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Adding in the recent MERS-CoV cases by chart...we're back to 2013

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According to my personal list...

Total cases globally: 714
Total deaths globally: 225
Proportion of fatal cases (PFC): 31.5%

My data still do not include the found113 cases, reported by the Command & Control Centre of the Ministry of Health (MOH) of the Kingdom of Saudi Arabia (KSA; gasp) 3-June because they can't be included. They have no accompanying data apart from some of them not being confirmed/sent for confirmation, by a second laboratory. And we see how that rolls in the recent Bangladesh case hmm?

This is the latest version of the case per day charts. This have dropped to 1/case per day on some days, since 10-June. Since the 3-June, the majority of KSA dates refer to the date the case was reported (not illness onset, the preferred norm for this sort of epidemiology); dates from cases in other countries that have been filtered through eh team at the World Health Organization, are more rich in data (and include 2 of the recent KSA cases).

The trend line is not really needed but shows the steady and very linear decline in new MERS-CoV detections since the new new acting Health Minister Adel M. Fakeih, took over the MOH's reigns in late April.
Click on chart to enlarge.

Just for interest, here is the very same period from 2013. If you exclude the massive healthcare-associated outbreak that was Jeddah-2014, the cases numbers look identical. 

Click on chart to enlarge.

So now we're "back to normal" MERS-CoV detections, unless another outbreak bypasses infection control and lifts the numbers of course. I guess we now wait to hear the results from the new studies being conducted in the KSA and nearby countries. Hopefully these will better explain how "back to normal" works? Including addressing...

  • How cases keep ticking over? This will be better understood once we know what the transmission method(s) from camels to humans is(are) e.g. mucous, ingestion, aerosol, splashing, sideways glances or YouTube video creation
  • What the community seroprevalence is, both overall in the KSA and in the recent hotspots of MERS-CoV activity
  • How many camels are actively infected with MERS-CoV at any given time, how many are obviously showing signs of illness (runny noses etc) and is active infection mostly restricted to juveniles (as the research studies suggest) or can older camels be a source of human infection (less often suggested)
  • Are infected camels being imported into the Arabian peninsula from outside the peninsula (see today's Storify collection with questions and data from @influenza_bio by visiting reference [1])?
And many more questions for which I know of no specific studies under way, that may nonetheless address whether there are human infections that have been acquired from within countries with MERS-CoV infected camels other than those in the Arabian peninsula. These include Egypt, Ethiopia, Nigeria and Kenya.

References...
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Back to 21 countries with MERS....still no party ensues

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Well, it looks like some of us jumped the gun and did not tick all of our self-imposed quality assurance boxes. Yes, definitely including me.

With the sample(s) from a Bangladeshi expatriate apparently testing negative at a second laboratory, the previous comments by Prof. Mahmudur Rahman announcing a MERS-CoV positive traveller returning form eh USA via the UAE, seem to have lacked solid support from reliable laboratory analysis. It certainly makes more sense for the test result to be a false positive than the alternative; a very strange concurrence of circumstances which lead to the MERS-CoV infection that was announced.

Since it was never formally announced, it may never be formally retracted, but it would be nice to know precisely what led to the positive result and how things proceeded from there.

So this puts another of those wonderfully wild, hypothesis-generating, hand-waving MERSmoments where we tried to bend reality into a shape capable of fitting in the box made out of everyone's overly eager need to report things fast and first....behind us.

Nothing to see here. Move along. D'Oh.

Click on map to enlarge.

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Ebola Virus Disease: Country contributors in 2014 West African outbreak...

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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.

As the Ebola Virus Disease (EVD) outbreak in West Africa continues [1], and grows larger, I thought it worth looking at which countries have contributed cases lately. 

  • In late May, Guinea started to see a new, and since then steady, ascension in the number of suspected / probable / confirmed cases and and deaths. 
  • In early June, a big jump occurred in Sierra Leone. 
  • In Liberia there was a rise not in cases, but in fatalities; for a while Liberia had an unusually low proportion of fatal cases (PFC), at just 8%, then something happened to the numbers and it climbed to the higher proportion we expect from Ebola virus.

As I noted last night,[2] and Maia Majumder has also noted on her blog [3] and via a very nice story by the Toronto Star's Jennifer Yang,[4] the PFC for this outbreak is lower than that seen in a number of previous EVD outbreaks (see last night's post for related charts from me [2]). In fact it has been lower than that from other outbreaks at all preceding data points in 2014. Of course this lower PFC, still sitting at a horrible 64%, may just be an artefact of the outbreak not being over yet, and the dust probably still being in the air and yet to settle. 

The PFC may rise as more information is gathered and testing completed, post-outbreak. It it may also be that due to the quick deployment of experts in healthcare, education and laboratory analysis, and perhaps new or different supportive methods, that this outbreak is not taking as many lives as previous outbreak have. But I can't speak authoritatively on any of that.

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,[5] 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 | 18-June-2014
    http://www.who.int/csr/don/2014_06_18_ebola/en/
  2. West African Ebola virus disease (EVD) outbreak flares up in late May and in early June...
    http://newsmedicalnet.blogspot.com.au/2014/06/west-african-ebola-virus-disease-evd.html
  3. Ebola 2014: Fatality & Lab-Confirmation Charts
    http://maimunamajumder.wordpress.com/2014/06/19/ebola-2014-fatality-lab-confirmation-charts/
  4. The Ebola outbreak that refuses to die
    http://www.thestar.com/news/the_world_daily/2014/06/the_ebola_outbreak_that_refuses_to_die.html
  5. Ebola virus disease and lab testing...http://newsmedicalnet.blogspot.com.au/2014/04/ebola-virus-disease-and-lab-testing.html
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West African Ebola virus disease (EVD) outbreak flares up in late May and in early June...[UPDATED]

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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...
  1. http://www.who.int/csr/don/2014_06_18_ebola/en/
  2. http://www.hpa.org.uk/Topics/InfectiousDiseases/InfectionsAZ/Ebola/GeneralInformation/
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Influenza in Queensland, Australia: 1-Jan (Week 1) to 8-June (Week 23)

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Map of Queensland's Hospital and Health service 
areas. Adapted from
Click on image to enlarge.
Waaaay back on 18-March we looked at how influenza notifications in Queensland (population ~5mill) were above the 5-year-to-date (YTD) average. 

"Woopty Doo" some, perhaps very few, of you said. "That number means nothing until you look back at it later". 

So, let's look back at it now that it's later. 

It was Autumn then and now its Winter which is Flu season and also the season when we get some more public info on a handful of other  respiratory viruses circulating here in Queensland thanks to the collatory (I don't care if a dictionary doesn't recognize it) genius of the crew at the State of Queensland, Queensland Health (SoQ|QH).

So what's happening with flu Down Under? For all the detailed detail, I recommend you check out the Open Access document, Statewide Weekly Influenza Surveillance Report that spans up to Week-23 (that's the week ending 8-June; we're in Week 25 now)

Turns out its still 2x (well,  1.987x but who;/s counting?) above the 5-year-to-date mean. No, this is not a "I told you so" - just that it's interesting to see that on this occasion at least, autumn trends predicted a winter event. Still, its only early winter. We've also had a very warm and dry autumn (see the Bureau of Meteorology for more on Autumn) for those who like to link weather and influenza activity.

I like to look at virus interactions as driving their own seasons. How is that possible I eerily hear you ask (I'm not listening to the "Oh what a load of..." comments by  the way, so sit back down and put up your hand)? Well, they don't do anything themselves of course, but my theory goes like this...

When there are enough of us in the community infected by one virus (say respiratory syncytial virus [RSV]) and our immune-thing-a-me-whats-it is all fired up and producing an inflammatory response to rid us off said pestilence, that responsey thing offers a kind of "Shield's Up" effect. 

For a short while we feel like rubbish but we also don't let other viruses get in as easily because we're in an "antiviral state". Enough of us in that state and we get a kind of short-term herd immunity (a fairy died) - where the number of people fully susceptible to another virus (say, an influenza virus) is too small for it to get a good toehold in us and the population. This pattern among seasonal respiratory viruses is most often observed, in my experience, for viruses with an RNA genome like RSV, rhinoviruses and influenza viruses. 

Thankfully for my hypothesis, the data from SoQ|QH show a nice example of this pattern of viruses interacting with viruses within us, projected to the level of the community. 

A snippet from the State of Queensland, Queensland 
Report  for 1-January-2014 to 8-June-2014.
Edited by Ian M Mackay, VDU.
Click to enlarge. 
Let's have a look at the adjacent figure I've mixed around from reference [1]. Hopefully I haven't broken any copyright laws in hacking pasting as I have.

Part A shows the notifications for influenza viruses in Queensland. Peaks and troughs, As and Bs. Cool

Part B shows some of the respiratory viruses, including RSV which has been having a bonza season this past autumn by the looks of things.

Can you see the pattern?

Part C is a cobbled together composite I made in Photoshop/Illustrator by laying B over A and making B partly transparent. It's a bit rough and has had the axis labels and legend trimmed off for clarity, but it makes the point. What it shows (to me anyway) is that when RSV numbers go up, influenza virus notifications head downwards. 

Is this due to RSV influencing influenza or influenza exerting its muscle on RSV? Can't tell from this sort of analysis. 

The fact that RSV can rise in the presence of influenza virus may speak to its dominance. But take a step back. Remember we're taking about people not cells in a dish. It may be that 2 distinct populations are at play initially; perhaps younger children with RSV versus older children and adults with influenza. Once infected people reach a critical mass, that virus may win out and "push put" the other.What's happening in a single household - kids bringing home one virus, parents another perhaps? That would be intriguing to know with these concepts in mind using molecular methods and longitudinal regular sampling of whole families, regardless of symptoms.

Statistically, when I've looked at this with other data, that negative association, more obvious and frequent between influenza virus and rhinoviruses, does reach significance. You can read one of my group's hospital-based studies in [4] and a collaborative community study in [5]. Rhinovirus seasons usually bracket influenza season. So I offer a different view of how seasonal viruses are seasonal. With the sources of variability I discuss above as well as genetics and differences in everyone's past virus exposures and immune-thing-a-me-whats-it status to each virus, some cross-protective, some not, some having got really sick last year, some not...its not hard to see how those virus seasons can shift around from year to year as well.

Yet another reason to test for viruses, and to include more than just 1 or 2 viruses in that testing; the more you test, the more you can observe and learn.

By the way, interferon-the major player in causing these virus:virus interactions, got its name because it could block a secondary viral infection much like those that I've described above, but on a population level.

Now, try and get some funding to do any research on that. I hate you if you do by the way (yes, I failed miserably).

References...

  1. Statewide Weekly Influenza Surveillance Report, 1-January to 8-June 2014.
    http://www.health.qld.gov.au/ph/documents/cdb/influenza-qld-140101-140608.pdf
  2. Queensland in autumn 2014: A warm autumn; coastal rainfall but dry inland of the Great Dividing Range
    http://www.bom.gov.au/climate/current/season/qld/summary.shtml
  3. Do rhinoviruses reduce the probability of viral co-detection during acute respiratory tract infections.
    http://www.ncbi.nlm.nih.gov/pubmed/19376742
  4. Community-wide, contemporaneous circulation of a broad spectrum of human rhinoviruses in healthy Australian preschool-aged children during a 12-month period.
    http://www.ncbi.nlm.nih.gov/pubmed/22829638
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MERS-CoV detections by week...

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Yeah, I got bored waiting. 

I finally came around to the fact that the data for MERS-CoV have always been so inconsistent that why worry about that now. So what about dates? I have no idea how long it will be until we see the WHO post data with dates for the hundreds of Kingdom of Saudi Arabia (KSA) cases we know nothing much about that occurred in the Jeddah-2014 healthcare outbreak. The WHO without Gregory Hartl is a much less interactive entity on social media these days. One person can make such a difference.

As it stands, the KSA Ministry of Health has clearly decided to hold fast on not releasing dates for symptom onset, hospitalisation and death for new cases; the new and improved Command & Control Center (CCC) colour scheme speaks for the data....instead of having the data....it seems.

Click on chart to enlarge.
So, the chart. It shows the end of the outbreak in western KSA...still...having been that way for a few weeks. Its hard to tell exactly when the cases have fallen out for the last 13 days or so, since we don't know when they became ill (which is what I use most often when plotting cases-and will again should those data ever become available). So take those dots over the last month with a grain of salt for now. I expect they will reduce in number as they sort into the preceding week(s). 

As I note in the chart - I do not include the "found113" cases here. They remain dodgy data for now. I'll also wait for the WHO to make sense of them.
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Epidemiology without dates is just -ology...

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Click on image to enlarge.
Data from the Kingdom of Saudi Arabia Ministry of Health MERS website.[1]

The above images give an indication of what the Kingdom of Saudi Arabia's Ministry of Health (MOH) considers to be case detail of immediate relevance to the public according to Prof. Tariq Madani, head of the scientific advisory board within the MOH's Command and Control Centre (CCC). 

Since the newly revised CCC MOH website came online, dates that describe key information have been absent (red dashed outline in the screen capture above). These dates include:
  • Date when symptoms began
  • Date of hospital admission
  • Date when a new fatal case was first reported (allowing a link to be made)
    • Click on image to enlarge.
    Where the re-defined 113 cases fall out across 2013 to
    1st week of May, 2014.[3]
  • Date when a recovered case was first reported (allowing a link to be made; actually this one hasn't ever been present)
Sure, we only had these dates for a short period, and relied heavily on the World Health Organization's (WHO) Disease Outbreak Notifications (DONs) to fill in and "scrub" the data once it was submitted to them, but it was so great while it lasted. 

I have had many emails and Tweets noting how useful it's been to others to see those data distilled into more digestible graphs and charts. These notes have come from both the public and from other scientists too.

This latest change to the MERS information provided us, came after a report on 3-June [2,3]. That is also the entry between where there were dates included [orange] and where dates stopped being included [red] again, in Part A above. The report described a review which started in May and found 113 un(publicly)reported MERS cases (see the bar chart above). Interestingly, 55 of these cases were either not sent to, or were not confirmed by, KSA governmental laboratories (thus should be better listed as probable cases IMO) while 58 results just hadn't been sent to the MOH, who "sign off" on the final reporting of MERS-CoV detections. Great that the CCC is able to track these down and admit to them. Good work. 

Not so great that 33 of the 55 cases are included in this tally despite not being able to be confirmed. 

In response to the "found 113", I halted my charting activities for MERS-CoV that week. I won't be resuming charting until the very long-awaited WHO's DON fills in the gaps on over 400 cases[6].

Much has been made by the media, some of it with comments from me[2,8], of these events. Some have noted that there is now a new sense of transparency about. While I don't argue with reports and comments about a range of collaborative efforts now/already underway (which is great news) and the need to acknowledge things when they improve, I do question how the retraction of some key data, essential for public epidemiology efforts, data that were fine to be included (inconsistent as they were even then) previously, can be labelled as transparency. I certainly don't think those actions meet up to this statement (bolding is mine)[3]...
"Based on the findings of the review, the Ministry has already put in place a number of measures to ensure that best practices of data gathering, reporting, transparency are being strictly observed.."
I've stated before, for H7N9[4] and for MERS[5] that we, the public, do not have a right to such data, even though its deidentified and the privacy of the patient is protected. We may feel entitled, but we are not. As long as the WHO and appropriate Committees or experts are aware of the facts and can judge the risk to the world, then that is the main issue.

Of course, I'd much rather we lived in a world where such relatively innocuous data were available, and complete. But whether or not we get to play with useful and rich data is a separate issue to the difference between saying something is so and it actually being the case. 

There has been an increase in the presentation quality (prettiness) of data but a decrease in the data presented, since the CCC website came online. That's a fact. 
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*POSSIBLY NOT* Country #22 to have been paid a visit by the MERS-CoV: Bangladesh [UPDATED x2]

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Looking like this result could not be confirmed 
by external testing.
June 20th 


The case, a 53-year old male (53M) returned to Dhaka, Bangladesh on 4-June from New York (the United States of America), via Abu Dhabi (United Arab Emirates). He became symptomatic on 6-June and was hospitalized 9-June.

Director of the Institute of Epidemiology, Disease Control and Research (IEDCR), Prof. Mahmudur Rahman, speculated that 53M was likely to have contacted MERS-CoV in the UAE. It's not clear whether he transited through the Abu Dhabi airport (apparently he was at the airport for 3-hours, h/t @influenza_bio; seems like a very unlucky acquisition then[4]), or stayed there for some time. 
It's also not clear how long he stayed the the USA for. The WHO have been informed, according to reports.

A 2-day incubation period is a bit on the short side for MERS-CoV though. Eagerly awaiting the WHO DON on this case.

[UPDATE] It looks like this sample could not be repeated. If I read any further announcements I'll post them here buit for now it appears that the two samples may have been false positive results. How that could happen I'm really not able to imagine. But we'd need to know more about the testing to answer that.

Sources...

  1. FluTrackers thread
    http://www.flutrackers.com/forum/showthread.php?p=537546#post537546
  2. Treyfish's H5N1 pandemic information news blog
    http://swineflumagazine.blogspot.com.au/2014/06/more-on-bangladesh.html
  3. The Daily Star
    http://www.thedailystar.net/mers-detected-first-time-in-bangladesh-28635
  4. Channel NewsAsia
    http://www.channelnewsasia.com/news/health/bangladesh-reports-first/1162024.html
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