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: 'Office life' of bacteria may be their weak spot

add to favorites email to friend print save as pdf

Related Stories

Study solves the bluetongue disease 'overwintering' mystery

Sep 12, 2014

The bluetongue virus, which causes a serious disease that costs the cattle and sheep industries in the United States an estimated $125 million annually, manages to survive the winter by reproducing in the insect that transmits ...

Bacteria harbor secret weapons against antibiotics

Sep 09, 2014

The ability of pathogenic bacteria to evolve resistance to antibiotic drugs poses a growing threat to human health worldwide. And scientists have now discovered that some of our microscopic enemies may be ...

Recommended for you

Transparent larvae hide opaque eyes behind reflections

7 hours ago

Becoming invisible is probably the ultimate form of camouflage: you don't just blend in, the background shows through you. And this strategy is not as uncommon as you might think. Kathryn Feller, from the University of Maryland ...

Peacock's train is not such a drag

8 hours ago

The magnificent plumage of the peacock may not be quite the sacrifice to love that it appears to be, University of Leeds researchers have discovered.

Iberian pig genome remains unchanged after five centuries

14 hours ago

A team of Spanish researchers have obtained the first partial genome sequence of an ancient pig. Extracted from a sixteenth century pig found at the site of the Montsoriu Castle in Girona, the data obtained indicates that ...

User comments : 0