Scientists will use RNA-Seq to draw a genetic map of how the Ebola outbreak changed as it passed from person to person

rna-seq(Reuters – By Julie Steenhuysen) – Etienne Simon-Loriere of the Pasteur Institut in Paris has his fingers crossed. He is heading to West Africa on Sunday to inspect blood samples gathered from Ebola patients in Guinea in hopes of tracing the path of the virus in the country where the current outbreak began.

Such samples are scarce and precious. So far, only a few scientists have them, and many more say they need them in order to do critical research on the virus.

If the samples are in good shape, Simon-Loriere will extract viral RNA and sequence the virus to draw a genetic map of how the Ebola outbreak changed as it passed from person to person.

“Having this complete picture will be extremely important to designing the best vaccines and the best treatments to make sure they are effective on all of the virus that is circulating now,” said Simon-Loriere.

Even slight changes in the right area of the virus could render new rapid diagnostic kits being built on specific genetic sequences obsolete. “We need to be sure the targets that we are picking are correct,” Simon-Loriere said.

So far, genetic sequencing has been done on only three samples taken from two locations in Guinea, and these were gathered at the beginning of the outbreak.

Simon-Loriere wants to sequence lots of samples from all over Guinea to understand transmission patterns of the virus before it crossed over to Sierra Leone, filling in the gaps about how the virus changed from the early days of the outbreak.

The blood samples were gathered by scientists at Institut Pasteur Dakar in Senegal. Simon-Loriere will extract viral RNA in Dakar and ship the vials back to Paris, where he and colleagues will use a technique called deep sequencing to detect slight changes within the genetic code of the virus.

The team is collaborating with researchers at the Broad Institute of Harvard University and the Massachusetts Institute of Technology, which conducted similar work tracing Ebola as it first crossed into Sierra Leone.

That study, published in August, found that Ebola was mutating twice as fast in humans as in fruit bats that carried the virus.

Simon-Loriere is hopeful that the Guinean samples were preserved well enough and frozen quickly enough after being collected from patients to be suitable for use.

Eddie Holmes, an evolutionary biologist at the University of Sydney who is not involved in the research, said key questions will be understanding whether the virus in Guinea differs from the one in Sierra Leone and whether there is anything “biologically different” that could explain why this outbreak is so much larger than any of the others.

Jim Kent of the University of California, Santa Cruz, which in late September started an Ebola genome browser for use by scientists studying the virus, said he wishes there were a “continuous stream” of genetic sequences coming in to help keep track of the virus.

“I just wish we could do something to get more samples,” he said.

(Reporting by Julie Steenhuysen; Editing by Leslie Adler)

Source – Reuters – US Edition

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