Artificial plasmid engineered to simulate multiple biological threat agents

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) combined with colorimetric gold nanoparticle (AuNP) probe assay for visual detection of Penaeus vannamei nodavirus (PvNV)

Penaeus vannamei nodavirus (PvNV) is an emerging viral infection that has caused muscle necrosis or a white tail disease in cultivated whiteleg shrimp Penaeus (Litopenaeus) vannamei, leading to loss in the productions. Rapid detection of PvNV is essential for further control disease. A combination between reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay and colorimetric gold nanoparticle (AuNP) probe was developed for rapid, sensitive and inexpensive detection of PvNV in this study. RT-LAMP reaction successfully detected PvNV at 63°C for 45 and 5 min for hybridization of LAMP amplified product, followed by salt-induced AuNP-labelled ssDNA probe aggregation to visual colour development. This method showed identical results to LAMP followed by gel electrophoresis and spectrophotometric detection, and it was 10 times sensitive more than conventional nested RT-PCR. The new method revealed negative results with other shrimp pathogens. This study provides the direct visualization of LAMP reaction by AuNP probe hybridization, that significantly reduces the time and cost required for the molecular diagnostic of infectious diseases and offers to use in aquaculture health management.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study represents the first report of Penaeus vannamei nodavirus (PvNV) detection using the colorimetric RT-LAMP technique. The application of RT-LAMP assay combined with colorimetric gold nanoparticle (AuNP) probe to detect the PvNV offers simple, rapid and sensitive technique and does not require sophisticated equipment with applicable for small or field laboratories. This method can further employ to screen broodstock before breeding, to screen postlarvae before ponds stocking, to monitor shrimp in rearing ponds and to assess the occurrence of this virus in shrimp farming.

Detection and tracking of a novel genetically tagged biological simulant in the environment

A variant of Bacillus thuringiensis subsp. kurstaki containing a single, stable copy of a uniquely amplifiable DNA oligomer integrated into the genome for tracking the fate of biological agents in the environment was developed. The use of genetically tagged spores overcomes the ambiguity of discerning the test material from pre-existing environmental microflora or from previously released background material. In this study, we demonstrate the utility of the genetically "barcoded" simulant in a controlled indoor setting and in an outdoor release. In an ambient breeze tunnel test, spores deposited on tiles were reaerosolized and detected by real-time PCR at distances of 30 m from the point of deposition. Real-time PCR signals were inversely correlated with distance from the seeded tiles. An outdoor release of powdered spore simulant at Aberdeen Proving Ground, Edgewood, MD, was monitored from a distance by a light detection and ranging (LIDAR) laser. Over a 2-week period, an array of air sampling units collected samples were analyzed for the presence of viable spores and using barcode-specific real-time PCR assays. Barcoded B. thuringiensis subsp. kurstaki spores were unambiguously identified on the day of the release, and viable material was recovered in a pattern consistent with the cloud track predicted by prevailing winds and by data tracks provided by the LIDAR system. Finally, the real-time PCR assays successfully differentiated barcoded B. thuringiensis subsp. kurstaki spores from wild-type spores under field conditions.

Testing and validation of high density resequencing microarray for broad range biothreat agents detection

Rapid and effective detection and identification of emerging microbiological threats and potential biowarfare agents is very challenging when using traditional culture-based methods. Contemporary molecular techniques, relying upon reverse transcription and/or polymerase chain reaction (RT-PCR/PCR) provide a rapid and effective alternative, however, such assays are generally designed and optimized to detect only a limited number of targets, and seldom are capable of differentiation among variants of detected targets. To meet these challenges, we have designed a broad-range resequencing pathogen microarray (RPM) for detection of tropical and emerging infectious agents (TEI) including biothreat agents: RPM-TEI v 1.0 (RPM-TEI). The scope of the RPM-TEI assay enables detection and differential identification of 84 types of pathogens and 13 toxin genes, including most of the class A, B and C select agents as defined by the Centers for Disease Control and Prevention (CDC, Atlanta, GA). Due to the high risks associated with handling these particular target pathogens, the sensitivity validation of the RPM-TEI has been performed using an innovative approach, in which synthetic DNA fragments are used as templates for testing the assay's limit of detection (LOD). Assay specificity and sensitivity was subsequently confirmed by testing with full-length genomic nucleic acids of selected agents. The LOD for a majority of the agents detected by RPM-TEI was determined to be at least 10⁴ copies per test. Our results also show that the RPM-TEI assay not only detects and identifies agents, but is also able to differentiate near neighbors of the same agent types, such as closely related strains of filoviruses of the Ebola Zaire group, or the Machupo and Lassa arenaviruses. Furthermore, each RPM-TEI assay results in specimen-specific agent gene sequence information that can be used to assess pathogenicity, mutations, and virulence markers, results that are not generally available from multiplexed RT-PCR/PCR-based detection assays.

Non-infectious plasmid engineered to simulate multiple viral threat agents

The aim of this study was to design and construct a non-virulent simulant to replace several pathogenic viruses in the development of detection and identification methods in biodefense. A non-infectious simulant was designed and engineered to include the nucleic acid signature of VEEV (Venezuelan Equine Encephalitis virus), Influenza virus, Rift Valley Fever virus, Machupo virus, Lassa virus, Yellow Fever virus, Ebola virus, Eastern Equine Encephalitis virus, Junin virus, Marburg virus, Dengue virus, and Crimean-Congo virus, all in a single construct. The nucleic acid sequences of all isolates available for each virus species were aligned using ClustalW software in order to obtain conserved regions of the viral genomes. Specific primers were designed to permit the identification and differentiation between viral threat agents. A chimera of 3143 base pairs was engineered to produce 13 PCR amplicons of different sizes. PCR amplification of the simulant with virus-specific primers revealed products of the predicted length, in bands of similar intensity, and without detectable unspecific products by electrophoresis analysis. The simulant described could reduce the need to use infectious viruses in the development of detection and diagnostic methods, and could also be useful as a non-virulent positive control in nucleic acid-based tests against biological threat agents.