IAB Life Science Hour Seminar Series
|Associate Professor of Virology, Institute of Arctic Biology, UAF. Deputy Director, Alaska State Virology Lab.|
|Title:||Public Health Related Virology Research and Diagnostics|
|Date:||Friday, 16 October 2015|
|Location:||Murie Life Science Bldg, Murie Auditorium.|
A major challenge facing current diagnostic laboratories is the gap between what the clinical lab can provide and what the patients want. While patients want to know the cause for infection, our current diagnostic practice can only tell, one test at a time, whether or not a specific human pathogen exists (or ever existed) in the clinical specimen. This gap has existed ever since the beginning of modern clinical microbiology. There seemed to be no solutions until very recently, with the development of next generation sequencing (NGS) technology.
NGS technology has started a revolution in genomics and has the potential for broad application in many fields, including the detection of viral pathogens. The current Illumina MiSeq system (including the FDA-approved version, MiSeqDx) can generate 44-50 million paired-end (PE) sequencing reads per run, which exceeds the sensitivity of current PCR-based assays for virus detection. NGS technologies continue to evolve, opening new and more affordable opportunities to implement this methodology in clinical laboratories.
Unlike PCR-based assays, which rely on knowledge of specific target viral sequences, NGS technology uses a target-independent approach, and therefore has the ability to identify all possible viral infections in the clinical samples. However, the high cost per sequencing run, the need for intensive bioinformatics analyses, and the long turnaround time make currently NGS impractical for application in clinical laboratories. In fact, the average proportion of viral sequences in an infected human blood sample is about 1 to 100 per 10 million human sequences. How to detect scarce viral sequences in a clinical sample is thus a huge challenge for clinical laboratories – akin to “searching for a needle in a haystack.”
We developed a method called “Preferential Amplification of Pathogenic Sequences (PATHseq®)” that can be used to greatly enrich pathogenic sequences in a NGS library. This method does not require prior knowledge of the pathogen or assumption of the infection, therefore, provides a fast and target-independent approach to identify human pathogens. The PATHseq method uses a set of short oligonucleotides (8-10 mer) called “non-human” primers that do not match the sequences of human transcripts (RNAs). Instead of using random primers in the construction of cDNA library for sequencing, the PATHseq method recruits these short non-human primers, which in turn, preferentially amplifies non-human, presumably pathogenic sequences. The PATHseq method is pending US patent. An international searching authority led by USPTO has thoroughly examined the novelty of this method but didn’t find a similar invention. Using this method, we are currently developing two clinical assays, one is a highly sensitive HIV assay for the detection and dynamic monitoring of cell-associated HIV RNA in infected individuals under antiretroviral therapy (ART), with the aim to achieve an HIV cure. The second is a sensitive and multiplex assay for detecting all blood-borne viruses simultaneously, including Hepatitis B and C, HBV, HCV, Human Immunodeficiency Virus 1 and 2, Human T-Lymphotropic virus (HTLV-I/II) and West Nile virus (WNV), for use in screening general populations or blood donations. Our goal is to develop an all-in-one assay that includes all viruses for blood testing in order to replace current multiple tests adopted by American Red Cross.
About the Speaker:
At 19, Jack Chen received a bachelor of science degree with honors (4.0 GPA) in microbiology from Nanchang University (China), a master's degree in virology from Chinese Academy of Sciences, and a Ph.D. from Osaka University Medical School (Japan).
He did his postdoctoral research at the University of British Columbia, Canada. In 2005, he moved to the U.S. and worked at the University of Texas Health Science Center at San Antonio and Mississippi State University. He joined the University of Alaska Fairbanks in 2012 as an associate professor and the deputy director of the Alaska State Public Health Virology Laboratory. He developed and is teaching a new course - “Principles of Virology”.
In 2013, he invented a method for the detection of unknown human pathogens using next generation sequencing technology. In 2014, he formed a startup company to commercialize his invention. Research activities in his lab include both clinical and basic research of public health related viral infection. His lab is a joint effort between the State of Alaska Division of Public Health and the University of Alaska Fairbanks.
The clinical research in his lab focuses on the molecular diagnostics of human viral pathogens and diagnostic assay development using next generation sequencing technology. Equipped with state-of-the-art technologies, Chen's lab provides diagnosis, surveillance, and reference for many human viruses including influenza virus A & B, hepatitis A, B, and C virus, human immunodeficiency virus (HIV), adenovirus, enterovirus, herpes viruses, rabies virus, etc.
Browse Life Science Hour Seminars
Beginning in 1966 and continuing today, IAB hosts a weekly seminar for faculty, students, staff and the public during the academic year. The series attracts life scientists from Alaska and around the world.
If you wish to meet with a particular speaker, please contact one of the seminar coordinators or the IAB director's office at 907-474-7649.The fall 2015 faculty coordinators for this seminar series are Todd Brinkman and Greg Breed. The staff coordinator is Marie Thoms. Beginning in 2013, many of the seminars were recorded and can be viewed online. Speakers are listed in chronological order within academic years.
- 8/28/15 (Sammy L. King)
- 9/4/15 (Jennifer Moss Burns)
- 9/11/15 (Mimi Koehl)
- 9/18/15 (Vadim B. Fedorov)
- 9/25/15 (Richard Boone)
- 10/2/15 (Kelly Drew)
- 10/9/15 (Andrej Podlutsky)
- 10/16/15 (Jack Chen)
- 10/23/15 (Knut Kielland)
- 10/30/15 (Robert "Trey" Coker)
- 11/6/15 (Bill Streever)