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: Fruit flies crucial to basic research

Related Stories

Vaccines from a reactor

Mar 02, 2015

In the event of an impending global flu pandemic, vaccine production could quickly reach its limits, as flu vaccines are still largely produced in embryonated chicken eggs. Udo Reichl, Director at the Max ...

Bi-annual bat birthing helps Ebola persist

Feb 11, 2015

A bat-filled tree has been touted as the source of the on-going Ebola epidemic in Western Africa – now research from Massey University suggests that the twice yearly birthing of bats may also be responsible ...

Recommended for you

Fruit flies crucial to basic research

35 minutes ago

The world around us is full of amazing creatures. My favorite is an animal the size of a pinhead, that can fly and land on the ceiling, that stages an elaborate (if not beautiful) courtship ritual, that can ...

Crete's mystery croc killed by cold snap

35 minutes ago

A man-eating crocodile that became an attraction on the Greek island of Crete last year after its mysterious appearance in a lake has died, probably of cold, an official said Monday.

Hunting for living fossils in Indonesian waters

1 hour ago

The Coelacanth (Latimeria menadoensis) was thought to be extinct for more than 60 million years and took the science world by storm in 1938 when it was re-discovered living in South Africa. This fish has ...

Equatorial fish babies in hot water

1 hour ago

Scientists have discovered that rising ocean temperatures slow the development of baby fish around the equator, raising concerns about the impact of global warming on fish and fisheries in the tropics.

Beneficial insect virus gets boost as crop pest fighter

1 hour ago

Common baking ingredients may offer a way to bolster the effectiveness of Cydia pomonella granulovirus (CpGV), a natural insect pathogen that's been commercially formulated to kill codling moth larvae, a ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.