the Ion AmpliSeqCancer Hotspot Panel, to show that the somatic mutation profile found in tissue and plasma can be quantified in paired urine samples from patients with HGSC. Our results suggest that HIST1H2BB and MAGI2 have growth-suppressing roles and can be used as HGSC precision medicine biomarkers.

Development and validation of multiplex real-time PCR assays for rapid detection of cytomegalovirus, Epstein-Barr virus, and polyomavirus BK in whole blood from transplant candidates

Transplant recipients are more susceptible to bacterial and viral infections. Cytomegalovirus (CMV), Epstein-Barr virus (EBV), and polyomavirus BK (BK) are risk factors for graft dysfunction. All three of them are latent viruses that can cause serious disease in immunocompromised patients. Mainly qualitative PCR tests are required for diagnosis and quantitative monitoring, which are used to follow the response to transplantation. We developed a multiplex real-time PCR (qPCR) method to detect these viruses during blood screenings of transplant recipients. We also validated analytical and clinical performance tests using the developed multiplex qPCR. The limit of detection (LOD) was 100, 125, and 183 copies/ml for CMV, EBV, and BK, respectively. These results had high linearity (R² = 0.997) and reproducibility (CV range, 0.95-2.38%, 0.52-3.32%, and 0.31-2.45%, respectively). Among 183 samples, we detected 8 samples that were positive for CMV, while only 6 were positive for EBV, and 3 were positive for BK. Therefore, the viral infection prevalence in transplant candidates was 4.40% for CMV, 3.29% for EBV, and 1.64% for BK. This multiplex qPCR method should be used widely for diagnosing and monitoring latent viral infections in transplant recipients.

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection

Background

Herpesviruses can infect a wide range of animal species. Herpes simplex virus 1 (HSV-1) is one of the eight herpesviruses that can infect humans and is prevalent worldwide. Herpesviruses have evolved multiple ways to adapt the infected cells to their needs, but knowledge about these transcriptional and post-transcriptional modifications is sparse.

Results

Here, we show that HSV-1 induces the expression of about 1000 antisense transcripts from the human host cell genome. A subset of these is also activated by the closely related varicella zoster virus. Antisense transcripts originate either at gene promoters or within the gene body, and they show different susceptibility to the inhibition of early and immediate early viral gene expression. Overexpression of the major viral transcription factor ICP4 is sufficient to turn on a subset of antisense transcripts. Histone marks around transcription start sites of HSV-1-induced and constitutively transcribed antisense transcripts are highly similar, indicating that the genetic loci are already poised to transcribe these novel RNAs. Furthermore, an antisense transcript overlapping with the BBC3 gene (also known as PUMA) transcriptionally silences this potent inducer of apoptosis in cis.

Conclusions

We show for the first time that a virus induces widespread antisense transcription of the host cell genome. We provide evidence that HSV-1 uses this to downregulate a strong inducer of apoptosis. Our findings open new perspectives on global and specific alterations of host cell transcription by viruses.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1329-5) contains supplementary material, which is available to authorized users.

Type-specific detection of herpes simplex virus type 1 and type 2 using the cobas® HSV 1 and 2 test on the cobas® 4800 platform

INTRODUCTION

HSV-1 and HSV-2 are among the most common causes of sexually transmitted infections (stis) globally. these infections are strongly associated with increased risk of hiv acquisition and rare, but devastating, neonatal disease. available treatment options can reduce HSV transmission and improve quality of life. accurate diagnosis early in disease can improve patient management. Areas covered: This paper describes the clinical manifestations of HSV infection often used for clinical diagnostic purposes. The paper then describes the evolution of laboratory diagnostic assays. Serology, culture and molecular diagnostics are described since all are currently in use. The features and performance characteristics of the cobas 4800 HSV1 and HSV2 Test (cobas HSV) on the cobas 4800® system (cobas 4800) are described in detail. Expert commentary: Diagnosis of HSV has historically been unreliable or technically difficult, but the availability of molecular assays such as the cobas HSV test for detection and typing of herpes can improve our ability to correctly manage this disease. Utilization of tools such as the cobas HSV assay may help shorten the time to accurate diagnosis and treatment thus potentially reducing the risk of transmission and the global burden of HSV.

Pyrosequencing as a fast and reliable tool to determine clade affiliation for equine Influenza A virus

The objective of our study was to determine the clade affiliation of 116 contemporary equine Influenza A virus (EIV) isolates using pyrosequencing. The EIV isolates originated from horses with clinical signs of equine influenza and laboratory confirmation of EIV by real-time quantitative PCR (qPCR) in nasal secretions. Clade affiliation was performed on the basis of a single nucleotide polymorphism at 2 positions of the hemagglutinin 1 gene. Pyrosequencing was able to clearly classify EIV Florida sublineage prototype A/equine/Ohio/1/2003 and prototype A/equine/Richmond/1/2007 as clade 1 and 2, respectively. Out of the 116 EIV qPCR-positive samples, 113 (97.4%) were classified as belonging to clade 1 Florida sublineage, whereas 3 (2.6%) were classified as clade 2. All clade 1 EIV strains were detected in domestic horses, whereas the 3 clade 2 EIV strains originated from horses recently imported to the United States. Although clade 1 EIV strains are endemic in the United States, international transportation of horses represents a real risk in introducing clade 2 EIV strains into North America.

Prevalence of 7 sexually transmitted organisms by multiplex real-time PCR in Fallopian tube specimens collected from Saudi women with and without ectopic pregnancy

Background

Ectopic pregnancy (EP) is associated with maternal morbidity and occasionally mortality during the first trimester. A history of sexually transmitted infection (STI) and pelvic inflammatory disease have been implicated as major risk factors for EP. Our aim was to measure the prevalence of Chlamydia trachomatis (CT), Neisseria gonorrhoeae, Mycoplasma genitalium (MG), Ureaplasma parvum/urealyticum, Gardnerella vaginalis, Trichomonas vaginalis and herpes simplex virus (HSV)-1&2 in Fallopian tubes collected from EP and the results were compared with those obtained from total abdominal hysterectomy (TAH) and tubal ligation.

Methods

This was a prospective case–control study and tubal samples were collected from 135 Saudi women recruited from 3 centres in the Western region as follow: 84 EPs, 20 TAH and 31 tubal ligations. Multiplex TaqMan PCR was performed using an IVD CE kit for the simultaneous detection of candidate pathogens following DNA extraction.

Results

Infections were detected in 31.8 % of the 135 participants either as single (11.1 %) or co-infections (20.7 %) and the frequencies were significantly higher in EP (42.85 %) compared with control (13.72 %). The rates of CT (27.4 %; P = 0.001); MG (20.2 %; P = 0.009) and HSV-1/2 (21.4 %; P = 0.01) were significantly higher in EP. No significant difference between the study groups was observed for the other pathogens (P > 0.05). Binary logistic regression also showed that infection with ≥ 2 pathogens (OR 4.9; 95 % CI: 2.2 – 11.6; P = 0.006), CT (OR 3.07; 95 % CI: 1.3 – 12.3; P = 0.002), MG (OR 2.3; 95 % CI: 1.1 – 8.6; P = 0.03) and HSV-1/2 (OR 1.7; 95 % CI: 0.75 – 5.7; P = 0.004) were associated with a significantly higher risk of developing EP.

Conclusions

STIs are frequent in the upper genital tract of Saudi women during the reproductive age and, CT, MG and HSV-1/2 were more prevalent in EP. The observed high rates of co-infection advocate the necessity of establishing national guidelines and/or screening program utilising multiplex PCR approach for the detection of common STIs among high risk groups in the kingdom. Further studies are needed to measure the adverse reproductive outcomes associated with STIs in Saudi Arabia.

Serum HSV-1 and -2 IgM in pregnant women in Port Harcourt, Nigeria

The present study was undertaken for the purpose of finding IgM antibodies against HSV-1 and 2 infections among pregnant women and also to evaluate correlation of Serum HSV-1 and 2 IgM in these pregnant women. A total of 180 pregnant women attending antenatal clinic at Braithwaite Memorial Specialist Hospital (BMSH) in Port Harcourt, Nigeria were consecutively recruited, after they had given consents to participate in the study. Serum of each sample was assayed for HSV-1&2 IgM antibody using a commercial ELISA. Five (2.8%) of the pregnant women were positive for IgM antibody against HSV-1&2. Marital status mainly correlated (χ(2) = 221.5, P < 0.05) with HSV-2 infection and HSV-1/HSV-2 co-infection. Age, educational level, occupation, and gestation were not consistently associated (P>0.05) with HSV-1/HSV-2 infection and co-infection. We also observed a high overall anti-HSV-1&2 IgM seronegativity of 97.2% among these pregnant women. Group-specific seronegativity was also high ranging from 93.3-100%. Although the age-groups significantly differed, none of their variables showed statistical association with the seronegativity. This represents the first analysis of HSV IgM antibody reported in Port Harcourt, Nigeria and has important public health implications, particularly for pregnant women. Consideration of this information would benefit physicians providing primary gynecological and obstetric care to this population of women.

Y chromosome DNA in cervicovaginal self-collected samples of childbearing age women: Implications for epitheliotropic sexually transmitted infections?

AIMS

Assuming a possible association between Y chromosome (Yc)-DNA and sexually transmitted infection (STI) transmission rate, could Yc-DNA be related to an increased prevalence of Human Papillomavirus (HPV), Herpes Simplex Virus (HSV-1/2) and Chlamydia trachomatis (CT)? Could Yc-DNA be used to validate self-reported condom use and sexual behaviors?

MAIN METHODS

Cervicovaginal (CV) self-collected samples of 612 Portuguese women at childbearing age were tested for Yc, HPV, HSV-1/2 and CT by polymerase chain reaction (PCR).

KEY FINDINGS

The prevalence of Yc, HPV, CT and HSV-2 was 4.9%, 17.6%, 11.6% and 2.8%, respectively. There was a statistically significant trend for increased Yc-DNA prevalence in HPV positive samples [odds ratio (OR) 2.35, 95% confidence interval (CI) 1.03-5.31] and oral contraceptive (OC) use (OR 4.73, 95% CI 1.09-20.44). A protective effect of condom use was observed in Yc-DNA detection (OR 0.40, 95% CI 0.18-0.89). No statistically significant difference was found between Yc-DNA, CT and HSV-2 infection. HPV infection risk increased with age (>20 years), young age at first sexual intercourse (FSI) (≤18 years), >1 lifetime sexual partner (LSP) and OC use. Risk factors for CT infection were young age (≤20 years) and young age at FSI (≤18 years). HSV-2 infection risk increased with age (>20 years) and >1 LSP.

SIGNIFICANCE

Considering the prevalence of HPV and CT in Yc positive samples, we hypothesize a current infection due to recent sexual activity. The study of Yc PCR may add information as (i) a predictor of STI transmission and (ii) an indicative biomarker to validate self-reported condom use.

Development of a pyrosequencing assay for the typing of alphaherpesviruses

Identification of herpesvirus in biological material is usually carried out by real-time PCR. With the aim to classify the strain of virus identified, real-time PCR must be often supported by time-consuming capillary electrophoresis sequencing analysis. Here we provide a protocol for the rapid and reliable identification of 5 closely related herpesviruses by PyroMark Q24 sequencing system. PyroMark performs DNA sequencing analysis using pyrosequencing, a technology based on the detection of released pyrophosphate during DNA elongation [1]. PyroMark is designed to detect changes in specified variable positions of the DNA. It can efficiently detect single nucleotide differences in sequences [2]. In the present paper we describe a protocol to pyrosequence a small polymorphic segment of the US8 gene. On the basis of the differences identified in the nucleotide sequence we could readily classify the herpesvirus as Bovine herpesvirus 1.1, Bovine herpesvirus 1.2, Bovine herpesvirus 5, Bubaline herpesvirus 1 or Caprine herpesvirus. The protocol set up offers several advantages with respect to the techniques commonly used:

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it requires less than one working day to be carried;

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it gives the possibility to analyze, at reasonable costs, up to 24 samples at a time; and

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it allows to detect with great reliability and specificity strongly genetically correlated organisms like the herpesviruses named above. The procedure can be easily applied to other families of viruses, with opportune modifications.

Diagnosis of genital herpes simplex virus infection in the clinical laboratory

Since the type of herpes simplex virus (HSV) infection affects prognosis and subsequent counseling, type-specific testing to distinguish HSV-1 from HSV-2 is always recommended. Although PCR has been the diagnostic standard method for HSV infections of the central nervous system, until now viral culture has been the test of choice for HSV genital infection. However, HSV PCR, with its consistently and substantially higher rate of HSV detection, could replace viral culture as the gold standard for the diagnosis of genital herpes in people with active mucocutaneous lesions, regardless of anatomic location or viral type. Alternatively, antigen detection—an immunofluorescence test or enzyme immunoassay from samples from symptomatic patients--could be employed, but HSV type determination is of importance. Type-specific serology based on glycoprotein G should be used for detecting asymptomatic individuals but widespread screening for HSV antibodies is not recommended. In conclusion, rapid and accurate laboratory diagnosis of HSV is now become a necessity, given the difficulty in making the clinical diagnosis of HSV, the growing worldwide prevalence of genital herpes and the availability of effective antiviral therapy.

Rapid strategy for screening by pyrosequencing of influenza virus reassortants--candidates for live attenuated vaccines

BACKGROUND

Live attenuated influenza vaccine viruses (LAIVs) can be generated by classical reassortment of gene segments between a cold adapted, temperature sensitive and attenuated Master Donor Virus (MDV) and a seasonal wild-type (wt) virus. The vaccine candidates contain hemagglutinin (HA) and neuraminidase (NA) genes derived from the circulating wt viruses and the remaining six genes derived from the MDV strains. Rapid, efficient selection of the viruses with 6∶2 genome compositions from the large number of genetically different viruses generated during reassortment is essential for the biannual production schedule of vaccine viruses.

METHODOLOGY/PRINCIPAL FINDINGS

This manuscript describes a new approach for the genotypic analysis of LAIV reassortant virus clones based on pyrosequencing. LAIV candidate viruses were created by classical reassortment of seasonal influenza A (H3N2) (A/Victoria/361/2011, A/Ohio/02/2012, A/Texas/50/2012) or influenza A (H7N9) (A/Anhui/1/2013) wt viruses with the MDV A/Leningrad/134/17/57(H2N2). Using strain-specific pyrosequencing assays, mixed gene variations were detected in the allantoic progenies during the cloning procedure. The pyrosequencing analysis also allowed for estimation of the relative abundance of segment variants in mixed populations. This semi-quantitative approach was used for selecting specific clones for the subsequent cloning procedures.

CONCLUSIONS/SIGNIFICANCE

The present study demonstrates that pyrosequencing analysis is a useful technique for rapid and reliable genotyping of reassortants and intermediate clones during the preparation of LAIV candidates, and can expedite the selection of vaccine virus candidates.

Apparent Rarity of Asymptomatic Herpes Cervicitis in a Woman with Intra-Uterine Contraceptive Device

Infection with genital herpes simplex virus (HSV) remains a common viral sexually transmitted disease, often subclinical and a major worldwide problem of women of reproductive age group. Herpes cervicitis is an unusual presentation of Herpes simplex virus infection in females. The finding of herpes cervicitis on routine pap smear of an asymptomatic woman on Intrauterine contraceptive device still further supports the need for increased awareness on the possibility of Herpes simplex virus infection among women, particularly those on Intrauterine contraceptive device. The index case is a 28 years old Nigerian female who was referred to our Special Treatment Clinic on account of an abnormal pap smear cytology which was in keeping with Herpes cervicitis. There was no history of genital ulcer in this patient; however ELISA for HSV 2 IgM was positive in her. We therefore describe a case of herpes cervicitis in an asymptomatic woman on intrauterine contraceptive device. This case highlights to clinicians the need to be aware of the possibility of this association and to carry out relevant investigations so as to identify and treat these patients appropriately. Therefore, there is a need to put in place adequate public health intervention strategy to prevent genital herpes in women of reproductive age group with a view to preventing the possibility of congenital herpes in subsequent pregnancy.

A miniaturized and integrated gel post platform for multiparameter PCR detection of herpes simplex viruses from raw genital swabs

Herpes simplex virus (HSV) is one of the most prevalent viruses, with acute and recurrent infections in humans. The current gold standard for the diagnosis of HSV is viral culture which takes 2-14 days and has low sensitivity. In contrast, DNA amplification by polymerase chain reaction (PCR) can be performed within 1-2 h. We here describe a multiparameter PCR assay to simultaneously detect HSV-1 and HSV-2 DNA templates, together with integrated positive and negative controls, with product detection by melting curve analysis (MCA), in an array of semi-solid polyacrylamide gel posts. Each gel post is 0.67 μL in volume, and polymerized with all the components required for PCR. Both PCR and MCA can currently be performed in one hour and 20 min. Unprocessed genital swabs collected in universal transport medium were directly added to the reagents before or after polymerization, diffusing from atop the gel posts. The gel post platform detects HSV templates in as little as 2.5 nL of raw sample. In this study, 45 genital swab specimens were tested blindly as a preliminary validation of this platform. The concordance of PCR on gel posts with conventional PCR was 91%. The primer sequestration method introduced here (wherein different primers are placed in different sets of posts) enables the simultaneous detection of multiple pathogens for the same sample, together with positive and negative controls, on a single chip. This platform accepts unprocessed samples and is readily adaptable to detection of multiple different pathogens or biomarkers for point-of-care diagnostics.

A novel multiplex real-time PCR assay for the detection and quantification of HPV16/18 and HSV1/2 in cervical cancer screening

Infection with human papillomavirus (HPV), particularly HPV16 and HPV18, is the main cause of invasive cervical cancer, although other factors such as herpes simplex virus (HSV) may act in conjunction with HPV in this context. To explore the possibility of developing a system for rapid diagnosis and clinical screening of cervical cancer, we developed a multiplex real-time PCR assay that can simultaneously detect and quantify HPV16/18 and HSV1/2. To evaluate its possibilities and practical uses, 177 samples collected from patients with suspected HPV and HSV infection in exfoliated cervical cells, genital herpes or labial herpes were tested by multiplex real-time PCR and compared with results obtained by DNA sequencing. Each virus was detected over a range from 1.0 × 10(1) to 1.0 × 10(7) copies/reaction. The clinical sensitivity was 100% for HPV16/18 and HSV1/2. The clinical specificity was 97.1% for HPV16, 98.1% for HPV18, 97.0% for HSV1 and 96.0% for HSV2. The kappa value was 0.96 for HPV16, 0.92 for HPV18, 0.94 for HSV1 and 0.93 for HSV2, when DNA sequencing was used as the reference standard. In summary, this novel multiplex real-time PCR allows the rapid and specific detection of HPV16/18 and HSV1/2, as well as coinfection with HPV and HSV, in clinical samples. In the future, this multiplex real-time PCR assay will assist in cervical cancer screening, viral treatment evaluation and epidemiological studies in which high throughput analysis is required.

Pyrosequencing for mini-barcoding of fresh and old museum specimens

DNA barcoding is an effective approach for species identification and for discovery of new and/or cryptic species. Sanger sequencing technology is the method of choice for obtaining standard 650 bp cytochrome c oxidase subunit I (COI) barcodes. However, DNA degradation/fragmentation makes it difficult to obtain a full-length barcode from old specimens. Mini-barcodes of 130 bp from the standard barcode region have been shown to be effective for accurate identification in many animal groups and may be readily obtained from museum samples. Here we demonstrate the application of an alternative sequencing technology, the four-enzymes single-specimen pyrosequencing, in rapid, cost-effective mini-barcode analysis. We were able to generate sequences of up to 100 bp from mini-barcode fragments of COI in 135 fresh and 50 old Lepidoptera specimens (ranging from 53–97 year-old). The sequences obtained using pyrosequencing were of high quality and we were able to robustly match all the tested pyro-sequenced samples to their respective Sanger-sequenced standard barcode sequences, where available. Simplicity of the protocol and instrumentation coupled with higher speed and lower cost per sequence than Sanger sequencing makes this approach potentially useful in efforts to link standard barcode sequences from unidentified specimens to known museum specimens with only short DNA fragments.

Genital herpes simplex virus type 1 in women: detection in cervicovaginal specimens from gynecological practices in the United States

Herpes simplex virus types 1 and 2 (HSV-1 and -2) are significant human pathogens causing clinically indistinguishable facial and genital lesions. Recently, the number of reported genital herpes cases caused by type 1 virus has increased. Identifying the HSV type is of clinical importance to determine proper treatment, as there is no licensed vaccine or cure. We assessed, by PCR, the frequency of HSV-1 and HSV-2 present in more than 60,000 clinical cervicovaginal specimens derived from samples originating from 43 continental U.S. states. Fourteen percent were positive for HSV-1 and/or HSV-2. This likely represents subclinal shedding. It was not a measurement of the prevalence of HSV infection. While the majority were HSV-2, 32% were HSV-1. The distribution of HSV types varied between the states with the largest number of specimens, New Jersey, Florida, and Texas. Specimens from women under the age of 24 had an HSV-1 positivity rate of 47 percent. Importantly, in New Jersey, an observed age effect was the disproportionately high prevalence of genital HSV-1 in young women. This represents the largest analysis of HSV types reported and has important public health implications, particularly for younger women.

Prospects for Developing an Effective Vaccine Against Ocular Herpes Simplex Virus Infection

One of the hallmarks of herpes simplex virus (HSV) infection is the establishment of a lifelong latent infection accompanied by periods of recurrent disease. Primary HSV infections or repeated clinical recurrences do not elicit immune responses capable of completely preventing recurrences of endogenous virus. It is therefore questionable if vaccination approaches that seek to mimic the immune response to natural infection will reduce infection or disease due to an exogenous viral challenge. Approaches to the induction of protective responses by altering or enhancing both innate and adaptive immunity, using novel vaccines specifically tested in models of HSV infections of the eye, such as recombinant viral vaccine vectors and DNA vaccines, are detailed in this review.

Rapid isolation of HSV-1 and HSV-2 from OneSwab cervicovaginal specimens

Herpes simplex viruses are significant human pathogens which remain latent in their hosts for life and reactivate to cause disease at or near the initial site of infection. Since HSV infections are associated with high morbidity, rapid detection and diagnosis of these viruses is imperative. While PCR technology for the diagnosis of HSV is now almost utilized universally, virus isolation from mucosa and skin in shell cultures is still applied in many clinical settings. Virus growth in cultured cells alone has the disadvantage that it cannot distinguish between HSV-1 and HSV-2. The aim of this study was to combine these two disparate methods. A protocol was developed to isolate clinical strains directly from the medium used for as the standard source of extraction to isolate DNA. Both HSV-1 and HSV-2 strains were isolated successfully from cervicovaginal swabs transported in OneSwab devices. It was found that the titers of these viruses did not correlate with the C(T) scores determined for the samples using real-time PCR. HSV-2 strains generally had lower titers than those of HSV-1, suggesting that the HSV-2 may be more sensitive to the sample handling procedures. These studies represent the first report of the culture and isolation of HSV from clinical samples using OneSwab intended exclusively for molecular diagnostic analyses.

Multiplex real-time PCR for the simultaneous detection of herpes simplex virus, human herpesvirus 6, and human herpesvirus 7

A simultaneous detection system to quantify HSV, HHV-6, and HHV-7 DNA via multiplex real-time PCR using different fluorochromes was developed. The minimum quantitative level established via this multiplex assay was four copies per reaction for HSV type 1, four copies for HHV-6, and three copies for HHV-7, respectively. The dynamic range encompassed at least six orders of magnitude. The system was specific and reproducible even in the presence of large amounts of other viral DNA. We then applied this multiplex real-time PCR assay to 105 CSF specimens obtained from subjects less than 15 years old in whom a diagnosis of viral encephalitis/encephalopathy was suspected on clinical grounds. The detection rate for each viral DNA was 6.7% for HSV, 9.5% for HHV-6, and 1.9% for HHV-7. These results indicate that our system is reliable and may be useful for the rapid diagnosis of viral encephalitis/encephalopathy.

[Utility of molecular biology techniques in the diagnosis of sexually transmitted diseases and genital infections]

Historically, the diagnosis of sexually transmitted diseases (STDs) has been difficult. The introduction of molecular biology techniques in microbiological diagnosis and their application to non-invasive samples has produced significant advances in the diagnosis of these diseases. Overall, detection of Neisseria gonorrhoeae by molecular biology techniques provides a presumptive diagnosis and requires confirmation by culture in areas with a low prevalence. For Chlamydia trachomatis infections, these techniques are considered to be the most sensitive and specific procedures for mass screening studies, as well as for the diagnosis of symptomatic patients. Diagnosis of Mycoplasma genitalium infection by culture is very slow and consequently molecular techniques are the only procedures that can provide relevant diagnostic information. For Treponema pallidum, molecular techniques can provide direct benefits in the diagnosis of infection. Molecular techniques are not established for the routine diagnosis of donovanosis, but can be recommended when performed by experts. Molecular methods are advisable in Haemophilus ducreyi, because of the difficulties of culture and its low sensitivity. In genital herpes, molecular techniques have begun to be recommended for routine diagnosis and could soon become the technique of choice. For other genital infections, bacterial vaginosis, vulvovaginal candidosis and trichomoniasis, diagnosis by molecular methods is poorly established. With genital warts, techniques available for screening and genotyping of endocervical samples could be used for certain populations, but are not validated for this purpose.

Studies of the human aortic intima by a direct quantitative assay of mutant alleles in the mitochondrial genome

A mutant allele quantitative assay was developed to study somatic mitochondrial mutations associated with human diseases. This assay may be used in the clinical diagnostics for diseases associated with somatic mutations. To detect somatic mutations associated with atherosclerotic lesions of the aortal intima, we analyzed 40 mitochondrial mutations previously identified in several pathological conditions. 10 mutations associated with lipofibrosis plaques were found in mitochondrial genes that encode rRNA 12S, tRNA-Leu (UUR recognition codon), tRNA-Leu (CUN recognition codon), subunits of 1, 2, 5, and 6 NADH-dehydrogenase, and cytochrome B.

Reconsideration of viral protein immunoblotting for differentiation of human herpes simplex viruses

Herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) are ubiquitous human pathogens that infect their hosts for life and reactivate to cause disease at or near the initial site of infection. As the incidence of genital HSV-1 infections increase, there is an increased demand for valid viral typing diagnostics. In this report, we reconsidered and developed a triple-phase immune-typing procedure that compares differences in electrophoretic mobilities of viral ICP4, ICP27, and VP22 proteins between HSV-1 and HSV-2 strains. We isolated and immunotyped 5 primary HSV-1 strains derived from orofacial, ocular, and genital areas along with 2 primary HSV-2 strains from the genital area. Advantages of this methodology include its general technical simplicity, sensitivity, and ability to definitively type HSV. It is anticipated that this methodology will be useful in distinguishing viruses obtained in clinical cultures.

Identification and genotyping of molluscum contagiosum virus from genital swab samples by real-time PCR and Pyrosequencing

BACKGROUND

Laboratory diagnosis of molluscum contagiosum virus (MCV) is important as lesions can be confused with those caused by Cryptococcus neoformans, herpes simplex virus, human papillomavirus, and varicella-zoster virus.

OBJECTIVES

To develop a rapid method for identifying patients infected with MCV via swab sampling.

STUDY DESIGN

Two dual-labeled probe real-time PCR assays, one homologous to the p43K gene and one to the MC080R gene, were designed. The p43K PCR was designed to be used in conjunction with Pyrosequencing for confirmation of PCR products and discrimination between MCV1 and MCV2.

RESULTS

Both PCR assays were optimized with respect to reaction components, thermocycling parameters, and primer and probe concentrations. The specificities of both PCR assays were confirmed by non-amplification of 38 known human pathogens. Sensitivity assays demonstrated detection of as few as 10 copies per reaction. Testing 703 swabs, concordance between the two real-time PCR assays was 99.9%. Under the developed conditions, Pyrosequencing of the p43K PCR product was capable of providing enough nucleotide sequence to definitively differentiate MCV1 and MCV2.

CONCLUSIONS

These real-time PCR assays can be used for the rapid, sensitive, and specific detection of MCV and, when combined with Pyrosequencing, can further discriminate between MCV1 and MCV2.

Simultaneous quantification of Epstein-Barr virus, cytomegalovirus, and human herpesvirus 6 DNA in samples from transplant recipients by multiplex real-time PCR assay

We developed a multiplex real-time PCR assay using 6-carboxyfluorescein, 6-carboxy-4',5'-dichloro-2',7'-dimethoxyfluorescein, and carbocyanine 5-labeled probes to simultaneously quantify Epstein-Barr virus (EBV), cytomegalovirus (CMV), and human herpesvirus 6 (HHV-6) DNA. When previously tested and stored DNA samples were examined, results of the multiplex real-time PCR assay were as sensitive and specific as those of a single real-time PCR assay. The multiplex assay was used to quantify the EBV, CMV, and HHV-6 DNA in 46 transplant recipients. A total of 303 whole-blood and plasma specimens were collected and analyzed. According to the results of the multiplex assay, the detection rates for viral DNA in whole blood and plasma were 23.8% and 5.9% for EBV, 11.2% and 5.3% for CMV, and 12.5% and 2.0% for HHV-6, respectively. All forms of viral DNA were detected more frequently in whole blood than in plasma. During the symptomatic period, EBV DNA was detected in all whole-blood specimens but not in all plasma specimens. Furthermore, the EBV DNA load in whole blood was higher during the symptomatic period than during the asymptomatic period, whereas the EBV DNA load in plasma was similar for both periods. These results demonstrate that whole blood is more suitable for the quantification of EBV DNA in transplant patients. However, a cutoff value with clinical relevance still needs to be determined.

Design and validation of an H5 TaqMan real-time one-step reverse transcription-PCR and confirmatory assays for diagnosis and verification of influenza A virus H5 infections in humans

Increasing diversity among influenza H5N1 viruses has resulted in the need for sensitive and specific diagnostic assays, fully validated for the detection of H5 viruses belonging to all hemagglutinin (HA) clades, particularly the recently circulating H5N1 viruses of clade 2. In this report, the development and validation of a real-time, one-step TaqMan reverse transcription-PCR (RT-PCR) assay specific for the detection of influenza A H5 viruses from clades 1, 1', 2, and 3 is described. The real-time assay for H5 virus was shown to be highly sensitive, detecting H5 virus levels of <1 PFU from each of the HA clades. Specificity of the H5 RT-PCR for influenza A H5 viruses was demonstrated by using influenza A viruses of different subtypes, clinical samples containing influenza A viruses H1N1, H3N2, and H5N1, influenza B viruses, and other respiratory viruses. The usefulness of the inclusion of a distinguishable assay positive control and of confirmatory assays for the laboratory diagnosis and verification of H5 virus infections was demonstrated. A real-time RT-PCR pyrosequencing assay, a restriction enzyme digestion assay, and direct sequencing of the H5 real-time RT-PCR amplicon were validated for the confirmation of H5 detection by the diagnostic real-time assay. The H5 real-time assay was applied to diagnostic testing for suspected cases of influenza A virus H5 infection in the United Kingdom. Influenza A H5 viruses were not detected in the cases analyzed; however, influenza A H3N2 virus was detected in 57% of the suspected cases of H5. The H5 TaqMan real-time RT-PCR and confirmatory assays will be useful tools for the laboratory surveillance and rapid diagnosis of H5 infections in humans.

Longitudinal evaluation of herpes simplex virus DNA load during episodes of herpes labialis

BACKGROUND

Few studies have performed sequential evaluation of the herpes simplex virus (HSV) load using quantitative PCR during episodes of herpes labialis.

OBJECTIVE

To determine HSV viral load kinetics during recurrences of herpes labialis.

STUDY DESIGN

Twenty-two subjects were monitored by daily swabs during recurrences of herpes labialis. A real-time PCR detecting both HSV-1 and HSV-2 was used to quantify the viral load.

RESULTS

Median duration of HSV-1 shedding was 60 h and 48 h by PCR and culture, respectively. No HSV-2 DNA was detected in that study. Peak viral DNA load (123.6 copies/cell) occurred at 48 h with no virus detected beyond 96 h of onset of symptoms.

CONCLUSIONS

These viral load kinetics data could be used as surrogate markers of antiviral activity in future clinical trials.