Diagnostics Breakthrough Brings Viral Sequencing to Doctors’ Toolkit

Posted 9/21/2015 2:48:55 PM


New Screening Tool Produces Up to 10,000-Fold Improvement in Viral Matches Compared With Traditional High-Throughput Methods

NEW YORK (Sept. 22, 2015)—Until now, there hasn’t been a fast, efficient way to broadly screen for viral infections. A breakthrough genetic testing method promises change this situation by giving clinicians a powerful new tool to detect and sequence viruses. Developed by scientists at the Center for Infection and Immunity (CII) at Columbia University’s Mailman School of Public Health, the Virome-Capture-Sequencing platform for Vertebrate viruses (VirCapSeq-VERT) is as sensitive as the gold standard polymerase chain reaction (PCR) assays while enabling simultaneous testing for hundreds of different viruses and providing near complete sequence of their genomes.

The system and its capabilities are described for the first time in a paper in the journal mBio.

To use VirCapSeq-VERT, scientists select 2 million genetic pieces from among known viruses, representing all viral taxa known to infect vertebrates. These genetic pieces are used to constitute a probe, which is introduced alongside material taken from the sample being tested. A magnetic process “pulls out” segments from the sample that match the probe; these segments are then analyzed using high-throughput sequencing. In a series of tests detailed in the study, scientists used VirCapSeq-VERT to test for a wide range of viruses in lung tissue, blood, nasal swabs, and feces. In tests of blood or tissue, the method resulted in 100 to 10,000-fold increases in viral matches compared with conventional high-throughput tests.


A Harbinger of Precision Medicine

Ian Lipkin, MD, CII director and John Snow Professor of Epidemiology, explains that heretofore high-throughput screening lacked the necessary sensitivity for detecting viruses. And PCR lacked the ability to test for multiple viruses simultaneously, making screening viruses time consuming and expensive.  By contrast, says Lipkin, senior author on the paper, “VirCapSeq-VERT is a specific, sensitive, powerful way of characterizing all of the viruses in a sample. This will be an important tool for precision medicine as well as basic and clinical research. 

A major advantage of VirCapSeq-VERT is that it can collect the entire genome of viruses detected in the sample. By contrast, PCR detects a much smaller segment of the viruses’ genome.


Captures Viruses Even After They Mutate

The method’s ability to detect a broader swath of the genome is especially useful in screening for viruses, which mutate many times faster than bacteria. VirCapSeq-VERT is able to detect and collect genetic information about viruses even if the sample doesn’t exactly match the probe. According to its developers, VirCapSeq-VERT can detect a novel virus when as much as 60 percent of its sequence doesn’t match the probe. When the suspect virus mutates, the technology is still able to catch it.  

VirCapSeq-VERT also gives researchers a new tool for efficient viral discovery to help them find all the viruses within a population, or shed light on an emerging infectious disease. CII is already using the tool in its research and is in talks with other labs interested in using it.

But VirCapSeq-VERT’s most important contribution, according to Thomas Briese, associate professor and first author, will be in the clinical setting. “If you have patients you suspect has a viral disease, you can now for a very reasonable amount of money, definitively characterize all the viruses present in those individuals in order to figure out how they should be treated,” he explains.

VirCapSeq-VERT costs approximately $40 when testing 20 samples, comparing favorably with other procedures like rRNA depletion (approximately $65 per sample).

Among the world’s best-known virus hunters, Ian Lipkin has a long track record of advances in microbiology. In the 1980s, he was the first to use subtractive cloning. A decade later, he used a similar approach to discover the first cases of West Nile virus in the Western Hemisphere. More recently, Lipkin and colleagues at CII developed mass-tag PCR and the first pan-microbial microarray. CII is also the first to use high-throughput sequencing for the discovery of novel microbes.

Co-authors include Thomas Briese, Amit Kapoor, Nischay Mishra, Komal Jain, Arvind Kumar, and Omar J. Jabado—all from the Center for Infection and Immunity.

The study was supported by the National Institutes of Health (AI109761, HL119485) and the Department of Homeland Security (S11045.01). The authors declare no conflicts.


About Columbia University’s Mailman School of Public Health

Founded in 1922, Columbia University’s Mailman School of Public Health pursues an agenda of research, education, and service to address the critical and complex public health issues affecting New Yorkers, the nation and the world. The Mailman School is the third largest recipient of NIH grants among schools of public health. Its over 450 multi-disciplinary faculty members work in more than 100 countries around the world, addressing such issues as preventing infectious and chronic diseases, environmental health, maternal and child health, health policy, climate change & health, and public health preparedness. It is a leader in public health education with over 1,300 graduate students from more than 40 nations pursuing a variety of master’s and doctoral degree programs. The Mailman School is also home to numerous world-renowned research centers including ICAP (formerly the International Center for AIDS Care and Treatment Programs) and the Center for Infection and Immunity. For more information, please visit www.mailman.columbia.edu.

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Chili ME Challenge: Make This Summer Red Hot for Research!

Posted 6/15/2015 3:45:56 PM

Watch Mady Hornig and Ian Lipkin take the Chili ME Challenge!

CFS, also known as Myalgic Encephalomyelitis, or ME/CFS, is a complex illness affects between 0.5 and 2 percent of adults in the U.S. It is characterized by a severe debilitating fatigue lasting at least six months. The causes of CFS are unknown and there is no approved diagnostic test or treatment.

On July 1, renowned researchers Ian Lipkin and Mady Hornig at the Center for Infection & Immunity (CII) at Columbia University’s Mailman School of Public Health will take the Chili ME Challenge via live webcast. CII challenges you to support this research to help unlock the mysteries of ME/CFS. Every dollar you give directly supports research.

The Chili ME Challenge harnesses social media to raise awareness and funding for important ongoing research. This grassroots campaign organized by four young women living with ME/CFS provides direct support for research by Drs. Lipkin and Hornig. Earlier this year, the Center published two high-profile papers reporting the discovery of robust evidence that ME/CFS is a biological illness, paving the way to improved diagnosis and treatment.

The funds raised will support comprehensive studies into the role of the bacteria, fungi and viruses in CFS. Research into the human microbiome is an exciting new pathway to advance understanding of the role more than a trillion microorganisms in our body play in health and in the development of disease. As one of the the world’s largest and most advanced centers in microbe discovery, identification and diagnosis, CII is optimally positioned to embark upon the challenge to determine how bacteria, fungi, viruses and toxins (and the immune response to them) contribute to ME/CFS.

Your support may show the way toward treatment strategies. With every gift, the Spice-O-Meter will climb. The more you give, the hotter it gets. Challenge your friends and family to join in on Facebook and Twitter. Simply include the tag #ChiliMEchallenge and link to this page.

Donate now and put the heat on ME/CFS!

Don't stop at giving. You, too, can eat a hot pepper and challenge others to do the same.

CII Partners with Bangladesh on Pathogen Discovery and Surveillance

Posted 4/16/2015 12:17:23 PM

April 15, 2015—The Center for Infection and Immunity at the Columbia University Mailman School of Public Health entered into an agreement with the People’s Republic of Bangladesh, furthering a series of international partnerships to undertake infectious disease surveillance and discovery in Bangladesh.

At the April 14 signing ceremony, Mailman School Dean Linda P. Fried and CII director W. Ian Lipkin met with representatives from the Institute of Epidemiology, Disease Control and Research, National Influenza Centre, and the Ministry of Health and Family Welfare of the People’s Republic of Bangladesh, who also signed the agreement.

“This relationship formalizes our commitment to continuing and expanding our current collaboration with the government of Bangladesh,” said Lipkin. “Through research and training programs, we will both yield scientific insights and build public health infrastructure.”

The agreement with Bangladesh follows on the heels of similar arrangements with People’s Republic of China and the Kingdom of Saudi Arabia, and furthers CII’s efforts to create a “global immune system” for emerging infectious disease threats. In Bangladesh, CII will employ genetic methods to rapidly identify infectious agents—methods pioneered by CII.

Among the poorest countries in the world, Bangladesh is marked by chronic malnutrition, faulty water and sanitation systems, and the highest infant mortality rate in Asia. It is also among the most densely populated, and populous, countries on the planet. The emergence of zoonotic viruses in Bangladesh could augur an almost immediate threat to regional stability and world health.



From left, seated: Linda P Fried, Dean, Mailman School of Public Health, Columbia University; Professor Dr. Deen Mohd. Noorul Huq, Directorate General of Health Services, Ministry of Health and Family Welfare, Government of the People’s Republic of Bangladesh; Roxana Quader, Additional Secretary, Ministry of Health & Family Welfare, Government of the People’s Republic of Bangladesh; Professor W. Ian Lipkin, MD Director, Center for Infection & Immunity, Mailman School of Public Health, Columbia University; 

From left, standing:Dr. M. Mushtuq Husain, Principal Scientist Officer & Head, Institute of Epidemiology, Disease Control and Research (IEDCR); Md. Helal Uddin, Joint Chief, Ministry of Health & Family Welfare; Professor Mahmudur Rahman, PhD, Director, Institute for Epidemiology, Disease Control & Research (IEDCR and National Influenza Centre (NIC), Bangladesh, Simon Anthony, D. Phil., associate research scientist, Center for Infection & Immunity, Mailman School of Public Health, Columbia University; Dr. Ahmad Raihan Sharif, Medical Officer, Institute of Epidemiology, Disease Control and Research (IEDCR)

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