Ebola Recombinant in Uganda?
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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 (http://www.recombinomics.com/News/11150702/Ebola_Recombination.html) was described (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=17942693&dopt=AbstractPlus) 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, (http://www.promedmail.org/pls/promed/f?p=2400:1202:15050356339388132085::NO::F2400_P120 2_CHECK_DISPLAY,F2400_P1202_PUB_MAIL_ID:X,28016) 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 (http://www.recombinomics.com/phylo/Canadian_Swine_PB2.html) of genes, short clusters, and single nucleotide polymorphisms (http://precedings.nature.com/documents/459/version/3).
Moreover, Zaire ebolavirus (see list here (http://www.flutrackers.com/forum/showpost.php?p=111945&postcount=14)) and influenza H5 envelope genes (see list here (http://www.flutrackers.com/forum/showpost.php?p=111877&postcount=8)) share a 18 BP region of identity (http://www.wipo.int/pctdb/en/wo.jsp?wo=2006033691&IA=WO2006033691&DISPLAY=DESC), 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 (http://flu.lanl.gov/search/view_record.html?accession=CY015081&database=fluA), although most of the H5 identities are in low path H5, which is transported and transmitted waterfowl, including waterfowl in Africa (http://flu.lanl.gov/search/view_record.html?accession=CY014984&database=fluA).
The current Ebola outbreak is near the Rift Valley and Lake Victoria, regions with significant biodiversity and potential co-infections and recombination.
The evelope sequence of the new Ebola species would be of interest.
Media Links (http://www.flutrackers.com/forum/showthread.php?t=42832)
Recombinomics Presentations (http://www.recombinomics.com/presentations.html)
Recombinomics Publications (http://www.recombinomics.com/publications.html)
Recombinomics Paper at Nature Precedings (http://precedings.nature.com/tags/Recombination)
http://www.recombinomics.com/News/12020701/Ebola_Recombination_Uganda.html
Recombinomics Commentary
December 4, 2007
Uganda's main referral hospital, Mulago has received its first Ebola patient since the deadly virus broke out in the country's southwestern district of Bundibugyo.
Dr Yonah Kule, an employee of the International Air Ambulance (IAA) who contracted the highly communicable haemorrhagic fever while treating patients at Bundibugyo hospital last week, was admitted to the top most government medical centre in Kampala at the weekend.
"Yes, he (Kule) is in our isolation unit and he is fair now," Dr Edward Ddumba, the director of Mulago hospital told Daily Monitor yesterday.
A blog by two doctors on site in Bundibugyo indicated Dr Kule died tonight (http://paradoxuganda.blogspot.com/2007/12/dr-jonah-kulekilled-by-ebola.html). The blog indicated he had a headache and fever (http://paradoxuganda.blogspot.com/2007/11/update-friday-mid-day.html) when he checked in Friday night, and was ambulatory today (http://paradoxuganda.blogspot.com/2007/12/ebola-in-bundibugyo-tues-day-6.html) after IV treatment.
The death of this health care workers hightens transmission concerns (http://www.recombinomics.com/News/12040703/Ebola_Uganda_Spread_Increase.html) for the Ebola in Uganda. The number of health care workers hospitalized (http://www.recombinomics.com/News/12020702/Ebola_Uganda_HCW.html) is high, and many did not return to their hospitalized patients.
Personel from WHO and Doctors Without Borders have arrived, but the situation in Uganda continues to deteriorate (http://www.recombinomics.com/News/12020703/Ebola_Uganda_Spread.html). Some hospitals have refused patients, while other agencies have limited movement.
The Ebola appears to be a new species and is likely a recombinant (http://www.recombinomics.com/News/12020701/Ebola_Recombination_Uganda.html).
Sequence data on the new isoaltes would be useful.
Media Links (http://www.flutrackers.com/forum/showthread.php?t=42832)
Recombinomics Presentations (http://www.recombinomics.com/presentations.html)
Recombinomics Publications (http://www.recombinomics.com/publications.html)
Recombinomics Paper at Nature Precedings (http://precedings.nature.com/tags/Recombination)
http://www.recombinomics.com/News/12040704/Ebola_Kampala.html
Recombinomics Commentary
December 4, 2007
The conventional wisdom was that Ebola is containable because it kills its victims faster than it can find new ones. However, conditions on the ground are now proving otherwise. While 61 cases have been identified, Zaramba says the health ministry is having difficulty detecting more cases or identifying people with whom patients had contact. And as of the weekend, the disease had spread to three new zones in Bundibugyo district. Local officials speaking on the condition of anonymity say that the death toll is almost twice that reported.
The above comments describe the worsening situation in Uganda. Recent media reports suggest the outbreak has spread further (http://www.recombinomics.com/News/12020703/Ebola_Uganda_Spread.html) this week, and the infections of health care workers (http://www.recombinomics.com/News/12020702/Ebola_Uganda_HCW.html)raise transmission concerns. The current strain was difficult to identify, and is likely a recombinant (http://www.recombinomics.com/News/12020701/Ebola_Recombination_Uganda.html). Recombination has been linked to the emergence of new Ebola strains, and some of these strains share a region of identity (http://www.wipo.int/pctdb/en/wo.jsp?wo=2006033691&IA=WO2006033691&DISPLAY=DESC) with H5 (http://www.flutrackers.com/forum/showpost.php?p=111877&postcount=8) influenza. Both influenza and filoviruses are negative sense RNA viruses and influenza is transported and transmitted by migratory birds that fly into Africa.
The new species may also have different transmission modes. The symptoms of the cases are closer to those associated with H5N1 than those associated with Ebola. The CDC has partial Ebola sequence data, but the relationship between those sequences and prior Ebola sequences remain unclear.
Release of the partial sequences would be useful. The Ebola / H5 identity is in the envelope gene, and the region has differences in strains of Ebola as well as high and low path H5.
Media Links (http://www.flutrackers.com/forum/showthread.php?t=42832)
Recombinomics Presentations (http://www.recombinomics.com/presentations.html)
Recombinomics Publications (http://www.recombinomics.com/publications.html)
Recombinomics Paper at Nature Precedings (http://precedings.nature.com/tags/Recombination)
http://www.recombinomics.com/News/12040703/Ebola_Uganda_Spread_Increase.html
Recombinomics Commentary
December 2, 2007
[/URL]The number of Ugandans infected by a new strain of the deadly Ebola virus has risen to 58, raising fears the death toll of 18 will also increase from the outbreak in a remote area near Democratic Republic of Congo.
The half dozen extra infections in recent days include some medical staff who were treating victims of the haemorrhagic fever which has swept the western Bundibugyo region since August.
"Four of our medical personnel, including a doctor and three nurses, have been isolated in Bundibugyo Hospital after catching the virus," said Dr. Sam Okware, head of Uganda's national hemorrhagic fever task force.
"We now have a team of experts on the ground to try and contain further spreading of the virus."
Genetic analysis of samples taken from some of the victims shows it is a previously unknown type of Ebola, making it the fifth strain, U.S. and Ugandan health officials say.
The above comments describe a worsening situation in Uganda. A new strain of Ebola, which could be a recombinant (http://www.recombinomics.com/phylo/Canadian_Swine_PB2.html), has infected at least 58 patients, including health care workers. The case fatality rate remains relatively low (http://www.recombinomics.com/News/04020502/Marburg_Ebola_CFR.html) for Ebola, which can kill (http://www.recombinomics.com/News/04020503/Marburg_Recombinant.html) more than 80% of infected patients.
The new strain may be less lethal, but more infectious.
The spread of the virus to health care workers, and reports of health care workers abandoning patients, is a cause for concern.
Media Links (http://www.flutrackers.com/forum/showthread.php?t=42832)
Recombinomics Presentations (http://www.recombinomics.com/presentations.html)
Recombinomics Publications (http://www.recombinomics.com/publications.html)
Recombinomics Paper at Nature Precedings (http://precedings.nature.com/tags/Recombination)
[URL]http://www.recombinomics.com/News/12020702/Ebola_Uganda_HCW.html
Recombinomics Commentary
December 5, 2007
A medical doctor and four health workers, who treated the first Ebola patients in Bundibugyo, have died of the disease. Dr. Jonah Kule, the medical superintendent of Kikyo Health Centre, succumbed on Tuesday night. He had been quarantined at Mulago Hospital.
Senior clinical officer Joshua Kule, senior nursing officer Rose Bulimpikya, matron Peluce Tabiita and another nurse not yet identified died yesterday in Bundibugyo Hospital, according to senior clinical officer James Agaba.
The above comments indicate two additional health care workers (http://www.recombinomics.com/News/12050701/Ebola_HCW_Fatalities.html) have died, raising the total to five fatalities in teh past 24 hours. These numbers suggest the number of infected patients may be markedly higher than reported to date.
The hospitalization and deaths of health care workers (http://www.recombinomics.com/News/12020702/Ebola_Uganda_HCW.html) has reduced the number of hospitalized patients significantly, and many with symptoms will avoid hospitals. Although some PPE’s are just arriving, most of the health care workers would have gloves, and would be aware of potential transmission of the infectious agent. Therefore, their fatal infections signal efficient transmission.
Media reports describe multiple suspect fatalities at more distant locations, and confirmation of cases will be reduced because the Ebola virus is a new species (http://www.recombinomics.com/News/12020701/Ebola_Recombination_Uganda.html) and PCR primers are still under development. Positives will be dependent on antibody tests, which may have a high specificity, but a low sensitivity. Similarly, infected patients that avoid hospitals will also reduce the number of confirmed cases.
More information on suspect Ebola fatalities at distant locations would be useful.
Media Links (http://www.flutrackers.com/forum/showthread.php?t=42832)
Recombinomics Presentations (http://www.recombinomics.com/presentations.html)
Recombinomics Publications (http://www.recombinomics.com/publications.html)
Recombinomics Paper at Nature Precedings (http://precedings.nature.com/tags/Recombination)
http://www.recombinomics.com/News/12050703/Ebola_HCW_5.html
Recombinomics Commentary
December 4, 2007
"The sad news is that our doctor who was admitted in Mulago died last night and a senior clinic officer who had been in critical condition died this morning," said Samuel Kazinga, district commissioner for Bundibugyo, the epicentre of the new outbreak.
Joshua Kule, the senior clinical officer, and the head nurse of the hospital (Peluce) also died this morning, so with Jonah that brings 3 of 6 health care workers admitted dying within 12 hours of each other.
The above comments describe the deaths of three health care workers (http://www.recombinomics.com/News/12020702/Ebola_Uganda_HCW.html) in the past 12 hours. One had been admitted to the hospital in Kampala (http://www.recombinomics.com/News/12040704/Ebola_Kampala.html), while two were admitted locally. The high fatality rate for the health care workers as well as clusters of cases, raise additional transmission concerns.
One group was linked to attendance at a funeral, raising concerns of transmission by casual contact. The CDC is setting up a local lab for testing, so the number of confirmed cases should rise shortly, which will help determine the spread (http://www.recombinomics.com/News/12020703/Ebola_Uganda_Spread.html) of the infections..
The sequence of the virus from patients is said to represent a new species, which is almost certainly a recombinant (http://www.recombinomics.com/News/12020701/Ebola_Recombination_Uganda.html).
Details on the sequence would be useful.
Media Links (http://www.flutrackers.com/forum/showthread.php?t=42832)
Recombinomics Presentations (http://www.recombinomics.com/presentations.html)
Recombinomics Publications (http://www.recombinomics.com/publications.html)
Recombinomics Paper at Nature Precedings (http://precedings.nature.com/tags/Recombination)
http://www.recombinomics.com/News/12050701/Ebola_HCW_Fatalities.html
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