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: Underground amphibians evolved unique ear

add to favorites email to friend print save as pdf

Related Stories

DNA based diagnostics 2.0

Jul 01, 2014

The latest generation of DNA sequencers allows all the genes of a plant, as well as any pathogens present, to be charted literally within a few days. "This provides unprecedented opportunities for the diagnosis ...

Recommended for you

Monkeys fear big cats less, eat more, with humans around

2 hours ago

Some Monkeys in South Africa have been found to regard field scientists as human shields against predators and why not if the alternative is death by leopard? The researchers found the monkeys felt far safer ...

Study indicates large raptors in Africa used for bushmeat

15 hours ago

Bushmeat, the use of native animal species for food or commercial food sale, has been heavily documented to be a significant factor in the decline of many species of primates and other mammals. However, a new study indicates ...

User comments : 0