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PostPosted: Thu Aug 28, 2014 3:48 pm 

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
28 August 2014 Last updated at 14:00 ET
Genetic clues to spread of Ebola
By Helen Briggs
Health editor, BBC News website
Augustine Goba, laboratory director at Kenema Government Hospital Lassa fever laboratory
Experts at Kenema Government Hospital in Sierra Leone have been monitoring the outbreak

Scientists have tracked the spread of Ebola in West Africa, revealing genetic clues to the course of the outbreak.

Genetic analysis of patient samples suggests the virus spread from Guinea to Sierra Leone at a single funeral.

The virus is mutating and must be contained rapidly, warn African and US experts. But they say there is no evidence the virus is changing its behaviour.

The current outbreak is the largest ever, with more than 3,000 cases.

The number of cases could exceed 20,000 before the outbreak is stemmed, according to the World Health Organization.

"We've uncovered more than 300 genetic clues about what sets this outbreak apart from previous outbreaks," said Stephen Gire from the Broad Institute and Harvard University in the US.

"Although we don't know whether these differences are related to the severity of the current outbreak, by sharing these data with the research community, we hope to speed up our understanding of this epidemic and support global efforts to contain it."

The data, published in Science, suggests the virus made the leap from animals to humans only once in the current outbreak.

“Clearly this virus is evolving, but what's not clear is whether or not the mutations it's accumulating affect the way it behaves.”

Prof Jonathan Ball
Nottingham University

The strain emerged in Central Africa in the past 10 years, probably carried by animals such as fruit bats or primates.

The first human cases appeared in Guinea, then the disease spread to Sierra Leone, reportedly at the funeral of a traditional healer.

There is evidence the virus is mutating, "underscoring the need for rapid containment", the team writes in Science.

"The longer the outbreak happens, the more opportunity the virus has to accumulate mutations," Dr Gire told the BBC.

But he said there was no evidence at present that the virus was changing its behaviour and becoming better adapted to humans.

Commenting on the research, Prof Jonathan Ball, a virus expert at Nottingham University, said: "Clearly this virus is evolving, but what's not clear is whether or not the mutations it's accumulating affect the way it behaves."

The genetic samples came from 78 patients at a hospital in Sierra Leone who were infected in May and June.

These were compared with existing virus samples from Guinea.

Five of the 58 experts named on the paper died from Ebola in Sierra Leone during the study.



PostPosted: Thu Aug 28, 2014 4:25 pm 

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
Ebola virus has mutated during course of outbreak

As the worst Ebola outbreak in history unfolds in West Africa, The Post's Joel Achenbach explains how the deadly virus wreaks havoc on the human body. (Davin Coburn/The Washington Post)

By Brady Dennis August 28 at 2:02 PM 

The Ebola virus sweeping through West Africa has mutated repeatedly during the current outbreak, a fact that could hinder diagnosis and treatment of the devastating disease, according to scientists who have genetically sequenced the virus in scores of victims.

The findings, published Thursday in the journal Science, also offer new insights into the origins of the largest and most deadly Ebola outbreak in history, which has killed more than 1,500 people in four countries and shows few signs of slowing. It also provided another reminder of the deep toll the outbreak has taken on health workers and others in the affected areas, as five of the paper’s more than 50 co-authors died from Ebola before publication.

In a collaboration led by scientists at Harvard University and aided by officials at Sierra Leone’s health ministry, researchers sequenced Ebola virus genomes from 78 patients beginning in the early days of the outbreak this spring. Those 99 samples — some patients were tested more than once — suggested that the outbreak began with a single human infection before spreading rapidly, like a spark that grows into a wildfire.

Ebola’s arrival in Sierra Leone in May started with a funeral, according to Thursday’s findings. A young pregnant woman tested positive for the virus and was treated at Kenema Government Hospital. Health workers who traced her contacts discovered that she and more than a dozen other women recently had attended the burial of a traditional healer who had been treating Ebola patients near the Sierra Leone-Guinea border. All of them had been infected.


“They realized she was not an isolated case,” said Pardis Sabeti, an associate professor at Harvard whose lab sequenced the Ebola genomes and quickly made public the data earlier this summer.

The Ebola outbreak in West Africa eventually could exceed 20,000 cases, more than six times as many as are known now, according to the World Health Organization. (AP)

The genomic sequencing also offers hints as to how the Ebola “Zaire” strain at the heart of the current outbreak — one of five types of Ebola virus known to infect humans — likely ended up in West Africa in the first place. Researchers said the data suggests that the virus spread from an animal host, possibly bats, and that diverged around 2004 from an Ebola strain in central Africa, where previous outbreaks have occurred.

“We don’t actually know where the virus has been since then,” said Sabeti, referring to the time between 2004 and when the virus resurfaced earlier this year. “We’re trying to piece together an historical record.”

Thursday’s study also details hundreds of genetic mutations that make the current Ebola outbreak different from any in the past. Some of those changes have the potential to affect the accuracy of diagnostic tests or the effectiveness of vaccines and treatments under development for the disease.

“We’ve uncovered more than 300 genetic clues about what sets this outbreak apart from previous outbreaks,” Stephen Gire, one of the study’s co-authors and an infectious disease researcher at Harvard, said in an announcement about the findings. “Although we don’t know whether these differences are related to the severity of the current outbreak, by sharing these data with the research community, we hope to speed up our understanding of this epidemic and support global efforts to contain it.”

Sabeti said researchers are expecting to receive additional Ebola samples soon from Nigeria. They plan to sequence those, as well, and release the data as soon as possible.

“The fact that we can do this in real time while the outbreak is still going is breathtaking,” said Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases at the National Institutes of Health, said of the group’s rapid genomic sequencing of the virus, which he said could have taken two years or longer in the past. “We didn’t have this technology years ago. What they did was really extraordinary.”


Fauci said Thursday’s findings also underscore the necessity to get the outbreak under control before the Ebola virus continues to morph.

“We’re left with a situation where if, in fact, this thing smolders on and on, we know mutations will accumulate,” he said. “And that has its own set of problems. We’ve really got to get this thing shut off.”

Sabeti said she that since she and her colleagues published the sequencing data, they have heard from companies working on vaccines and treatments, as well as by researchers developing new diagnostic tests, who want to understand how the mutations could affect those efforts. Only through such collaboration, she said, can scientists tackle the current outbreak with the speed it deserves.

“There’s nothing you should crowdsource more than an epidemic. It has this urgency where we need every person working on it,” Sabeti said. “It took a village to make this paper happen. It will take a planet to help get this virus under control.”

http://www.washingtonpost.com/national/ ... ml?hpid=z2


PostPosted: Thu Aug 28, 2014 9:41 pm 

Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
WHO launches road map for containing Ebola in West Africa
Filed Under: Ebola; VHF
Lisa Schnirring | Staff Writer | CIDRAP News | Aug 28, 2014

WHO's road map to containing West Africa's Ebola epidemic has a goal of stopping transmission in 6 to 9 months.
The World Health Organization (WHO) today unveiled a road map to step up the global response to West Africa's intensifying Ebola virus outbreak, at an estimated price tag of $490 million, and to limit spread to other countries, with a goal of stopping transmission in 6 to 9 months.

In a separate development, scientists today provided a blueprint of the outbreak virus's genome, which tracks its evolution and sheds new light on West Africa's epidemic.

The WHO called the need to scale up the response urgent and said the actual number of cases may be 2 to 4 times higher than the 3,069 currently reported. The agency estimated that the number of people sickened by Ebola virus disease (EVD) could reach 20,000 over the course of the outbreak.

Plan spells out priorities, tasks, troubleshooting
The 27-page WHO plan, a follow-up to an initial strategy released Jul 31 after a health minister's meeting in Accra, reflects an intensifying outbreak, with more than 40% of the cases occurring in just the past 21 days, said the group Alarms have been sounded recently about the heavy toll the outbreak is taking on health workers at the frontlines and difficulties border and flight restrictions are having on getting supplies and personnel into affected countries to battle the outbreak.

A large number of partners had input on the plan, including the affected countries, the African Union, development banks, other United Nations (UN) agencies, Doctors Without Borders (MSF), and countries that are providing direct financial support, the WHO said in a press release.

The top priorities are treatment and management centers, social mobilization, and safe burials, with plans based on site-specific data that will appear in regular situation reports starting this week that will map out hot spots and show how the outbreak is evolving, according to the WHO. The plan outlines potential bottlenecks that will require international coordination, such as the need for personal protective equipment (PPE), disinfectants, and body bags.

The group said it hopes air traffic restrictions to the affected countries will be addressed within 2 weeks, and it said by the end of September the UN will launch a complementary plan that provides a common operational platform for enhancing the response steps and addressing the outbreak's broader consequences, such as problems related to food security, water, sanitation, and healthcare infrastructure.

Today's plan spells out roles and responsibilities for different groups, from the WHO to the private sector, as well as steps for monitoring the plan's implementation, which will be evaluated twice a week.

MSF response
In response to today's WHO release, Brice de la Vinge, director of operations for MSF, said in a statement that he welcomed the plan but cautioned that it should not give a false sense of hope. He questioned who will implement the plan and who has the right training for taking on the variety of tasks that it details.

De le Vigne also said it's not clear how long it will take to train organizations to establish and run more Ebola treatment centers or how long it will take them to become operational. He also wondered who will shoulder the important tasks of health education, contact tracing, and safe burials.

"We have learned an uncomfortable lesson over the past six months: none of the organizations in the most affected countries—the UN, WHO, local governments, [nongovernmental organizations] (including MSF)—currently have the proper set-up to respond at the scale necessary to make a serious impact on the spread of the outbreak," de le Vigne said.

He added that some groups simply have no capacity to do more, "and others may need to be encouraged to demonstrate more willingness to push the boundaries and scale up effective activities at a meaningful scale."

Outbreak escalation concentrated at hot spots
In its latest update on the outbreak, the WHO today put the latest outbreak total at 3,069, with the number of deaths at 1,552. The numbers reflect an increase of 454 EVD infections and 125 deaths since the WHO's last case update on Aug 22. The official numbers are thought to dramatically underestimate the true burden of the disease.

So far the overall case-fatality rate is 52%, ranging from 42% in Sierra Leone to 66% in Guinea, the WHO said.

Though the outbreak continues to escalate, most of the cases are concentrated in a few localities, and while a detailed analysis is still needed, early results show that 62% of all cases reported so far are still concentrated in the outbreak epicenter: the Gueckedou region of Guinea, the Lofa area of Liberia, and the Kenema and Kailahun areas of Sierra Leone.

The WHO added that infections occurring in the capital cities of the three countries are especially worrisome, given population density and the impacts on travel and trade.

Gene study yields outbreak clues
In other developments today, an international research team, with help from Sierra Leone's health ministry, published a detail genetic sequencing study on samples from 78 patients sickened with EVD in the country during the first 24 days of the outbreak, which showed mutations and clues about how the outbreak evolved. Their findings appear in the latest online edition of Science.

They looked at 99 Ebola virus genomes. Some were from the same patient, allowing researchers to watch how the virus can change in a patient over the course of an infection.

Based on sequence variations in the genomes they analyzed, they estimated that the EVD outbreak started from a single introduction into humans, spreading between humans over many months. They also found more than 300 genetic changes that make the outbreak virus distinct from Ebola viruses that have sparked other outbreaks.

Some of the variations they observed were often seen in the parts of the genome that encode proteins, which they said might affect the primers used in diagnostic tests, one reason why genetic surveillance and vigilance are so important.

The team released the full-length sequences to the National Center for Biotechnology Information (NCBI) DNA database before publication, which they said could help with response efforts.

Their sequencing study suggests that the strains fueling the current outbreak likely have a common ancestor dating back to 1976 when the first Ebola outbreak was recorded. West Africa's lineage diverged from the Middle African version within the last decade and spread from Guinea to Sierra Leone by 12 people who had attended the same funeral, according to the report.

In an unusual and sad twist, one of the senior authors of the study, Dr. Humarr Kahn, who was with Sierra Leone's Ministry of Health and Sanitation, died from an EVD infection in late July. Before his death he had been overseeing an Ebola treatment program at Kenema Government Hospital, where he headed a Lassa fever program..

Pardis Sabeti, MD, PhD, another senior author of the study and associated member at the Broad Institute and associate professor at Harvard University, said in a statement from the Broad Institute, "There is an extraordinary battle still ahead, and we have lost many friends and colleagues already like our good friend and colleague Dr. Humarr Khan."

She continued, "By making the data immediately available to the community, we hope to accelerate response efforts." She added that demonstrating transparency and partnership is one way she and her colleagues hope to honor Humarr's legacy. "We are all in this fight together," she said.

See also:

Aug 28 WHO statement

Aug 28 WHO Ebola response blueprint

Aug 28 MSF statement

Aug 28 WHO outbreak update

Aug 28 Science abstract

Aug 28 Broad Institute press release

http://www.cidrap.umn.edu/news-perspect ... est-africa


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