An international team of researchers led by the Univ. of Florida has created a new way to analyze the spread
of dangerous viruses, according to a study published online in Nature Communications.
The method uses sets of mathematical rules to do
something software cannot easily accomplish—analyze subtle DNA differences to
more fully understand health threats such as HIV, hepatitis, or even influenza.
“We applied this technique to more than 7,000 patients
with a subtype of HIV-1,” said Mattia Prosperi, a postdoctoral associate at
UF’s Emerging Pathogens Institute and the Genetics Institute. “We were able to
confirm transmission within established risk groups, identify infection hubs,
and we also saw that transmission does not respect the boundaries of the risk
Information about sexual habits, intravenous drug use,
and other behaviors or characteristics that play a role in HIV transmission can
be found through comprehensive interviews with large numbers of people. But
even with that exhaustive analysis, the fine elements concerning the
distribution of the virus can be unclear.
The new technique can ascertain similar information by
taking DNA sequences from patients and partitioning them according to
differences in how the virus evolved. By quickly characterizing how the virus
spreads, researchers can discover information about the demographics of the
people being infected and the drug-resistance of the virus. The information can
shape prevention measures to thwart potential epidemics.
“Ways to look at DNA sequences and compare how a
pathogen moves from one person to the next has been a computational problem for
more than 10 years,” said co-author Marco Salemi, an assistant professor of
pathology, immunology and laboratory medicine and a member of and graduate
instructor with the UF Genetics Institute. “It is important to have a
statistically sound method to follow the spread of viruses in populations and
detect transmission chains—the networks of people who transmit the infection to
each other—to develop strategies to control an epidemic.”
The technique in the Nature
Communications study could be applied to any bacterial or viral threat, but
UF researchers along with colleagues from the Univ.
of Rome studied how an emerging HIV-1
subtype circulated among different risk groups in Italy.
Using data obtained from the Antiretroviral Resistance
Cohort Analysis, a nationwide Italian HIV resistance data repository,
scientists discovered people who recently acquired HIV-1 were effectively
acting as infection hubs, playing a dramatic role in the spread of the disease
before they actually displayed any symptoms. In addition, the study showed
infections were not exclusive to the risk groups.
“The HIV example shows a strong strategy needs to be in
place to educate people that if they are in a risk group, they shouldn’t wait
until symptoms appear before being tested,” Prosperi said. “It also shows the
transmission route is not always clear, and people should not assume that they
are excluded from contracting HIV.”
Researchers said the technique can reveal valuable
information in viruses as common as the flu, such as whether it is spreading
along transportation routes or among people in certain occupations.