Recombinomics Commentary
December 2, 2007
Samples arrived at CDC's Biosafety
Level 4 labs in Atlanta on Monday [26 Nov 2007]. 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 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.
http://www.recombinomics.com/News/12020701/Ebola_Recombination_Uganda.html