Featured Research

from universities, journals, and other organizations

False alarm on hepatitis virus highlights challenges of pathogen sleuthing

Date:
September 26, 2013
Source:
University of California, San Francisco (UCSF)
Summary:
A report by scientists on a new hepatitis virus earlier this year was a false alarm, according to the researchers who correctly identified the virus as a contaminant present in a type of glassware used in many research labs.

A new hepatitis virus discovered earlier this year was a false alarm, according to UC San Francisco researchers, who correctly identified the virus as a contaminant present in a type of glassware used in many research labs.
Credit: Vasiliy Koval / Fotolia

The report by scientists of a new hepatitis virus earlier this year was a false alarm, according to UC San Francisco researchers who correctly identified the virus as a contaminant present in a type of glassware used in many research labs. Their finding, they said, highlights both the promise and peril of today's powerful "next-generation" lab techniques that are used to track down new agents of disease.

Related Articles


In research published online September 11, 2013, in the Journal of Virology, researchers led by Charles Chiu, MD, PhD, director of the UCSF Viral Diagnostics and Discovery Center, traced the source of the contamination back to tiny diatoms, a type of oceanic algae having nothing to do with human disease.

A scientific team led by researchers from the National Institutes of Health (NIH) first identified the virus as a potential cause of hepatitis in their study of blood samples from 92 people from China who had serious cases of hepatitis not caused by any of the five known hepatitis viruses. Chiu and colleagues discovered the same virus, which they called parvovirus-like hybrid virus (PHV), independently, in a different set of hepatitis patients whose disease was not caused by known viruses.

To further investigate the origin of the virus, Chiu's UCSF team tracked down its true source by applying next-generation DNA sequencing techniques in a set of carefully controlled experiments, and by referencing the ever-expanding scientific databases that spell out and catalog viral genomes.

"At first we thought this was a genuine hepatitis virus, but later we found it in data sets from patients with many other diseases and even from animals," said Chiu, a professor of laboratory medicine at UCSF.

The researchers also found that the virus sequenced from samples around the world strangely exhibited almost no genomic diversity. The research team strongly suspected that PHV was a laboratory contaminant and began probing other databases in search of the true source of the virus.

"We did some data mining of environmental databases and found matching DNA sequences from viruses originating in coastal waters off California and Oregon, but not elsewhere" Chiu said.

A developer of sampling and testing technologies may have sourced silica from diatoms in the ocean to make a popular glass column used in the studies, Chiu said. The columns are used to centrifugally spin biological samples to extract nucleic acids -- DNA and RNA. Viral DNA that may have once infected the diatoms was also likely extracted as a contaminant during the procedure, along with DNA from biological samples, he said.

"The silica used in nearly all commercial spin columns is derived from the cell walls of diatoms," he said. "We believe that PHV may be a diatom virus that had inadvertently contaminated the silica-based spin columns during manufacture."

The scientists do not know what caused the cases of hepatitis examined in the studies.

Earlier techniques developed to read out the sequence of DNA building blocks extracted from biological samples permitted the stepwise decoding of genes and eventually the characterization of entire genomes of humans and other organisms.

But in recent years game-changing technological advances referred to as next-generation sequencing have permitted exponentially faster and cheaper sequencing of millions of DNA molecules in a single run through a lab protocol.

These state-of-the-art techniques for piecing together the genomes of organisms from tiny amounts of DNA can be used to efficiently detect pathogens previously unknown to science, but they also are so sensitive that they easily pick up contaminants, Chiu said.

It is not clear why the NIH-led team did not also detect the contaminating DNA in the control samples, Chiu said. Different techniques may have been used in the analysis of control samples in comparison to samples from hepatitis patients, or there may have been lot-to-lot variations in glassware, Chiu speculates.

A similar viral false-alarm scenario unfolded in recent years with a mouse virus called XMRV, first reported in 2006. The virus initially was thought to be associated with human prostate cancer and chronic fatigue syndrome, but last year Chiu and others, including original XMRV co-discoverer Joseph DeRisi, PhD, Howard Hughes Medical Institute Investigator and professor of biochemistry at UCSF, confirmed that XMRV was actually a viral contaminant of laboratory cell cultures and was not present in prostate cancer tissue.

These studies highlight the importance of repeating experiments with good controls to ensure that results are accurate, Chiu said. "Reproducibility is a cornerstone of science, yet far too few studies are validated by follow-up investigation," he said. Next-generation sequencing is a promising approach to rapidly confirm and validate discoveries of new disease agents, saving investments in time and money that might otherwise be spent pursuing false leads, he added.


Story Source:

The above story is based on materials provided by University of California, San Francisco (UCSF). Note: Materials may be edited for content and length.


Journal Reference:

  1. S. N. Naccache, A. L. Greninger, D. Lee, L. L. Coffey, T. Phan, A. Rein-Weston, A. Aronsohn, J. Hackett, E. L. Delwart, C. Y. Chiu. The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns. Journal of Virology, 2013; DOI: 10.1128/JVI.02323-13

Cite This Page:

University of California, San Francisco (UCSF). "False alarm on hepatitis virus highlights challenges of pathogen sleuthing." ScienceDaily. ScienceDaily, 26 September 2013. <www.sciencedaily.com/releases/2013/09/130926102308.htm>.
University of California, San Francisco (UCSF). (2013, September 26). False alarm on hepatitis virus highlights challenges of pathogen sleuthing. ScienceDaily. Retrieved October 31, 2014 from www.sciencedaily.com/releases/2013/09/130926102308.htm
University of California, San Francisco (UCSF). "False alarm on hepatitis virus highlights challenges of pathogen sleuthing." ScienceDaily. www.sciencedaily.com/releases/2013/09/130926102308.htm (accessed October 31, 2014).

Share This



More Health & Medicine News

Friday, October 31, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Melafind: Spotting Melanoma Without a Biopsy

Melafind: Spotting Melanoma Without a Biopsy

Ivanhoe (Oct. 31, 2014) The MelaFind device is a pain-free way to check suspicious moles for melanoma, without the need for a biopsy. Video provided by Ivanhoe
Powered by NewsLook.com
Battling Multiple Myeloma

Battling Multiple Myeloma

Ivanhoe (Oct. 31, 2014) The answer isn’t always found in new drugs – repurposing an ‘old’ drug that could mean better multiple myeloma treatment, and hope. Video provided by Ivanhoe
Powered by NewsLook.com
Chronic Inflammation and Prostate Cancer

Chronic Inflammation and Prostate Cancer

Ivanhoe (Oct. 31, 2014) New information that is linking chronic inflammation in the prostate and prostate cancer, which may help doctors and patients prevent cancer in the future. Video provided by Ivanhoe
Powered by NewsLook.com
Sickle Cell: Stopping Kids’ Silent Strokes

Sickle Cell: Stopping Kids’ Silent Strokes

Ivanhoe (Oct. 31, 2014) Blood transfusions are proving crucial to young sickle cell patients by helping prevent strokes, even when there is no outward sign of brain injury. Video provided by Ivanhoe
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Health & Medicine

Mind & Brain

Living & Well

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins