In-house quantitative real-time PCR for the diagnosis of hepatitis B virus and hepatitis C virus infections

Clinical diagnosis of viral hepatitis: Current status and future strategies

Viral hepatitis (VH) is a significant public health issue with tremendous potential to aggravate into chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Recent decade has witnessed remarkable uprising in the drug development and effective treatment of VH. An upsurge is seen in identification of antiviral therapies with low rates of viral resistance, the improvement of Hepatitis B Virus (HBV) vaccination and the development of direct-acting antivirals for Hepatitis C Virus (HCV). But unfortunately, the "2030 worldwide eradication" objective of World Health Organization (WHO) is still unmet. It can be largely attributed to the deficit faced by the healthcare system concerning screening and diagnosis. A timely, accurate and comprehensive screening; encompassing maximum population coverage is essential to combat this disease. However, advancements in VH diagnostics remain inadequate and with a marginal use in routine practice. This paper deliberates upon the lacunae in traditional and prevailing diagnostic methodology of viral hepatitis, especially their inadequacy in meeting the unique situations prevailing low- and middle-income countries (LMIC).

Engineering highly thermostable Cas12b via de novo structural analyses for one-pot detection of nucleic acids

CRISPR-Cas-based diagnostics have the potential to elevate nucleic acid detection. CRISPR-Cas systems can be combined with a pre-amplification step in a one-pot reaction to simplify the workflow and reduce carryover contamination. Here, we report an engineered Cas12b with improved thermostability that falls within the optimal temperature range (60°C-65°C) of reverse transcription-loop-mediated isothermal amplification (RT-LAMP). Using de novo structural analyses, we introduce mutations to wild-type BrCas12b to tighten its hydrophobic cores, thereby enhancing thermostability. The one-pot detection assay utilizing the engineered BrCas12b, called SPLENDID (single-pot LAMP-mediated engineered BrCas12b for nucleic acid detection of infectious diseases), exhibits robust trans-cleavage activity up to 67°C in a one-pot setting. We validate SPLENDID clinically in 80 serum samples for hepatitis C virus (HCV) and 66 saliva samples for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high specificity and accuracy. We obtain results in as little as 20 min, and with the extraction process, the entire assay can be performed within an hour.

Screening of Occult Hepatitis B and C Virus Infection in Working Children, Tehran, Iran

Background: Working children are susceptible to infection with various infectious microorganisms. Unfortunately, the difficulties of working children are growing at a remarkable speed worldwide. Objectives: The aim of this research was to determine the prevalence of hepatitis B virus (HBV) and hepatitis C virus (HCV) infection, as well as to evaluate the level of anemia, calcium, and phosphorus in working children. Methods: This cross-sectional research was performed on 370 Iranian and Afghan working children from February 2018 to May 2019. Hepatitis B surface antigen (HBsAg), hepatitis B surface antibody (HBsAb), hepatitis B core antibody (HBcAb), and anti-HCV Ab were evaluated using an enzyme-linked immunosorbent assay (ELISA). Furthermore, HCV-RNA and genomic HBV-DNA in the plasma and peripheral blood mononuclear cell (PBMC) specimens of the participants were investigated. The restriction fragment length polymorphism (RFLP) method was used to determine the genotype of HCV, and sequencing was performed to confirm. Results: The mean age of the participants was 10.1 ± 2.1 years (range, 6 - 15 years), and 229 (61.9%) were male. None of the studied children had any detectable HBV-DNA in the plasma and PBMC. The HCV genome was not detected in the plasma of the children, but HCV-RNA was assessed in the PBMC sample of 1 child (0.3%). Therefore, one of the children had occult HCV infection (OCI). The genotype of HCV in this child was subtype 1a. Furthermore, HBsAb was detected in Iranian (41.5%) and Afghan children (40.0%), and 2 (0.54%) of the working children were HBsAg positive. In 3 participants (0.8%), a positive HBcAb test result was noted. Conclusions: The prevalence of HCV and HBV infection in working children in Iran is extremely rare. However, there is a possibility of the presence of OCI in these children.

Adenovirus load correlates with respiratory disease severity among hospitalized pediatric patients

OBJECTIVES

Human adenoviruses (HAdVs) are common pathogens that can cause respiratory, gastrointestinal and other infections. We investigated the correlation between adenovirus viral load in clinical respiratory samples and the respiratory disease severity in pediatric patients.

METHODS

Medical records of patients hospitalized in the Sheba Medical Center (SMC) with confirmed adenovirus infection were retrospectively analyzed. The possible correlation between disease severity score and Real time PCR 'cycle threshold' (Ct), a proxy of viral load, was assessed in patients aged 9 years and under. In addition, Ct values of hospitalized versus community-care patient samples, positive for various respiratory viruses including adenovirus, were compared.

RESULTS

Adenovirus load in respiratory samples, as measured by Ct values, was found to be negatively correlated with respiratory disease severity in hospitalized pediatric patients aged under 9 years. Moreover, hospitalized patients presented with significantly higher Ct levels for various respiratory viruses as compared to community-care patients.

CONCLUSION

In this study we found a correlation between Ct values obtained from adenovirus q-PCR analysis of respiratory clinical samples and disease severity in patients aged 9 years and under. Such finding may serve as a predictor of respiratory disease course in pediatric patients and will be beneficial for the differential diagnosis and treatment of pediatric patients.

Copy number-based quantification assay for non-invasive detection of PVT1-derived transcripts

Background

One of the most important susceptibility loci for cancer is the 8q24 human chromosomal region. The non-protein coding gene locus plasmacytoma variant translocation 1 (PVT1) is located at 8q24 and is dysregulated in prostate cancer. PVT1 gives rise to multiple transcripts which may have different functions. Here, we describe a real-time quantitative polymerase chain reaction (qPCR)-based assay for copy number-based quantitation of PVT1 exons 4A, 4B, and 9 to enable accurate, reproducible, and quantifiable detection.

Methods

PVT1 exons 4A, 4B, and 9 were cloned into a plasmid vector to create standards for subsequent creation of linear standard curves representing a broad range of concentrations. PCR was carried out using SYBR-Green signal detection to quantify PVT1 exons 4A, 4B, and 9. The efficacy of this assay was evaluated by using it to detect these transcripts in prostate epithelial and prostate cancer cell lines, normal and cancerous human prostate tissues, human serum, mouse plasma, and urine samples.

Results

The results indicate that the assay can be used to quantify both low and high copy numbers of PVT1-derived transcripts. This is the first report of a copy number-based quantification assay for non-invasive detection of PVT1 derived transcripts.

Conclusions

This novel assay holds promise for routine non-invasive testing in diseases where PVT1 is dysregulated.

Performance characteristics of a fast real-time PCR assay for hepatitis B virus DNA quantification

Detection of hepatitis B virus (HBV) DNA is particularly important for detection of early acute and of occult HBV infection. On the other hand, HBV DNA detection and quantification are essential to diagnose and treat chronic HBV infection. In this study, we evaluated the performance of the real-time PCR SUMASIGNAL VHB (un paso) (Immunoassay Center, Cuba). The clinical and analytical specificity of the assay was 100%. Intra-assay and inter-assay coefficients of variation ranged from 0.50 to 2.53% and from 1.23 to 3.03%, respectively. A strong correlation (r=0.926; P<0.001) with the COBAS^® AmpliPrep/COBAS^® TaqMan^® HBV Test, v2.0 (Roche Molecular Systems, Inc.) was obtained. The limit of detection using the third WHO international standard for HBV DNA was 377.47 IU/mL. The test was able to detect the most prevalent HBV genotypes (A-G) equally well. In conclusion, the SUMASIGNAL VHB (un paso) is a sensitive, specific, precise and accurate assay for the quantification of serum and plasma HBV DNA. Thus, this simple and fast real-time PCR test can be used as an aid in diagnosing an HBV infection and monitoring drug efficacy.