FRIDAY, SEPTEMBER 30, 2016

Scientists use gene sequencing to identify Lone Star virus

Researchers at UC San Francisco recently used new faster gene sequencing to conclusively identify that the tick-borne Lone Star virus is part of a family of other tick-borne viruses.

The scientists used ultra-rapid deep sequencing to reconstruct the previously unknown genome of the virus in less than 24 hours. They determined the virus is part of the bunyavirus family, the members of which often cause respiratory problems, fever and bleeding.

"We did not show that Lone Star virus causes disease in humans, although the laboratory and sequencing data suggest that this is a distinct possibility," Charles Chiu, the study's principal investigator, said.

The new sequencing technique combines deep sequencing, an emerging technology that uses a tiny snippet of DNA to reconstruct an entire DNA sequence, with advanced computational techniques and algorithms developed in the laboratories of Chiu and his collaborators. Conventional DNA sequencing techniques can take days to weeks. Chiu and his team plan to introduce a graphical user interface to let small laboratories analyze and access ultra-rapid, deep-sequencing data through cloud computing.

"This will mean that any remote laboratory in Asia or Africa -- where a lot of these recent outbreaks have occurred -- will be able to use a portable, field-ready benchtop sequencer hooked up to a smartphone or laptop with an Internet connection, to obtain a complete genetic sequence of a novel pathogen within hours," Chiu said. "Our hope is that these efforts will democratize the surveillance and investigation of infectious diseases."

Chiu said the study may also prove to be significant in light of the fact that most emerging diseases discovered in the last two decades originated in animals.

"Nature is continually throwing us curveballs," Chiu said. "We will likely always be faced with the threat of novel outbreak viruses originating in animals or insects. It will be extremely important to identify and characterize those viruses as quickly as possible -- to get a head start on the development of diagnostic assays for surveillance and drugs, or vaccines for treatment -- before they have a chance to really spread."

Chiu and his colleagues recently published the results of the study in PloS ONE.