Two-color multiplex assay for the identification of orthopox viruses with real-time LUX- PCR

Molecular detection of monkeypox and related viruses: challenges and opportunities

The recent widespread emergence of monkeypox (mpox), a rare and endemic zoonotic disease by monkeypox virus (MPXV), has made global headlines. While transmissibility (R₀ ≈ 0.58) and fatality rate (0-3%) are low, as it causes prolonged morbidity, the World Health Organization has declared monkeypox as a public health emergency of international concern. Thus, effective containment and disease management require quick and efficient detection of MPXV. In this bioinformatic overview, we summarize the numerous molecular tests available for MPXV, and discuss the diversity of genes and primers used in the polymerase chain reaction-based detection. Over 90 primer/probe sets are used for the detection of poxviruses. While hemagglutinin and A-type inclusion protein are the most common target genes, tumor necrosis factor receptor and complement binding protein genes are frequently used for distinguishing Clade I and Clade II of MPXV. Problems and possibilities in the detection of MPXV have been discussed.

Are We Prepared in Case of a Possible Smallpox-Like Disease Emergence?

Smallpox was the first human disease to be eradicated, through a concerted vaccination campaign led by the World Health Organization. Since its eradication, routine vaccination against smallpox has ceased, leaving the world population susceptible to disease caused by orthopoxviruses. In recent decades, reports of human disease from zoonotic orthopoxviruses have increased. Furthermore, multiple reports of newly identified poxviruses capable of causing human disease have occurred. These facts raise concerns regarding both the opportunity for these zoonotic orthopoxviruses to evolve and become a more severe public health issue, as well as the risk of Variola virus (the causative agent of smallpox) to be utilized as a bioterrorist weapon. The eradication of smallpox occurred prior to the development of the majority of modern virological and molecular biological techniques. Therefore, there is a considerable amount that is not understood regarding how this solely human pathogen interacts with its host. This paper briefly recounts the history and current status of diagnostic tools, vaccines, and anti-viral therapeutics for treatment of smallpox disease. The authors discuss the importance of further research to prepare the global community should a smallpox-like virus emerge.

Detection of human-pathogenic poxviruses

With the eradication of smallpox about 30 years ago, the identification and differentiation of other poxviruses with varying pathogenicity in humans present a challenge for diagnostic facilities. While a clinical differentiation can be demanding, electron microscopy is the fastest approach to identify poxviruses. Molecular techniques, based on specific genomic sequences, are routinely applied to identify poxvirus species and distinguish between individual virus variants. In this chapter, we present detailed protocols for both techniques and discuss questions relevant to fast and reliable diagnostics of poxviruses.

A novel real-time PCR assay for determination of viral loads in person infected with hepatitis B virus

A novel LUX (Light Upon eXtension) primer-based real-time PCR assay was developed and evaluated in this study, which was designed to provide a cost-effective, specific and highly sensitive method for viral load determination of hepatitis B virus (HBV). The assay employed an effective and rapid nucleic acid extraction system based on magnetic beads. To evaluate its efficacy, this new viral DNA preparation method was compared with QIAamp Blood Mini Kit and the results showed a good correlation (r=0.971; P<0.001). The performance of the LUX real-time assay was validated by testing serial dilutions of HBV plasmid DNA (5 to 5 x 10(8)copies/reaction) and a good linear relationship was obtained between the Ct values and the log(10) concentration of the HBV DNA. The assay possessed high sensitivity and the detection limit of this system was as few as 25 copies/ml of serum. A total of 91 positive serum samples were detected to evaluate further the assay and the high specificity was confirmed by melting curve analysis. This assay provides an ideal tool for monitoring the treatment efficacy and studying the relationship between HBV viral load and the stage of disease.

Loop-mediated isothermal amplification-based diagnostic assay for monkeypox virus infections

Monkeypox virus (MPXV) causes a smallpox-like disease in non-human primates and humans. This infection is endemic to central and western Africa. MPXV is divided into two genetically different groups, Congo Basin and West African MPXV, with the former being the more virulent. A real-time quantitative MPXV genome amplification system was developed for the diagnosis of MPXV infections using loop-mediated isothermal amplification (LAMP) technology. Primers used for genome amplification of Congo Basin (C-LAMP), West African (W-LAMP), and both Congo Basin and West African (COM-LAMP) MPXV by LAMP were designed according to the nucleotide sequences of the Congo Basin-specific D14L gene, the West African-specific partial ATI gene, and the partial ATI gene that is shared by both groups, respectively. The sensitivity and specificity of the LAMP were evaluated with nested PCR using peripheral blood and throat swab specimens collected from Congo Basin MPXV or West African MPXV-infected monkeys. The sensitivity and specificity of COM-LAMP, C-LAMP, and W-LAMP were 80% (45/56) and 100% (64/64); 79% (19/24) and 100% (24/24); and 72% (23/32) and 100% (40/40), respectively. The viremia level determined by LAMP assays increased with increases in the severity of the monkeypox-associated symptoms. The newly developed LAMP assay was confirmed to be a rapid, quantifiable, and highly sensitive and specific system effective in the diagnosis of MPXV infections. The LAMP assays made it possible to discriminate between Congo Basin and West African MPXV. The LAMP developed in this study is useful not only for diagnosis of but also for the assessment of MPXV infections.

Dual-probe real-time PCR assay for detection of variola or other orthopoxviruses with dried reagents

A real-time, multiplexed polymerase chain reaction (PCR) assay based on dried PCR reagents was developed. Only variola virus could be specifically detected by a FAM (6-carboxyfluorescein)-labeled probe while camelpox, cowpox, monkeypox and vaccinia viruses could be detected by a TET (6-carboxytetramethylrhodamine)-labeled probe in a single PCR reaction. Approximately 25 copies of cloned variola virus DNA and 50 copies of genomic orthopoxviruses DNA could be detected with high reproducibility. The assay exhibited a dynamic range of seven orders of magnitude with a correlation coefficient value greater than 0.97. The sensitivity and specificity of the assay, as determined from 100 samples that contained nucleic acids from a multitude of bacterial and viral species were 96% and 98%, respectively. The limit of detection, sensitivity and specificity of the assay were comparable to standard real-time PCR assays with wet reagents. Employing a multiplexed format in this assay allows simultaneous discrimination of the variola virus from other closely related orthopoxviruses. Furthermore, the implementation of dried reagents in real-time PCR assays is an important step towards simplifying such assays and allowing their use in areas where cold storage is not easily accessible.

Orthopoxvirus detection in environmental specimens during suspected bioterror attacks: inhibitory influences of common household products

After terrorists attacked the United States in 2001, the appearance of letters and other objects containing powdery substances with unknown potentials for biological threat focused attention on the speed, sensitivity, and reliability of diagnostic methods. This study summarizes the abilities and limitations of real-time PCR, electron microscopy (EM), and virus isolation when used to detect potential bioweapons. In particular, we investigated the inhibitory influences of different common household products present in environmental specimens on PCR yield, EM detection, and virus isolation. We used vaccinia virus as a model for orthopoxviruses by spiking it into specimens. In the second part of the study, we describe modifications of diagnostic methods to overcome inhibitory effects. A variety of PCR amplification enhancers, DNA extraction protocols, and applications of internal controls were evaluated to improve diagnostic simplicity, speed, and reliability. As a result, we strongly recommend using at least two different frontline techniques in parallel, e.g., EM and PCR. A positive result obtained by any one of these techniques should be followed by a biological method to confirm the putative diagnosis. Confirmatory methods include virus isolation followed by an agent-specific immunofluorescence assay to confirm the presence of replication-competent particles.

Fast and reliable diagnostic methods for the detection of human poxvirus infections

Although the most prominent poxvirus, Variola virus, was successfully eradicated in the last century, several other poxviruses cause zoonotic infections that, in the early stages, resemble Variola virus infections with varying pathogenicity in humans. Over recent decades, numerous diagnostic methods for the detection of poxviruses have been established. As a result of technical progress and the advancement in molecular techniques, only a small selection of these methods meet the demands of being rapid and reliable. This review briefly introduces human poxviruses, summarizes the methods available, discusses their pros and cons and provides recommendations for a ‘fast and reliable diagnostic approach.

Orthopoxvirus pan-genomic DNA assay

A genome-spanning assay is described that enables laboratory confirmation of infections with orthopoxviruses (OPVs), particularly Vaccinia, Monkeypox, and Variola viruses, which can cause vesiculo-pustular rash illnesses in humans. The assay uses a series of polymerase chain reaction (PCR) amplicons that overlap to span the approximately 200kilobase pair linear DNA genome of OPVs. Corresponding amplicons of different viral isolates can then be compared by matching their restriction fragment length polymorphism (RFLP) gel electrophoresis patterns. The PCR step does not necessarily require viral growth to produce sufficient DNA for the RFLP comparisons. The assay would be useful as a prelude to sequencing entire or partial DNA genome regions of various OPVs, including natural or recombinant OPVs and potentially dangerous bioengineered OPVs designed to express foreign DNA or other viruses.

A PCR-based assay for detection of emerging vaccinia-like viruses isolated in Brazil

We report 2 strategies to identify Brazilian vaccinia virus (VACV) isolates related to Cantagalo virus (CTGV) based on the amplification of the hemagglutinin (HA) gene by the polymerase chain reaction (PCR). One PCR protocol was combined with restriction analysis using the endonuclease SnaB I, generating a unique digestion pattern for CTGV amplicons. The restriction profile could identify 41 CTGV-related isolates in 43 clinical specimens and clearly differentiated them from other orthopoxviruses and strains of VACV. Alternatively, we used a 1-step PCR assay with primers that specifically targeted CTGV HA sequence. This protocol produced similar results more rapidly than the 1st strategy, eliminating post-PCR procedures. The results were supported by Western blot analysis of the viral protein profile in infected cells. Both PCR-based methods enabled a fast, sensitive, and cost-effective detection of new isolates of VACV related to CTGV directly from clinical samples without requiring virus isolation.

Detection and monitoring of virus infections by real-time PCR

The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.