Virus Diseases: Guinea

Showing posts with label Guinea. Show all posts

Friday, August 29, 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...

Sunday, July 27, 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.

Thursday, June 19, 2014

West African Ebola virus disease (EVD) outbreak flares up in late May and in early June...[UPDATED]

Data are based on WHO DONs. Lines use the numbers on the vertical axis on the left, bars use the right hand axis. The percentages are the proportion of fatal cases at the time point indicated.
Click on chart to enlarge.

The chart tells a pretty grim story of an outbreak that has flared up, after what looked like some weeks of things settling down. I'd said I would stop charting this outbreak back at 5-May, unless anything major happened. Well it did. In late May in Guinea and then in early June in Sierra Leone.

The causes seem to be the heartbreaking stories of family members sequestering ill loved ones or removing them from isolation wards, and in so doing, getting infected themselves, and so spreading infection.

Click on image to enlarge.

Maps purchased from maptorian and adapted by VDU

The adjacent map has been updated to help communicate an idea of the number of cases in each country.

The number of cases and deaths, not all of which are laboratory confirmed as being ebolavirus disease (EVD), are now the highest of any known outbreak of EVD (see the chart below). A grisly fact and one that doesn't change anything. But one I note nonetheless. Also worthy of note is that throughout this outbreak, the proportion of fatal cases (PFC; check the disclaimer in the legend below) has not reached the heights of the Zaire outbreak of 1976, or the Democratic Republic of Congo (DRC) outbreak of 1995, or that in the Republic of Congo (RC) during 2002-3, and others. So that's a small silver lining.

A guide to confirmed EVD cases and those who died from EVD over time.
The data for the non-West Africa-2014 outbreaks, sourced from Public Health England website [1], are defined as "confirmed". Not all of the Wet Africa-2014-related clinical cases or deaths have been laboratory confirmed so these bars are probably a little high (highlighted in the key). Note that looking at proportions alone can be confusing. For example, if 1 of 1 cases is fatal, that's a PFC of 100% but it may not reflect the situation accurately. So please interpret the grey mountains alongside the read and blue bars to get the complete picture. DRC-Democratic Republic of Congo; RC-Republic of Congo

Click on chart to enlarge.

I'll try and keep the charts up-to-date as this outbreak continues to burn.

References...

Sunday, May 4, 2014

Ebola virus disease (EVD) West Africa update for 02-May, WHO-AFRO update...

Click on image to enlarge.

Thankfully the latest World Health Organisation update includes figures for Liberia. The last West Africa update did not, so I didn't post a chart.

Summary..

Total suspected/probable/confirmed cases: 244
Total suspected/probable/confirmed deaths: 162 (66.4%)
Total lab confirmations: 133 (54.5% of 227)

These figures are very important for two reasons...

Firstly they show a drop in suspect/probable cases after data scrubbing by the Liberian Ministry of Health and Social Welfare. This reinforces that the outbreak is being well controlled.;The date of isolation of the most recent confirmed cases is 30-April from Conakry and Guekedou (Guinea).

Secondly there has been a concomitant rise in the proportion of fatal cases of EVD due toZaire ebolavirus (see the percentages above the orange line in the chart). This is not because the numbers have jumped, it's because the denominator has shrunk for the relevant calculation:

No. EVD fatalities/No. total susp/prob/conf cases.

We've known this rise in proportion was coming because it was highly likely that case numbers would change as the dust settles and the susp/prob EVD patient numbers get discarded because they are found to be infected by something else; clinically similar disease, but not because of infection with Zaire ebolavirus. I've written about it previously if you'd like some background.

With the use of more antibody testing, the numbers will continue to change, as they always do in outbreaks.

This will be my last update on this outbreak linked to the WHO-AFRO announcements unless anything major happens.

A reminder - the chart above is made for general interest. It may be that I have misinterpreted the language in the report (sometimes a little tricky to wade through these reports) but the trends should still be informative even if a number or data point is out of place.

Sources...

http://www.who.int/csr/don/don_updates/en/
http://reliefweb.int/report/liberia/unicef-liberia-ebola-virus-disease-sitrep-20-2-may-2014
http://virologydownunder.blogspot.com.au/2014/04/ebola-virus-disease-and-lab-testing.html

Sunday, April 20, 2014

Ebola update: some additional numbers for Guinea from 17-April, WHO-AFRO update

These numbers slightly change the numbers I last posted from 18-April.

A small uptick in deaths and lab confirmations and a change to the most recent illness onset which is now 17-Apr. The clock is still waiting to start on the 2-incubation periods required, without new cases, before the region will be declared free of Zaire ebolavirus.

18 healthcare workers are lab confirmed with Ebola virus disease, 6 are probables (24 in total) of which 15 have died (11 are lab confirmed).

Source..

http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4104-ebola-virus-disease-west-africa-19-april-2014.html

Thursday, April 10, 2014

Update on Ebola virus disease (EVD) case accumulation chart with new WHO African Regional Office data...[UPDATED].

UPDATED with 2 Sierra Leone probable deaths.
Click on image to enlarge

Not much of a change to be seen with the data from WHO following that from UNICEF yesterday.

No Species Zaire ebolavirus cases have been confirmed in Sierra Leone nor any in Mali (6 suspected cases however; 2 other samples tested negative) or elsewhere.

Click on image to enlarge.
Maps purchased from maptorian and adapted by VDU

EVD cases are still restricted to Guinea and Liberia and all cases remain linked to infections in Guinea.

As I understood the recent WHO virtual press conference, because the index case was known, the transmission chain of contacts is mostly already under observation. While Ebola virus disease (EVD) has a grisly progression, once experts are in place to help track, test and educate, with the help of local and international governments, the spread of EVD can be contained.

But it will still take time to be sure the outbreak has been contained; 2 full incubation periods worth of time.[3] As the maximum incubation period is 21-days (2-21 days being the full range), you start to see why the WHO speaks in terms of "months" [2,3] before the outbreak can be considered over. And that clock starts sometime around the end of the last case's disease onset I'd guess.

“We fully expect to be engaged in this outbreak for another two, three, four months”

Dr Kenji Fukuda, WHO[3]

So as the outbreak comes under control, as seems to be the case, we should pay attention to when new cases stop appearing. Then it becomes about waiting until everyone can safely say there are no new cases.

The most recent case had an onset of illness on 08-April-2014.

Sources...

WHO-AFRO Ebola virus disease, West Africa (Situation as of 10 April 2014)http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4093-ebola-virus-disease-west-africa-10-april-2014.html
Ebola expected to terrorise West Africa for ‘months’–WHO - Euronewshttp://www.euronews.com/2014/04/09/ebola-expected-to-terrorise-west-africa-for-months-who/
Officials Say Ebola Outbreak Could Last Months - Timehttp://time.com/54299/officials-say-ebola-outbreak-could-last-months/

Wednesday, April 9, 2014

Update on Ebola virus disease (EVD) case accumulation chart with new UNICEF data...

Click on chart to enlarge.

Thanks to a UNICEF Australia's update I've added a few cases to the produce a new chart; I expect we'll see some WHO numbers soon, and I'll update if there are any differences.

Check the version number in the bottom left hand corner - it defines whether it is the only chart of the day from VDU, or one of several.

The new version shows the proportion of fatal cases holding fairly steady at ~60% of all cases. This calculation includes those cases that also that look like EVD but have not been laboratory confirmed as EVD, as well as those that have been confirmed.

As I went into yesterday, these are very volatile numbers, so regard this chart for its trends only.

Sources...

UNICEF Australia's PDF of numbers from ~3-hours ago
http://ow.ly/d/24bM

Recorded Ebola virus disease (EVD) outbreaks throughout time...

A guide of case total confirmed cases and those who died from
Ebola virus over time.
Sourced from Public Health England website [1]:
Click on chart to enlarge.

A quick chart to highlight the larger and smaller outbreaks and importations of EVD and Ebola viruses, respectively, that have been recorded worldwide since 1976.

I've added in the current tally of 167 suspected/probable/confirmed cases for the 2014 Guinea outbreak but this number is inflated compared to the other entries on the chart because those are reportedly based on confirmed cases; only around a third (59) of Ebola cases in the current outbreak have been confirmed to date.

Thanks to @Pawixx for steering me to the PHE page.

Please note that these numbers differ a little from the World Health Organization's Table [2]. Solving that discrepancy is a problem for another day.

Source...

Sunday, April 6, 2014

Ebola virus disease (EVD) outbreak in West Africa: chart of cases to 04-Apr

Data are based on WHO DONs, French Embassy Conakry
figures and WHO Tweeted information.
Click on image to enlarge.

The Ebola virus disease (EVD) case chart adjacent is based on the latest Disease Outbreak News (DON) from the World Health Organization (WHO) posted at the Global Alert and Response (GAR) site [1] and at the African Regional Office (WHO-AFRO) [2].

There are roughly 163 suspected, probable and laboratory-confirmed cases including 95 deaths (58.3% proportion of fatal cases) for which only 56 (34.4%) have been confirmed by laboratory tetsing.

I'm also maintaining a curated Storify timeline here which lists some key Tweets and links on this outbreak.

A few things to note about the chart and the outbreak:

The susp/prob/conf (shorthand I use on Twitter) numbers change - the 1st 2 numbers can go down as well as up as cases that cannot be laboratory confirmed as due to EVD are discarded from the tally. Other diseases with similar presenting signs and symptoms occur in the West African region so this is not at all unexpected. We see the same thing for other viral outbreaks, like influenzavirus, all the time.
The WHO does not posted "grand totals". The DONs present totals for each region (currently Guinea, Sierra Leone and Liberia), which I've tallied up above.
Its worth remembering that this outbreak was happening back in early Feb, so there was a passage of time during which people were exposed and did not know precisely what was causing illness. This creates a lag between the time of the first announcement and when the situation can come under some semblance of control. Control requires that the various teams arrive, are coordinated and set up in the area to test, trace, educate and reduce virus spread. Each time a new region has a case, the same flurry of activity may well ensue, so case numbers will seem suddenly spike - but as we can see, they do not continue to rise exponentially, or even at all in some regions. This is thanks to the expert teams including those from the WHO, jurisdictional Ministries of Health, UNICEF, the Red Cross and Médecins Sans Frontières (apologies to all those I've missed - you are all doing a fantastic job under extreme conditions and you are extremely appreciated)
Posts on this outbreak do not occur daily - I presume, as for avian influenza virus outbreaks etc, posting of numbers is based on when those data are collated, summarized and provided to the WHO.
There are reports of 4 haemorrhagic fever cases from Mali (some of whom had traveled to Guinea; a suspect case is also reported in Ghana coming from Mali although there are questions about where from precisely) that are not, at writing, laboratory confirmed.[5] Samples are being sent to the United States for confirmation. Why not to the Institute Pasteur in Dakar, or Guinea field labs I do not know; presumably because of pre-existing arrangements?
Liberia has 1 suspected EVD case in a hunter who seems to have acquired his infection locally (no contact with know EVD cases or with Guinea). This suggests to me that the vector is actively infected in the region. Perhaps this is a migratory season (seasonal change, following food sources, breeding) for this Ebola virus's animal hosts, previously found to be fruit bats, chimpanzees, gorillas, monkeys, forest antelope and porcupines in particular, eaten as "bushmeat". I admit to knowing nothing about animal movement in the region however.
While EVD is "highly contagious", close contact with an infected animal host or an infected human cases' bodily fluids (blood, organs, mucous, urine, vomit, faeces and semen for up to 7-weeks post-infection) is required to acquire an infection. Generally the virus doesn't spread across distance as well or quickly as for example, influenzavirus does. This is largely because the virus is not spread the same way:

Sneezing and coughing is not considered a method of EVD transmission
Once the patient is symptomatic, they do not move around as much; from that point, spread of the virus to new people requires those people to come to the ill person. This is why healthcare workers, especially early on in an uncharacterized outbreak, and close family members caring for an ill or deceased relative number highly in new cases of EVD.
Basic levels of infection prevention and control can interrupt transmission. These include good hand hygiene, use of personal protective equipment and prevention of needle stick injuries.

Airborne transmission is not considered a risk factor for acquiring EVD; this is not the movie Outbreak where the fictional "Motaba" virus mutates into an airborne ebolavirus-like pathogen. Also unlike the movies, bleeding from orifices and the skin can occur, but much more rarely than the movies lead us to believe
EVD signs and symptoms start suddenly 2-21-days (8-10 more common[3]) after virus acquisition and usually include fever, headache, joint and muscle aches, weakness, diarrhoea, vomiting, stomach pain, loss of appetite and may also include rash, sore throat, red eyes, hiccups, cough, chest pain, breathing and swallowing difficulties and sometimes internal and external bleeding. Not everyone dies from infection however the higher end of the mortality spectrum for the species Zaire ebolavirus can reach 90% in outbreaks with >1 case identified.[4]
A person with no signs or symptoms of disease is not considered contagious.
While a border closure (Senegal) and some flight restrictions have come into play, these may only serve to disadvantage the outbreak region rather than provide any true risk mitigation. Closing a border may hinder the flow of food, medical supplies and daily goods as well as interrupting the normal commerce of the country, impacting both economically and directly on the lives of the overwhelming majority of people who are not infected. I'm not aware of any evidence that shows closing a border has any reducing effect on an Ebola outbreak. Closures are a knee-jerk reaction caused by the fear of a scary disease.

And that last point is an important one. Ebola evokes some scary images outside of Africa. And so it's important for us not to run around like a decapitated Gallus gallus domesticus. We need to rein in the excessive over-reaction. As Maryn McKenna aptly noted recently over on Superbug, many things are killing more people, more regularly every day both in and outside of Africa. Having said that, I can totally understand the reactions of those living inside of West Africa just now. Among them, those who both have or have never looked this pathogen in its filovirusy-eye and stared down the barrel of its disease before.

Viruses can be pretty scary things indeed.

References..

WHO Global Alert and Response (GAR) Disease Outbreak News (DONs) Articles
http://www.who.int/csr/don/en/
WHO African Regional Office (WHO-AFRO)
http://www.afro.who.int/en/media-centre/pressreleases.html
Signs and symptoms of EVD or Ebola haemorrhagic fever (HF) from US Centers for Disease Control and Prevention
http://www.cdc.gov/vhf/ebola/symptoms/index.html
WHO EVD fact sheet
http://www.who.int/mediacentre/factsheets/fs103/en/
WHO AFRO EVD West Africa SitRep for 4-April-2014
http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4079-ebola-virus-disease-west-africa-5-april-2014.html
A Patient in Minnesota Has Lassa Haemorrhagic Fever. (Don’t Panic.)
http://www.wired.com/2014/04/minnesota-lassa/

Monday, March 24, 2014

Ebola outbreak in Guinea: 13-lab confirmed cases, 73 more suspect, includes 59 deaths

Schematic of an Ebola virus virion.
Its a work in progress but feel free to use.
Just cite Ian M. Mackay, PhD and
http://virologydownunder.blogspot.com.au/
Click to enlarge.

There's an outbreak of Ebola virus (species Zaire ebolavirus) haemorrhagic fever going on in Guinea just now (see the map for where that is within Africa).

Haemorrhagic fever? That's the scary stuff that books get written about and movies based on - bleeding from tissues and person-to-person spread to infected healthcare workers and grieving family carers...horrible, scary stuff for those in the thick of it. If anything can be said to be good news to this, it is that usually (to date) cases do not pass several hundred (see Storify article of tonight's Twitter information [5]) because the virus does not transmit as easily as influenza for example (no aerosol route; spread is by bodily secretions); scary bleeding from everywhere is not as common as the movie make out and there are survivors of infection.

A very digestible backgrounder on Ebola that will get you up to speed on this virus and disease can be found at Mike Coston's Avian Flu Diary, here [9].

On 22-March, the World Health Organization (WHO) was made aware of an outbreak in the west African country by its Ministry of Health [1]. The outbreak of febrile disease commenced 9-Feb. When the Minister of Health released a statement, 22-Mar, he noted the disease was characterized by fever, diarrhoea, vomiting, fatigue and sometimes bleeding.

Guinea and surrounds, Africa.
Maps purchased from maptorian.
Click on image to enlarge.

Since then, haemorrhagic fever cases in the country's capital, Conakry, have been shown to be due to something other than the Ebola virus according to testing results from the Pasteur Institute Dakar [3].

The Institut Pasteur in Lyon had earlier identified Ebola virus (so far in 13 cases) in Guekedou, Macenta, Nzerekore and Kissidougou districts; they also genotyped some strains using the L gene as a PCR target[10]. This led to identifying the species Zaire ebolavirus.

The Emerging and Dangerous Pathogens Laboratory Network (EDPLN) is working with the Guinean VHF Laboratory in Donka, the Institut Pasteur in Lyon, the Institut Pasteur in Dakar, and the Kenema Lassa fever laboratory in Sierra Leone to make available appropriate Filo-virus diagnostic capacity in Guinea and Sierra Leone [1]

There is no specific treatment or vaccine for Ebola disease. The first Ebola virus outbreak was identified in 1976. Ebola virus is the conversational name of the viruses that are members of the Family Filoviridae, Genus Ebolavirus and exist as 5 species [4]:

Species: Tai Forest ebolavirus ("Tai Forest virus")
Species: Reston ebolavirus ("Reston virus")
Species: Sudan ebolavirus ("Sudan virus")
Species: Zaire ebolavirus ("Ebola virus")
Species: Bundibugyo ebolavirus ("Bundibugyo virus")

"Multidisciplinary teams have been deployed to the field to actively search and manage cases; trace and follow-up contacts; and to sensitize communities on the outbreak prevention and control. Médecins Sans Frontières, Switzerland (MSF-CH) is working in the affected areas and is assisting with establishment of isolation facilities, and also supported transport of the biological samples from suspect cases and contacts to international reference laboratories for urgent testing." [1]

But where was the crack team of experts laden with ultra cool tech capable of diagnosing the tiny beast within minutes, containing it within hours and saving more people from becoming afflicted in days?

Unfortunately no such crack team or timeline exists, except in the movies anyway. But as we are going to see in the coming days as diagnostic delays cause headaches for those multidisciplinary teams trying to educate the locals and begin helping contain, confirm cases and trace the disease, there is a real need for faster identification of the causes of acute and serious disease outbreaks worldwide.

Wouldn't it be great if the world's governments and biotech industries could come together to assemble and maintain some sort of rapidly deployable multinational pathogen detection force? Several teams of scientists and healthcare workers assembled and trained by the world's best, and remaining linked to them, carrying with them all the (perhaps bespoke) tech they'd need to identify any pathogen (unbiased molecular methods). They could analyse their data on the fly or rapidly send it to others for help using satellite links. The "Force" could be funded by the contributing States, biotech and Pharma; coordinated by the WHO perhaps. I'd love to see a dedicated set-up for pathogen identification; a kind of virus/bacteria/parasite-hunting fire department that can down its regular tools and jump on a plane ASAP; someone whose number is on every country's speed dial.

Ahh 'tis to dream.

In the meantime, I have a lot to learn about Ebola; something that is more nightmare than dream to me.

References..

WHO situation report as of 22-Mar-2014 [PDF]
http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4063-ebola-hemorrhagic-fever-in-guinea.html
Epidemic hemorrhagic fever in Guinea after 29 deaths, the Health Minister announces new measures
http://www.lejourguinee.com/index.php/fr/societe/3072-epidemie-de-fievre-virale-hemorragique-en-guinee-apres-29-morts-le-ministre-de-la-sante-annonce-des-nouvelles-mesures
Guinea: fever cases detected in Conakry are not due to Ebola.
http://www.france24.com/fr/20140324-guinee-conakry-ebola-virus-fievre-hemorragique-epidemie-institut-pasteur/
Prof Vincent Racaniello's Virology blog on Ebola virus naming
http://www.virology.ws/2012/08/07/is-it-ebolavirus-or-ebola-virus/
Storify: Early timeline of the events in the Guinea Fever outrbreak
http://storify.com/MackayIM/early-timeline-of-the-eventsin-the-guinea-fever-ou
WHO webpage on the Guinea Ebola outbreak
http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4063-ebola-hemorrhagic-fever-in-guinea.html
WHO primer on Ebola haemorrhagic fever
http://www.who.int/mediacentre/factsheets/fs103/en/
Avian Flu Diary (Mike Coston) on WHO Twitter Messaging On Ebola
http://afludiary.blogspot.com.au/2014/03/who-twitter-messaging-on-ebola.html
Avian Flu Diary (Mike Coston) on A Brief History Of Ebola
http://afludiary.blogspot.com.au/2014/03/a-brief-history-of-ebola.html
Guinea Ebola outbreak believed to be deadly Zaire strain
http://www.reuters.com/article/2014/03/24/us-guinea-ebola-idUSBREA2L0MI20140324

Virus Diseases