A new test detects virtually any virus that infects
people and animals, according to research at
Washington University School of Medicine in St.
Louis, where the technology was developed.
Many thousands of viruses are known to cause illness
in people and animals, and making a diagnosis can be
an exhaustive exercise, at times requiring a battery
of different tests. That’s because current tests
aren’t sensitive enough to detect low levels of
viral bugs or are limited to detecting only those
viruses suspected of being responsible for a
patient’s illness.
“With this test, you don’t have to know what you’re
looking for,” said the study’s senior author,
Gregory Storch, MD, the Ruth L. Siteman Professor of
Pediatrics. “It casts a broad net and can
efficiently detect viruses that are present at very
low levels. We think the test will be especially
useful in situations where a diagnosis remains
elusive after standard testing or in situations in
which the cause of a disease outbreak is unknown.”
Results published online in September in the journal
Genome Research demonstrate that in patient samples
the new test – called ViroCap – can detect viruses
not found by standard testing based on genome
sequencing. The test could be used to detect
outbreaks of deadly viruses such as Ebola, Marburg
and severe acute respiratory syndrome (SARS), as
well as more routine viruses, including rotavirus
and norovirus, both of which cause severe
gastrointestinal infections.
Developed in collaboration with the university’s
McDonnell Genome Institute, the test sequences and
detects viruses in patient samples and is just as
sensitive as the gold-standard polymerase chain
reaction (PCR) assays, which are used widely in
clinical laboratories. However, even the most
expansive PCR assays can only screen for up to about
20 similar viruses at the same time.
The Washington University researchers are making the
technology they developed publicly available to
scientists and clinicians worldwide, for the benefit
of patients and research.
The researchers evaluated the new test in two sets
of biological samples – for example, from blood,
stool and nasal secretions – from patients at St.
Louis Children’s Hospital. In the first, standard
testing that relied on genome sequencing had
detected viruses in 10 of 14 patients. But the new
test found viruses in the four children that earlier
testing had missed. Standard testing failed to
detect common, everyday viruses: influenza B, a
cause of seasonal flu; parechovirus, a mild
gastrointestinal and respiratory virus; herpes virus
1, responsible for cold sores in the mouth; and
varicella-zoster virus, which causes chickenpox.
In a second group of children with unexplained
fevers, standard testing had detected 11 viruses in
the eight children evaluated. But the new test found
another seven, including a respiratory virus called
human adenovirus B type 3A, which usually is
harmless but can cause severe infections in some
patients.
In all, the number of viruses detected in the two
patient groups jumped to 32 from 21, a 52 percent
increase.
“The test is so sensitive that it also detects
variant strains of viruses that are closely related
genetically,” said corresponding author Todd Wylie,
an instructor of pediatrics. “Slight genetic
variations among viruses often can’t be
distinguished by currently available tests and
complicate physicians’ ability to detect all
variants with one test.”
In addition, because the test includes detailed
genetic information about various strains of
particular viruses, subtypes can be identified
easily. For example, the study showed that while
standard testing identified a virus as influenza A,
which causes seasonal flu, the new test indicated
that the virus was a particularly harsh subtype
called H3N2.
Last flu season, H3N2 contributed to some 36,000
deaths in the United States. And in some patients –
particularly young children, older adults and people
with weakened immune systems – knowing that the H3N2
strain is present may alter treatment.
To develop the test, the researchers targeted unique
stretches of DNA or RNA from every known group of
viruses that infects humans and animals. In all, the
research team included 2 million unique stretches of
genetic material from viruses in the test.
These stretches of material are used as probes to
pluck out viruses in patient samples that are a
genetic match. The matched viral material then is
analyzed using high-throughput genetic sequencing.
As completely novel viruses are discovered, their
genetic material could easily be added to the test,
Storch said.
The researchers plan to conduct additional research
to validate the accuracy of the test, so it could be
several years before it is clinically available.
“It also may be possible to modify the test so that
it could be used to detect pathogens other than
viruses, including bacteria, fungi and other
microbes, as well as genes that would indicate the
pathogen is resistant to treatment with antibiotics
or other drugs,” said co-author Kristine Wylie, PhD,
assistant professor of pediatrics.
In the meantime, the technology can be used by
scientists to study viruses in a research setting.
Kristine Wylie investigates the viruses that set up
residence in and on the human body, collectively
known as the virome. The new test will provide a way
to capture the full breadth and depth of such
viruses, and deepen understanding of how they play a
role in keeping the body healthy.
For more information
Genome Research - Wylie TN, Wylie KM, Herter BN and
Storch GA
Enhanced virome sequencing using targeted sequence
capture.
Link...
Washington University in St. Louis
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