The Microbial Detection Array for Detection of Emerging Viruses in Clinical Samples - A Useful Panmicrobial Diagnostic Tool

Abstract

Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travel, climate change and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. Many of these viruses cause similar disease symptoms as other emerging viruses or common infections, making these unexpected pathogens difficult to diagnose. Broad-spectrum pathogen detection microarrays containing probes for all sequenced viruses and bacteria can provide rapid identification of viruses, guiding decisions about treatment and appropriate case management. We report a modified Whole Transcriptome Amplification (WTA) method that increases unbiased amplification, particular of RNA viruses. Using this modified WTA method, we tested the specificity and sensitivity of the Lawrence Livermore Microbial Detection Array (LLMDA) against a wide range of emerging viruses present in both non-clinical and clinical samples using two different microarray data analysis methods.

Microbiome associations in pigs with the best and worst clinical outcomes following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2)

“…The LLMDA oligonucleotide probes are around 60 nucleotides in length and were designed to detect all sequenced microbial families with a large number of probes per sequence (average of 30 probes) to improve sensitivity in the evaluation of microbial nucleic acids in a variety of samples. The high-density oligo LLMDA microarray and statistical analysis method have been extensively tested in numerous studies for viral and bacterial detection in pure or complex environmental and clinical samples (Gardner et al, 2010;Jaing et al, 2015;Rosenstierne et al, 2014).…”

“…Since less extracted nucleic acid was obtained from the fecal and serum samples, a random amplification was performed on these samples as described previously (Rosenstierne et al, 2014). For each amplification reaction, 5µL each of extracted DNA and RNA was input into the reaction.…”

Proteomics analysis of liver tissues from C57BL/6J mice receiving low-dose 137Cs radiation

“…In vivo studies on mouse liver or kidney with low-dose-rate irradiation demonstrate distinct differences between high-and low-dose exposures (Taki et al 2009;Uehara et al 2010). These results showed few genes in common between low-dose exposures in the different time points (Rosenstierne et al 2014). However, specific radiation exposure-related molecular events have yet to be identified.…”

Design of genomic signatures for pathogen identification and characterization

“…Glass-slide platforms containing up to 400,00 total probes and capable of running 1, 2, 4, or 8 samples at a time were used for a very wide range of studies on human, animal, environmental, and product samples. This includes finding vaccine contaminants (Victoria et al, 2010), viral association with bladder cancer (Parad zik et al, 2013), identifying ancient pathogen DNA in archaeological samples (Devault et al, 2014), combat wound infection analysis , and finding emerging viruses in clinical samples (Rosenstierne et al, 2014).…”