Ebola Recombinant in Uganda?
Recombinomics Commentary
December 2, 2007
Samples arrived at CDC's Biosafety Level 4 labs in Atlanta on Monday [26 Nov 20007]. By Tuesday [27 Nov 2007], Ksiazek said, it was apparent this was not a typical Ebola virus. Dr. Stuart Nichol, a CDC special pathogens team leader, said some molecular tests for Ebola were coming back negative, when another type of test came back positive. The CDC lab was then able to extract a small fragment of the virus' genome. "It looks, based on this, like it's a new species of Ebola," Nichol said Friday evening. Previously, there were only 4 known types of Ebola. The Sudan and Zaire species were discovered in 1976. A strain called Reston was identified in 1989 among monkeys imported to a lab in Virginia. And in 1994, the Ivory Coast strain was identified. Depending on the strain, the death rate varies. Ebola-Zaire kills about 80 percent of its victims, while the Sudan strain kills about 50 percent, Ksiazek said. Ebola Reston is not lethal for humans.
The above comments describe a new species of Ebola that is spreading along the west coast of Uganda, just east of the Democratic Republic of the Congo. The description of the new species sounds like a recombinant. Recently homologous recombination was described for Ebolavirus. These recombinations may have led to prior human outbreaks involving the Zaire species. Ebola is negative sense RNA virus. Prior to the report of Ebolavirus recombination, homologous recombination in negative sense RNA viruses was discounted, although recombination in positive sense RNA viruses including coronaviruses was widely accepted. However, since both negative and positive sense virus use the same base pairing rules to replicate, using one strand as a template for the other strand, the rationale for the distinction remains unclear.
Similarly, homologous recombination in influenza, another negative sense RNA virus, has been discounted, although clear examples of recombination are present in the influenza sequence database. Examples include long stretches of genes, short clusters, and single nucleotide polymorphisms.
Moreover, Zaire ebolavirus (see list here) and influenza H5 envelope genes (see list here) share a 18 BP region of identity, raising the possibility of recombination between the two negative sense RNA viruses. The identity in H5 traces back to the first H5N1 sequences, from a chicken in Scotland in 1959, although most of the H5 identities are in low path H5, which is transported and transmitted by waterfowl, including waterfowl in Africa.
The current Ebola outbreak is near the Rift Valley and Lake Victoria, regions with significant biodiversity and potential co-infections and recombination.
The envelope sequence of the new Ebola species would be of interest.
Media Links
Recombinomics Presentations
Recombinomics Publications
Recombinomics Paper at Nature Precedings