VDU's blog: Ebola virus

Showing posts with label Ebola virus. Show all posts

Sunday, 9 July 2017

Ebola virus disease over in the DRC....

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Sunday, 21 May 2017

Ebola in the DRC: list of border-checking countries at seven...

Starting from WHO Regional Office for Africa Ebola Virus Disease (EVD) Situation Report No. 2,[1] there have been an increasing number of countries that are screening ill-looking people for EVD at their ports of entry. Currently [7] there are 7 and they are:

Kenya
Nigeria
Rwanda
South Africa
United Republic of Tanzania
Zambia
Zimbabwe

Quite a few more than I listed yesterday.

Latest EVD figures form the DRC.
Click on image to enlarge.

No borders are closed to travellers from, or who have travelled through, the Democratic Republic of the Congo, which is good news.

Screenshot from SitRep No.5.[1]
Click on image to enlarge.

Presumably this screening relies on the appearance of signs of illness, questionnaires and perhaps thermal camera images to identify feverish people.

As I alluded to yesterday, these efforts are not very effective at actually picking up EVD cases from among a milieu of other febrile illness that stumble through a port of entry.

Studies - some of which are summed up in this Canadian review [2] - are usually not supportive of any practical benefit from using fever as a screening tool to pick out a single disease in passing travellers.[3,4,5]

However, these screening efforts do play a role in making citizens and politicians feel better and more useful. The precautions may also be helpful in keeping travel flowing.[6] Whether the continued flow of travel during an epidemic that may leak from a hotzone is a good thing or not will no doubt (once again) be dissected after a more more transmissible pathogen sweeps across the world I expect.

References....

Saturday, 20 May 2017

Ebola virus disease in the DRC: first graphs...

The World Health Organization have apparently found an outlet for their Ebola virus disease (EVD) reports for 2017's Democratic Republic of the Congo outbreak.

It's not the Disease Outbreak News site. It's not the WHO media page. It's not any of the past EVD outbreak pages on the central WHO site.

Turns out the Situation Reports (SitReps) are to be found on a new page on the WHO African site.[1] Okay. Why not? Found it eventually. I've plotted the first 4 (they started from 15th of May) below. Not much to say about trends at this early stage obviously!

Click on image to enlarge.

Don't go expecting to find how we got to the totals shown on the 15th - those may well be lost details. Or they may come out later. We'll have to wait and see. Outbreaks viewed from the public point of view are very much about patience and trying not to leap to any dramatic conclusions - like those decisions taken by at least one country in Africa to start screening passengers for signs of EVD.[2] It's your budget guys - spend up if it makes you feel safe. At this stage, and perhaps ever, its a pretty wasteful exercise though; apart from your citizens seeing you doing something.

Back to numbers. I'm pretty impressed with the WHOAfro SitRep - the 4th Report carries a detailed table of cases, deaths and locations and also a timeline graphic (below) which is fantastic.

Click on image to enlarge.This image is part of SitRep No.4.[3]

And to wrap up, just for a glimpse of what has come before and where we are now (and because I promised @kristindownie I would!), I've also added an updated "EVD through time" bar graph. Where we are with the current outbreak total is highlighted using a red arrow and the towering totals of West Africa are indicated by yellow arrows.

Click on image to enlarge.

References...

Saturday, 13 May 2017

Ebola returns to the Democratic Republic of the Congo (DRC): Zaire...

UPDATE No.1 14MAY2017 AEST

UPDATE No.2 15MAY2017 AEST

UPDATE No.3 17MAY2017 AEST

UPDATE No.4 18MAY2017 AEST

UPDATE No.5 18MAY2017 AEST

UPDATE No.6 10MAY2018 AEST

The World Heath Organization alerted the world on May 12th [1] to an outbreak of Ebola virus disease (EVD) in Likati, a remote region in the Bas-Uele province of the Democratic Republic of the Congo (DRC).[4] The news had been communicated to them on the 11th May by the DRC Ministry of Heath.[6]

This is the 8th recorded outbreak in the DRC and it is hoped that their expertise, together with a range of rapidly mobilised outside expertise, will contain this one quickly and with a minimal loss of life.[5]

It reportedly took 10 days for the first samples to reach the lab in Kinshasa for testing.[8] Google estimates about 47 hours to travel the ~3,000km from Kinshasa to Aketi (about 50km beyond Likati via Google's inland suggested route - doesn't account for off the 'main' road and forest parts) - it doesn't give estimates for Likati direct. The WHO explained...

See thread here if you use Twitter.

The journey to Likati is not an easy one.[16] Planes and helicopters are being used and there are questions around how secure the area is.[18] While remoteness is anecdotally beneficial for containing the spread of an outbreak, there are 2 clusters of illness and death outside of Bas-Uele, marked on the Ebola SitRep maps, which may test this theory.[17]

There are reportedly 300,000 (GAVI/Merck emergency stockpile [13])-700,000 doses of the rVSV-ZEBOV vaccine which has been reported to be highly effective at preventing EVD.[3,9,10]

Early numbers were a bit confusing [2] - as often happens in the fog of announcement of an outbreak - but since 22nd April there seem to have been:

20 suspected and confirmed cases in total [17]

3 fatal cases (proportion of fatal cases: 15%)

1 of 5 samples was initially laboratory confirmed (PCR) at Institut National de Recherche Biomédicale (INRB) in Kinshasa - it tested positive for Zaire ebolavirus
a 2nd case has since been Zaire ebolavirus lab confirmed [12]; 3 have tested negative [17]

at least 6 cases hospitalised [7]
≧416 contacts being traced [17]
1st case - 45 year old (or 39yo) male (45M) transported by taxi; died on arrival [11]

driver fell ill and died
carer of 45M fell ill and died (=25 contacts)

Nambwa health district has notified the greatest number of the earliest cases: 13 in all, with 2 deaths (case fatality: 15%).[15]

References...

Maps used to help place Likati and Bas-Uele...

Updates...

Fixed spelling mistakes in Likati, added detail about sampling delays

Added references 10-12; noted 2 cases now confirmed, 19 suspect cases in total
Update on where the 300,000 vaccines come from [13]
Update on contacts and ReliefWeb and WHO references
New SitRep from WHOAfro - altered case & testing numbers
Replaced maps to add in the correct population!

Thursday, 14 January 2016

Ebola virus disease is not known to be occurring in humans anywhere in the world right now...but the virus is probably everywhere it was before..

"Ebola" is not "extinct"

Ebola virus is not kicked out of West Africa.

West Africa is not "Ebola free".

It is just wrong to say there is no more Ebola virus in Liberia, Guinea or Sierra Leone.

But - as of right now - there are no known human cases of Ebola virus disease (EVD) in Guinea, Liberia, Sierra Leone, or anywhere else in the world for that matter.

That does not mean there are not cases we don't know about. It certainly does not mean that Ebola virus is not still to be found in one or more species of animal reservoir in the forests throughout Africa.

Of course we still don't know every way in which Ebola virus can re-occur in and from humans. We hardly know all the details of what it has done during the past 2 years thanks to slow and old fashioned ideas about publishing important clicnial data during times of wide need.

Do we have reliable antivirals to use after this epidemic? We do not. We have a pretty good looking vaccine - and lots of other potential things. We did show what the world can do when it works together in trying to get a vaccine to people. But we started much too late, in every aspect of the response. Everyone did. Except those on the ground already.

Is Ebola virus persisting in an unknown number of EVD survivors? Undoubtedly. Sorry - but stigmatisation aside - that is a fact. Sticking our heads in the sand and not looking closely enough at events are two of the many reasons EVD was able to sow the destruction it did in West Africa.

Let's face the facts. Not hide from them or fail to fully explore them.

For the 900 health workers, of whom >500 died; for the >28,000 EVD case and >11,000 deaths; for the many families and friends, villages and communities who lost someone dear to them - we are all so glad it is nearly over. There will be more challenges in the coming month and years, but the constant Ebola-driven fear, sickness and death is behind you now.

One way or another.

For the rest of us, it is our responsibility to do honour to those who have and still are suffering by never again being so slow, so arrogant and so limited in our imagination as to let this happen - to any country - again.

But of course, we will.

We do.

We are.

Tuesday, 29 December 2015

Congratulations to Guinea for defeating its Ebola virus disease epidemic!

CONGRATULATIONS!!!
After a very long and painful battle with many, many losses, Guinea has stopped the Ebola virus epidemic that began there in December 2013; two years ago.[1]

From Guinea, the Makona variant of a Zaire ebolavirus spread to and throughout Liberia and Sierra Leone. For Liberia, the wait for its third declaration of freedom from any new acute human cases, must continue until 14 January.[2] Two weeks and a bit.

Sierra Leone has remained free any human cases since early November.[3]

My family and I were out having lunch when the clock ticked over and my 10-year old boy (10M) said "Dad, no-one at any of these other tables will know how good it is to hear this news". My family has talked a lot about Ebola virus and Ebola virus disease in the past year and a half. And we've all learned a lot by talking and sharing and generally communicating. We've also been frequently reminded of all that we have. But 10M was likely very right.

From http://virologydownunder.blogspot.com.au/2014/07/ebola-virus-disease-evd-2014-west.html

For those of us that have been watching this tragedy unfold from the sidelines since the numbers started rolling out 23 March 2014, much more so for those citizens of Guinea and Liberia and Sierra Leone who have lived and died through this, for those who went to their aid, for those who facilitated that aid and for those in countries all around the world who received and treated cases - we are happy today in a way we have not been for nearly two years. Longer for some who were involved in caring for and trying to understand and diagnose the disease in the suspected index case, a small child from Meliandou village, Guéckédou in Guinea who became ill 26 December 2013.

While cases and clusters may yet flare up in Guinea and elsewhere in West Africa there remain many thousands of survivors who are still suffering the consequences of infection and of viral persistence.

Good luck Guinea on your 90-day period of vigilance - and beyond. You have earned some dancing!

References...

Friday, 20 November 2015

Liberia reports another case of Ebola virus infection...

Reset the contacts clocks. Liberia has had a second setback in the fight to rid West Africa of human Ebola virus (EBOV) infections.

While we were academically aware this could happen again, I'd venture to say we probably thought the next case of Ebola virus disease (EVD) would return to Sierra Leon or Guinea. Liberia which was declared free of known transmission back in 03-SEPT-2015...78-days or 2-months and 17-days ago, and was without a case for 42 days before that.

This was where I learned about the new case from...

Looks like new case of #Ebola here in #Liberia. I'm confident that the Govt will again contain it effectively. Hope the poor boy recovers.
— Sinead Walsh (@SWalshIRL) November 20, 2015

It has now been confirmed that a 15-year old male, the beginning of Liberia's "fourth wave" of EVD, acquired EBOV from....somewhere...somehow.[9]

15M became ill from 13-Nov and was confirmed as EBOV infected 19-Nov.[7,8,9] He died 24-NOV.[12]

UPDATE #1: tally now stands at 3 cases - the 2 new cases among family members of 15M include his 8-year old brother and his father.[8,9] It has been said that 15M had no known contact with a survivor or relevant travel history.[9] 15M was previously described as 10M, but age amended in [9])
UPDATE #2: 153 contacts being monitored.[10]
UPDATE #3: WHO lists boy as 10-year old in 23NOV update. Aiyahh!
UPDATE #4: Announcement of 10M death.[12]
UPDATE #5: Guess what? WHO says 15M.[13] Father, 40M.[13] 149 contacts including 10 healthcare workers.
UPDATE #6: 40M and 8M were discharged from hospital but some contacts still have a week of observation to complete.[14]

Information on how the initial infection for this cluster was acquired.

Time ~~will~~ may tell us more.

Reference...

http://www.reuters.com/article/2015/11/22/health-ebola-liberia-idUSL8N13H0CM20151122#Ug24kslkc6Qo48g0.97

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/

Monday, 12 October 2015

Jon Snow is remarkably well informed compared to us...

...because we clearly know almost nothing when it comes to the specifics of where Ebola virus (EBOV) can, in some portion of survivors, hide.

What triggers EBOV to come out of hiding? If indeed that is what it has done within PC, the United Kingdom nurse who seems to have recently become ill while (or due to) hosting a reappearance of EBOV in her blood - 9 months after her blood was defined as containing no detectable EBOV.

This is not a new infection - but a return of a virus that had not been cleared from its hidey hole(s).

There are obvious concerns to be discussed around this, including:

What triggered its re-emergence
Is this a strange and rare event or a more common one?
Was the virus hiding in PC's central nervous system (she has meningitis-like symptoms reportedly) or in another place or places?
Is the thyroid a site of persistence?
Did the mysterious antiviral treatment she was given alongside a plasma treatment in 2014/15 act to push the virus into hiding?
Has the activated virus mutated in any significant way during its holiday out of the bloodstream?
Can EBOV become truly latent or at least dormant (still producing proteins, but not infectious virus particles) when off the beaten track, or is it constantly replicating?
Is PC suffering from full-blown Ebola virus disease (EVD) now, or a disease due to tissue or organ damage from her earlier infection - although if she has detectable EBOV in her blood, one would assume it is EVD.
What the hell are a "lucky set of genes" in the context of a return to systemic EBOV infection?

Below are some known and some proposed/possible/unproven sites at which EBOV may linger, avoiding or not exposed to clearance by the full force of our immune response.

In the future, perhaps tomorrow, in a non-rich nation, will others become infected from a convalescent patient who experience a return of EBOV long after they were declared virus-free based on a their blood test results. Has that happened already? Will they be our colleagues, friends or family members? The sooner we hear more about what is going on with PC, the better prepared those on the ground will be to intervene. Also, those tending to convalescent health workers in countries around the globe.

Communication has always been a key issue for EVD and other emerging diseases. Have we been listening?

We know nothing but we can learn. Will we?

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..

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Sunday, 9 July 2017

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