The proportion of fatal cases (PFC)...

This is excerpted and altered a little, from a more influenza A(H7N9) virus slanted article to be found here. But I think it deserves its own page.

In July 2013 I coined a term on VDU to avoid the use of the term Case Fatality Ratio/Rate/Risk (CFR). 

My term was the Proportion of Fatal Cases (PFC). I use the term on VDU and have published it an article.[1] I have no expectations that anyone else will use it although I notice it made an appearance in a HeathMap story[2] by Maia Majumder.

The PFC is a percentage calculated as the currently known number of fatalities divided by the number of total lab-confirmed cases including fatalities, regardless of whether surviving cases are inpatients (hospitalized) or outpatients.

The PFC is just a number - it's not meant to imply that every case that ever happened is included - it never could. It does not account for those cases who will die later on, either directly or indirectly, as a result of their infection but who may be alive at the time of calculation. 

The PFC is a snapshot to be used before an outbreak is done and dusted. It is meant as a guide to what is happening right now using the data we can get our hands on. Sometimes that means lots of data and sometimes they are very limited or just plain behind closed doors.

The CFR makes use of the number of recovered cases in its denominator.[3] So it's important to know survivor numbers. As suggested above, this requires that all the people who will recover from their infection, have recovered (and been discharged) from their infection. 

Using the CFR early in an emerging virus/disease outbreak, when what usually brings in outbreak to our attention is death, is great for selling papers, but not helpful realistic in a bigger picture sense. 

The CFR is most useful at the end of an epidemic/pandemic, but not so much when data-in-hand is poor during the early days of many outbreak. 

Of course, some will take a PFC and multiply it by the world's population as an estimate of how many are going to die if the virus reaches pandemic levels. That's not helpful or accurate. Just accept it as that snapshot of what's happening now.

References...

1. J. P. Dudley and I. M. Mackay. Age-Specific and Sex-Specific Morbidity and Mortality from Avian Influenza A(H7N9). J. Clin. Virol. 2013. Nov;58(3):568-70. ePub Sept.
   http://www.ncbi.nlm.nih.gov/pubmed/24091087
2. http://www.healthmap.org/site/diseasedaily/article/estimating-fatality-2014-west-african-ebola-outbreak-91014
3. http://en.wikipedia.org/wiki/Case_fatality_rate

Ebolavirus disease (EVD) cases, clusters and outbreaks mapped out...

The West African region outbreak (top map) and the totals from past Ebola outbreaks and the few imported monkey cases (the US & Philippines; hence zero human cases) plotted by total numbers and country (bottom map)

These maps are best viewed alongside my Ebola numbers page found here.

The WHO have commenced creating multi-page Situation Reports.[2] They contain more granular data than is publicly available. They will be reported at least once per week.

If I become impatient, I'll cobble together the individual country's numbers via reliefweb.int, then update that once WHO data are available (which may result in a drop in totals as WHO numbers may have been collected a littler earlier).

This is a static page - it will be updated with new numbers but the website address will remain the same.

Latest data taken from: http://apps.who.int/iris/bitstream/10665/135029/1/roadmapupdate26sept14_eng.pdf?ua=1
Date of DON: 26-Sept
Dates covered: 23-Sept

Learn About Tableau

A note about the proportion of fatal cases (PFC): 
On these graphs, my PFC calculations for West African countries and the DRC are based on dividing the total number of suspect/probable/confirmed deaths by the number of total suspect/probable/confirmed cases for the same date. This is crude and may be a sizable underestimate of the true PFC.

It may be better to use the deaths at the most recent date divided by the total cases from 9-14-days  earlier (this number is not precisely known) to better account for the lag in time between presenting to a treatment facility and dying (for those who do not recover). 

Some estimates suggest the true PFC may be closer to 80%. I don't have enough data (or smarts) to be able to calculate that for now so please be aware the PFC above is likely an underestimate

Reminders:

• 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. 
• Sometimes there are very country-specific differences in what gets presented to/via the World WHO DONs/SitReps which make this process less clear than it could be. I recommend you have a read and compare the data from each of the countries for yourself to understand these issues. 
• As I've talked about previously,[1] these numbers are all volatile for a variety of reasons, some Ebola-specific, so regard this chart for its trends only.
• I am only able to plot what is publicly available. To date, this does not include granular data with dates of onset, or daily data of any kind. The WHO have these data and you will see them become more available through their Situation Reports found here http://www.who.int/csr/disease/ebola/situation-reports/en/

References... 

1. Ebola virus disease and lab testing...
   http://virologydownunder.blogspot.com.au/2014/04/ebola-virus-disease-and-lab-testing.html
2. Ebolavirus outbreak Situation Reports
    http://www.who.int/csr/disease/ebola/situation-reports/en/

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

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.

MERS-CoV: another emerging virus that just...stopped emerging?

Click on image to enlarge.
Data are plotted using sites of acquisition of MERS-CoV
infection. Dates are of illness onset when reported, 
otherwise the date the case was announced

Two charts by way of an update on cases of infection by the Middle East respiratory syndrome coronavirus (MERS-CoV)...which shows that there is not much to update from my last charts on Jan-17 here and here.

Click on image to enlarge.
Same accumulation graph (green) together with the
accumulated fatal cases and the proportion of fatal cases (PFC)

The main feature of these two charts is that cases have plateaued. There has been little recent reporting of new MERS-CoV infections...from anywhere.. for some weeks.

Has something been done within the Kingdom of Saudi Arabia (KSA) to interrupt the transmission chain between whatever the MERS-CoV source(s) was(were) and humans? 

We have not heard of any measures and of course no-one is generously offering to clarify this obvious and abrupt change in epidemiology. As has always been the case with the MERS story, this new turn of events leaves one unsure of what to think about this apparent sudden decline of case announcements. 

I'm wondering if reporting has simply ceased. Two reasons for this personal view:

1. The most recent MERS-CoV case was a 55-year old male healthcare worker (HCW; Bangladeshi surgeon working at Prince Salman Hospital) who died 15-Jan in Riyadh. Now sure, he may have acquired MERS from an animal source (camel, bat, mouse, or cow, we don't know) but the odds, to my mind and with the MERS-CoV picture to date, it seem much more likely that he was caring for someone afflicted with MERS-CoV, which would mean 1 or more other cases exist but have not been reported.
2.  The level of communication from the KSA about many aspects of MERS-CoV has not been of the quality that could foster any trust. It often appears that free communication of has been stifled or strangled rather than nurtured or nourished. The specifics to support that opinion can be found in browsing through my posts on MERS-CoV this past year or so.

So its impossible to say more about what's happening with MERS-CoV infections beyond the fact that they have not spread, noticeably, beyond the bounds of the Arabian peninsula.

Tracking virus-related deaths using publicly available data...

Click on image to enlarge.

Here's the cumulative case chart overlaid with the cumulative deaths and PFC. see the story behind the term PFC here, created by VDU to avoid issues around case fatality rate/ratio (CFR) which relies on knowing when cases have recovered.

I have two PFC values charted here. In black dots, is my curated list based on fatal cases (n=40; red dots) that have been announced publicly. 

In yellow are the numbers gleaned from media releases and the WHO - the latest number being 52 fatal H7N9 outcomes. 

Somewhere towards the end of the initial H7N9 outbreak in May, we stopped seeing reports from China that could link fatal cases with those H7N9 cases they initially announced. If anyone knows of a complete public list of fatal H7N9 outcomes that contains all 52 cases with age/sex/date of illness onset/date of death/province, I would be most grateful to be made aware of it.

MERS-CoV cases #82 and #83 are mildly ill outpatients.

Hat tip to Crawford Kilian.

Two new MERS-CoV cases reported on the Kingdom of Saudi Arabia's Ministry of Health website.

Both cases are from Asir (Southwestern KSA), the 42F (F=female) is possibly a healthcare worker and the other, a 26M, had contact with another MERS case. No dates. No details of which case.

The KSA has now hosted 86% of known MERS-CoV cases. 64% of all cases with data being male. The new PFC is 53.6%.