Ebola virus disease (EVD) West Africa: 24-June WHO-AFRO update...

Apart from something unexplained going on with the wording &/or numbers in the Sierra Leone portion of the report, the latest Disease Outbreak News (DON) from the World Health Organization (WHO) reports a continuing climb in the case numbers, particularly those from Sierra Leone.

The cumulative totals of suspected/probable/ fatal EVD cases, just fatal cases and the numbers confirmed by laboratory analysis. Latest data are based on WHO DON.[1] 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 country-based EVD cumulative totals. Latest data are based on WHO DONs (see latest, [1]). Lines use the numbers on the vertical axis on the left. The percentages are the proportion of fatal cases at the time point indicated.

Click on image to enlarge

A reminder:

The chart above, as with all on VDU, is made for general interest only. It is also freely available for anyone's use, just cite the page and me please. It may be that I have misinterpreted the language in the reports (sometimes a little tricky to wade through) or miscalculated some totals based on the way data have been presented. 

There are very country-specific differences in what gets presented to/via the World Health Organization's Disease Outbreak News which make this process less clear than it could be. I recommend you have a read and compare the data from each of the 3 countries for yourself to understand these issues. 

As I've talked about previously,[2] these numbers are all volatile for a variety of reasons, some Ebola-specific, so regard this chart for its trends only.

References...

1. Ebola virus disease, West Africa - update
   http://www.who.int/csr/don/2014_06_24_ebola/en/
2. Ebola virus disease and lab testing...
   http://virologydownunder.blogspot.com.au/2014/04/ebola-virus-disease-and-lab-testing.html

Ebola virus disease (EVD) West Africa update for 22-June, WHO-AFRO update...

[CHECK OUT TAB ALONG TOP FOR LATEST EBOLA NUMBERS]

A new Disease Outbreak News has appeared. It shows that cases have risen by ~39 since the last report.

Total suspected/probable/confirmed cases: 567
Total suspected/probable/confirmed deaths: 350 (61.7%)
Total lab confirmations: 385 (67.9% of 567)

The cumulative totals of suspected/probable/ fatal EVD cases, just fatal cases and the numbers confirmed by laboratory analysis. 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.

Reported cases continue to rise most rapidly in in Sierra Leone as we can see from the country-specific chart below..

The country-based EVD cumulative totals. Data are based on WHO DONs (see latest, [1]). Lines use the numbers on the vertical axis on the left. The percentages are the proportion of fatal cases at the time point indicated.

Click on image to enlarge.

A reminder:

The chart above, as with all on VDU, is made for general interest only. It is also freely available for anyone's use, just cite the page and me please. It may be that I have misinterpreted the language in the reports (sometimes a little tricky to wade through) or miscalculated some totals based on the way data have been presented. 

There are very country-specific differences in what gets presented to/via the World Health Organization's Disease Outbreak News which make this process less clear than it could be. I recommend you have a read and compare the data from each of the 3 countries for yourself to understand these issues. 

As I've talked about previously,[2] these numbers are all volatile for a variety of reasons, some Ebola-specific, so regard this chart for its trends only.

References...

1. Ebola virus disease, West Africa - update (awaiting move out of the Latest News section)
   http://www.who.int/csr/don/2014_06_22_ebola/en/
2. Ebola virus disease and lab testing...
   http://virologydownunder.blogspot.com.au/2014/04/ebola-virus-disease-and-lab-testing.html

Snapdate: Charting up MERS-CoV numbers..

Another quick chart update.

Nothing too drastic to add since cases have been infrequent over recent days (see previous post for recent dailies on this [1])

Same caveats apply about the found113 (they are not included here [1]).

Detections and fatal outcomes have slowed to a plateau.

Next stop, Ramadan.

Click on chart to enlarge

References...

1. Adding in the recent MERS-CoV cases by chart...we're back to 2013
   http://virologydownunder.blogspot.com.au/2014/06/adding-in-recent-mers-cov-cases-by.html

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..

1. 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

Update on Ebola virus disease (EVD) case accumulation chart with new WHO African Regional Office data for 16-Apr-2014.

Click on image to enlarge.

Since the last update [2] there looks to have been a big jump in cases, but that is mostly be because its been a while since that WHO update. 

You could draw a straight line between the dot from the update on 11-Apr and it would maintain the overall gradual slope. 

Total suspected/probable/confirmed cases: 227
Total suspected/probable/confirmed deaths: 135 (59.5%)
Total lab confirmations: 114 (50.2% of 227)
What I find encouraging in the latest numbers [1] is that the lab confirmations have jumped up by nearly 10% so we now have 50.2% of all the (227) cases listed having been confirmed up from 41.6%. Also, none of the Mali suspect cases tested positive for this variant of the Zaire ebolavirus species (by the way, you can tell I meant species because I called out the full species name and used italics - just fyi). And the proportion of fatal cases has dropped because the suspect/probable case numbers have gone up faster than the fatal case number. A good thing for now, but that may well change in the future for reason I've written about recently.[4]

Less encouraging is that I couldn't find the number of lab confirmations for Liberia so that number may shift a little. When the most recent case became ill was not listed. Also, healthcare worker (HCW) numbers have jumped from 15 suspect and confirmed with 11 fatalities to 24 and 13 fatalities but I'm not sure just how many are currently lab confirmed. HCWs suffer a lot to be at the forefront of these outbreaks. We should never forget that.

We also learned today, thanks to a very speedy and nicely laid out New England Journal of Medicine article [3] by Baize and colleagues from Europe and Africa, that the particular variant of this species that has ravaged Guinea is a virus distinct from those found in other African Ebola virus outbreaks. I wonder if it has evolved in the local bats of Guinea or the greater West African region? I'm ignorant of how wide-ranging bat travels are or how friendly different region's bat colonies are. More testing is needed to answer the virology underneath all that...as always. 

The Guinea Ebola virus variant is still a member of the species Zaire ebolavirus, genus Ebolavirus, family Filoviridae, but it has enough genetic variation across its genome to mark it as different from those found variants of Zaire ebolavirus identified in 1976, 1994-1995, 2002, 2007-2008.[3] How different? That will take more research to answer. What's its new name? We don't know yet but the Filoviridae Study Group can tells us that they would rather not use a country or patient name, prefer to avoid any "unusual" characters, choose easy to pronounce designations - and contact them for guidance! They'd like to see something that rolls off the tongue and includes...

<virus name> <isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation> 

e.g. Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621

Source...

1. Ebola virus disease, West Africa (Situation as of 16 April 2014)
   http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4100-ebola-virus-disease-west-africa-16-april-2014.html
2. Update on Ebola virus disease (EVD) case accumulation chart with new WHO African Regional Office data for 11-Apr-2014.
   http://virologydownunder.blogspot.com.au/2014/04/update-on-ebola-virus-disease-evd-case_15.html
3. Emergence of Zaire Ebola Virus Disease in Guinea — Preliminary Report
   http://www.nejm.org/doi/pdf/10.1056/NEJMoa1404505
4. Ebola virus disease and lab testing...
   http://virologydownunder.blogspot.com.au/2014/04/ebola-virus-disease-and-lab-testing.html

MERS-CoV: sex, age and accumulating death

A few more charts, just to fill out the set for today's Middle East respiratory syndrome coronavirus (MERS-CoV) update.

First Chart.
Click on chart to enlarge.

The first chart shows what everyone knows; MERS, as it has been for the past 2-years, is a severe disease principally of the people of the Kingdom of Saudi Arabia (KSA). 

The route of human acquisition of MERS-CoV remains unknown and will not soon be discovered judging by the lack of any evident plan in the most recent Editorial on MERS-CoV from the KSA's lead author, Prof Ziad Memish. An even less addressed topic is why this disease has such an impact in this particular country given that neighbouring States share aspects of lifestyle, belief and habit.

Second chart.
Click on chart to enlarge.

The second chart reinforces that MERS, in the severe form we see in hospitals, is principally a disease of men (66% of all case are male;  77% among the fatal cases) aged 50 and above (median age is currently 53-years). Something this chart does not show is the that MERS-CoV is a particularly opportunistic virus causing serious disease and death particularly among those who present with an underlying disease (at least a third of cases have a comorbidity of some sort).

Third chart.
Click on chart to enlarge.

In the third chart we can see the human cases by month. Nothing to add for 2012 or 2013 but that steady climb in 2014 should be watched. Why is it there? Why, 2.04 years since we learned of MERS-CoV thanks to the endeavours of an Egyptian scientist named Dr Ali Zaki, are there no public conversations on what is/could/should be done to staunch the trickle of new infections and deaths? Will we see a take-off of cases in April 2014 as we did in 2013? What is happening in Riyadh (where most cases have been of late)? I've added in the Janadriyah festival too because why not?

And in the fourth chart we can see that trickle of new cases but they have thankfully not (yet) been matched by an equivalent rise in fatalities judging by the proportion of fatal cases (PFC) which has dropped a little. The PFC still sits at the "killer virus" level of 42% of all laboratory confirmed cases dying. Not my phrase. 

To generalise, MERS-CoV infection is mainly a cause for serious concern among a particular adult population within the KSA. 

A question I'd like to see answered by studies from the KSA is what is the epidemiology and clinical spectrum of human coronaviruses 229E, NL63, HKU1 and NL63? I believe that would be an interesting study yielding results  that may well put MERS-CoV in a very different context.

Yet another reason for every State to test its population for respiratory viruses I suppose, because then one has a baseline for the known viruses which can help judge the impact of newly identified or emerging viruses.

An update on avian influenza A(H7N9) virus cases in humans: Week 56

As we currently stand (this minute), there are 389 laboratory confirmed human cases of infection including perhaps 122 deaths (31% PFC). 

H7N9 cases are mostly noted in older males (Average age 54-years; Wave 1 57-years; Wave 2 53-years) with the major risk being exposure to birds and "poultry markets" (commas because it is not just poultry being sold at these markets). No sustained human-to-human transmission has been noted and no specific vaccine exists although one is coming soon apparently. Oseltamivir or zanamivir are useful antivirals while adamantanes are of no use because H7N9 is resistant. to them. The second wave has peaked but we are still seeing a shoulder off the main peak from Wave 2; smaller numbers of cases each week (no longer occurring every day), often from regions other than those with closed poultry markets or with only recently closed or temporarily closed markets.

First chart.
Click on chart to enlarge.

First chart: where is H7N9? It's in Southeast China, most cases having been acquired in Zhejiang province (139/389 cases; 36%) during both Waves of human infection and Guangdong province is currently a very close second place (95/389 cases; 24%).

Second chart.
Click on chart to enlarge.

Second chart: where has H7N9 been focused over time? We can see from this chart that Zhejiang and Guangdong provinces have accrued H7N9 cases most rapidly. While Zhejiang featured in both waves, Guangdong is of Wave 2. It will be interesting to see what happens if there is a Wave 3; without finding and controlling the source of human acquisitions and if the birds with the virus continue to have the virus, I expect we will see future waves.

Third chart.
Click on chart to enlarge.

Third chart: the waves of an outbreak. Wave 1 was 2013 while Wave 2 started in Oct-2013 but really kicked off in Jan-2014. Cases dived in Feb-2014 but there are still sporadic cases being reported each week. The Week (#53) beginning 17-Feb-2014 saw 8 cases followed by 7, 4 and 0 for subsequent weeks. Keeping in mind that there are around 4-12-days (currently averaging 8-days overall) between onset of illness and when a case get confirmed by a laboratory (or reported publicly if no specific lab date is available), we may see a few more cases assigned to the last week of February yet.

Fourth chart.
Click on chart to enlarge.

Fourth chart: Age and sex of H7N9 cases. The age pyramid shows a decidedly upside down pyramid indicating that H7N9 disease is one of the older age bands. It also shows that it is a disease of men morseo than women.

Fifth chart.
Click on chart to enlarge.

Fifth chart: age by week and proportion female. This is an interesting one. There was a dip in the proportion of female cases for the week the week beginning in 3-Feb (right hand y-axis) which bounced back up a week or two later. 

Sixth chart.
Click on chart to enlarge.

Sixth chart: H7N9 cases per day and the rolling average. The decline in Wave 2 cases continues with multiple recent days recently in which no new cases occurred.

Middle East respiratory syndrome coronavirus (MERS-CoV): summing up 100 weeks

We stand at 182 cases with 78 deaths. The proportion of fatal cases (PFC) stands at 43%.

• Median age of all cases, including deaths, sits at 53-years (missing data on 13 cases); median age of fatal cases is 60-years
• 47% of all MERS cases with data are >55-years of age; 36% are >60-years
• 65% of cases are male (missing data on 18 cases)
• Underlying comorbidities feature in most severe disease MERS cases
• Approximately 18% of MERS-CoV cases are in healthcare workers; 2.7% of all fatal MERS cases are HCWs
• 81% of case are from the Kingdom of Saudi Arabia (KSA); the Arabian peninsula is the zone of case origin
• Reliable real-time reverse transcription polymerase chain reaction (RT-rtPCR) assays exist for detection, confirmation and genotyping
• Camels have been found on multiple occasions at multiple sites in the region to have antibodies to an antigenically similar virus to the MERS-CoV and nasal swabs have been found to be MERS-CoV RNA positive, as have humans in contact with the same camels (infection direction unknown). 
• Camel, goat, monkey, alpaca and human cells lines efficiently replicate MERS-CoV (multiple intermediate sources?)
• 1 diagnostic sequence of MERS-CoV RNA has been identified in a Taphozus perforatus bat (origin of animal other infections?)
• MERS-CoV uses DPP4 (CD26) as its receptor on host cells, a molecule found on some cell lines and epithelial cells of kidney, small intestine, liver and prostate. DPP4 has a standard role in hormone and chemokine activation
• No viable antiviral therapy or cocktail exists to treat infection. No vaccine exists.
• MERS-CoV replicates well in the lower respiratory tract of lab-infected macaques
• Person-to-person (p2p) transmission of MERS-CoV is sporadic
• Genetic variation among MERS-CoV genomes suggests multiple insertions into humans from the source(s)
• Fever, cough and shortness of breath in >70% of 47 cases in KSA; runny nose in 4%; abnormal chest X-Ray in 100%
• Sample often, sample lower respiratory tract to increase chance of successful RT-PCR result 
• Testing 5,065 hospitalized patients, healthcare worker contacts and family contacts found 2% (n=106) positivity over 12-months, in Saudi Arabia 
• MERS-CoV has circulated in KSA during several mass gatherings (2x Hajj pilgrimages and Umrah) providing ample opportunity for p2p transmission. There has been no evidence for an uptick in p2p transmission. We are nowhere near the verge of a pandemic.

Latest confirmed cases and a probable new MERS-CoV case(s) in France [UPDATED]

It's been a couple of days since the last report of a new MERS-CoV case, that of an expatriate, 23-year old asymptomatic male contact of another case in Doha, Qatar (the 7th seemingly acquired on Qatari soil). 23M (FT#150) was mildly ill and was diagnosed through routine screening of contacts. The man worked with animals in a barn owned by a previous case according to the latest WHO update. Once again this highlights that the MERS-CoV can move on from an infected person and it can do it stealthily. However, the next "round" of infection seems to be (a) milder in severity and (b) the end of the transmission event.

Unfortunately the recently described MERS-CoV-positive 83-year old woman in Jubail on the eastern coast of Saudi Arabia, has reportedly died. Apparently she was hospitalised a month ago.

Buzzing around on Twitter (thanks to @makoto_au_japon) and the web nothing is the story of a probable case in a 43-year old in France. The man returned from a stay in Saudi Arabia and he is currently described as stable. There areno more details on France's Department of Health and Social Affairs website but they have noted it on their Twitter feed (@Minist_Sante) and have the media release. The various translations mention the plural, "cases" (machine glitch?). An article in the Khaleej Times notes it is unclear whether this person was a pilgrim to the Hajj. My Form 3 French is very rusty and didn't covered public health so I eagerly await laboratory confirmation. 

If this imported case is confirmed [UPDATE: it was not] it will be France's 3rd detection, only 1 of which has been transmitted locally.

The MERS-CoV laboratory confirmed count currently stands at 148 cases with 63 deaths (PFC of 45.6%) .

MERS-CoV update...

Click to enlarge. Schematic of the MERS-CoV.
Feel free to use, please just cite 
Virology Down Under and Dr Ian M Mackay

No major jump in Middle East respiratory syndrome coronavirus (MERS-CoV) cases over the past 2 weeks. Great to see.

In parallel to this slow-down in new announcements, the World Health Organization's last few MERS Disease Outbreak News (DONs; 19th Sept, 20th Sept and 4th Oct) announcements have have given no specific detail but rather age ranges, date of onset ranges and comments in a general and format that is not linked to specific cases.

While the 3rd Emergency Committee convened by the Director-General under the International Health Regulations decreed September 25th that the conditions for a Public Health Emergency of International Concern (PHEIC) have not been met, it did conclude the following:

• strengthening surveillance, especially in countries with pilgrims participating in Umrah and the Hajj;
• continuing to increase awareness and effective risk communication concerning MERS-CoV, including with pilgrims;
• supporting countries that are particularly vulnerable, especially in Sub-Saharan Africa taking into account the regional challenges;
• increasing relevant diagnostic testing capacities;
• continuing with investigative work, including identifying the source of the virus and relevant exposures through case control studies and other research; and
• timely sharing of information in accordance with the International Health Regulations (2005) and ongoing active coordination with WHO.

The following press briefing by Dr Keiji Fukuda noted that:

• cases have been found in 9 countries
• no umrah visitors were infected
• more cases in men than women (~59% male)
• about a third of (so-called sporadic) cases occur in the community; acquired there via an unknown exposure.
• older, male, underlying conditions have most severe outcomes
• suspicion is that exposure is related to animals but how remains unknown
• another group is person-to-person (family and hospital settings) that lead to clusters but no translation to community case spreads
• we are seeing the emergence of a new virus, limited to the Middle East, but the full picture remains to be captured
• we are seeing more mild cases as surveillance picks up but the disease should not be considered mild
• overall levels of testing after umrah is variable and overall  testing in a number of countries at particular risk of infection is sub-optimal
• an ideal level of surveillance should be sustained, not bankrupt the country or exhaust resources but identify whether infections are coming into a country or if infection trends are changing. The level of detail depends on the country.
• WHO is, in general, providing all the information they have

My count seems to be 139 cases with 58 deaths among those giving a PFC of 41.7%. This included the reclassification of 2 "local" Italian cases as probable rather than laboratory confirmed. FluTrackers and I keep the continuous numbering system though, we just deduct 2 from the tally.

Click to enlarge. A map showing countries where cases have
been detected (orange) and those where local transmission
has occurred (red).

In context of global infectious diseases, that is not a large number of cases but it remains a high proportion of deaths. 

To tackle this high PFC, we really need to do something, on a research basis (so as not to bankrupt or over-tax already strained diagnostic services), that was not specifically listed above; test more well people prospectively. This will address how widespread the virus is among those who are not older, male and sick with comorbidities.

Seems like a job for local academic medical researchers - with some special government funding made available perhaps?

H7N9 in Shanghai...

7th H7N9 death, 64M retiree from Shanghai.

First new death from infection initiated after the WHO notification date.

Two new positive cases also. See time line for the 24 H7N9 cases so far