DNA microarray technology for simultaneous detection and species identification of seven human herpes viruses

CovidArray: A Microarray-Based Assay with High Sensitivity for the Detection of Sars-Cov-2 in Nasopharyngeal Swabs

A new coronavirus (SARS-CoV-2) caused the current coronavirus disease (Covid-19) epidemic. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is used as the gold standard for clinical detection of SARS-CoV-2. Under ideal conditions, RT-qPCR Covid-19 assays have analytical sensitivity and specificity greater than 95%. However, when the sample panel is enlarged including asymptomatic individuals, the sensitivity decreases and false negatives are reported. Moreover, RT-qPCR requires up to 3–6 h with most of the time involved in RNA extraction from swab samples. We introduce CovidArray, a microarray-based assay, to detect SARS-CoV-2 markers N1 and N2 in the nasopharyngeal swabs. The method is based on solid-phase hybridization of fluorescently-labeled amplicons upon RNA extraction and reverse transcription. This approach combines the physical-optical properties of the silicon substrate with the surface chemistry used to coat the substrate to obtain a diagnostic tool of great sensitivity. Furthermore, we used an innovative approach, RNAGEM, to extract and purify viral RNA in less than 15 min. We correctly assigned 12 nasopharyngeal swabs, previously analyzed by RT-qPCR. Thanks to the CovidArray sensitivity we were able to identify a false-negative sample. CovidArray is the first DNA microarray-based assay to detect viral genes in the swabs. Its high sensitivity and the innovative viral RNA extraction by RNAGEM allows the reduction of both the amount of false-negative results and the total analysis time to about 2 h.

Optimizing a custom tiling microarray for low input detection and identification of unamplified virus targets

Viruses are major pathogens causing foodborne illnesses and are often present at low levels in foods, thus requiring sensitive techniques for their detection in contaminated foods. The lack of efficient culture methods for many foodborne viruses and the potential for multi-species viral contamination have driven investigation toward non-amplification based methods for virus detection and identification. A custom DNA microarray (FDA_EVIR) was assessed for its sensitivity in the detection and identification of low-input virus targets, human hepatitis A virus, norovirus, and coxsackievirus, individually and in combination. Modifications to sample processing were made to accommodate low input levels of unamplified virus targets, which included addition of carrier cDNA, RNase treatment, and optimization of DNase I-mediated target fragmentation. Amplification-free detection and identification of foodborne viruses were achieved in the range of 250-500 copies of virus RNA. Alternative data analysis methods were employed to distinguish the genotypes of the viruses particularly at lower levels of target input and the single probe-based analysis approach made it possible to identify a minority species in a multi-virus complex. The oligonucleotide array is shown to be a promising platform to detect foodborne viruses at low levels close to what are anticipated in food or environmental samples.

Development of a multiplex real-time PCR for the simultaneous detection of herpes simplex and varicella zoster viruses in cerebrospinal fluid and lesion swab specimens

Herpes simplex viruses (HSV) and varicella zoster virus (VZV) can have very similar and wide-ranging clinical presentations. Rapid identification is necessary for timely antiviral therapy, especially with infections involving the central nervous system, neonates, and immunocompromised individuals. Detection of HSV-1, HSV-2 and VZV was combined into one real-time PCR reaction utilizing hydrolysis probes. The assay was validated on the LightCycler(®) (Roche) and Applied Biosystems 7500 Real-Time PCR System (Thermo Fisher Scientific Inc.) to detect alphaherpesviruses in cerebral spinal fluid (CSF) and lesion swab specimens, respectively. Validation data on blood and tissue samples are also presented. The multiplex assay showed excellent sensitivity, specificity and reproducibility when compared to two singleplex real-time PCR assays for CSF samples and direct fluorescent antigen/culture for lesion swab samples. Implementation of the multiplex assay has facilitated improved sensitivity and accuracy as well as reduced turn-around-times and costs. The results from a large data set of 16,622 prospective samples tested between August 16, 2012 to February 1, 2014 at the Provincial Laboratory for Public Health (Alberta, Canada) are presented here.

Evaluation of a viral microarray based on simultaneous extraction and amplification of viral nucleotide acid for detecting human herpesviruses and enteroviruses

In this study, a viral microarray based assay was developed to detect the human herpesviruses and enteroviruses associated with central nervous system infections, including herpes simplex virus type 1, type 2 (HSV1 and HSV2), Epstein-Barr virus (EBV), cytomegalovirus (CMV), enterovirus 71 (EV71), coxsackievirus A 16 (CA16) and B 5(CB5). The DNA polymerase gene of human herpesviruses and 5’-untranslated region of enteroviruses were selected as the targets to design primers and probes. Human herpesviruses DNA and enteroviruses RNA were extracted simultaneously by using a guanidinium thiocyanate acid buffer, and were subsequently amplified through a biotinylated asymmetry multiplex RT-PCR with the specific primer of enteroviruses. In total, 90 blood samples and 49 cerebrospinal fluids samples with suspected systemic or neurological virus infections were investigated. Out of 139 samples, 66 were identified as positive. The specificities of this multiplex RT-PCR microarray assay were over 96% but the sensitivities were various from 100% for HSV1, HSV2, EV71 and CB5, 95.83% for CMV, 80% for EBV to 71.43% for CA16 in comparison with reference standards of TaqMan qPCR/qRT-PCR. The high Kappa values (>0.90) from HSV1, HSV2, CMV, EV71 and CB5 were obtained, indicating almost perfect agreement in term of the 5 viruses detection. But lower Kappa values for EBV (0.63) and CA16 (0.74) displayed a moderate to substantial agreement. This study provides an innovation of simultaneous extraction, amplification, hybridization and detection of DNA viruses and RNA viruses with simplicity and specificity, and demonstrates a potential clinical utility for a variety of viruses’ detection.

Comparison of two multiplexed PCR assays for the detection of HSV-1, HSV-2, and VZV with extracted and unextracted cutaneous and mucosal specimens

BACKGROUND

Several analyte specific reagents (ASRs) are available for the detection and differentiation of HSV-1, HSV-2, and VZV in clinical specimens. However, there is limited data on the test performance of these reagents used in multiplexed PCR assays.

OBJECTIVE

This study compared the performance of two multiplexed ASR sets for detection of HSV-1, HSV-2, and VZV in dermal specimens.

STUDY DESIGN

Two commercially available ASRs were combined to produce multiplexed PCR assays for simultaneous detection of HSV-1, HSV-2, and VZV. Seeded samples were used to determine the limit of detection (LOD) for each assay. Patient samples (n=156) were tested in duplicate and results for each method compared to the reference standard of culture. Both extracted and unextracted specimens were used in the study.

RESULTS

Both multiplexed PCR assays showed similar test performance, with minimal LOD differences observed. The LOD was 10(3) copies/mL for HSV-1 and HSV-2 using the Focus assay compared to 5×10(3) copies/mL and 2×10(4) copies/mL, respectively for the EraGen assay. Both assays showed equal performance for VZV with a LOD of 5×10(3) copies/mL. Analytical specificity testing showed no cross reactivity with other selected DNA viruses. Both assays showed similar performance when clinical samples were tested using both extracted and unextracted specimens.

CONCLUSION

Commercially available ASRs can be successfully multiplexed for the PCR detection of HSV-1, HSV-2, and VZV using dermal specimens. Either direct testing or nucleic acid extracted specimens can be used with similar performance in these assays.

Candida infections and their prevention

Infections caused by Candida species have been increased dramatically worldwide due to the increase in immunocompromised patients. For the prevention and cure of candidiasis, several strategies have been adopted at clinical level. Candida infected patients are commonly treated with a variety of antifungal drugs such as fluconazole, amphotericin B, nystatin, and flucytosine. Moreover, early detection and speciation of the fungal agents will play a crucial role for administering appropriate drugs for antifungal therapy. Many modern technologies like MALDI-TOF-MS, real-time PCR, and DNA microarray are being applied for accurate and fast detection of the strains. However, during prolonged use of these drugs, many fungal pathogens become resistant and antifungal therapy suffers. In this regard, combination of two or more antifungal drugs is thought to be an alternative to counter the rising drug resistance. Also, many inhibitors of efflux pumps have been designed and tested in different models to effectively treat candidiasis. However, most of the synthetic drugs have side effects and biomedicines like antibodies and polysaccharide-peptide conjugates could be better alternatives and safe options to prevent and cure the diseases. Furthermore, availability of genome sequences of Candida   albicans and other non-albicans strains has made it feasible to analyze the genes for their roles in adherence, penetration, and establishment of diseases. Understanding the biology of Candida species by applying different modern and advanced technology will definitely help us in preventing and curing the diseases caused by fungal pathogens.

Molecular and nanotechnologic approaches to etiologic diagnosis of infectious syndromes

Infectious diseases are a major global public health problem. Multiple agents are now recognized to cause indistinguishable illnesses. The term 'syndrome' applies to such situations, for which early and rapid diagnosis of the infecting agent would enable prompt and appropriate therapy. Public health physicians would also get timely information on the specific etiology of the infectious syndrome, facilitating intervention at the community level in the face of outbreaks or epidemics. A variety of molecular techniques have been evaluated for rapid diagnosis of infectious syndromes. These techniques include real-time multiplex PCR, DNA microarray, loop-mediated isothermal amplification, and other similar assays. This review surveys such state-of-the-art technologies.

Subtype-specific, probe-based, real-time PCR for detection and typing of human herpesvirus-6 encephalitis from pediatric patients under the age of 2 years

To investigate the frequency of human herpesvirus-6 (HHV-6) encephalitis in pediatric patients under 2 years of age, we developed a method for the simultaneous detection and differentiation of the 2 variants of HHV-6 (HHV-6A and HHV-6B) using subtype-specific, probe-based, real-time PCR (SSPBRT-PCR) and which were further evaluated on 405 cerebrospinal fluid (CSF) specimens from children with suspected encephalitis. A total of 23 (5.70%) out of 405 CSF specimens were positive by SSPBRT-PCR, including 3 cases of HHV-6A and 20 cases of HHV-6B. The positive rate of HHV-6B was significantly higher than that of HHV-6A (P = 0.0004). Compared with the results of the conventional real-time PCR, the sensitivity and specificity of the SSPBRT-PCR assay were 95.24% and 99.22%, respectively. This study suggests a role for both variants of HHV-6 in the pathogenesis of viral encephalitis. SSPBRT-PCR can provide rapid, sensitive, and specific results for identification of HHV-6A and HHV-6B and management of HHV-6 encephalitis.

Quantitative and qualitative RNA-Seq-based evaluation of Epstein-Barr virus transcription in type I latency Burkitt's lymphoma cells

RNA-seq provides a rich source of transcriptome information with high qualitative and quantitative value. Here, we provide a pipeline for Epstein-Barr virus (EBV) transcriptome analysis using RNA-seq and we apply it to two type I latency cell lines, Mutu I and Akata. This analysis revealed substantial average expression levels of many lytic genes in predominantly latent cell populations. The lytic transcripts BHLF1 and LF3 were expressed at levels greater than those for 98% of all cellular polyadenylated transcripts. Exon junction mapping accurately identified the Qp-derived EBNA1 splicing pattern, lytic gene splicing, and a complex splicing pattern within the BamHI A region.

Rapid diagnosis of herpetic encephalitis in children by PCR-microarray technology for simultaneous detection of seven human herpes viruses

The aim of the study was to evaluate retrospectively the usefulness of polymerase chain reaction (PCR)-microarray technology, which can simultaneously detect seven human herpes viruses for rapid and accurate diagnosis of herpetic encephalitis in children. We simultaneously amplified herpes simplex virus type 1 and type 2 (HSV-1 and HSV-2); varicella-zoster virus; Epstein-Barr virus (EBV); cytomegalovirus (CMV); and human herpes virus 6 (HHV-6A and HHV-6B) by multiplex PCR, and genotyped by DNA microarray technology. The multiplex primers and oligonucleotide probes were designed and synthesized based on the highly conserved regions of the DNA polymerase gene in human herpes viruses. Two hundred ninety cerebrospinal fluid (CSF) specimens from children with clinical suspicion of viral encephalitis were screened by PCR-microarray technology. The results were compared with those of TaqMan PCR kits of common herpes virus. The PCR-microarray technology could detect as few as 10 copies of viral loads. There was no nonspecific hybridizing signal between probes and no cross-reaction to DNA extracted from the pathogens we used. Of 290 cases, 11 were tested positive by PCR-microarray technology. Among them, three were positive for HSV-1, two were positive for HSV-2, one was positive for EBV, two were positive for CMV, two were positive for HHV-6A, one was positive for HHV-6B, and one showed mixed infection of HSV-2 and CMV, and the positive rate was 3.8%. Compared with the results of TaqMan PCR, the sensitivity of PCR-microarray technology was 91.7%, the specificity was 100%, and the index of accurate diagnosis was 0.917. None of the 30 control CSF specimens was tested positive in both methods. Our study suggests that the simultaneous detection of seven human herpes viruses by PCR-microarray technology is the method of choice for rapid, accurate, and specific etiological diagnosis of herpetic encephalitis in children.

Fatal herpes virus type I infection in a newborn

The authors present a case of environmentally acquired fatal herpes virus type I infection in a newborn after cesarean section and a discussion of the clinical presentation, pathogenesis and diagnosis of herpes simplex type I (HSV-1) at autopsy. Herpes simplex virus, both type I and type II, are well described infectious agents in newborns. Though herpes simplex type II (HSV-2) is commonly associated with fatal neonatal infections, it is important to consider HSV-1 to make the correct diagnosis. Additionally, although HSV infections are typically acquired during parturition, it is possible to be infected postpartum from the environment as occurred in this case. The diagnosis of neonatal HSV must also be communicated by the forensic pathologist to applicable healthcare providers and health care facilities, because of public health and medicolegal issues.

The hospitalized patient with abnormal liver function tests

Evaluation of abnormal liver function tests (LFTs) in the hospitalized patient is typically more urgent than the outpatient setting. This process is best organized into four steps. The first step is to determine whether the abnormal LFTs are associated with the illness resulting in the admission to the hospital or preceded the present illness. The second is to determine the etiology of the underlying liver disease. The third step is to evaluate the severity of the liver dysfunction and determine if acute liver failure (ALF) or acute decompensation of chronic liver failure is present. The final step is to look for the presence of associated complications-either those of ALF or chronic liver failure as appropriate.

Molecular diagnostics of infectious diseases

PURPOSE OF REVIEW

The purpose of this article is to review the molecular methods commonly used in medical microbiology as well as to update the clinician as to newer molecular technologies that show promise in the identification of microorganisms as well as evaluation of the presence of virulence factors and antibiotic resistance determinants.

RECENT FINDINGS

Numerous molecular assays have been developed recently using a variety of technologies. Direct hybridization techniques have allowed analysis of blood culture bottles for organisms such as methicillin-resistant Staphylococcus aureus. Target amplification methods allow postamplification analysis using a variety of technologies depending on the clinical needs for the assay. Postamplification analysis includes methods such as Sanger sequencing, pyrosequencing, reverse hybridization, and Luminex analysis, which are becoming more widely utilized. In the future, whole genome sequencing, mass spectrometry, and microarray analysis may provide a wealth of information that can be used to specifically tailor the treatment of infectious diseases.

SUMMARY

The implications of current trends in molecular infectious diseases are moving towards high-throughput, simple, array-type technologies that will provide a wealth of data regarding types of organisms present in a sample and the virulence factors/resistance determinants that influence the severity of disease. As a result of these developments, infectious diseases will be more accurately and effectively treated.