Comparison of Simplexa HSV 1 & 2 PCR with culture, immunofluorescence, and laboratory-developed TaqMan PCR for detection of herpes simplex virus in swab specimens

Control of HSV-1 Infection: Directions for the Development of CRISPR/Cas-Based Therapeutics and Diagnostics

It is estimated that nearly all individuals have been infected with herpesviruses, with herpes simplex virus type 1 (HSV-1) representing the most prevalent virus. In most cases, HSV-1 causes non-life-threatening skin damage in adults. However, in patients with compromised immune systems, it can cause serious diseases, including death. The situation is further complicated by the emergence of strains that are resistant to both traditional and novel antiviral drugs. It is, therefore, imperative that new methods of combating HSV-1 and other herpesviruses be developed without delay. CRISPR/Cas systems may prove an effective means of controlling herpesvirus infections. This review presents the current understanding of the underlying molecular mechanisms of HSV-1 infection and discusses four potential applications of CRISPR/Cas systems in the fight against HSV-1 infections. These include the search for viral and cellular genes that may serve as effective targets, the optimization of anti-HSV-1 activity of CRISPR/Cas systems in vivo, the development of CRISPR/Cas-based HSV-1 diagnostics, and the validation of HSV-1 drug resistance mutations.

Diagnostic Methods and Management Strategies of Herpes Simplex and Herpes Zoster Infections

Herpesviruses are medium-sized double-stranded DNA viruses. Of more than 80 herpesviruses identified, only 9 human herpesviruses have been found to cause infection in humans. These include herpes simplex viruses 1 and 2 (HSV-1 and HSV-2), varicella-zoster virus (VZV), human cyto-megalovirus (HCMV), Epstein-Barr virus (EBV), and human herpesvirus (HHV-6A, HHV-6B, HHV-7, HHV-8). HSV-1, HSV-2, and VZV can be problematic given their characteristic neurotropism which is the ability to invade via fusion of its plasma membrane and reside within neural tissue. HSV and VZV primarily infect mucocutaneous surfaces and remain latent in the dorsal root ganglia for a host's entire life. Reactivation causes either asymptomatic shedding of virus or clinical manifestation of vesicular lesions. The clinical presentation is influenced by the portal of entry, the immune status of the host, and whether the infection is primary or recurrent. Affecting 60% to 95% of adults, herpesvirus-associated infections include gingivostomatitis, orofacial and genital herpes,and primary varicella and herpes zoster. Symptomatology, treatment, and potential complications vary based on primary and recurrent infections as well as the patient's immune status.

A rapid isothermal CRISPR-Cas13a diagnostic test for genital herpes simplex virus infection

Prompt diagnosis is essential for managing herpes simplex virus types 1 and 2 (HSV-1/2). Existing diagnostic methods are not widely available that required expensive or additional equipment for conducting examinations and result readouts, which can limit their utility in resource-constrained settings. We successfully developed a CRISPR-Cas13a-based assay for the detection and genotyping of HSV. Our assay demonstrated a high sensitivity of 96.15% and 95.15% for HSV-1 and HSV-2, respectively, with a specificity of 100% compared to a commercial qPCR assay when tested on 194 clinical samples. Remarkably, the assay enables a limit of detection of 1 copy/μL of viral DNA, facilitated by an enhanced input of RPA product and is designed for both mobile app integration and colorimetric interpretation, allowing for semiquantitative readings. These findings highlight the excellent performance of our CRISPR-based diagnostic in detecting HSV and its potential for point-of-care testing in resource-constrained settings.

Diagnosis and Management of Genital Herpes: Key Questions and Review of the Evidence for the 2021 Centers for Disease Control and Prevention Sexually Transmitted Infections Treatment Guidelines

Genital herpes, caused by herpes simplex virus (HSV) type 1 or type 2, is a prevalent sexually transmitted infection (STI). Given that HSV is an incurable infection, there are important concerns about appropriate use of diagnostic tools, management of infection, prevention of transmission to sexual partners, and appropriate counseling. In preparation for updating the Centers for Disease Control and Prevention (CDC) STI treatment guidelines, key questions for management of genital herpes infection were developed with a panel of experts. To answer these questions, a systematic literature review was performed, with tables of evidence including articles that would change guidance assembled. These data were used to inform recommendations in the 2021 CDC STI treatment guidelines.

Sexually Transmitted Infections Treatment Guidelines, 2021

These guidelines for the treatment of persons who have or are at risk for sexually transmitted infections (STIs) were updated by CDC after consultation with professionals knowledgeable in the field of STIs who met in Atlanta, Georgia, June 11-14, 2019. The information in this report updates the 2015 guidelines. These guidelines discuss 1) updated recommendations for treatment of Neisseria gonorrhoeae, Chlamydia trachomatis, and Trichomonas vaginalis; 2) addition of metronidazole to the recommended treatment regimen for pelvic inflammatory disease; 3) alternative treatment options for bacterial vaginosis; 4) management of Mycoplasma genitalium; 5) human papillomavirus vaccine recommendations and counseling messages; 6) expanded risk factors for syphilis testing among pregnant women; 7) one-time testing for hepatitis C infection; 8) evaluation of men who have sex with men after sexual assault; and 9) two-step testing for serologic diagnosis of genital herpes simplex virus. Physicians and other health care providers can use these guidelines to assist in prevention and treatment of STIs.

Bayesian Evaluation of Solana HSV 1+2/VZV Assay Compared to Viral Culture and Commercial PCR Assay for Cutaneous or Mucocutaneous Specimens

Results from the Solana HSV 1+2/VZV assay for the detection of herpes simplex virus 1 (HSV-1), HSV-2, and varicella-zoster virus (VZV) in cutaneous or mucocutaneous specimens were compared with that of viral culture and a commercial PCR assay (RealStar alpha herpesvirus PCR kit). Three hundred two mucocutaneous specimens, for which HSV-1, HSV-2, or VZV viral culture or PCR detection have been requested, were randomly selected and prospectively processed on the Solana assay and viral culture or the RealStar assay. Discordant results between culture and the Solana assay were further analyzed using the RealStar assay. A Bayesian latent class model was developed to estimate the performance of each method. Viral culture detected 123 positive specimens (85 HSV-1, 36 HSV-2, and 2 VZV), while the Solana assay detected 27 additional positive specimens (4 HSV-1, 11 HSV-2, and 12 VZV), in agreement with the RealStar PCR assay. The estimated sensitivity of the Solana assay according to our model was 92.7% to 98.7%, 87.1% to 97.8%, and 94.9% to 98.8% (95% confidence interval [CI]) for HSV-1 HSV-2, and VZV, respectively, while the estimated sensitivity of viral culture was 85.2% to 95.0%, 73.6% to 89.6%, and 30.9% to 45.8% (95% CI), respectively. A nonsignificant tendency toward increased sensitivity was noted for the Solana assay compared with culture for HSV-1 and HSV-2, and the Solana assay was significantly more sensitive than culture for the detection of VZV. The Solana assay performed comparably to the RealStar assay. Processing time was reduced with the Solana assay compared with viral culture.

Tools for the Diagnosis of Herpes Simplex Virus 1/2: Systematic Review of Studies Published Between 2012 and 2018

Background

Herpes simplex virus (HSV)-1 and HSV-2 are common infections affecting the global population, with HSV-1 estimated to affect 67% of the global population. HSV can have rare but severe manifestations, such as encephalitis and neonatal herpes, necessitating the use of reliable and accurate diagnostic tools for the detection of the viruses. Currently used HSV diagnostic tools require highly specialized skills and availability of a laboratory setting but may lack sensitivity. The numerous recently developed HSV diagnostic tools need to be identified and compared in a systematic way to make the best decision about which diagnostic tool to use. The diagnosis of HSV is essential for prompt treatment with antivirals. To select the best test for a patient, knowledge of the performance and limitations of each test is critical.

Objective

This systematic review has summarized recent studies evaluating HSV-1 and HSV-2 diagnostic tools.

Methods

Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, selection criteria, data extraction, and data analysis were determined before the commencement of the study. Studies assessing the specificity/sensitivity of HSV-1 or HSV-2 diagnostic tools published between 2012 and 2018 were included. Quality assessment of included studies was performed using the quality assessment of diagnostic accuracy studies (QUADAS-2) tool.

Results

Searches of the PubMed database yielded 264 studies; 11 studies included 11 molecular assays, and 8 studies included 19 different serological assays for the detection of HSV-1, HSV-2, or both. A greater proportion of molecular assay–based tools are being developed by commercial entities. Studies that tested molecular assays mostly focused on cutaneous and mucosal HSV infections (n=13); 2 studies focused on ocular disease, whereas only 1 study focused on the central nervous system manifestations. The Simplexa HSV 1 & 2 Direct is currently the only Food and Drug Administration–approved device for use on cerebrospinal fluid. No tools focused on prenatal screening. We also present performance metrics of tests for benchmarking of future technology. Most of the included studies had a high risk of bias rating in half of the QUADAS-2 tool risk of bias domains.

Conclusions

The use of serologic tests to diagnose genital lesions is inappropriate because positive results may be due to chronic infection, whereas negative results may overlook recent infection. The incidence of acute infections is rising. As these infections present the greatest risk to fetuses, work needs to be done to prevent vertical transfer. Prenatal screening for primary infection and subsequent medical intervention will assist in lowering the rate of neonatal herpes. In conclusion, HSV diagnosis is moving away from culture-based methods to serology-based or polymerase chain reaction–based methods. Sensitive, rapid, and efficient HSV diagnostic tools should be adopted for the prevention of acute infections and neonatal herpes.

Economic analysis of rapid multiplex polymerase chain reaction testing for meningitis/encephalitis in adult patients

PURPOSE

Many patients with suspected meningitis do not require hospitalization yet are admitted, often resulting in unnecessary care and additional cost. We assessed the possible economic impact of a rapid multiplex test for suspected adult community-acquired meningitis/encephalitis.

METHODS

A model simulated diagnosis, clinical decisions, resource use/costs of standard of care (SOC) and two cerebrospinal fluid (CSF) testing strategies using the FDA-cleared BioFire® FilmArray® System (FA) which provides results in approximately one hour.

RESULTS

Pathogens detected by FA caused approximately 74% of cases, 97% of which would be accurately diagnosed with FA. False positives and false negatives more often led to extended/unnecessary admission than inappropriate discharge/missed admission. Mean cost per case ranged from 16829 to 20791. A strategy of testing all suspected cases yielded greater savings (2213/case) than testing only those with abnormal CSF (812/case) and both were less expensive than SOC.

CONCLUSION

This economic analysis demonstrates that FA can inform more appropriate clinician decisions resulting in cost savings with greater economic benefits achievable with syndromic testing of all cases, rather than SOC or targeted syndromic testing.

A comparison of the Quidel Solana HSV 1 + 2/VZV Assay, the Focus Diagnostics Simplexa HSV 1 & 2 Direct Assay and the Luminex Aries HSV 1&2 Assay for detection of herpes simplex virus 1 and 2 from swab specimens

BACKGROUND

Molecular methods enable more rapid and sensitive detection of herpes simplex virus (HSV) than viral culture.

OBJECTIVE

Three commercial molecular methods, all of which detect both HSV-1 and HSV-2, were compared to viral culture for the detection of HSV from swab specimens.

STUDY DESIGN

Pediatric and adult patient viral swab specimens were cultured for HSV. Residual swab fluid was frozen at -80 °C until tested with the 3 molecular methods: the Quidel Solana HSV 1 + 2/VZV Assay, the Focus Diagnostics Simplexa HSV 1 & 2 Direct Assay and the Luminex Aries HSV 1&2 Assay. A true positive was defined as positive by culture or positive by ≥ 2/3 molecular methods.

RESULTS

177 specimens were studied. The sensitivity of culture was 81.3% (61/75, 95% CI 70.7-89.4%) and specificity was 100% (102/102, 95% CI 96.4-100%). The sensitivities of both the Solana and Simplexa were 100% (75/75, 95% CI 95.2-100%) and specificities were also both 100% (102/102, 95% CI 96.4-100%). The Aries had a sensitivity of 98.7% (74/75, 95% CI 92.8-99.97%) and specificity 99.0% (101/102, 95% CI 94.7-99.98%). All three molecular methods were significantly more sensitive than culture (p ≤ 0.0005 for Solana and Simplexa and p ≤ 0.0012 for Aries).

CONCLUSION

All the molecular methods studied provided a significantly higher sensitivity than culture. In addition, the molecular methods took 1-2 hours to perform compared to a mean of 2.1 days for culture results. Use of any of the three molecular methods could lead to improved patient care.

Detection of Herpes Simplex Virus and Varicella-Zoster Virus by Traditional and Multiplex Molecular Methods

Objectives

To compare multiplex nucleic acid amplification tests (NAATs) that detect and differentiate herpes simplex virus (HSV) and varicella-zoster virus (VZV) with traditional virologic assays.

Methods

The HSV ELVIS Test System (Quidel, San Diego, CA) and/or Light Diagnostics VZV direct fluorescent antibody (DFA) kit (Millipore Sigma, Billerica, MA), as well as an ARIES HSV 1&2/VZV assay (Luminex, Austin, TX) and the Solana HSV1 + 2/VZV Assay (Quidel), were performed on non-cerebrospinal fluid specimens.

Results

The sensitivities/specificities for the ELVIS, Aries, and Solana assays for HSV were 71.1%/93.2%, 94.9%/93.2%, and 94.7%/100%, respectively. The sensitivities/specificities for the DFA, Aries, and Solana assays for VZV were 71.4%/100%, 100%/96.0%, and 95.3%/100%, respectively. HSV and VZV were detected but clinically unsuspected in 5.4% and 4.2% of the specimens, respectively.

Conclusions

Both NAAT assays were comparable and more sensitive than traditional methods. The recovery of unsuspected HSV and VZV from clinical specimens supports the implementation of a combined HSV/VZV assay.

Comparison of Herpes Simplex Virus PCR with Culture for Virus Detection in Multisource Surface Swab Specimens from Neonates

The American Academy of Pediatrics currently recommends herpes simplex virus (HSV) culture or PCR for testing of swabs of the conjunctivae, mouth, nasopharynx, and rectum (surface swabs) from neonates. The objectives of this study were to compare the performance and time to results of HSV PCR with those of HSV culture with surface swabs from neonates. Banked multisource surface swab samples that were collected from infants less than or equal to 30 days old from January 2017 to December 2017 and that had previously been cultured for HSV were identified and tested retrospectively by HSV PCR. Surface swab samples from 97 patients were included in the study. Of these 97 patients, 7 (7%) had clinical HSV disease. Of the 7 neonates with HSV disease, 3 (42.9%) had surface swabs positive by culture and 6 (85.7%) had swabs positive by PCR. Limiting the analysis to specimens that were positive only by culture or only by PCR, the specificity for both methods was 100%, but the sensitivity of PCR was 100%, whereas it was 50% for culture. During the study period, 341 HSV cultures and 426 HSV PCRs were performed. The median time from swab collection to reporting of results was 7.6 days (interquartile range [IQR], 7.1 to 7.9 days) for culture and 0.8 days (IQR, 0.6 to 1.0 days) for PCR. HSV PCR of surface swabs from neonates was considerably more rapid and sensitive than HSV culture without yielding false-positive results. Although larger studies are needed to support our findings, strong consideration should be given to utilize PCR instead of culture for the detection of HSV in surface swabs from neonates.

Influenza and respiratory syncytial virus screening for the detection of asymptomatically infected patients in hematology and oncology

Introduction: Respiratory syncytial virus (RSV) and influenza virus infections are a significant healthcare risk for immunocompromised patients. In addition to community onset, nosocomial acquisition and transmission may also occur. Detection of asymptomatic shedders (e.g., patients in the incubation period or immunosuppressed long term shedders) facilitates control of nosocomial transmission.

Methods: To strengthen the existing infection control concept, a PCR-based screening for RSV and influenza virus was implemented for all patients lacking respiratory symptoms (asymptomatic patients) who were hospitalized on an adult and a pediatric hemato-oncological ward. Laboratory results of this screening were analyzed retrospectively.

Results: 665 respiratory specimens were obtained for screening from 251 patients (26% were 18 years and younger) from December 2016 to April 2017. In 23 patients without respiratory symptoms, either influenza virus or RSV infection was found, resulting in a detection rate of about 9%. In 6 patients, the infection was presumably detected during the incubation period, because an increase of viral load was observed in subsequent specimens. Positive screening results facilitated timely implementation of adequate infection control precautions. Nosocomial clusters of RSV or influenza were not detected during the screening period on the two wards.

Conclusion: The seasonal screening program expanded our existing infection control concept in terms of patients lacking respiratory symptoms who shed influenza virus or RSV. It enabled us to identify 23 RSV or influenza infections in patients lacking respiratory symptoms in a 4-month period and thus to rapidly take isolation precautions.

Economic analysis of rapid multiplex polymerase chain reaction testing for meningitis/encephalitis in pediatric patients

AIM

We assessed the possible economic impact of a rapid test in pediatric patients with suspected community-acquired meningitis/encephalitis.

MATERIALS & METHODS

Modeling simulated diagnosis, clinical decisions, resource use/costs of standard of care (SOC) and two cerebrospinal fluid testing strategies using FilmArray^® (FA), a US FDA-cleared system that provides results in approximately 1 h.

RESULTS

Pathogens detected by FA caused approximately 75% of cases, 97% of which would be accurately diagnosed with FA.  Mean cost/case ranged from $17,599 to $22,025.  Syndromic testing is less expensive than SOC. Testing all suspected cases yielded greater savings ($3481/case) than testing only those with abnormal cerebrospinal fluid ($2157/case).

CONCLUSION

Greater economic benefits are achievable with syndromic testing of all cases, rather than SOC or targeted syndromic testing.

Characteristics of pediatric recurrent erythema multiforme

BACKGROUND

Erythema multiforme (EM) is an acute condition characterized by distinctive target lesions of the skin often accompanied by mucosal ulcers. A subset of individuals experience frequent episodes of recurrent EM, which is rare and poorly understood, especially in children.

OBJECTIVE

To characterize clinical features, laboratory findings, and treatment responses of pediatric recurrent EM.

METHODS

A retrospective chart review was conducted at the Children's Hospital of Wisconsin in Milwaukee, Wisconsin (2000-2015) and the Mayo Clinic in Rochester, Minnesota (1990-2015). Inclusion criterion was a diagnosis before age 18 years with recurrent EM, defined as a symmetrically distributed, fixed eruption, including target lesions, with or without mucous membrane involvement, occurring on at least three occasions. A literature review was conducted to include individuals who met the inclusion criterion.

RESULTS

Twenty-six patients were included, of whom 16 (62%) were male. The median age of onset was 9.1 years (range 0-15.7 years). Nine patients (35%) required hospitalization. Herpes simplex virus testing was positive in 9 of 17 (65%) patients. Remission was achieved in 5 of 16 (31%) patients while taking suppressive antivirals. Eight patients received continuous anti-inflammatory treatment, two (25%) of whom experienced remission.

CONCLUSION

This study of pediatric recurrent EM found a greater male predominance, more hospitalizations, fewer cases caused by herpes simplex virus, and a lower response to immunosuppression in children than in the general population.

[Genital herpes and pregnancy: Serological and molecular diagnostic tools. Guidelines for clinical practice from the French College of Gynecologists and Obstetricians (CNGOF)]

OBJECTIVES

To describe serological and molecular tools available for genital and neonatal herpes, and their use in different clinical situations.

METHODS

Bibliographic investigations from MedLine database and consultation of international clinical practice guidelines.

RESULTS

Virological confirmation of genital herpes during pregnancy or neonatal herpes must rely on PCR (Professional consensus). HSV type-specific serology (IgG) will allow determining the immune status of a patient (in the absence of clinical lesions). However, there is currently no evidence to justify universal HSV serological testing during pregnancy (Professional consensus). In case of genital lesions in a pregnant woman that do not report any genital herpes before, it is recommended to perform a virological confirmation by PCR and HSV type-specific IgG in order to distinguish a true primary infection, a non-primary infection associated with first genital manifestation, from a recurrence (Grade C). HSV IgM is useless for diagnosis of genital herpes (Grade C). If a pregnant woman has personal history of genital herpes but no lesions, whatever the gestational age, it is not recommended to perform genital sampling nor serology (Professional consensus). In case of recurrence, if the lesion is characteristic of herpes, virological confirmation is not necessary (Professional Agreement). However, if the lesion is not characteristic, virological confirmation by PCR should be performed (Professional consensus). At birth, HSV PCR samples should be collected as soon as neonatal herpes is suspected (symptomatic neonate) (best before beginning antiviral treatment but must not delay the treatment), or after 24hours of life in case of asymptomatic neonate born to a mother with herpes lesions at delivery (Professional consensus). Clinical samples for virological confirmation should include at least blood and a peripheral location. In case of clinical manifestations of herpes in the neonate, first samples PCR positive, preterm birth, or maternal primary infection or non-primary infection associated with first genital manifestation at delivery, CSF should also be collected as well as samples of lesions in the neonate if present (Professional consensus). Sampling should be repeated in case of PCR negative but strong evidence of neonatal herpes (Professional consensus). HSV serology is useless for diagnosis of neonatal herpes (Grade C).

CONCLUSIONS

Virological confirmation for diagnosis of genital herpes during pregnancy or neonatal herpes must rely on PCR. PCR assays available in France are very reliable. Specific IgG are dedicated to restricted indications.

Saliva and viral infections

Over the last 10 years there have been only a handful of publications dealing with the oral virome, which is in contrast to the oral microbiome, an area that has seen considerable interest. Here, we survey viral infections in general and then focus on those viruses that are found in and/or are transmitted via the oral cavity; norovirus, rabies, human papillomavirus, Epstein‐Barr virus, herpes simplex viruses, hepatitis C virus, and HIV. Increasingly, viral infections have been diagnosed using an oral sample (e.g. saliva mucosal transudate or an oral swab) instead of blood or urine. The results of two studies using a rapid and semi‐quantitative lateral flow assay format demonstrating the correlation of HIV anti‐IgG/sIgA detection with saliva and serum samples are presented. When immediate detection of infection is important, point‐of‐care devices that obtain a non‐invasive sample from the oral cavity can be used to provide a first line diagnosis to assist in determining appropriate counselling and therapeutic path for an increasing number of diseases.

Impact of a Rapid Herpes Simplex Virus PCR Assay on Duration of Acyclovir Therapy

Herpes simplex virus (HSV) infections of the central nervous system (CNS) are associated with significant morbidity and mortality rates in children. This study assessed the impact of a direct HSV (dHSV) PCR assay on the time to result reporting and the duration of acyclovir therapy for children with signs and symptoms of meningitis and encephalitis. A total of 363 patients with HSV PCR results from cerebrospinal fluid (CSF) samples were included in this retrospective analysis, divided into preimplementation and postimplementation groups. For the preimplementation group, CSF testing was performed using a laboratory-developed real-time PCR assay; for the postimplementation group, CSF samples were tested using a direct sample-to-answer assay. All CSF samples were negative for HSV. Over 60% of patients from both groups were prescribed acyclovir. The average HSV PCR test turnaround time for the postimplementation group was reduced by 14.5 h (23.6 h versus 9.1 h; P < 0.001). Furthermore, 79 patients (43.6%) in the postimplementation group had dHSV PCR results reported <4 h after specimen collection. The mean time from specimen collection to acyclovir discontinuation was 17.1 h shorter in the postimplementation group (31.1 h versus 14 h; P < 0.001). The median duration of acyclovir therapy was also significantly reduced in the postimplementation group (29.2 h versus 14.3 h; P = 0.01). Our investigation suggests that implementation of rapid HSV PCR testing can decrease turnaround times and the duration of unnecessary acyclovir therapy.

Automated processing, extraction and detection of herpes simplex virus types 1 and 2: A comparative evaluation of three commercial platforms using clinical specimens

BACKGROUND

Recently, automated platforms have been developed that can perform processing, extraction and testing for herpes simplex virus (HSV) nucleic acid on a single instrument.

OBJECTIVES

In this study, we compared three commercially-available systems; Aptima^®/Panther (Hologic, San Diego, CA), ARIES^® (Luminex Corporation, Austin, TX), and cobas^® 4800 (Roche Molecular Systems Inc, Pleasanton, CA) for the qualitative detection of HSV-1/2 in clinical samples.

STUDY DESIGN

Two-hundred seventy-seven specimens (genital [n=193], dermal [n=84]) were submitted for routine HSV-1/2 real-time PCR by a laboratory developed test. Following routine testing, samples were also tested by the Aptima, ARIES, and cobas HSV-1/2 assays per the manufacturer's recommendations. Results were compared to a "consensus standard" defined as the result obtained from ≥3 of the 4 assays.

RESULTS

Following testing of 277 specimens, the cobas and ARIES assays demonstrated a sensitivity of 100% for HSV-1 (61/61) and HSV-2 (55/55). The Aptima assays showed a sensitivity of 91.8% (56/61) for HSV-1 and 90.9% (50/55) for HSV-2. Percent specificities for HSV-1 were 96.2% (202/210) by cobas, 99.5% (209/210) by ARIES and 100% (236/236) by Aptima. For HSV-2, the specificities were 98.1% (211/215) by cobas, 99.5% (215/216) by ARIES and 100% (216/216) by Aptima. The turnaround time for testing 24 samples was 2.5h by the cobas 4800, 3.1h by Aptima/Panther, and 3.9h by ARIES.

CONCLUSIONS

The three commercial systems can perform all current functions on a single platform, thereby improving workflow and potentially reducing errors associated with manual processing of samples.

Laboratory Diagnosis of Central Nervous System Infection

Central nervous system (CNS) infections are potentially life threatening if not diagnosed and treated early. The initial clinical presentations of many CNS infections are non-specific, making a definitive etiologic diagnosis challenging. Nucleic acid in vitro amplification-based molecular methods are increasingly being applied for routine microbial detection. These methods are a vast improvement over conventional techniques with the advantage of rapid turnaround and higher sensitivity and specificity. Additionally, molecular methods performed on cerebrospinal fluid samples are considered the new gold standard for diagnosis of CNS infection caused by pathogens, which are otherwise difficult to detect. Commercial diagnostic platforms offer various monoplex and multiplex PCR assays for convenient testing of targets that cause similar clinical illness. Pan-omic molecular platforms possess potential for use in this area. Although molecular methods are predicted to be widely used in diagnosing and monitoring CNS infections, results generated by these methods need to be carefully interpreted in combination with clinical findings. This review summarizes the currently available armamentarium of molecular assays for diagnosis of central nervous system infections, their application, and future approaches.

Evaluation of a transcription mediated amplification assay for detection of herpes simplex virus types 1 and 2 mRNA in clinical specimens

BACKGROUND

Herpes simplex viruses (HSV) are double-stranded DNA human herpesviruses (HHVs) that have the capacity to cause significant morbidity and mortality in humans. Like HHV5 (Cytomegalovirus) and HHV8 (Kaposi's sarcoma virus), HSV type 1 (HSV-1), and HSV type 2 (HSV-2) (HHV1, HHV2) selectively package certain viral messenger RNAs inside mature virions, as well as expressing those mRNAs in infected cells.

OBJECTIVES

To evaluate the clinical and analytical performance of Aptima HSV 1&2 assay (AHSV), a newly developed automated real time transcription-mediated amplification (TMA) nucleic acid amplification test (NAAT) for HSV-1 and 2 UL42 mRNAs, compared to viral culture and HSV DNA NAAT.

STUDY DESIGN

Cutaneous and mucocutaneous lesion swab specimens from a population of symptomatic female and male subjects attending a U.S. public health clinic (n=758) were evaluated by shell vial culture with fluorescent antibody staining for HSV-1 and 2. Specimens were then tested with AHSV for HSV-1 and 2 on the Panther instrument. Specimens from subjects with discordant culture-TMA paired results were tested using an FDA-cleared test for HSV-1 and 2 viral DNA. Analytical performance of AHSV was evaluated using test panels consisting of laboratory strains of HSV-1 and 2 and a variety of non-target human DNA viruses.

RESULTS

Compared to culture, AHSV was sensitive and specific for detection of HSV-1 and 2 in patient lesion swab specimens, exhibiting clinical sensitivities of 98.2% (95% CI: 92.9-99.7) and 99.4% (95% CI: 96.0-99.9), respectively. Addition of HSV DNA NAAT discordant resolution testing results to culture results improved AHSV sensitivity for HSV-1 and 2-99.2% (95% CI: 94.7-99.9) and 100% (95% CI: 97.5-100), respectively. Clinical specificity of AHSV for HSV-1 and 2 detection was 97.8% (95% CI: 96.3-98.8) and 94.5% (95% CI: 92.2-96.1), respectively, compared to culture; and 99.5% (95% CI: 98.5-99.9) and 99.5% (95% CI: 98.3-99.7), respectively, compared to culture with discordant resolution. Analytical sensitivity (95% limit of detection) of AHSV for HSV-1 (McIntyre strain) was 28.9 TCID50/mL (95% FL: 23.4-37.9), and 0.54 TCID50/mL (95% FL: 0.42-0.75) for HSV-2 (MS strain). AHSV did not cross-react with laboratory strains of HHV-3, HHV-4, HHV-5, HHV-6, and four other non-HHV human DNA viruses.

CONCLUSIONS

Real time transcription-mediated amplification NAAT for HSV viral mRNA is a sensitive and specific method for detection of herpes simplex virus infection in symptomatic patients.

Multiplexed Recombinase Polymerase Amplification Assay To Detect Intestinal Protozoa

This work describes a proof-of-concept multiplex recombinase polymerase amplification (RPA) assay with lateral flow readout that is capable of simultaneously detecting and differentiating DNA from any of the diarrhea-causing protozoa Giardia, Cryptosporidium, and Entamoeba. Together, these parasites contribute significantly to the global burden of diarrheal illness. Differential diagnosis of these parasites is traditionally accomplished via stool microscopy. However, microscopy is insensitive and can miss up to half of all cases. DNA-based diagnostics such as polymerase chain reaction (PCR) are far more sensitive; however, they rely on expensive thermal cycling equipment, limiting their availability to centralized reference laboratories. Isothermal DNA amplification platforms, such as the RPA platform used in this study, alleviate the need for thermal cycling equipment and have the potential to broaden access to more sensitive diagnostics. Until now, multiplex RPA assays have not been developed that are capable of simultaneously detecting and differentiating infections caused by different pathogens. We developed a multiplex RPA assay to detect the presence of DNA from Giardia, Cryptosporidium, and Entamoeba. The multiplex assay was characterized using synthetic DNA, where the limits-of-detection were calculated to be 403, 425, and 368 gene copies per reaction of the synthetic Giardia, Cryptosporidium, and Entamoeba targets, respectively (roughly 1.5 orders of magnitude higher than for the same targets in a singleplex RPA assay). The multiplex assay was also characterized using DNA extracted from live parasites spiked into stool samples where the limits-of-detection were calculated to be 444, 6, and 9 parasites per reaction for Giardia, Cryptosporidium, and Entamoeba parasites, respectively. This proof-of-concept assay may be reconfigured to detect a wide variety of targets by re-designing the primer and probe sequences.

Development and evaluation of the quantitative real-time PCR assay in detection and typing of herpes simplex virus in swab specimens from patients with genital herpes

Genital herpes (GH), which is caused mainly by herpes simplex virus (HSV)-2 and HSV-1, remains a worldwide problem. Laboratory confirmation of GH is important, particularly as there are other conditions which present similarly to GH, while atypical presentations of GH also occur. Currently, virus culture is the classical method for diagnosis of GH, but it is time consuming and with low sensitivity. A major advance for diagnosis of GH is to use Real-time polymerase chain reaction (PCR). In this study, to evaluate the significance of the real-time PCR method in diagnosis and typing of genital HSV, the primers and probes targeted at HSV-1 DNA polymerase gene and HSV-2 glycoprotein D gene fraction were designed and applied to amplify DNA from HSV-1 or HSV-2 by employing the real-time PCR technique. Then the PCR reaction system was optimized and evaluated. HSV in swab specimens from patients with genital herpes was detected by real-time PCR. The real-time PCR assay showed good specificity for detection and typing of HSV, with good linear range (5×10(2)~5×10(8) copies/ml, r=0.997), a sensitivity of 5×10(2) copies/ml, and good reproducibility (intra-assay coefficients of variation 2.29% and inter-assay coefficients of variation 4.76%). 186 swab specimens were tested for HSV by real-time PCR, and the positive rate was 23.7% (44/186). Among the 44 positive specimens, 8 (18.2%) were positive for HSV-1 with a viral load of 8.5546×10(6) copies/ml and 36 (81.2%) were positive for HSV-2 with a viral load of 1.9861×10(6) copies/ml. It is concluded that the real-time PCR is a specific, sensitive and rapid method for the detection and typing of HSV, which can be widely used in clinical diagnosis of GH.

Development and Validation of a Laboratory-Developed Multiplex Real-Time PCR Assay on the BD Max System for Detection of Herpes Simplex Virus and Varicella-Zoster Virus DNA in Various Clinical Specimens

A multiplex real-time PCR (quantitative PCR [qPCR]) assay detecting herpes simplex virus (HSV) and varicella-zoster virus (VZV) DNA together with an internal control was developed on the BD Max platform combining automated DNA extraction and an open amplification procedure. Its performance was compared to those of PCR assays routinely used in the laboratory, namely, a laboratory-developed test for HSV DNA on the LightCycler instrument and a test using a commercial master mix for VZV DNA on the ABI7500fast system. Using a pool of negative cerebrospinal fluid (CSF) samples spiked with either calibrated controls for HSV-1 and VZV or dilutions of a clinical strain that was previously quantified for HSV-2, the empirical limit of detection of the BD Max assay was 195.65, 91.80, and 414.07 copies/ml for HSV-1, HSV-2, and VZV, respectively. All the samples from HSV and VZV DNA quality control panels (Quality Control for Molecular Diagnostics [QCMD], 2013, Glasgow, United Kingdom) were correctly identified by the BD Max assay. From 180 clinical specimens of various origins, 2 CSF samples were found invalid by the BD Max assay due to the absence of detection of the internal control; a concordance of 100% was observed between the BD Max assay and the corresponding routine tests. The BD Max assay detected the PCR signal 3 to 4 cycles earlier than did the routine methods. With results available within 2 h on a wide range of specimens, this sensitive and fully automated PCR assay exhibited the qualities required for detecting simultaneously HSV and VZV DNA on a routine basis.

Evaluation of 2 multiplex real-time PCR assays for the detection of HSV-1/2 and Varicella zoster virus directly from clinical samples

We compared the performance of 2 multiplex assays (Focus Simplexa and Quidel Lyra) to individual real-time PCR for the detection of herpes simplex virus-1 (HSV-1), HSV-2, and Varicella zoster virus (VZV) from clinical specimens. Results were compared to a consensus standard, defined as the result obtained by at least 2 of the 3 molecular methods. The sensitivity of the Quidel assay ranged from 92.0% for HSV-1 to 97.7% for HSV-2, while the specificity for all targets was 100%. The Focus assay demonstrated 100% sensitivity for all targets, and the percent specificity ranged from 96.8% for HSV-1 to 100% for HSV-2 and VZV.

Equipment-free incubation of recombinase polymerase amplification reactions using body heat

The development of isothermal amplification platforms for nucleic acid detection has the potential to increase access to molecular diagnostics in low resource settings; however, simple, low-cost methods for heating samples are required to perform reactions. In this study, we demonstrated that human body heat may be harnessed to incubate recombinase polymerase amplification (RPA) reactions for isothermal amplification of HIV-1 DNA. After measuring the temperature of mock reactions at 4 body locations, the axilla was chosen as the ideal site for comfortable, convenient incubation. Using commonly available materials, 3 methods for securing RPA reactions to the body were characterized. Finally, RPA reactions were incubated using body heat while control RPA reactions were incubated in a heat block. At room temperature, all reactions with 10 copies of HIV-1 DNA and 90% of reactions with 100 copies of HIV-1 DNA tested positive when incubated with body heat. In a cold room with an ambient temperature of 10 degrees Celsius, all reactions containing 10 copies or 100 copies of HIV-1 DNA tested positive when incubated with body heat. These results suggest that human body heat may provide an extremely low-cost solution for incubating RPA reactions in low resource settings.

Development and clinical evaluation of a novel fully automated qualitative PCR assay for the diagnosis of anogenital herpes simplex virus infection

Molecular detection of viral infections has the potential to improve microbial diagnostics, particularly with the emergence of rapid automated systems. We describe the design of the IDbox fully automated cassette-based system for nucleic acid extraction and real-time PCR amplification and perform a clinical evaluation for the diagnosis of genital herpes simplex infections. At optimal cutoff values determined by receiver-operator curves, the IDbox showed sensitivities of 94.9% (95% confidence interval [CI] 84.9-98.7%) and 97.0% (95% CI 88.5-99.5%) and specificities of 96.7% (95% CI 91.2-98.9%) and 97.3% (95% CI 91.9-99.3%) relative to herpes simplex virus culture and PCR, respectively. We discuss relevant design characteristics and approaches used for each step of the analytical process to enhance assay sensitivity and provide accurate results in the presence of potential cross-reactive organisms and interfering substances.