Rapid detection of common viruses using multi-analyte suspension arrays

Multiplexed microarrays based on optically encoded microbeads

In recent years, there has been growing interest in optically-encoded or tagged functionalized microbeads as a solid support platform to capture proteins or nucleotides which may serve as biomarkers of various diseases. Multiplexing technologies (suspension array or planar array) based on optically encoded microspheres have made possible the observation of relatively minor changes in biomarkers related to specific diseases. The ability to identify these changes at an early stage may allow the diagnosis of serious diseases (e.g. cancer) at a time-point when curative treatment may still be possible. As the overall accuracy of current diagnostic methods for some diseases is often disappointing, multiplexed assays based on optically encoded microbeads could play an important role to detect biomarkers of diseases in a non-invasive and accurate manner. However, detection systems based on functionalized encoded microbeads are still an emerging technology, and more research needs to be done in the future. This review paper is a preliminary attempt to summarize the state-of-the-art concerning diagnostic microbeads; including microsphere composition, synthesis, encoding technology, detection systems, and applications.

Establishment and optimization of a liquid bead array for the simultaneous detection of ten insect-borne pathogens

Background

Insect-borne diseases could induce severe symptoms in human and clinical signs in animals, such as febrility, erythra, arthralgia and hemorrhagic fever, and cause significant economic losses and pose public health threat all over the world. The significant advantages of Luminex xMAP technology are high-throughput, high parallel and automation. This study aimed to establish a liquid bead array based on Luminex xMAP technology that was able to simultaneously detect multiple insect-borne pathogens.

Methods

Specific probes and primers to detect the nucleic acid of 10 insect-borne pathogens were designed. Probes were coupled with fluorescent carboxylated microspheres. The parameters of the system were optimized, including ratio of forward/reverse primers (1:2), hybridization temperature (50 °C) and duration (30 min) and quantity of PCR product (2 μl). The sensitivity and specificity of the system were also evaluated. Moreover mixed nucleic acid of 10 insect-borne pathogens, including Bluetongue virus, Epizootic hemorrhagic disease virus of deer, Coxiella burnetii, African swine fever virus, West Nile fever virus, Borrelia burgdorferi, vesicular stomatitis virus, Rift Valley fever virus, Ebola virus and Schmalenberg’s disease virus, and 3000 clinical samples were tested for practicability.

Results

The optimized detection system showed high sensitivity, specificity and reproducibility. Each probe showed specific fluorescence signal intensity without any cross-hybridization for the other insect-borne pathogens tested, which included dengue virus, tick-borne encephalitis virus, Japanese encephalitis virus, Xinjiang hemorrhagic fever virus, spotted fever group rickettsiae, ehrlichiae and chikungunya virus. The limit of detection was 10 copies of target gene. Insect-borne pathogens were successfully detected among the 3000 clinical samples, and the results were consistent with those obtained using gold-standard assays or commercial nucleic acid detection kits.

Conclusions

This optimized liquid array detection system was high-throughput and highly specific and sensitive in screening of the insect-borne pathogens. It was promising in detection of these pathogens for molecular epidemiological studies.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-2996-0) contains supplementary material, which is available to authorized users.

Development of multiplexed bead arrays for the simultaneous detection of nucleic acid from multiple viruses in bat samples

Virus surveillance of wildlife populations is important for identifying, monitoring, and predicting the emergence of pathogens that pose a potential threat to animal and human health. Bats are identified as important wildlife hosts of many viruses capable of causing fatal human disease, including members of the henipaviruses, coronaviruses, rhabdoviruses and filoviruses. As global warming and habitat change are thought to impact upon pathogen transmission dynamics and increase the risk of spillover, virus surveillance in bat populations remains a significant component of efforts to improve the prediction and control of potential future disease outbreaks caused by bat-borne viruses. In this study we have developed two fluid bead array assays containing customized panels that target multiple bat-borne viruses. These assays detect up to 11 viral RNA's simultaneously in urine samples collected from wild bat populations in Australia and Bangladesh. The assays developed show high specificity for the target viruses and the analytical sensitivity compares favorably to qRT-PCR. These assays enhance the ability to monitor multi-pathogen dynamics and identify patterns of virus shedding from bat populations, thus informing key approaches to outbreak response and control.

Variation-tolerant capture and multiplex detection of nucleic acids: application to detection of microbes

In contrast to ordinary PCRs, which have a limited multiplex capacity and often return false-negative results due to target variation or inhibition, our new detection strategy, VOCMA (variation-tolerant capture multiplex assay), allows variation-tolerant, target-specific capture and detection of many nucleic acids in one test. Here we demonstrate the use of a single-tube, dual-step amplification strategy that overcomes the usual limitations of PCR multiplexing, allowing at least a 22-plex format with retained sensitivity. Variation tolerance was achieved using long primers and probes designed to withstand variation at known sites and a judicious mix of degeneration and universal bases. We tested VOCMA in situations where enrichment from a large sample volume with high sensitivity and multiplexity is important (sepsis; streptococci, enterococci, and staphylococci, several enterobacteria, candida, and the most important antibiotic resistance genes) and where variation tolerance and high multiplexity is important (gastroenteritis; astrovirus, adenovirus, rotavirus, norovirus genogroups I and II, and sapovirus, as well as enteroviruses, which are not associated with gastroenteritis). Detection sensitivities of 10 to 1,000 copies per reaction were achieved for many targets. VOCMA is a highly multiplex, variation-tolerant, general purpose nucleic acid detection concept. It is a specific and sensitive method for simultaneous detection of nucleic acids from viruses, bacteria, fungi, and protozoa, as well as host nucleic acid, in the same test. It can be run on an ordinary PCR and a Luminex machine and is suitable for both clinical diagnoses and microbial surveillance.

A new molecular diagnostic approach to assess Y chromosome microdeletions in infertile men

OBJECTIVE

A key cause of spermatogenetic failure in infertile males is microdeletions in the azoospermia factor (AZF) regions of the Y chromosome. This study screened for microdeletions in the AZF regions using suspension array technology and compared the results with those from polymerase chain reaction (PCR).

METHODS

Patients with spermatogenetic failure (n=507) and healthy control sperm donors (n=100) were recruited. DNA samples were analysed using both multiplex PCR with gel electrophoresis and suspension array technology.

RESULTS

The suspension array method identified 45 infertile males with Y chromosome microdeletions, while none was found in the controls. Amongst the AZF subregions, two cases had deletions in AZFa, three in AZFb, 35 in AZFc, three in AZFbc and two in AZFabc. The results from 507 patients were identical when analysed with either suspension array or multiplex PCR, however suspension array technology offered improved sensitivity, may be more accurate and could give time and cost savings.

CONCLUSIONS

Suspension array technology offers a rapid and high-throughput method for Y chromosome microdeletion screening in infertile men.

Miniaturized immunoassays: moving beyond the microplate

After more than 40 years, immunoassays are still the backbone of protein biomarker analysis in clinical diagnostics and drug development. They have come a long way since their inception, incorporating technical developments including monoclonal antibodies, novel labels and lately microfluidics. A number of microfluidic platforms have been tested, such as centrifugational compact disc assays, lab-on-a-chip, arrays and digital electrochemical assays. This review focuses on commercial applications of microfluidic immunoassays with reference to some applied academic examples of interest. Advantages and disadvantages of the platform technologies are discussed in general.

Multi-analyte suspension arrays for the detection of common viruses: how viable are these assays in clinical laboratories?

This article assesses the viability of a recently described multi-analyte suspension array for the detection of herpes simplex viruses-1 and -2, cytomegalovirus, Epstein-Barr virus, human papillomavirus and hepatitis B virus. This methodology was identified by the authors as a means of providing rapid, high-throughput multiplex assays that were easy to use. When paired with PCR assays, multi-analyte suspension arrays have the ability to overcome drawbacks associated with conventional detection methods such as long turnaround time, detection sensitivity and the ability to detect only one pathogen in each round of testing. However, the assays described in this article are still hampered by some key issues including limit of detection, the fact that median fluorescence intensity is not truly a quantitative diagnostic method, and that open molecular diagnostic systems can lead to contamination and/or increased operator-based errors. Although modern pressures on clinical virology laboratories have increased the need to develop a system that can detect pathogens in multiplexed assays, in the future these assays will only become more clinically relevant if they are designed with greater stakeholder input.