New cost-effective means to reconstruct virus populations

May 09, 2008

Researchers from the United States and Switzerland have developed mathematical and statistical tools for reconstructing viral populations using pyrosequencing, a novel and effective technique for sequencing DNA. They describe their findings in an article published May 9th in the open-access journal PLoS Computational Biology.

The scientists knew that pyrosequencing reads are short and error-prone, and thus set out to improve upon this process. The new computational method they developed reduces the error rate and yields information faster and more efficiently. The method has been applied to four independent, diverse HIV-1 populations from drug-resistant patients and compared to 165 sequences obtained directly from clonal sequencing of the same samples.

“These new techniques produce results quite close to accepted techniques at a lower cost and potentially higher resolution,” says Niko Beerenwinkel from ETH Zurich, one of the researchers.

Knowledge of the genetic structure of virus populations is critical for furthering biomedical research on disease progression, vaccine design, and drug resistance. The ability to better estimate the structure of virus populations holds great promise for new insights into viral evolution and disease control strategies.

Citation: Eriksson N, Pachter L, Mitsuya Y, Rhee S-Y, Wang C, et al. (2008) Viral Population Estimation Using Pyrosequencing. PLoS Comput Biol 4(4): e1000074. doi:10.1371/journal.pcbi.1000074

Source: Public Library of Science

Explore further: Pollen on birds shows feeding grounds

add to favorites email to friend print save as pdf

Related Stories

Amazing raw Cassini images from this week

2 hours ago

When Saturn is at its closest to Earth, it's three-quarters of a billion miles away—or more than a billion kilometers! That makes these raw images from the ringed planet all the more remarkable.

Recommended for you

Researchers look at small RNA pathways in maize tassels

14 hours ago

Researchers at the University of Delaware and other institutions across the country have been awarded a four-year, $6.5 million National Science Foundation grant to analyze developmental events in maize anthers ...

How plant cell compartments change with cell growth

14 hours ago

A research team led by Kiminori Toyooka from the RIKEN Center for Sustainable Resource Science has developed a sophisticated microscopy technique that for the first time captures the detailed movement of ...

Plants can 'switch off' virus DNA

14 hours ago

A team of virologists and plant geneticists at Wageningen UR has demonstrated that when tomato plants contain Ty-1 resistance to the important Tomato yellow leaf curl virus (TYLCV), parts of the virus DNA ...

User comments : 0