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Publications

Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool

By:
Contributors: Gane Ka-Shu Wong Research Group, Eric John Carpenter, Glenn Ford, Jordan Dacey Lee Patterson, Sandra Lynn O'Keefe, Tracy Nicole Jordan, Troy Anthony Mitchell, Weiwei Wang, PhD

 

PLoS One. 2013 Apr 17;8(4):e60595. doi: 10.1371/journal.pone.0060595. Print 2013.

Law J1, Jovel J, Patterson J, Ford G, O’keefe S, Wang W, Meng B, Song D, Zhang Y, Tian Z, Wasilenko ST, Rahbari M, Mitchell T, Jordan T, Carpenter E, Mason AL, Wong GK.

Abstract

We conducted an unbiased metagenomics survey using plasma from patients with chronic hepatitis B, chronic hepatitis C, autoimmune hepatitis (AIH), non-alcoholic steatohepatitis (NASH), and patients without liver disease (control). RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Hepatitis viruses were readily detected at high coverage in patients with chronic viral hepatitis B and C, but only a limited number of sequences resembling other viruses were found. The exception was a library from a patient diagnosed with hepatitis C virus (HCV) infection that contained multiple sequences matching GB virus C (GBV-C). Abundant GBV-C reads were also found in plasma from patients with AIH, whereas Torque teno virus (TTV) was found at high frequency in samples from patients with AIH and NASH. After taxonomic classification of sequences by BLASTn, a substantial fraction in each library, ranging from 35% to 76%, remained unclassified. These unknown sequences were assembled into scaffolds along with virus, phage and endogenous retrovirus sequences and then analyzed by BLASTx against the non-redundant protein database. Nearly the full genome of a heretofore-unknown circovirus was assembled and many scaffolds that encoded proteins with similarity to plant, insect and mammalian viruses. The presence of this novel circovirus was confirmed by PCR. BLASTx also identified many polypeptides resembling nucleo-cytoplasmic large DNA viruses (NCLDV) proteins. We re-evaluated these alignments with a profile hidden Markov method, HHblits, and observed inconsistencies in the target proteins reported by the different algorithms. This suggests that sequence alignments are insufficient to identify NCLDV proteins, especially when these alignments are only to small portions of the target protein. Nevertheless, we have now established a reliable protocol for the identification of viruses in plasma that can also be adapted to other patient samples such as urine, bile, saliva and other body fluids.

journal.pone.0060595.g001

PubMed

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Dr. John Lewis recognized for a breakthrough innovation with commercial application: ClarityDX Prostate

Alberta’s life sciences industry association; BioAlberta, hosted its 2018 awards gala in Calgary, September 24. BioAlberta honoured Dr. John Lewis, the Frank and Carla Sojonky Chair in Prostate Cancer Research and an Associate Professor at the University of Alberta, with its Scientific Achievement and Innovation Award.

The Scientific Achievement and Innovation award recognizes an individual or a team responsible for a breakthrough innovation with commercial application. John Lewis and his research team based with his spin-off company Nanostics Inc. developed ClarityDX Prostate, a blood test designed to accurately diagnose aggressive prostate cancer. ClarityDX Prostate will give clinicians and physicians another tool to help them and their patients decide to perform a biopsy, or not. When the test becomes commercially available it is expected to reduce the number of prostate biopsies by 50%.

BioAlberta also gave out The Company of the Year award to Circle Cardiovascular Imaging Inc. for significant achievement within the marketplace and Alberta’s business community. It has developed technology to produce an innovative post-processing cardiovascular imaging solution to improve patient outcomes that provides fast, accurate and reproducible images to assist physicians in earlier diagnosis and treatment.

Mel Wong, President and CEO of BioAlberta presented the awards with these comments, “We commend Circle Cardiovascular Imaging and Dr. John Lewis for their exceptional achievements in life sciences, Alberta’s life sciences industry is maturing and these award winners exemplify Alberta’s capacity for global impact.”

More than 200 representatives from industry, the investment community, government and innovation support organizations attended the awards gala that was held in partnership with TEC Edmonton, and with generous event sponsors. Read more in this Financial Post article.

Congratulations to John Lewis on receiving BioAlberta’s Scientific Achievement and Innovation Award!

- Perrin Beatty