VDU's blog: Sierra Leone

Showing posts with label Sierra Leone. Show all posts

Saturday, 7 November 2015

Congratulations to Sierra Leone for defeating its Ebola virus disease epidemic!

Edited by Katherine Arden, PhD.

"On Behalf of the Sierra Leone National Ebola Response Centre (NERC) and the World Health Organisation (WHO)

Note to Correspondents

Subject: Ebola transmission in Sierra Leone over.

Nation enters 90-day enhanced surveillance period
On 7 November 2015, if no new case of Ebola virus disease is recorded, Sierra Leone will have met the criteria set by the World Health Organization (WHO) for declaring the end of Ebola transmission. If Sierra Leone meets that milestone, on that day, the WHO will declare the end of Ebola transmission in Sierra Leone, at an event organised by the Government of Sierra Leone through the National Ebola Response Centre (NERC)."

This is the message that greets you on the NERC website today. Ebola virus transmission has finally been kicked out of Sierra Leone after a 42 period with no cases confirmed. Getting to zero is now, Got to zero!

CONGRATULATIONS!!!

It has been a hard fought battle with many, many losses. Battling the Ebola virus has also provided many teaching moments for the nation...as it has been for Liberia and still is for Guinea...and the world.

Within the next 90 day enhanced surveillance period and in the months and months to come, we may see a case or cases pop up and clusters may result. But Sierra Leone knows what Ebola virus disease is and how to deal with it. It won't be caught out the same way again.

Many more teaching moments undoubtedly remain. But each will surely be faced with the same strength and passion that drove the nation to defeat an epidemic the likes of which the world had never before seen.

The people of Sierra Leone made many new friends during this tragedy and hopefully they will always be but a call or a text or an email away. Far too many of those incredibly brave local and international health workers, burial teams, laboratory specialists and ambulance drivers paid for their efforts with their lives. So to them, to those who survived, to all the contact tracers, the social anthropologists, the psychosocial experts, the survivor clinics, the organizers, the facilitators, the doers and the thinkers from within and outside Sierra Leone, we give our heartfelt thanks for your work and your many sacrifices. You together with the people of Sierra Leone all contained and defeated Ebola virus disease and you did it in the face of often overwhelming odds.

Enjoy the parties. Remember the lessons. Be vigilant.

References...

http://nerc.sl/

Saturday, 10 October 2015

Is the next Ebola virus revelation...reactivating infection?

Update #1 11OCT2015 AEST
Update #2 11OCT2015 AEST
Update #3 22OCT2015 AEST

Great. Are members of the Zaire ebolavirus (EBOV) species the most educational viruses of modern times or what? I mean, we've "known" about EBOV since 1976, but the West Africa Ebola virus disease (EVD) epidemic is the epidemic that keeps on giving - we seem to learn a brand new thing every few months.

And the latest is a doozy although we don't know many of the details yet.

So what do we know about this new finding of a seeming return of infection in a former EVD case? Or is this new disease because of damage from the old infection?

A 39 year old nurse, PC, was originally infected with EBOV while working for 3 weeks in the Save the Children’s Kerry Town Treatment Centre in Sierra Leone. She did not show signs of illness until after arriving home in Scotland [1,11]
PC was believed to have become infected while treating EVD patients in some way related to her use of a visor as part of her personal protective equipment, rather than goggles, [10]
PC entered a Gartnavel Hospital isolation unit on 29-DEC-2014, and was subsequently flown to the Royal Free Hospital (RFH) in Hampstead, North London on 30-DEC-2015. She stayed there for around a month [2,4]
During her time in the RFH, PC was treated with convalescent blood plasma and an experimental antiviral drug
PC was declared free of EBOV and discharged from the RFH on 24-JAN-2015 but continued to report thyroid problems afterwards as she described just a week ago [3,4,12]
On Monday evening, PC went to a GP service at Victoria Hospital with a temperature, headache, sore neck and sensitivity to light (photophobia). [15] She was sent home.
On Wednesday 07-OCT-2015, PC was admitted to the Queen Elizabeth University Hospital (QEUH) in Glasgow, Scotland. Tests revealed that EBOV (presumably) RNA was present.[13]
On Friday 09-OCT-2015, PC was admitted to the RFH, 8 months and 15 days after being declared free of Ebola virus and discharged.[16]
She is described as being in serious condition. However, it is unclear what her signs and symptoms were at presentation, or have become since.[4]
On Wednesday 14-Oct-2015, PC's conditions was described as having deteriorated and was now classified as in critical.[16,19,20]
On Monday 19-Oct-2015, PC's condition was described as improved.[16,21]
On Thursday 22-Oct-2015, at a press conference made possible because PC had given permission for her case to be publicly discussed, PC was described as having significantly improved. She had meningitis and has received a "highly experimental" drug, GS-5734, under development by Gilead Sciences, and proven highly effective in the lab and in monkeys post-infection.[22,23,25,26]

Descriptions note that PC is "not thought to be contagious". Presumably this means she is not symptomatic with EVD and if so the testing that must have identified EBOV somewhere in her system must have does so from a part of her system that is not readily in contact with the environment. In one report, laboratory staff in Glasgow who handled PC's samples, were not wearing the most basic of personal protective equipment (PPE) for lab staff-gloves.[24] All of that side, she is once again isolated at one of the world's best infectious diseases hospitals.[4]

There are also recent reports of PC having had thyroid problems after recovering-perhaps virus has been replicating in this tissue. PC's "condition is a complication of a previous infection with the Ebola virus".[4] Which leaves a lot of room for idle speculation but could just be that she is ill because of what the fallout from what EBOV previously did to a tissue/organ rather than because of EVD itself. Perhaps follicles in the scalp have been a site for virus replication, relating to her earlier hair loss. Another site may be the central nervous system...

@amymaxmen I've heard she has a meningitis like syndrome, probably CSF is where #Ebola virus is replicating
— Ahmed Tejan-Sie MD (@AhmedTejanSie) October 9, 2015

@MackayIM @amymaxmen CSF and blood (later) positive
— Ahmed Tejan-Sie MD (@AhmedTejanSie) October 15, 2015

All speculation. Again, nothing is known about PC's signs and symptoms of disease when she presented herself to the QEUH, what tissue(s) are involved in her current illness, which samples tested positive first, whether viral culture has been conducted or just RT-PCR and where the virus may have been replicating all this time. While we understand that some tissues are sites for EBOV persistence, there is clearly much more to learn about the frequency and full range of tissues that harbour infectious EBOV once it becomes undetectable in the blood.

Apart from how shocking and scary this must be for PC herself, another issue is how this will impact on the fragile processes of accepting of EVD survivors back into their West African communities. Extending the length of time that some male survivors are known to harbour EBOV already put pressure on their acceptance by some, but the potential for virus to return to the blood or other tissues - if indeed that is what has happened here - even after that time frame, will require a lot of communication to explain. It will be vitally important for this process that the facts underpinning what's happened here are deduced soon and communicated in ways that can be understood in West Africa. This is a chance for the World Health Organization to show off their shiny new intent to do better at communicating and reacting.

This is not the first time EBOV has been found to persist in a convalescent former EVD case.[5,6,7,8,9] But this may be the first documented time that the virus has re-emerged from an immune privileged site and returned to the blood, possibly causing EVD symptoms in the same former EVD case (recent media article mentions that this is the 2nd such case[15]).

The comments about PC's photophobia are similar to those from Dr Ian Crozier - who was found to have persistent infectious virus in the aqueous humor collected by needle from the anterior chamber of his eye causing uveitis-14 weeks after his EVD diagnosis.[6,17] His blood did not become EBOV positive again.[17] The virus found in his blood earlier and his ocular fluid 14 weeks later were nearly identical-just five mutations differentiating the genomes. Could the eye be a site of PC's hidden virus also? Perhaps the central nervous system the reservoir given the meningitis-like symptoms PC's family mentioned early and which was confirmed 22OCT.[15,18] Again, lots of speculation.

Shingles has been thrown up as an example of a similar disease that results from a virus recurring but it's not the same thing at all. Although, we don't know that with absolute certainty. The viruses are very different - that we know for certain. Varicella zoster virus (VZV) is the herpesvirus that first causes chickenpox (doctors call it 'varicella'), usually in childhood. The virus then goes dormant in your nerves. In this state, the virus is not producing full virus particles and so VZV no longer excites our (cellular) immune system, which can eventually "forget" it. Decades later (again, usually) after lying dormant and because of triggers and a lack of suitable immune memory VZV may arise from dormancy (reactivate) to produce lots of whole virus and cause shingles (doctors call this 'herpes zoster' - still the VZV though).[14] As far as we know, EBOV does not go dormant or become latent, but remains active at some sites, like the testes and the eyeball,[5,7] where our immune system is programmed not to venture in full force, so as to protect those sites from unwanted inflammation (in a nutshell). There may well be other sites.

Hopefully, more official key information will be made clear soon (as opposed to in the scientific literature weeks or months from now) as it will be vitally important for the continued management and support of EVD survivors in West Africa. It is also important knowledge for communicating real risks, and informing and toning down perceived but unrealistic ones. What falls into which category is however becoming harder and harder to discern.

I'll update this blog post as more information comes to hand.

References...

Updates...

Added dates for PC being initially released from the RFH and that she was tested at the QEUH; described "dormant" and qualified that chickenpox and shingles can occur at any times but usually as a child and adult respectively; provided references about chickenpox
Updated information from Ref 15 including dates, new calculation of time between RFH 1st discharge and admission and some symptom information from family
Added CSF+Blood Tweet; some tiny bits of new info from the RFH press conference; links to GS-5734 info

Sunday, 16 August 2015

Snapdate: Ebola virus diseaseClick on image to enlarge.

This is one of the data visualizations from my Ebola virus disease (EVD) graphs and tallies page.[1]

A crude extrapolation from current publicly available Ebola virus disease (EVD) confirmed case numbers. To see how I made this please visit here.[2]
The P-value for this linear trend model is <0.0001.
The standard error = 6.13; R-squared = 0.20.
Click on graph to enlarge.

The first time I posted it I wondered if the end was in sight. That was 6th of May. Over three months later I'm wondering that again - but this time things are a bit different. There has been a steady decline in new cases, also in cases that cannot be tracked back to a known source and in cases found only after they have died of EVD. There have also been the first very promising results from one of the vaccine candidates in Guinea [4] - which has always been a difficult locale for the control of EVD case activity.

So it does look much more likely that the end to EVD in West Africa, or at least an end, is nigh.

By "an end" I mean that we may be close to seeing the cessation of new cases popping up in transmission chains each and every week. We may soon be seeing zero new cases for long periods of time. Those blissful stretches however, may be punctuated by a case arising from parts unknown. They may be tracked to a sexual transmission event, or their origin may never be fully understood. We saw this scenario in Liberia.[3] Virus characterisation indicated that the Ebola virus variant from the young Liberian man was most closely resembled other viruses that had been circulating in Liberia weeks before; the exact source of his infection though, remains unknown.

So we're not at all free and clear of this virus yet - but we are getting very close to shifting into another phase. It's still a long haul with many weeks of anxious waiting and heightened vigilance as well as the need to retain the capacity to cope with a new case or cases. But that said, we do seem to have taken one more step back from the precipice we once stared into as we imagined an Africa fending off a rolling EVD epidemic - and a world at risk as well - however unlikely that should have been.

References..

Friday, 8 May 2015

iBola and the speed of research reporting during outbreaks and epidemics...

My thanks to Dr Judy Stone who pointed out the New York Times Health article.[1]

Ebola virus takes advantage of privileged sites

The New England Journal of Medicine (NEJM) has been one of the greatest publishers of high quality clinical information throughout the Ebola virus disease (EVD) epidemic in 2014.

NEJM has just published an article on a 43 year old male physician who was evacuated from Sierra Leone after an EVD diagnosis, for treatment at the Emory University Hospital Serious Communicable Disease Unit (SCDU). But 14 weeks after his EVD diagnosis, he developed eyesight and hearing problems and was found to have infectious Ebola virus, and viral RNA...In. His. Eyeball.[2] No viral RNA was found on his conjunctiva or his tears. He hearing loss was on the same side as his declining vision.[1]

An approximate timeline of the Emory patient.
Coloured balloons with vertical lines indicate specific dates.
The absence of a vertical line indicates a general time frame only.
Click on figure to enlarge.

Emory has treated at least four EVD cases evacuated to the United States [17] and has done so with exceptional care and enviable professionalism.[19] They produced a protocols website that became a beacon to the world's public health efforts to prepare for an imported case of EVD.[18]

This latest finding may go a long way towards explaining some of the issues suffered by survivors of EVD - headaches, eyesight and hearing issues, muscle and joint pain, tingling or other sensations and extreme weakness. Some of these symptoms have affected 50% of survivors by some counts.[4]

Eyesight problems may not be a long term effect from damage during the earlier infection, but the result of a persistent infection - active virus replication at body sites like the eyeball, that have immunological (e.g. expression go anti-inflammatory chemicals) and physical methods (e.g. cellular barriers) of keeping out molecules, viruses and bacteria, but not necessarily host cells.[5,6,7] Such sites do not usually have a strong inflammatory immune response to pathogens - perhaps to avoid the collateral damage that occurs during inflammation. Should a pathogen get into one of these sites, perhaps by riding in via an immune cell it infected, it can set up house for an indeterminate amount of time and with an unquantified spectrum of damage - from direct viral cell deaths to inflammation. It may also be difficult to get a drug into these sites because of the very discriminatory barriers mentioned earlier. Apart from the eye, such protected tissues include the testes (and we know Ebola virus can be maintained there for half a year) and brain and they are very generally described as 'immune privileged' sites.

The NEJM study also reported that the patient's semen contained RNA at 44 days after illness onset, and was still being monitored at publication. During his initial illness he had received the Ebola virus RNA-binding drug, TKM-100802 (or 'TKM-Ebola'[15]). It seems - for this one case anyway - that TKM-Ebola did not prevent persistence in at least two privileged sites.

This was not the first time an eye infection of this sort, called uveitis (inflammation of a region inside the eye), has been described in the EVD literature. In a study published about four years after an EVD outbreak in the Democratic Republic of the Congo, four ophthalmologist-confirmed cases were described. They developed symptoms between 42 and 72 days after onset of EVD, but no virology testing was reported.[9] In 1975, a report described a Marburg virus isolate grown from a fluid sample from the eye of a female with uveitis nearly three months after EVD onset.[10] All cases recovered their sight following treatment with atropine and steroid.

Apart from the NEJM story being a fascinating discovery and a tribute again to Emory's tenacity in trying to understand EVD, I have two concerns:

According to the Disclosure forms attached to the NEJM article and signed by the authors, the article was likely submitted around February 2015 (amendment: Dr Varkey-lead author, confirmed via a Tweet to me, that the paper was submitted in January). It's now May 2015 and the EVD epidemic, while vastly reduced in scale compared to what it was in December, is ongoing. There have been growing reports of clinics devoted to dealing with the survivors of EVD and the description of post-Ebola syndrome is also growing.[8]
The New York Times article included the following (bold is mine)...

Dr. Jay Varkey, an infectious-disease specialist who had handled much of Dr. Crozier’s care, got special permission from the Food and Drug Administration to use an experimental antiviral drug taken in pill form. (The doctors declined to name it, preferring to save that information for future publication in a medical journal.)

There is currently no evidence for or against any successful intervention using this unnamed drug. But the fact that the authors are considering publishing its use in a separate article could be interpreted as there being a chance it was helpful. Also, because the drug was obtained with special permission - it needed the drug company to agree to it being named. Perhaps they did not. But if this drug helped, it is a drug that should be made known, or available, to all who are seeing and treating EVD survivors. If the drug was of substantive use, then it might also be of helpful for survivors in Guinea, Liberia and Sierra Leone for slowing/eradicating virus in other immune privileged sites. I hope the company is considering this at least as urgently as vaccine companies did, before they eventually ramped up production of their products.

Publishing can often be slow

The traditional process of publishing research results through scientific journals is a lot slower than many would like. This four month lag is an example of that. There are some journals that are faster than others and some that are slower. Publishing in some journals is traditionally considered to guarantee (you and) your data greater exposure. Some journals are where your data go to die. This is not just because of the journal per se, but also because of your data and because some journals are watched more closely than others by those who can make the complex science more understandable - the science communicators. They write the stories that draw attention to the big discoveries.

But peer-review is an important part of publishing quality science. Peer reviewing - finding expert reviewers who will review a manuscript in their own time and getting them to return their comments in a reasonable time frame - it is quite a challenge and it can be the cause a lot of delay to the process of manuscripts becoming published papers. It is also often argued that peer-review is a broken system, nonetheless it is (still) what we have now.[11,12,13]

Publishing should sometimes be fast

When there is an active or ongoing outbreak of infectious disease, knowledge is power; the power to perhaps help save lives, reduce the burden of the disease, halt transmission, find the source, change the diagnostics, manage infected patients differently, alter the message, use a new drug - generally the power do good things for people at risk, as fast as possible.

On these occasions when time is so important to health, putting new data related to an outbreak through the scientific publication pipeline may be the least effective way to get important messages out in a timely manner. Before and after an outbreak - whatever - but during the outbreak - think differently. We've seen some great leaps in free genomic (viral sequence) data from Ebola virus variants - with the important detailed scientific papers following up later.[14] We still have a way to go to embrace not just a culture of openness, but one of speedy openness.[16] Not just for sequence data but for clinical data and for use of investigational drugs at times of crisis too.

All of the important aspects of the latest Ebola virus findings may have been passed quickly along to public health institutions that disseminate the information and act upon it if and as necessary. Nonetheless such behind-the-scenes information has remained behind-the-scenes.

While eye surgery is unlikely to be very frequent in west Africa, a risk is now known for ophthalmologists who may operate on, or collect samples from, EVD survivors. We now know of at least two immune-privileged sites that can harbour infectious Ebola virus, many months after signs of disease have passed and the surviving patient has left care; the other site being the testes.[20,21]

Could the central nervous system be yet another site? Could much of the remaining post-Ebola syndrome symptoms be related to virus replicating here causing headaches and nerve-related pain and tingling/burning?[8] Perhaps Emory medical researchers are working on this next.

Ebola virus continues to challenge us as we learn important lessons about managing its many and newly discovered impacts on the health of the host. This virus excels at revealing and exploiting our weaknesses. For something that is not alive, it has certainly played merry havoc in showing up our many failures to communicate.

References...

Weeks After His Recovery, Ebola Lurked in a Doctor’s Eye
http://www.nytimes.com/2015/05/08/health/weeks-after-his-recovery-ebola-lurked-in-a-doctors-eye.html?smid=tw-share
Persistence of Ebola Virus in Ocular Fluid during Convalescence
http://www.nejm.org/doi/full/10.1056/NEJMoa1500306
Mystery ‘post-Ebola syndrome’ emerges in West Africa
http://www.japantimes.co.jp/news/2015/05/03/world/science-health-world/mystery-post-ebola-syndrome-emerges-in-west-africa/#.VUwe9vnzp1N
Sierra Leone: Helping the Ebola survivors turn the page
http://www.who.int/features/2014/post-ebola-syndrome/en/
Immune privilege or privileged immunity?
http://www.nature.com/mi/journal/v1/n5/full/mi200827a.html
The testis in immune privilege.
http://www.ncbi.nlm.nih.gov/pubmed/16972897
Immune Privilege of the Testis: Meaning, Mechanisms, and Manifestations
http://link.springer.com/chapter/10.1007%2F978-3-0348-0445-5_2
Mystery ‘post-Ebola syndrome’ emerges in West Africa
http://www.japantimes.co.jp/news/2015/05/03/world/science-health-world/mystery-post-ebola-syndrome-emerges-in-west-africa/#.VUvhNfnzp1N
Late Ophthalmologic Manifestations in Survivors of the 1995 Ebola Virus Epidemic in Kikwit, Democratic Republic of the Congo
http://jid.oxfordjournals.org/content/179/Supplement_1/S13.long
Outbreake of Marburg virus disease in Johannesburg
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1675587/
Scientific Peer Review Is Broken. We’re Fighting to Fix It With Anonymity
http://www.wired.com/2014/12/pubpeer-fights-for-anonymity/
Is the Peer Review Process for Scientific Papers Broken?
http://time.com/81388/is-the-peer-review-process-for-scientific-papers-broken/
Is Peer Review Broken?
http://www.the-scientist.com/?articles.view/articleNo/23672/title/Is-Peer-Review-Broken-/
Using Genomics to Follow the Path of Ebola
http://directorsblog.nih.gov/2014/09/02/using-genomics-to-follow-the-path-of-ebola/
Ebola: Tracking the Latest Measures Against a Killer
http://sciencewatch.com/articles/ebola-tracking-latest-measures-against-killer
Data sharing: Make outbreak research open access
http://www.nature.com/news/data-sharing-make-outbreak-research-open-access-1.16966
Status of U.S. Ebola cases
http://apps.washingtonpost.com/g/page/national/status-of-us-ebola-cases/1406/
Emory Healthcare Ebola Preparedness Protocols
http://www.emoryhealthcare.org/ebola-protocol/ehc-message.html
Emory's "Team Ebola" to receive National Patient Safety DAISY Award for exceptional nursing
http://news.emory.edu/stories/2015/04/team_ebola_npsf_daisy_award/
Ebola virus in semen is the real deal....
http://virologydownunder.blogspot.com.au/2014/08/ebola-virus-in-semen-is-real-deal.html
Ebola virus in the semen of convalescent men
http://www.thelancet.com/journals/laninf/article/PIIS1473-3099%2814%2971033-3/fulltext?rss=yes

Saturday, 21 February 2015

Ebola virus disease: obliterating a variant and stalled case decline...

We've seen the words vigilant and vigilance used widely in recent weeks, ever since we entered a "new phase" of the Ebola virus disease (EVD) battle/fight/war.

The reason for vigilance in all things to do with this campaign has become obvious as the weeks have passed; the reduction in cases has stalled.

I've very crudely drawn in some trends below. Whether you agree with them or not, it is clear that since the fast fall in confirmed cases reported between November-January, it seems to have become very difficult to stamp out the last fires of EVD.

The phases.
(Very) rough trends in the number of EVD cases over time.
Date from World Health Organization situation reports (SitReps)
and situation summaries (SitSumms).
Click on image to enlarge.

Liberia has come the closest to completing this goal of obliterating the Makona variant of the Zaire ebolavirus (EBOV|Makona) with just 3-9 confirmed cases between World Health Organization (WHO) Situation Report (SitReps) during any of the past 7 weeks. It seems that recent cases can be traced to known transmission chains too and that means no surprise outbreaks.

However, the people of Guinea and Sierra Leone have not quite got the messages that those in Liberia seem to have embraced (without touching!) so admirably.

In the last WHO SitRep [1] it was noted that 39-45 unsafe burials (probably not all that occurred) occurred in a week and >40 EVD cases were identified post-mortem. This last observation means exposure of the community to the virus, not getting help and treatment for ill people, and unnecessarily requiring contact tracers to play catch-up. Bad for the infected people their friends and families and the response to EVD. It doesn't have to be that way.

This paints a picture of problems with Ebola outreach and education, communication and cooperation. Those things will keep the latest EVD "phase" chugging along.

We do need to destroy this variant of Ebola virus by isolating it in the last human cases in each of Guinea, Liberia and Sierra Leone. Once those people recover or regrettably die, EBOV|Makona will be gone, except for what's in lab freezers around the world and in sequence databases thanks to the efforts of a few expert research teams. Once gone from "the wild", the evolutionary clock resets back to the EBOV variants in the animals of the forest.

EBOV|Makona knows too much; it has seen too much; it has learned too much, to be allowed to "live". It has been passed through humans too many times and while there is a vanishingly small chance it will sprout wings, it is still a virus that spreads relatively easily under the right conditions and circumstances. Explosive loss of 8 litres of fluids a day provides many ways to pass along this blood/gastro virus. EBOV|Makona may also have adapted, and continues to adapt, in other ways that would mean its stay among humans becomes lengthy and its dissemination more widespread.

More bad news from an unsuccessful obliteration of EBOV|Makona-smouldering EVD in Sierra Leone and Guinea may release new case embers that drift across borders and set new fires in other countries. We don't need hundreds of cases a day for that to happen.[3] We know cases also fly with the aid of planes (not wings). And the cycle could renew. I don't think we'll see such big outbreaks of EBOV|Makona again, for reasons I laid out here, but chasing new fires is more work than stamping out the remnants of old ones. Vigilance and action.

I think vaccines still have an important role to play in the final phase of this epidemic, even if only 3 new healthcare worker cases were noted in the past SitRep week. Vaccine given to more than just healthcare workers could be useful here if others will accept the needle.

Ebola outreach
Education
Communication
Cooperation

Oh, and vigilance.

References...

Thursday, 5 February 2015

Cases of Ebola virus infection can be exported any old time...

I'm adding my two cents on the issues around remaining vigilant about Ebola virus disease (EVD) cases.

There are far fewer weekly EVD cases than there used to be but it remains absolutely essential to "kill off" this particular highly-passaged Zaire ebolavirus variant. In other words, push new cases down to zero per day in all three countries, keep it there for 42-days, and thus declare all three nations free of Ebola virus transmission.

Apart from the obvious desire to see these countries rid of this horrible and deadly pestilence, another, less likely thing to consider is that more spillovers to other countries can still happen at any time. And apart from the costs, the reaction from a certain country to its first imported case, just does not bear living through again.

Whether human cases were just kicking off, or after they began accruing at an exponential rate of hundreds per day, the hotspot countries have been the source of export of a case to another country.

That said, in my opinion we are in a much better global position today than we were six to twelve months ago. We can much more effectively engage and thwart the spread of infection from an EVD case that appears on our doorstep because we now know Ebola virus is out there and can hop on a plane, and many countries and regions within countries have done something to prepare for that rare arrival. Some countries were already in a better position than others, simply because they have (relatively) huge healthcare
processes in place and are now aware of how to help, and how quickly to respond, should a foreign neighbour acquire a case.

None of that is to say zero spread in other countries is a given in the near future; humans being humans, accidents and mistakes will always happen. But we are just very unlikely to see EVD spread in a new country to the extent that we saw last year. Hopefully I'm not being too naive on that call.

If we look at the images below, it's plain to see that EVD cases were exported from these countries both early on and late in the outbreaks and later epidemic. Guinea being slightly more of a culprit than the other two countries of intense and widespread transmission (Liberia and Sierra Leone).

Guinea's Ebola virus disease experience. The approximate time at which
another country receives a person infected by Ebola virus, most likely acquired
from within Liberia, are indicated by an arrow.
Click on graph to enlarge.

Sierra Leone's Ebola virus disease experience. The approximate time at which
another country receives a person infected by Ebola virus, most likely acquired
from within Liberia, are indicated by an arrow.
Click on graph to enlarge.

Liberia's Ebola virus disease experience. The approximate time at which
another country receives a person infected by Ebola virus, most likely acquired
from within Liberia, are indicated by an arrow.
Click on graph to enlarge.

Saturday, 31 January 2015

The filovirus tree has been shooting wildly

While there are not a lot of new branches, there are many, many new leaves on this growing tree. That is overwhelmingly due to the fantastic work of Dr Pardis Sabeti, and Stephen Gire at the Sabeti lab, Harvard University, and their many collaborators.

It sounds like even more sequences will be coming out in the future. This group is the face of the molecular epidemiology of history's largest Ebola virus disease epidemic in Sierra Leone. If a team of scientists could be said to embody an aspect of an epidemic, it has been these guys and their virus characterization. Hugely impressive stuff.

I only wish we could see more Guinean and Liberian sequences - they are both hugely under-represented in this tree of complete genomes downloaded from GenBank a week or so ago.

Click on tree to enlarge even further.
Coloured boxes surround those sequences generated during the
2014 EVD epidemic. Orange boxes point out the nearest neighbours
and the year from which the sample that was sequenced, originated.
The West African Ebola virus Makona variant has been
traced back to sharing an ancestor in common with a 2007
variant in 2004.

References

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC.
Science. 2014 Sep 12;345(6202):1369-72. doi: 10.1126/science.1259657. Epub 2014 Aug 28.

Friday, 12 December 2014

WHO Media Release: Sierra Leone reacts swiftly in the face of desperate need

I am reprinting in full, with permission, what I think is a really well written "story behind the numbers". These stories provide invaluable context around the various individual human and community tragedies that are constantly occurring during this epidemic. They also highlight the many difficulties faced by those trying to help people, track and contain spread and and collate all the numbers. Those numbers may be dispassionate in their quantification of aspects of the epidemic, but they are so important to guide timely aid to the right areas and at the right scale

Freetown – 10 December 2014 - Racing to fact check an ominous spike in Ebola cases from the remote diamond district of Kono in eastern Sierra Leone, bordering Guinea, a World Health Organization rapid response team found a worse-than-expected scene. WHO and the U.S. Center for Disease Control (CDC) joined forces with the Sierra Leone National Ebola Response Center (NERC) and Ministry of Health and Sanitation (MoHS) to sound the alarm and are now rallying all-comers in a massive build up to contain this burgeoning Ebola outbreak which ran the risk of continuing to grow and remaining hidden as world attention focuses on urban centers.

“Our team met heroic doctors and nurses at their wits end, exhausted burial teams and lab techs, all doing the best they could but they simply ran out of resources and were overrun with gravely ill people,” explains Dr Olu Olushayo, WHO National Coordinator, Ebola Epidemic Response. “In districts like Kono, with moderate transmission confined to limited villages and chiefdoms, the best chance of eliminating transmission is through aggressive and comprehensive case investigation and contact tracing,” he said. Scattered villages in 8 of the 15 chiefdoms are affected.

Reacting on intel from the Ministry of Health of Sierra Leone, WHO sent a seasoned field epidemiologist to Kono 10 days ago to tease out whether reported Ebola cases told the whole story. Cases go unreported for a variety of reasons and are exacerbated when overwhelmed and under-resourced frontline workers are unable to reach remote areas to get the truth from reluctant villagers. The surveillance officers had no vehicles. WHO and CDC quickly sent more investigators and rugged trucks.

They uncovered a grim scene. In 11 days, 2 teams buried 87 bodies, including a nurse, an ambulance driver, and a janitor drafted into removing bodies as they piled up at the only area hospital, ill-equipped to deal with the dangerous pathogen. In the 5 days before the team arrived, 25 people died in the hastily cordoned off section of the main hospital serving as a makeshift Ebola holding center.

As of 9 December 2014, this district of over 350 000 people officially has 119 reported cases. Upon hearing the WHO findings, Dr. Amara Jambai, MoHS Director of Disease Prevention and Control harkened a local saying to describe what remains yet to be discovered, "we are only seeing the ears of the hippo."

Help is arriving daily. The NERC and MoHS for the Government of Sierra Leone and UNMEER with WHO support are connecting ready-to-help partners with an all-out multi-agency response to critical needs on the ground. WHO field staff are sharing their expertise with surveillance investigators, community mobilizers, infection controllers, and coordinators. The doctors from Partners in Health and Wellbody Alliance who supported the overwhelmed holding center, are willing to stay on board to support care at the source in outlying health posts. The International Federation of the Red Cross will build a new Ebola Treatment Center on a tight timetable, while they disinfect the hospital with MoHS and create a temporary safe holding unit. The IFRC Kenema Ebola Treatment Center will take Kono patients until these solutions are in place. CDC has staff on the ground. UNMEER has lent it’s helicopters to the effort in support of the UN family (WHO, UNICEF, UNFPA, WFP, and others) engaged in building up capacity for staff and volunteers through training, materials and logistical support. International Rescue Committee is supporting infection prevention activities in the district. Funders such as DIFD and USAID are making much of the fast response possible. The race is on in this frontier fight against the virus, as Ebola responders dash to get ahead of the epidemic rather than chasing its tail.

Saturday, 30 August 2014

The fifth I give you...[UPDATED]

Senegal.
According to it's Minister of Health, Awa Marie Coll Seck[1,2], a case of Ebola virus disease (EVD) has been imported from Guinea and it is confirmed by testing at the World Health Organization's collaboration Centre, the Pasteur Institute in Dakar.

Interesting that this occurred one week after Senegal closed its borders (again) with Guinea.[3,4] The infected 21-year old Guinean student travelled on 21-August to Dakar. On the 23rd he presented to a hospital but did not admit to being in contact with known EVD cases; Guinea issued an alert that a person with EVD contact has escaped surveillance 27-Aug; Senegal closed its borders around 22-August.[5,6,7,8].
[WHO Disease Outbreak News places his movements ahead of the closure of the border, arriving in Senegal 20-Aug [8]]

These borders are leaky and so the effect of "closure" essentially hinders aid, trade and economy (all very important to the region, especially right now) but ~~very clearly~~ ~~does~~ may not stop the spread of human hosts~~-as we have seen here~~.

Humans are the variable in outbreaks.

They behave differently each time.

They respond differently each time.

This is why no two outbreaks are identical.

It's why you're a mug to assume this outbreak will be like the last outbreak.

While it looks like this is now a case study in why closing a border is ineffective, I maintain a position that border closures can't contain infectious disease. And please, do not point me to "temperature measurement" as a way to ensure capture of infected individuals. You could easily be harbouring an infection that does not yet express the symptom of fever.

Click on image to enlarge.
Graphic lifted from a great CNN video narrated by
Dr Sanjay Gupta. The video describes an example of
contact tracing and its importance to the fight
to contain EVD.[2]

The contact tracing starts in Senegal now. A 42-day clock starts for the country and a signs and symptoms watch continues on all this case's contacts for 21-days.

References...

Monday, 28 July 2014

Ebola West Africa numbers in context...[AMENDED]

A quick glance at how the suspect, probable and laboratory confirmed (susp/prob/conf) cases of Ebola virus disease (EVD) stack up in the 3 countries with local spread of Zaire ebolavirus.

Please note that I have separated Guinea-2014, Sierra Leone-2014 and Liberia 2014 only to highlight that each country in the single "West Africa" outbreak (involving a single viral variant as far as we know) has greater case numbers than those found in many of the earlier outbreaks.

I have not yet listed the case imported to Nigeria here.

Click on chart to enlarge.

Friday, 11 April 2014

When 2 - 2 = 2: Ebola case numbers in Sierra Leone

I've been having a little trouble following some aspects of the World Health Organization's (WHO) updates on the Zaire ebolavirus outbreak. There have been a few things - tiny little things - that have made it more confusing for a simple chap like me to track. One of them follows.

Don't get me wrong; this is not a criticism of the fantastic job the social comms team (@HaertlG, @setiogi and @MonikaGehner and no doubt many others I am completely ignorant of) have been doing. I've openly congratulated these guys before, and do so again here; they get so much information out on so many topics to so many endpoints...staggering. The 2014 #ebola communication has been an stunning process/event/big-word-full-of-respect-awe-and-bigness to behold from the outside looking in. It should be a shining example of a multifaceted social media education, updating and mobilisation campaign.

Tonight however, I write about the case numbers from Sierra Leone...and I'm essentially "typing out loud" to work through my confusion here so I forgive you for reading no further.

Lets go back (wavy hands)...

Ebola virus disease, West Africa – update

WHO, 01-Apr-14
The Ministry of Health of Sierra Leone is maintaining a high level of vigilance following the deaths of 2 probable cases of EVD in one family who died in Guinea and their bodies repatriated to Sierra Leone. To date, active surveillance activities have identified no new suspected cases and all contacts of the deceased have remained well.
http://www.who.int/csr/don/2014_04_01_ebola/en/

Ebola virus disease, West Africa – update

WHO, 02-Apr-14
There has been no change in the situation in Sierra Leone following the deaths of 2 probable cases of EVD in one family who died in Guinea and their bodies repatriated to Sierra Leone. As this is a rapidly changing situation, the number of reported cases and deaths, contacts under medical observation and the number of laboratory results are subject to change due to enhanced surveillance and contact tracing activities, ongoing laboratory investigations and consolidation of case, contact and laboratory data.
http://www.who.int/csr/don/2014_04_02_ebola/en/

Ebola virus disease, West Africa – update

WHO, 05-Apr-14
There has been no change in the situation in Sierra Leone following the deaths of 2 probable cases of EVD in one family who died in Guinea and their bodies repatriated to Sierra Leone. The office of the Chief Medical Officer (CMO) is coordinating all operations involving suspected cases of Ebola as well as the follow-up investigations. Enhanced surveillance and public education activities are continuing.
http://www.who.int/csr/don/2014_04_05_ebola/en/

Ebola virus disease, West Africa – update

WHO, 07-Apr-14
There has been no change in the epidemiological situation of EVD in Sierra Leone. The Ministry of Health and Sanitation of Sierra Leone has confirmed that 2 suspected cases of viral haemorrhagic fever are laboratory confirmed as Lassa fever which is endemic in Sierra Leone.
http://www.who.int/csr/don/2014_04_07_ebola/en/

Ebola virus disease, West Africa – update
WHO, 10-Apr-14
Although the epidemiological situation in Sierra Leone remains unchanged, the Ministry of Health and Sanitation (MOHS) continues to lead intensive EVD preparedness activities.
http://www.who.int/csr/don/2014_04_07_ebola/en/

Okay. Cool. So what was all that for?

WHO's super-human Tweeter and communicator, Gregory Härtl (also called Head of Public Relations/Social Media for the WHO) posted a Tweet today...

#Ebola in West Africa:101 suspect/probable/confirmed deaths in #Guinea,12 s/p/c deaths in #Liberia,2 in SierraLeone. http://t.co/qPvh09yLHB
— Gregory Härtl (@HaertlG) April 10, 2014

What I didn't understand was where these 2 cases from Sierra Leone had come from? See-toldya I was a simple chap.

So by listing them out, it seems they must be the 2 suspected cases - highlighted in yellow in the 07-Apr update above.

They were 2 cases distinct from the the 2 fatal EVD cases in Sierra Leone. As it turns out those 2 fatal cases will forever remain "probable EVD cases" because they died and were not sampled. As Gregory Hartl Tweeted...

@MackayIM @Pawixx the 2 probables will never be tested because they died. hence they will remain probables. #ebola
— Gregory Härtl (@HaertlG) April 11, 2014

If you'd like to read more of a timeline about these two - have a look at a very detailed analysis prepared by Cedric Moro (@Moro_Cedric).

This case study also confirms that at least some of the EVD cases will not ever be getting a laboratory confirmation as I wondered about in my Ebola virus sampling issues post 09-Apr. Not only do EVD case numbers change, occasionally in slippery ways, but there are also occasions when they won't ever change despite us wanting them too. If I was a pedant this could drive me to insane.

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