Science: Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

[Treyfish]

Ebola Outbreak Strains Sequenced

Ninety-nine publicly available genomes could help researchers working to develop diagnostics, vaccines, and therapies.
By Tracy Vence | August 28, 2014

• 
  

Augustine Goba of Kenema Government Hospital diagnosed the first case of Ebola in Sierra Leone.STEPHEN GIRE


An international team led by investigators at Harvard University has sequenced 99 Ebola virus genomes isolated from the blood of 78 patients in Sierra Leone—one of four countries at the center of the largest-ever Ebola outbreak. Within these sequences, which were each made public within a matter of days post-assembly, the researchers found evidence of the rapid accumulation of mutations affecting biologically meaningful targets, which could have implications for the development of diagnostics, vaccines, and therapies. The team’s analysis of all 99 genomes was published today (August 28) in Science.

“This analysis will provide the backbone for tracking the virus as it spreads, and to see if future outbreaks outside of these countries are connected both epidemiologically and genetically,” emerging infectious diseases researcher Matthew Frieman from the University of Maryland School of Medicine who was not involved in the work told The Scientist in an e-mail. “The ability to deep sequence virus samples rapidly, inexpensively, and safely has opened up a window in to genomic surveillance that did not exist before.”

snip

“We’ve been really overwhelmed by what’s going on,” said Sabeti. “This is an extraordinary emergency on an unprecedented scale.”

Five healthcare workers who assisted the team on the ground in Sierra Leone died of Ebola. All five were infected with the virus while caring for sick patients or family members, Sabeti said. In their paper, the authors honored their deceased colleagues—five would-be coauthors on the work—who gave their lives to help others.
“These individuals were heroic and battling something extraordinarily dangerous,” said Sabeti. “Without them, this wouldn’t be possible.”
S.K. Gire et al., “Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak,” Science, doi: 10.1126/science.1259657, 2014.http://www.the-scientist.com/?articl...ins-Sequenced/

[Treyfish]

Re: Ebola Outbreak Strains Sequenced

28 August 2014 Last updated at 14:00 ET




Genetic clues to spread of Ebola

By Helen Briggs Health editor, BBC News website

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.
The isolation ward at Kenema Government Hospital in Kenema, Sierra Leone
"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.

“Start Quote

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

snip

Five of the 58 experts named on the paper died from Ebola in Sierra Leone during the study.http://www.bbc.com/news/health-28958495

[Treyfish]

Re: West Africa: Ebola Outbreak Strains Sequenced

...For starters, the data show that the virus is rapidly accumulating new mutations as it spreads through people. "We've found over 250 mutations that are changing in real time as we're watching."
While moving through the human population in West Africa, she says, the virus has been collecting mutations about twice as quickly as did while circulating in animals for the last decade or so.
"The more time you give a virus to mutate and the more human-to-human transmission you see," she says, "the more opportunities you give it to fall upon some [mutation] that could make it more easily transmissible or more pathogenic.".. http://www.npr.org/blogs/goatsandsod...ss-west-africa

[sharon sanders]

Re: West Africa: Ebola Outbreak Strains Sequenced

<cite>
Science DOI: 10.1126/science.1259657 </cite>

• Report

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

1. Stephen K. Gire¹,²,*,
2. Augustine Goba³,*,?,
3. Kristian G. Andersen¹,²,*,?,
4. Rachel S. G. Sealfon²,⁴,*,
5. Daniel J. Park²,*,
6. Lansana Kanneh³,
7. Simbirie Jalloh³,
8. Mambu Momoh³,⁵,
9. Mohamed Fullah³,⁵,?,
10. Gytis Dudas⁶,
11. Shirlee Wohl¹,²,⁷,
12. Lina M. Moses⁸,
13. Nathan L. Yozwiak¹,²,
14. Sarah Winnicki¹,²,
15. Christian B. Matranga²,
16. Christine M. Malboeuf²,
17. James Qu²,
18. Adrianne D. Gladden²,
19. Stephen F. Schaffner¹,²,
20. Xiao Yang²,
21. Pan-Pan Jiang¹,²,
22. Mahan Nekoui¹,²,
23. Andres Colubri¹,
24. Moinya Ruth Coomber³,
25. Mbalu Fonnie³,?,
26. Alex Moigboi³,?,
27. Michael Gbakie³,
28. Fatima K. Kamara³,
29. Veronica Tucker³,
30. Edwin Konuwa³,
31. Sidiki Saffa³,
32. Josephine Sellu³,
33. Abdul Azziz Jalloh³,
34. Alice Kovoma³,?,
35. James Koninga³,
36. Ibrahim Mustapha³,
37. Kandeh Kargbo³,
38. Momoh Foday³,
39. Mohamed Yillah³,
40. Franklyn Kanneh³,
41. Willie Robert³,
42. James L. B. Massally³,
43. Sin?ad B. Chapman²,
44. James Bochicchio²,
45. Cheryl Murphy²,
46. Chad Nusbaum²,
47. Sarah Young²,
48. Bruce W. Birren²,
49. Donald S. Grant³,
50. John S. Scheiffelin⁸,
51. Eric S. Lander²,⁷,⁹,
52. Christian Happi¹⁰,
53. Sahr M. Gevao¹¹,
54. Andreas Gnirke²,?,
55. Andrew Rambaut⁶,¹²,¹³,?,
56. Robert F. Garry⁸,?,
57. S. Humarr Khan³,??,
58. Pardis C. Sabeti¹,²,??

+ Author Affiliations

1. <address>¹Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. </address>
2. <address>²Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. </address>
3. <address>³Kenema Government Hospital, Kenema, Sierra Leone. </address>
4. <address>⁴Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. </address>
5. <address>⁵Eastern Polytechnic College, Kenema, Sierra Leone. </address>
6. <address>⁶Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK. </address>
7. <address>⁷Systems Biology, Harvard Medical School, Boston, MA 02115, USA. </address>
8. <address>⁸Tulane University Medical Center, New Orleans, LA 70112, USA. </address>
9. <address>⁹Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. </address>
10. <address>¹⁰Redeemer?s University, Ogun State, Nigeria. </address>
11. <address>¹¹University of Sierra Leone, Freetown, Sierra Leone. </address>
12. <address>¹²Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. </address>
13. <address>¹³Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK. </address>

+ Author Notes

• ↵? Deceased.

1. ↵?Corresponding author. E-mail: andersen@broadinstitute.org (K.G.A.); augstgoba@yahoo.com (A.G.); psabeti@oeb.harvard.edu (P.C.S.)

1. ↵* These authors contributed equally to this work.
2. ↵? These authors jointly supervised this work.

• Abstract

In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2,000x coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from Middle African lineages ~2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Since many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.

• Received for publication 5 August 2014.
• Accepted for publication 21 August 2014.

http://www.sciencemag.org/content/early/2014/08/27/science.1259657.abstract?sid=1da1a723-ac42-480d-8206-96feb3fcb57c

[Shiloh]

Re: West Africa: Ebola Outbreak Strains Sequenced

Source: http://www.npr.org/blogs/goatsandsod...ss-west-africa


Ebola Is Rapidly Mutating As It Spreads Across West Africa
by Michaeleen Doucleff
August 28, 2014 2:08 PM ET


"In general, these viruses are amazing because they are these tiny things that can do a lot of damage," says the study's lead author, . She's a computational biology at Harvard University...

...For starters, the data show that the virus is rapidly accumulating new mutations as it spreads through people. "We've found over 250 mutations that are changing in real time as we're watching."

While moving through the human population in West Africa, she says, the virus has been collecting mutations about twice as quickly as did while circulating in animals for the last decade or so.

"The more time you give a virus to mutate and the more human-to-human transmission you see," she says, "the more opportunities you give it to fall upon some [mutation] that could make it more easily transmissible or more pathogenic."
A scientist tests a patient's blood for Ebola at the European Mobile Laboratory in Gueckedou, Guinea. The first cases reported in the outbreak occurred in a small village about eight miles outside Gueckedou.

Sabeti says she doesn't know if that's happening yet. But the rapid change in the virus' DNA could weaken the tools we have to detect Ebola or potentially treat patients...

[sharon sanders]

Re: West Africa: Ebola Outbreak Strains Sequenced

GenBank sequences:

http://www.ncbi.nlm.nih.gov/nuccore/?term=ebola+zaire+2014

[JJackson]

Re: West Africa: Ebola Outbreak Strains Sequenced

Do any of you understand EBOV sequences? I have downloaded and aligned some of the genebank sequences but have no understanding of the important sites on the genes, as I would for flu sequences. Where are the primary antigenic sites, binding sites, sites know to relate to virulance or transmission etc?

Its an -ssRNA virus, like flu, but with a single strand. It is slightly larger overall but seems to have more non-coding AAs. As with all negative sense viruses it must provide its own RNP components which I would expect to take up about half the genome - assuming they are much like influenza's.

[Donners]

Re: West Africa: Ebola Outbreak Strains Sequenced

While moving through the human population in West Africa, she says, the virus has been collecting mutations about twice as quickly as did while circulating in animals for the last decade or so.

That line is confusing.

Do they mean it is mutating at twice the normal rate (as "twice as quickly" seems to indicate) or twice the level of mutations that would be expected over a decade (as the latter part of the sentence seems to say).

[JJackson]

Re: West Africa: Ebola Outbreak Strains Sequenced

That line is confusing.

Do they mean it is mutating at twice the normal rate (as "twice as quickly" seems to indicate) or twice the level of mutations that would be expected over a decade (as the latter part of the sentence seems to say).

I think they mean the same. You count the number of single nucleotide changes that occur over a given time.
They found a given rate of change over time while it was replicating in its wild host but over the same period of time in humans they got twice that rate.
An increase in the rate of mutations is found when any organism is adapting to a new environment. Here I suspect the virus is adapting to its new host so the rate of apparent change has doubled. Note it is apparent rate that has changed i.e. the rate that changes have become fixed in the population. The actual rate of SNP substitution probably will not have changed but, absent selection pressure, they are out performed by the wild type. To get actual rate change I would go for an energetic ionizing radiation source - plutonium would do the trick.

[Vibrant62]

Re: West Africa: Ebola Outbreak Strains Sequenced

Powerful article from Washington Post

Ebola virus has mutated during course of outbreak

Ebola virus has mutated during course of outbreak

By Brady Dennis August 28 at 2:02 PM

http://www.washingtonpost.com/national/health-science/ebola-virus-has-mutated-during-course-of-outbreak/2014/08/28/98235aaa-2ecb-11e4-bb9b-997ae96fad33_story.html

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.

snip

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.

snip

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.

snip

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.

snip

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.?

[Donners]

Re: West Africa: Ebola Outbreak Strains Sequenced

This part is fascinating:

The analysis reveals that the outbreak in Sierra Leone was sparked by at least two distinct viruses, introduced from Guinea at about the same time. It is unclear whether the herbalist was infected with both variants, or whether perhaps another funeral attendee was independently infected. One Ebola virus lineage disappears from patient samples taken later in the outbreak, while a third lineage appears. That lineage—tied to a nurse who was traveling to reach a hospital but died along the way—seems to have originated when one of the lineages present at the funeral gained a new mutation. This third lineage was spread, Garry says, via a truck driver who transported the nurse, as well as others who cared for her in the town where she died.

[Gemineye]

Genomic sequencing reveals more than 300 mutations in 2014 Ebola virus

From Healio Infectious News
Gire SK. Science. 2014;doi:10.1126/science.1259657.

August 28, 2014

...With collaboration with the Sierra Leone Ministry of Health and Sanitation, Pardis Sabeti, MD, DPhil, of the Broad Institute and Harvard University, and colleagues sequenced Ebola virus genomes collected from 78 patients with the virus in Sierra Leone during the first 24 days of the outbreak. Along with the mutations, which make the 2014 Ebola virus distinct from the viral genomes tied to previous Ebola outbreaks, the researchers found sequence variations indicating that the outbreak started from a single introduction into humans...

http://www.healio.com/infectious-disease/zoonotic-infections/news/online/%7Bca3aa4e3-2af5-4813-8e02-c0b552f404a0%7D/genomic-sequencing-reveals-more-than-300-mutations-in-2014-ebola-virus

[gsgs]

Re: Science: Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

http://www.virology.ws/2014/09/18/wh...t-ebola-virus/

http://www.twiv.tv/2014/09/21/twiv-303/

here http://www.sciencemag.org/content/345/6202/1369.full they gibe 8e-4 mutations per site per year,
which would be roughly 1/4 of influenza-A, 1/2 of influenza-B.
they don't mention the 1997 paper which wikipedia refers to when they say
ebola mutates 100 times slower than influenza :

http://mbe.oxfordjournals.org/content/14/8/800

only the glycoprotein, the rest mutates faster ?
the full 1976 virus is at genbank, it has 561 differences to the 2014 strain,
it seems to be a (almost) direct ancester, thus giving a rate of
561/18000/38=8e-4 mutations per site per year

5 types of ebola, the other 4 types are very different, e.g. Reston-Ebola
has 6184 differences (--> >300years)

-----------------------------

http://www.ncbi.nlm.nih.gov/nuccore/?term=ebola

Zaire Ebola virus virion spike glycoprotein and small secreted non-structural glycoprotein
sGP (GP) gene, complete cds
2,408 bp linear RNA

http://www.ncbi.nlm.nih.gov/nuccore/U77384.1

positions 5898-8344 out of 18959 in my (1976,1996,2014) alignment
83 mutations 1976-2014 in that area --> rate = 83/2447/38 = 8.9e-4 per site per year
-------------------------------

ahh, the 1997 paper considers _nonsynonymous mutations_ !
> Molecular evolutionary analyses for Ebola and Marburg viruses were conducted with the
> aim of elucidating evolutionary features of these viruses. In particular, the rate of
> nonsynonymous substitutions for the glycoprotein gene of Ebola virus was estimated
> to be, on the average, 3.6 X 1O-5 per site per year.
> Marburg virus was also suggested to be evolving at a similar rate. Those rates were
> a hundred times slower than those of retroviruses and human influenza A virus,

so it seems they compared nonsynonymous ebola mutations with synonymous influenza
to arrive at their "hundred times slower" , which would be really silly.
And wikipedia repeats it.

http://en.wikipedia.org/wiki/Ebolavirus

incredible ... one of the co-authors himself examined the influenza mutation rate in 1994
and that paper was referred to :

GOJOBORI, T., Y. YAMAGUCHI, K. IKEO, and M. MIZOKAMI.
1994. Evolution of pathogenic viruses with special refer-
ence to the rates of synonymous and nonsynonymous sub-
stitutions. Jpn. J. Genet. 69:48 l-488.

https://www.jstage.jst.go.jp/article...5_481/_article

they give 13.1e-3 for synonymous flu-A-HA and 3.59e-3 for nonsynonymous
(only at antigenic sites ?)

referring to Gojobori et.al., 1990 , molecular clock ... :

---------------------------------------------------
Collecting the reports on human H3 hemagglutinin gene
sequences, K. Oguchi and T. Gojobori (personal communi-
cation) estimated the rates of synonymous and nonsynony-
mous substitutions by the method of Nei and Gojobori (12).
The rate (13.1 x 10-3 per site per year) of synonymous
substitutions was much higher than that (3.59x 10-3 per site
per year) ofnonsynonymous substitutions (Fig. 1).
------------------------------------------------------
12. Nei, M. & Gojobori, T. (1986) Mol. Biol. Evol. 3, 418-426.
so, now we are at 1986 as the base for the wiki-quote.
Much happened since then wrt. sequencing.

the word "influenza" was not found with OCR in that 1986 article

so they didn't compare nonsynonymous ebola with synonymous influenza
but it remains unclear how they arrived at their erraneous influenza
mutation rates in the first place in 1986 and maintained that until
at least 1994. [and wikipedia still has it in 2014 !]


however, checking mutations in HA of nowadays available
H3N2 , I get ~4e-3 mutations per nucleotide-position per year in HA,
upto 5e-3 after hostswitch or important reassortments and
about 1/3 of these are nonsynonymous.
4e-3 in HA, 3e-3 in other segments. Nothing whatsoever justifies
that "100 times slower". Maybe 5 times slower when compared with
flu-A HAs in humans.

[gsgs]

Re: West Africa: Ebola Outbreak Strains Sequenced

GenBank sequences:

http://www.ncbi.nlm.nih.gov/nuccore/...ola+zaire+2014

I'm not sure how to get all the sequences.
You may have to search also for "ebolavirus" (one word)

I have got 296 full genomes of the ebola (Zaire) now. (fasta)
And the headers are not so nice as with flu, dates and locations



when I have several of the 5 ebolatypes (Zaire,Bundibugya,Reston,Sudan,Tai_Forest)
mixed in one file, then I can't align them with mafft or kalign

[gsgs]

Re: West Africa: Ebola Outbreak Strains Sequenced

Do any of you understand EBOV sequences? I have downloaded and aligned some of the genebank sequences but have no understanding of the important sites on the genes, as I would for flu sequences. Where are the primary antigenic sites, binding sites, sites know to relate to virulance or transmission etc?

Its an -ssRNA virus, like flu, but with a single strand. It is slightly larger overall but seems to have more non-coding AAs. As with all negative sense viruses it must provide its own RNP components which I would expect to take up about half the genome - assuming they are much like influenza's.

7 proteins, genbank also lists them, but I don't know yet what they do,
where antigenic sites are etc.

http://en.wikipedia.org/wiki/Ebolavirus

gb