There (might be) something in the air tonight... [UPDATE]

UPDATE No.1 06SEPT2016

One of the early pieces of science-based news to come out of the May-2015 Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak in South Korea was a June-2015 piece asking whether air conditioning may have played one (of many?) key role in facilitating the spread of virus from infectious patients, within healthcare facilities.[1]

In a publication that came out in April 2016 (yes, the literature did not see much detail on the South Korean outbreak for quite some time), authors described a study to collect and test air and swabs from surfaces in and outside patient's rooms, and their restrooms, in 2 hospitals that housed 3 male cases of MERS pneumonia.[2]

Whenever RT-PCR is used for this sort of work, it brings with it the question of whether infectious virus-containing droplets were captured, or only bits of non-infectious RNA viral genome was detected. This group, like those in the last post (who did not collect air samples), attempted to grow infectious virus. They could confirm that it was infectious virus by observing cell changes in infected laboratory cultures which were also RT-PCR positive. Also the same approach as that described by the South Korean study reviewed in the last post.[3] Additionally, the infected cell cultures also reacted to an anti-Spike protein antibody in a fluorescent test and they even saw some actual virus from swab cultures (not captured air samples?) using electron microscopy.

Some interesting findings from the use of these test on air and swabs samples included:

• All air samples from both hospitals were RT-PCR positive and these included the detection of MERS-CoV of RNA in room, restroom and common corridor air. Infectious virus was grown in cells from from 4 of 7 (57%) samples.
• 42 of 68 (62%) surface swab samples tested positive for MERS-CoV RNA by RT-PCR and included elevator button and rails, doorknobs and handrails inside and outside a patient's room, telephone button, toilet seat, call button, patient pillow, nasal prong, toilet seat, TV, keyboard, stethoscope and air exhaust dampers. Infectious MERS-CoV was isolated from 15 swabs of some of these items including an elevator button, nasal prong, patient pillow, TV, bed handrail, keyboard, stethoscope, toilet seat and an air exhaust damper

This study really addresses three big issues. 

Firstly MERS-CoV from very ill patients late in their disease course, thoroughly contaminates a hospital room and its surrounds - not just with detectable genetic material, but with infectious, viable MERS-CoV virus. 

Secondly, surface contamination was detected from swabs collected 3-7 hours after daily room cleaning suggesting either that cleaning was insufficient or that new virus was quickly laid down on cleaned surfaces (with no lasting anti-viral effect from the cleaning solution). 

Thirdly, the capture of infectious virus from the air implies that the virus maybe present in droplets or droplet nuclei with implications for the level of personal protective equipment required for healthcare workers and visitors to an infected person bedside. It also pertains to the distance away from a case that is considered "safe" for an uninfected person to be. Six feet may not be nearly enough distance, at least if that is a prolonged period in a room.

This provides some more data to explain how MERS-CoV may be associated with hospital outbreaks. Why it has been allowed to get away with this is a matter for infection prevention and control specialists in each and every healthcare facility to address.

UPDATE.

After this was published, Van Kerkhove and colleagues wrote a letter to the editor to make some points about the study noting:

• an absence of negative control sampling from areas where MERS-CoV patients were not housed.
  Absolutely. I'd even suggest a few different sites in very distant hospital areas from where MERS patients were housed, given the possible human-spread of virus around a facility during and the possibility of silent or subclinical infection in patients admitted to hospitals for other reasons during times of outbreak. This will explore whether false positive laboratory results are occurring.
• other studies have reported surface contamination that did not yield viable virus. Van Kerkhove note that these negative findings need to be published to balance the literature. Always.
  However, it's well known that virus culture is insensitive compared to RT-PCR methods so it may fail to detect infectious virus which may be enough to infect a human . It may also be that infectious virus capable of infecting another person who comes into contact with it is not always present in the air or on surfaces. It may be that the surfaces often simply have non-infectious "bits" of virus detected by RT-PCR -these cannot cause a new infection. But in this study infectious virus was able to be isolated from air and surfaces...unless Van Kerkhove and colleagues are implying contamination of the cultures in some way.
• the need to replicate these findings in other studies.
  Always.
  But as is often the case, let's not wait on those findings to recognise that infectious droplets and contaminated surfaces now have some more data to support them and that they fit nicely into a picture of hospital transmission. Precautionary principle.

A second letter was also written by Myoung-don Oh,[7] noting:

• few infected cells in the cultures / slow growth.
  This isn't too surprising, it may just reflect that there was a low amount of virus in the air, added to the cell cultures compared to that used from the control virus (cell adapted?) stock.
  This may mean that the risk from airborne transmission in these rooms is low. However, since we don't know what amount of MERS-CoV is required to start a new human infection, this is a moot point.
• the sequences of the room samples were too different from each other.
  This is a bit surprising since within an outbreak, MERS-CoV doesn't usually vary much at all. I'll have a look at how much South Korea's MERS-CoV Spike gene sequences varied and come back to this point.

Both letters were replied to.[8]

References...

1. Did poor ventilation lead to MERS 'superspread' in Korea?
   http://www.sciencemag.org/news/2015/06/did-poor-ventilation-lead-mers-superspread-korea
2. Extensive Viable Middle East Respiratory Syndrome (MERS) Coronavirus Contamination in Air and Surrounding Environment in MERS Isolation Wards
   http://cid.oxfordjournals.org/content/early/2016/06/08/cid.ciw239.abstract
3. Korea contamination: Middle East respiratory syndrome coronavirus in the room..
   http://virologydownunder.blogspot.com.au/2016/09/korea-contamination-middle-east.html
4. Interpreting Results From Environmental Contamination Studies of Middle East Respiratory Syndrome Coronavirus
   http://cid.oxfordjournals.org/content/early/2016/08/09/cid.ciw478.full.pdf
5. STABILITY OF MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS (MERS-COV) UNDER DIFFERENT ENVIRONMENTAL CONDITIONS
   http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20590
6. Transmissibility of Middle East Respiratory Syndrome by the Airborne Route
   http://cid.oxfordjournals.org/content/early/2016/08/09/cid.ciw479.full.pdf
7. Interpreting Results From Environmental Contamination Studies of Middle East Respiratory Syndrome Coronavirus
   http://cid.oxfordjournals.org/content/early/2016/08/09/cid.ciw478.full.pdf
8. Reply to Kerkhove et al and Oh
   http://cid.oxfordjournals.org/content/early/2016/08/09/cid.ciw480.extract

Update...

1. Added in detail on letter by Van Kerkhove and colleagues [4], and rebuttal authors [5]

Korea contamination: Middle East respiratory syndrome coronavirus in the room..

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Research on MERS in South Korea seems fractured...

I would be remiss if I didn't point out that the Kingdom of Saudi Arabia (KSA) is not the only country that can be seen as slow to initiate local research on local cases of Middle East respiratory syndrome (MERS), MERS-coronavirus (MERS-CoV) or the epidemiology thereof.

The outbreak in South Korea began when an incubating person flew in from Qatar, arriving 4th May. He became ill while in South Korea, with symptoms beginning on the 11th May 2015. This was to become the largest MERS-CoV outbreak outside of the Arabian Peninsula and it is still to be investigated as the overarching single event that it really was. Scientific papers, letters, media and case reports all look at small groups of specimens, this or that specific hospital, a particular slice in time or an interesting group of cases and they reach a range of conclusions. But there appears to be no over-arching all-encompassing study of the outbreak. We did eventually see such a report from the KSA in its description of four dozen early MERS cases - 13 months after the first case became ill.[4] South Korea only had 185 cases in total (exporting one to southern China) so this should not be a great task.

A recent article in The Korea Times noted that "while the initial tests were conducted on a limited number of patients, research is underway to screen clinical specimens from 32 people that will help shed better light on the matter."[1] Well, perhaps a part of the matter. [1]
The article focusses on Spike gene mutations that were found in the MERS-CoV variants from 8 human cases - which is not a remarkable discovery and has been happening since we first saw sequenced MERS-CoV from humans (see "Tracking MERS-CoV through time: a spikey problem" [2]). 

The article also goes on to say that "There is a need to focus the country’s research capability on finding the reason for the change." Those will be dollars wasted since one cannot "find the reason" for a virus mutating because that is akin to asking why we exist. 

Scientific studies can determine that the variants have mutated at certain points and they can seek out whether those changes have any effect on the efficiency of viral replication, transmission or on our immune response to infection. This will be achieved by comparison to other non-mutated MERS-CoV variant viruses and will need more than one older variant to be included so as to encompass all of the different Spike gene mutations that have been determined to date. But these studies cannot find the reason for these mutations. Yes, that is a pedantic point.
We are about 6 months out from when the final MERS case first became ill in the South Korean outbreak. This media report sadly highlights that the world is still far away from seeing comparative experimental data defining whether or not there was anything special about the MERS-CoV variants in the outbreak. Strangely though, it has already been concluded that the rapid spread of MERS-CoV in South Korea was not due to viral changes but instead because of the poor control of transmission in healthcare settings.[3] That makes this report and its message to the public both a little stale and perhaps even unnecessarily alarming.

Clearly, the KSA was not alone in needing to improve its collaboration, communication and organization of research in response to the appearance of a new virus. 

References...

1. http://www.koreatimesus.com/mutation-detected-in-s-korean-mers-virus-govt/
2. http://virologydownunder.blogspot.com.au/2013/08/tracking-mers-cov-through-time-spikey.html
3. http://www.who.int/csr/disease/coronavirus_infections/situation-assessment/update-15-06-2015/en/
4. http://www.ncbi.nlm.nih.gov/pubmed/23891402

A place to be critical...

Around May/June 2015, the Middle East respiratory syndrome (MERS) coronavirus escaped its Arabian Peninsula bonds and exploded...still associated with the circumstances created under lax hospital conditions...into another part of the world entirely - South Korea.

About 20% of South Korean MERS cases were fatal. In contrast, nearly twice that proportion have died after MERS-CoV infection among 26 countries (36% fatal).[1] Meanwhile, a little over twice the SOuth Korea proportion of fatal cases occurs in the Kingdom of Saudi Arabia (KSA; 42%).[2] 

It is interesting to look at another possible measure of clinical impact - how often a MERS patient is publicly described via official channels as being in "critical" condition. I suspect that this term could be applied as arbitrarily as anything else used by humans, nonetheless, see the figure below.

Total MERS-CoV detections (mustard bars; left-hand axis)
and mentions of cases in "critical" condition (red bars; right-hand axis).
Taken from the MERS-CoV data visualizations page.[3]
Click on image to enlarge.

A few things:

• Sadly, you have to ignore the biggest peak - the Jeddah-2014 hospital outbreak (March to June) - as data during that time were rare and detail was mostly absent both from the KSA Ministry of Health and the World Health Organization
• If we look at the South Korea peak (May/June 2015) versus the most recent Riyadh outbreak (July/August 2015), there seem to be a lot more mentions of critical cases. There is also more red visible during the Eastern Region/Ar Riyadh region peak around January/February 2015. 

There may be little to conclude from observations such as this, but it is yet another interesting pattern to muse upon.  

Older males with comorbidities are heavily represented among MERS disease cases that present to hospitals (younger people among those with mild or no notable disease) and older  males and females with comorbidities among the fatal outcomes. A shared risk is that comorbidities are preyed upon by MERS-CoV.

Comorbidities include diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions. All of these are diseases of concern among countries with abundant unhealthy food options, weight issues and ageing populations. Is your country one of those? Even familiar old viruses could re-emerge as threats to this subgroup as the years go by. In the meantime, emerging newly identified viruses create an atmosphere of concern.

MERS-CoV detections broken down by age bands and into total cases
(left hand graphs), and those with a fatal outcome (right-hand grpahs).
Taken from the MERS-CoV data visualizations page.[3]
Click on image to enlarge.

References..

1. http://www.who.int/csr/don/01-october-2015-mers-jordan/en/
2. http://www.moh.gov.sa/en/CCC/PressReleases/Pages/Statistics-2015-10-04-001.aspx
3. http://virologydownunder.blogspot.com.au/2014/08/mers-cov-daily-monthly-and-cumulative.html

MERS around the world...

China was the 26th country to host a MERS-CoV infected person, when a 44-year old symptomatic male (onset 21-May-2015) travelled from South Korea, through Hong Kong to Huizhou in Guangdong Province,  China on 26-May-2015.[1] 

Click on it!
It gets bigger!!!

Reference...

1. http://www.who.int/csr/don/30-may-2015-mers-china/en/

MERS simmers down in South Korea...did we learn anything this time?

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Matching MERS case identification numbers from two differing sources...

Update #1 27JUNE2015
Update #2 28JUNE2015

Sometimes people work from different playbooks.

Figure 1. MERS in South Korea. Most cases now plotted
on graph using their dates of illness onset.
An outbreak in decline. This is up-to-date - 3 new cases
from 21JUN2015 added (column at right hand side -
onset dates unknown)
Click on graph to enlarge

In this instance, the data from the World Health Organization's (WHO) new list of Middle East respiratory syndrome (MERS) cases - with extra detail - uses a case identification key that's out of synchrony with that produced by the South Korean (SK) Health Authority which can be found in each of its posts announcing new MERS cases and deaths. 

Attempting to link the two lists has mostly been an exercise in pedantry, but sometimes it is useful to know which case one is talking about when discussing an outbreak or cluster of disease....'Hey Bill, what didja think of that 70 year old MERS case who drove the ambulance carrying that infected 75 year old MERS case and then those others got MERS as well..?' doesn't really roll off the tongue does it?

Figure 2. What the graph above looked like before
we had dates of illness onset. Many cases
were 'moved' to earlier time points because
report dates always follow onset of illness dates
and they can follow by varying periods of time -
sometimes a day, sometimes a week or more.

Two file formats are in the folder I've linked to below. This is my first attempt - yes, it is a work in progress - to match up the new WHO case list from the 19th June which includes the highly prized date of illness onset (DOOs) for most cases - with that of the South Korean (SK) Health Authority. They do differ. Quite a bit. And in several ways. For example, the numbering scheme is off by one or more, SK69 seems to be missing from the WHO list, there is a question mark hanging over SK152 & SK156 and the WHO data seem to have a number of different ages from the SK data- mostly differing by one year (presumably someone is rounding up or down). 

If I've stuffed anything up or if you can solve my problem cases - please pass that info along and I'll update the files on this page. Hopefully the next WHO version will have addressed all of this anyway (it didn't but perhaps a future one will).

These are publicly available and you can download them for your own interest.

There is a download arrow at the top of the Google Drive page.

1. Google Drive folder with MERS data files
   https://drive.google.com/open?id=0B5sEcTjB5Ailfm1PcU1oNDF6M2hiaDduUDgzQUdxNlZxeHBkU0FHeVBRRFJkbHIxTmdjX3c&authuser=0

Updates...

1. With the help of FluTrackers updated line list to cross check against, the first half of my list has been updated - some bugs fixed. 
2. After about 5 hours - on and off - FluTrackers helped me sort out a few errors and the latest version of my list has been uploaded into the the folder linked above. Some typos corrected.

MERS-CoV in South Korea - other data formats for data provided by WHO...

The following links take you to different version of the PDF if you want to harvest those data...

1. Excel version, Office 2010
   https://drive.google.com/open?id=0B5sEcTjB5Aila3c5WXI4bzlkLWc&authuser=0
2. MS DOS CSV file
   https://drive.google.com/open?id=0B5sEcTjB5AilTHRub1FRZnhpQmM&authuser=0
3. Original WHO PDF
   https://drive.google.com/open?id=0B5sEcTjB5AilWlo0UDZwVzRpdVE&authuser=0

Its taken a week to get these data, and its unclear why detail data dried up from the 12th June to the 19th, or why the data have appeared now, but they are here at last and that's great.

Middle East respiratory syndrome (MERS) coronavirus: Outbreak maps and graphs, South Korea

This static data visualization was created using data from FluTrackers, the World Health Organization and the Korean Broadcasting System (KBS).

Wherever possible, the dates are those for a case's onset of illness, but if that is unavailable then the date for hospitalization or if that is unclear, the date that case was reported.

Because the WHO obviously have more detailed information, I recommend you keep an eye on their site, so long as it is being maintained, for more accurate epidemic curves.

References...

1.  FluTrackers' line list of MERS-CoV around the world
https://flutrackers.com/forum/forum/novel-coronavirus-ncov-mers-2012-2014/146270-2012-2015-case-list-of-moh-who-novel-coronavirus-mers-ncov-announced-cases?t=205075

2. The Korean Broadcasting System's News websites
http://dj.kbs.co.kr/resources/2015-06-08/ &
http://dj.kbs.co.kr/resources/2015-06-04/

3.  World Health Organization pages
Main landing page on MERS and MERS-CoV (includes link to WHO line list under General Information)
http://www.who.int/emergencies/mers-cov/en/
Disease Outbreak News pages
http://www.who.int/csr/don/don_updates/en/ 
News on the current situation
http://www.wpro.who.int/outbreaks_emergencies/wpro_coronavirus/en/
Summary of Korean statistics-rapidly updated
http://www.wpro.who.int/outbreaks_emergencies/summary.of.MERS.stats/en/

Translating from the Korean for MERS epidemiology...

I absolutely love the graphic the Korean Broadcasting Service (KBS) have been putting up. Love 'em. Great job!  I just wish they were in English too. I understand that the first priority is to your own population - totally get that. But I do wish that, like the Saudi Ministry of Health, every country could do an English version as well as the native language. 

But processes, time money and stuff...

Anyway - to help me try and get more detail on the South Korean clusters I have added some translation to one of the KBS pages which, when you click on the icon of a person, gives you a popup box with some detail. I've added translation to the contents of that box (see the figure below). 

I don't know how accurate the "Date of infection" field is but will be comparing it to the World Health Organization (WHO) data from earlier to see if it can be useful. This is all because the date of reporting is almost always different from the date of illness onset - and the latter are much better to plot to get an idea of whether an outbreak is rising, peaking or slowing. Having the ability to crowd-plot these numbers is great and (I think) useful to inform the public and our clinical and scientific peers when included alongside some discussion about trends and reason for changes, risk etc. Often (always?) more personable banter, and engagement, seems to be lacking from 'bigPublicHealth' sources.

Click on image to enlarge.
Adapted from http://dj.kbs.co.kr/resources/2015-06-08/[1]

This sort of data mining seems essential if the recent WHO publication of a minimalist 33-word summary of the last 62 cases is now the norm - or perhaps the provision of information from the South Korean health authority to the WHO has changed in format. And that has become acceptable to the WHO, who have not commented on the change. Such summaries, and lack of comment, are also business-as-usual for 'updating' us on human cases of influenza A(H7N9) virus in China.

References...

1. http://dj.kbs.co.kr/resources/2015-06-08/

Tracing the MERS-CoV cases in South Korea...

The Korean Broadcasting System (KBS) News channel has made an awesome "bump map" or force diagram (thanks @Casillic) showing the layout of cases and the hospitals they passed through or were admitted to or transferred to.[1] It shows sex, deaths (9 across multiple facilities), profession, rounds of transmission and some dates (written as month.day)

Unfortunately for some of us, it's in Korean. If you, like me, are having trouble remembering your grade school Korean, I'm here to help (a little).

I've put together a screenshot of this awesome map as of today's count of  - no doubt the values will change tomorrow - and added onto it the hospital names in English. I highly recommend you visit the actual site though - the map is scalable and interactive. This snapshot does not do it justice and won't be updated like the map seems to be.

I've interpreted the hospital names by eye from the Hong Kong Centre for Health Protection's (CHP) excellent multi-lingual list of all the "MERS hospitals" released by the Korean health authority.[2,3] They may not be perfect and I'd be happy to take any suggestions and corrections (including what is in the orange boxes).

The index case, #1, is shown in green and is linked here to 2 clinics and a hospital - which differs a bit from the WHO story which includes a final move..."whereupon he was transferred to the nationally designated treatment facility for isolation".

The most recent additions seem to have a pulsing arrow (only visible at the source).

Made using a combination of sources. [1,2]
Click on image to enlarge.

References...

1. http://dj.kbs.co.kr/resources/2015-06-04/
2. http://www.chp.gov.hk/files/pdf/distribution_of_mers_cases_en.pdf
3. http://www.chp.gov.hk/files/pdf/korean_hospital_list.pdf

MERS-CoV and opportunity to spread...

1,500 people were exposed via direct or indirect contact, to one Doctor who was already ill and later tested positive for the Middle East respiratory syndrome coronavirus (MERS-CoV).[1]

So what?

If this were measles virus - that sort of exposure could spell disaster for infection control and measles containment. In measles, every infected person can infect about 18 other people...but that's an average of course and on an individual basis, the number of new cases can move around that value depending on the number of contacts each person has...and the type of contact...and how much virus the index case sheds... and everyone's their immune function...etc, etc, etc.

But MERS-CoV ain't no measles virus. 

Time and again we've seen that MERS-CoV does not pass easily to new people. Around 4% of household contacts were deemed infected, across 26 households,  in a study from 2014.[2] About 2-3% in some other analyses.[3] And by 'easily' I mean lots and lots of contact becoming ill from each case they are exposed too. If 4% of those 1,500 hundred contacts of the South Koran Doctor had been exposed to an infectious dose of MERS-CoV from this Doctor - who really does get around - and the incubation period is as short as the 3 or 4 days it has been in some cases in South Korea...then any minute now, we'll expect to see 60 more cases in the community and in hospitals, all with links to this health professional. 

I'm not holding my breath (pardon the pun) for this though, because I doubt the contact was often very close. I also won't go into the fact that there maybe no actual testing of contacts happening - we have no idea of that aspect of the South Korean incident. I really hope the South Koreans are testing. It would be a great study producing some valuable transmission data outside of Saudi Arabia. And not just PCR testing but collecting blood for serology (antibody studies) testing later too.

Google tells me that South Korea has a population of 50,220,000 in 2013. So there have been 87 cases of MERS since May...about 0.0002% of the population are infected. At this point, perhaps we should start assembling a list of how many people went through the hospitals with the most cases, that did not acquire MERS-CoV...just to provide some added context to the cluster. In other words - the past few days have seen case numbers growing day on day - but infections are still contained within the hospital setting. Close contact. No community spread. No camels infected in zoos.

Tomorrow is another day and we'll see what is added to the tally resulting from the arrival of a single infected traveller.

References..

1. http://www.koreaherald.com/view.php?ud=20150604001315 
2. MERS-CoV around the house-yes, it does transmit at home
   http://virologydownunder.blogspot.com.au/2014/08/mers-cov-around-house-yes-it-doers.html
3. If this is what MERS-CoV detections look like with more testing...what is the "normal" community level of virus?? [UPDATED]
   http://virologydownunder.blogspot.com.au/2014/04/if-this-is-what-mers-cov-detections.html

Middle East respiratory syndrome coronavirus (MERS-CoV): unhappy trails...

An updated map of the countries that have had a visit from, and in 52% of those, had some local transmission of, the MERS-CoV.

South Korea is the first country I have seen that has jumped three colour levels between updates. No mean feat.

So we have 25 countries that have hosted a MERS-CoV infected person, and 13 of those have gone on to have local transmission - new cases from that case on their soil.

Click on it!
It gets bigger!!!

In the meantime, 7,000,000 pilgrims are expected in Saudi Arabia to perform Umrah between mid-May (around the 19th May) and mid-July.[1] Over 2,000,000 had already performed the Umrah pilgrimage to The Holy City of  Makkah in Makkah province, between November 2014 and May 2015.[1,2] We're in the second phase of Umrah now - in the lead-up to the fasting month of Ramadan which begins on the 18th June 2015. 

Remember Saudi Arabia? That's where over 80% of all MERS-CoV cases have originated. That percentage has dropped a little of late thanks to the clusters in South Korea. Given the amazingly, incredibly, ultra-tiny (yes, that small) number of cases that have reportedly arisen during Umrah or Hajj (Septembee 21-26 in 2015)  in previous years, there is absolutely no reason to think 2015 will differ. Even if there have been recent cases in Makkah province. And a hospital cluster in Ash Sharqiyah (eastern province).

Clearly, MERS-CoV is not easy to catch even when so many different people, so many different states of underlying chronic disease, immune compromise, pre-existing infection, height, weight, age all come into contact within the zone of hotness that is Saudi Arabia.  

Which leaves me with one comment after a large batch of 23 cases was announced this morning - bringing the total to 87 from South Korea....look to the infection control South Korea!

References..

1. http://english.alarabiya.net/en/News/middle-east/2015/05/19/7-million-Umrah-pilgrims-expected-in-Saudi-in-next-2-months.html
2. http://english.alarabiya.net/en/News/middle-east/2015/01/28/Over-one-million-Umrah-pilgrims-pass-through-Jeddah.html

South Korean MERS cluster keeps growing..

version 3.

This cluster of hospital-related infections in South Korea has now reached 64 Middle East respiratory syndrome (MERS) cases. And no camel meat or milk, no route of ingestion yet fond in fact not even a camel to be seen - except the ones quarantined in the South Korean zoo - I can't even....

Anyway, thanks to a week long internet outage in my house (yes, I do these blogs from home) I've been unable to blog on any of this. 

Surprisingly though, after a week, the cluster is still going pretty strong. The recent tallies include 6 cases then 5, then 5, then 6, 9 and last night 14. These include 5 deaths (10%). 

As you'll see from the first 11 cases I've plotted below, this is similar to a bunch of incidents we've followed in Saudi Arabia in 2013 to today (Hafoof seems to have a pretty good cluster going at the moment). They have usually been the result of poor infection prevention and control creating a perfect storm of circumstance for viral spread. 

Timelines of the first 11 cases of MERS-CoV infection in South Korea.Click on image to enlarge based on World Health Organization and  FluTrackers information with help from this timeline. Hospital names have been published here and here - I'm not sure if this is how they are ordered so please consider this a work in progress.

Click on image to enlarge

It's looking like this will be the case in South Korea too. 

A couple of interesting things to note:

1. Cases are still popping up - a month later
2. A viral genome sequenced in China (ChinaGD01), from a South Korean case that flew out of South Korea to Guangdong, does not show any obvious genetic differences compared to other MERS-CoV genome sequences. Its sequence identity falls in the range that we can fit around all the MERS-CoV genomes - whether from humans, camels, from Saudi Arabia, Qatar or the United Arab Emirates, 2012 or 2015.
3. MERS cases in South Korea are tightly linked to hospitals - healthcare workers feature prominently as do other "close contacts" including relatives who stay at the hospital to help care for their loved ones. There are no indications of escape outside those hospitals so the closing of schools, the wearing of masks (which don't cover eyes) and the increased border measures offered to North Korea have no support from science or facts
4. Some incubation times are pretty short - just 3 or 4 days between exposure (in whatever form that is taking) and symptom onset - yet we haven't seen any not-so-close contacts come down with infections, despite that same time frame having passed long ago for them.
   Spread of virus is not very different to what we've observed in Saudi Arabia for 3 years
5. A few people have called the index case a "super-spreader" because of all the contacts he's had that have developed MERS (what about those who haven't developed disease by the way, are they being tested?) - I've come to loathe that term. It lazily defines the person as super-spreader while ignoring the context in which that person has been managed - namely whether infection control measures are well used, or in place at all. A super spreading event I like a little more - but even that makes something, special scary or different  out of what may be something completely normal in infectious disease biology
6. Testing times are all over the place - in just those first 11 cases it could be 9 days before a test result confirmed MERS-CoV infection. Therein may lie a reason for why MERS cases are still appearing now - no-one knew then, nor for a decent while, what they had. Although...they did know that they had an acute respiratory infection and I can't for the life of me work out why these viruses seem to get away from us time and time, and time again. Well, yeah I do - it's because people.

"Are we ready for the next pandemic?" is a question that has been asked a lot since the peak of the peak of Ebola virus disease epidemic in West Africa. The answer is that there is no way in a million years we're ready.

Version history.

• v2-fixed graphic's transparent background & changed case tally from 50 to 64
• v3-added in hospital names and a few more cases.

A good week for viruses...not so great for humans...

Edited for clarity 25MAY2015

Middle East respiratory syndrome coronavirus (MERS-CoV) managed to get out for some sightseeing - travelling to South Korea this week - and Ebola virus|Makona was given a helping hand to spread to new people in Guinea and Sierra Leone with a small splurge of new confirmed cases.

MERS has now trickled into 24 countries world wide as shown in the European Centre for Disease Prevention and Control's (ECDC) epic 'travel-by-plane' map.

The original of this is created by the ECDC and is presented here.
Click on image to enlarge.

Meanwhile, a crude extrapolation from current Ebola virus disease (EVD) case numbers saw the predicted date when we might reach zero cases, move further into June. 

This could pull back again or it could move further away if the EVD clusters and sporadic cases continue to spread. We can't model that because it's entirely down to unpredictable human variables. We can list what those are, we can better prepare for them, we can educate about them and how to prevent them and we can acknowledge that they are real, but we cannot know when and in what mix they will come into play.

Extrapolation of the public data for confirmed Ebola virus disease cases from
WHO. The most recent week is boxed in red and bucked the trend of declining
 cases. To see how I made this please visit here.
Click on image to enlarge. 

The newest EVD cases remain mostly clustered around the Forecariah prefecture of western Guinea, on the north west border with Sierra Leone but also 5 new cases appeared in the north west of Guinea in Boke prefecture, which borders Guinea-Bissau. 

From the World Health Organization's Ebola virus disease Situation Report, 20MAY2015.
Click on image to enlarge.

Since the last EVD SitRep, two days of reporting have seen fewer cases than in the same two days of the week before. 

So there's that. 

Quickly reporting what is actually happening is invaluable for all sorts of reasons. Modelling and prediction allow us to get ahead of the virus. But having the data, and having them available publicly remains a challenge for every country and for every outbreak. 

Public health data are about the public's health. If it has been considered worth collecting and collating, why not communicate it too?

MERS-CoV jumps a flight to South Korea...but from where?

It could be Qatar, Bahrain, the United Arab Emirates (UAE) or the Kingdom of Saudi Arabia (KSA). Any of these may have been the country of origin for the infected person who returned with a bunch of microscopic passengers, to the 24th country to host a case of Middle East respiratory syndrome coronavirus (MERS-CoV) infection - South Korea. 

The infected man then passed the spiky parasites on to his 63-year old wife and to a 76-year old man with whom he shared his hospital room. Close contact. From what we know of the MERS-CoV - it's a pretty ineffective transmitter among us humans types, preferring instead to give the hump to dromedaries.

Qatar seem less likely as it appears to have only been an airport transit point. If it's Bahrain, then we have 25 countries as Bahrain has not yet reported a MERS-CoV positive person. Both the people and the camels of the UAE and KSA are well known to this virus both in humans and camels. 

We await the clarity of the World Health Organization's analysis in a Disease Outbreak News (DON) article - although this might be a tough one to unravel.

Click on image to enlarge.