The microbial detection array for detection of emerging viruses in clinical samples - a useful panmicrobial diagnostic tool

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

Modified WT amplification of non-clinical samples containing emerging virus.

<p>Purified viral RNA from a wide range of virus-positive cell culture supernatants (SN) or QCMD panel samples was amplified by WTA using the P-N6/SSIII RT-reaction. Virus-specific real-time PCR was performed before and after the amplification step, and fold increase was calculated using ΔC_t-values and dilution factors for each sample tested. (A) Fold increase of WT-amplified emerging viruses belonging to different virus genera. The two QCMD panel samples (WNV10-01 and WNV10-07) containing mixtures of different flaviviruses are highlighted. (B) The correlation between fold increase in WT amplification and viral sample content (C_t before WT amplification).</p

Microarray results on clinical samples containing emerging viruses.

<p><b>NOTE</b>. Conc, Concentration; DENV; Dengue virus, WNV, West Nile virus; JCV, JC polyomavirus; BKV, BK polyomavirus; CCHFV, Crimean-Congo haemorrhagic fever virus; Neg. ctrl, Negative control; GBV-C, hepatitis GB virus C; JEV, Japanese encephalitis virus; CSF, Cerebrospinal fluid; HERV, human endogenous retrovirus; TTV, torque teno virus; ND, not determined. Bold represents correctly identified virus.</p><p>*Viruses are grouped based on nucleic acid content, according to the Baltimore Classification.</p>95<p>results obtained using a 95 percentile threshold.</p>a<p>Difference in C_t-value in real-time PCR before and after WT amplification.</p>b<p>Fold increase after WT amplification, calculated from ΔC_t combined with dilution factors for each sample.</p>c<p>Copies/ml (HCV; IU/ml).</p

Microarray results on non-clinical samples using two different data analysis methods.

<p><b>NOTE</b>. EEEV, Eastern equine encephalitis virus; WNV, West Nile virus; CCHFV, Crimean-Congo haemorrhagic fever virus; RVFV, Rift-Valley fever virus; TBEV, Tick borne encephalitis virus; OHFV, Omsk hemoratic fever virus; YFV, yellow fever virus; PV, poliovirus; HERV, human endogenous retrovirus; JEV, Japanese encephalitis virus; DENV, Dengue virus; DOBV, Dobrava-Belgrade virus; RV-A, rotavirus A; PRV-C, porcine rotavirus C; BEV, baboon endogenous virus; SRV-1, simian retrovirus 1; MuLV, murine leukemia virus; SV40, simian virus 40; MDEV, <i>mus dunni</i> endogeneous virus; MMTV, mouse mammary tumour virus; MRV, mammalian orthoreovirus; BVDV, bovine viral diarrhea virus; SV5, simian virus 5; pur. DNA, purified DNA; SN, cell culture supernatant; pur. RNA, purified RNA; WNV10-01, sample from QCMD EQA WNV panel 10-01; WNV10-07, sample from QCMD EQA WNV panel 10-07 Bold represents correctly identified virus.</p><p>∧Viruses with fragmented alignment plots.</p><p>*Viruses are grouped based on nucleic acid content, according to the Baltimore Classification.</p

Microarray detection range on WT-amplified samples.

<p><b>NOTE</b>. Conc, Concentration; SN, supernatant; RVFV, Rift-Valley fever virus; WNV13-01, sample from QCMD EQA WNV panel 13-01; WNV, West Nile virus; JEV, Japanese encephalitis virus; TBEV, tick borne encephalitis virus; DENV13-01, sample from QCMD EQA DENV panel 13-01; DENV, Dengue virus; HCV, hepatitis C virus; ND, not detected; na, not analysed.</p>§<p>WNV13-10 contain additional viruses (DENV-1, DENV-2 and DENV-4).</p>#<p>WNV13-11 contain addition viruses (YFV, DENV-3).</p>95<p>results obtained using a 95 percentile threshold.</p>a<p>copies/ml (HCV; IU/ml).</p>b<p>ml (volume of sample for purification).</p>c<p>Number of copies into reaction.</p><p>*Difference in C_t-value in real-time PCR before and after WT amplification.</p><p>+Fold increase after WT amplification, calculated from ΔC_t combined with dilution factors for each sample.</p

Microarray analysis correctly identifies emerging viruses in clinical samples.

<p>The results of microarray analysis of WT-amplified virus-positive clinical samples, using the SSI analysis method. Graphs show the signal mean for the probe intensities for each detected virus. The bar across the graph demonstrates the signal threshold at the 99^th percentile of the random control intensities. (A) Microarray analysis of a Dengue-positive serum sample. (B) Microarray analysis of another Dengue-positive serum sample. (C) Microarray analysis of a WNV-positive urine sample. (D) Microarray analysis of another WNV-positive urine sample.</p

Improved WT amplification when using 5′-phosphorylated random hexamers in RT-reaction.

<p>Comparison of three different RT-reactions in the Whole Transcriptome Amplification (WTA) protocol. Purified viral RNA was amplified by WTA using VILO, T-Script or P-N6/SSIII RT-reaction. Virus-specific real-time PCR was performed before and after the amplification step, and fold increase was calculated using ΔC_t-values and dilution factors for each sample tested. (A) WTA-protocols tested with a 10-fold serial dilution of an HCV-positive serum sample with known concentration. (B) WTA-protocols tested with two different virus-positive cell culture supernatants, Puumala virus and Dobrava-Belgrade virus (DOBV), respectively. (C) WTA-protocols tested with five HCV-positive serum samples with estimated concentration (IU/ml). (D) WTA-protocols tested with five HCV-positive plasma samples with estimated concentration (IU/ml).</p

CLiMax analysis detects Puumala virus in a non-clinical sample.

<p>The results of microarray analyses of WT-amplified viral DNA-samples, using CLiMax analysis. (A) Log-odds scores for a Puumala virus-positive sample. The lighter and darker-coloured portions of the bars represent the unconditional and conditional log-odds scores, respectively. The conditional log-odds scores shows the contribution from a target that cannot be explained by another, more likely target above it, while the unconditional score illustrates that some very similar targets share a number of probes. (B) Target sequence-probe alignment plots for segment L of the Puumala virus genome and for BVDV-1, showing probe intensity vs probe position in the viral genome. Plot symbol and color indicates positive (>99^th percentile), negative (<95^th percentile), or equivocal hybridisation signals; hollow symbols indicate probes found to hybridise non-specifically. The pattern seen for BVDV-1, in which positive probes are restricted to a few narrow genome regions, is a typical cross-hybridisation result.</p