Showing posts with label MERS. Show all posts
Showing posts with label MERS. Show all posts

Saturday, 24 June 2017

Another canary in the same coalmine - mild MERS may be bad news...

Sometimes, the Middle East respiratory syndrome coronavirus (MERS-CoV) is detected in a person who is not ill. 

Weird huh? 

Not really. This is the result of laboratory testing of contacts of a known and infected person during the process of containing a potential outbreak.


For me personally, this is one big question about new or emerging viral infections or infections we are still learning about - like new influenza viruses, MERS-CoV, ebolaviruses and Zika virus. Do we really know how often a laboratory-confirmed infected person with mild or no illness can spread virus to a new person - an uninfected potential host? Are our tools up to the job of detecting what's happening and are we using them properly?

Conventional wisdom is that truly asymptomatic but virus infected people do not infect others around them, or if they do, it's a pretty rare event. Because the risk is seen as low, studies around this issue are often down the list of research priorities.

The importance of this issue lies in whether mild or asymptomatic people need to be more closely considered as having a role in spreading virus and contributing to community or hospital outbreaks.

Emerging from the 2015 South Korean MERS-CoV outbreak, a recent report described the findings from laboratory testing of 82 contacts of an asymptomatic healthcare worker.[1] No other person became MERS-CoV positive. I have some issues with the fact that the nurse herself does not seem to have been tested to show that she developed antibodies to MERS-CoV and there also isn't a lot of discussion about how the PCR testing for MERS-CoV can be a bit "flaky" when sampling once from the upper respiratory tract. Although, there aren't any sampling details in this paper either (I'll blog about this paper another day)!

But I digress. 

I've plotted the all the publicly available mentions of asymptomatic MERS-CoV infections, by week, in the graph below (the bottom panel). 

Click on image to enlarge.
The yellow peaks show that cases without illness usually correlate with healthcare workers in the graph above, during hospital and healthcare facility outbreaks (see my previous post describing the pink graph in the top panel).[2] 

This isn't too surprising. The majority of disease associated with MERS-CoV infection arises in older males who already have an underlying disease including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions. Healthcare workers however are usually younger and do not have, or have not yet developed, such comorbidities. 

MERS-CoV is often a shown to be a bit of a bully when challenged by a healthy younger host's immune system. Although, when hit with a larger primary dose of virus from an infected camel, even the healthy can get hit very hard.

Healthcare workers can be the 'canary in the coalmine', except singing about a healthcare outbreak rather than a gas leak. Similarly, laboratory confirmed MERS-CoV infection manifesting with only mild or no signs and symptoms of disease, also serve this role as a sentinel of hospital, rather than camel-to-human, transmission of MERS-CoV.

References...

Tuesday, 20 June 2017

Working for health can make you sick....

Below is a quick look at the percentage of total Middle East respiratory syndrome coronavirus (MERS-CoV) cases reported each week that are listed as being healthcare workers (HCWs).



The sources of the numbers used in this graph.

These data are curated by me for this blog in my spare time and are compiled from the Kingdom of Saudi Arabia'a Ministry of Health (MOH) daily reports, the World Health Organization (WHO) disease outbreak notifications (and relatively new line lists) and from the FluTrackers line list

I use the same numbering as FluTrackers use in an attempt to produce at least two lists that agree on numbering and content. 

Some other things to note about this graph..

Each of the pink "spikes" is a percentage calculated by dividing the number of MERS-CoV laboratory confirmed HCW by ALL of the MERS-CoV laboratory-confirmed cases that were reported in that same week... 
Sometimes there might be just 1 HCW and 1 patient - which would give a pretty big looking 50% positive (1 divided by 2). But clearly, it is just 1 HCW. 

So proportion (%) alone is not a whole lot of use sometimes. One needs to know the denominator (the bottom number of a fraction) to get a gauge of how big the problem really is. 

The current June hospital outbreak in Saudi Arabia includes three facilities in Saudi Arabia according to the WHO and the MOH.[1,2] From the 47-year old male reported on the 1st June as an index case in one facility, there have been about 44 secondary MERS-CoV detections (cases) in Riyadh. 

Of the 44 MERS cases, 26 are listed as HCWs; 18 of 25 HCW MERS cases occurring in a single week (week beginning 5th June) and accounting for the 72% spike seen at the end of the graph above. 

Just to confuse things, there were 3 distinct hospital outbreaks that occurred previously,  in April and May, but it's not clear whether they contribute any cases to the June tally.[3]

Why can't we have nice things?

There has been no other successful effort, by anyone, to produce a single public MERS case list with a universally agreed upon numbering scheme that contains useful but deidentified case detail, that everyone could refer to and use. The same applies to the influenza A (H7N9) virus as well. This has only been achieved by public volunteer bloggers; FluTrackers and this blog. Pretty poor when you think on it.

References...

  1. http://www.cidrap.umn.edu/news-perspective/2017/06/who-details-saudi-mers-clusters-outbreak-grows
  2. http://www.who.int/csr/don/13-june-2017-mers-saudi-arabia/en/
  3. http://www.cidrap.umn.edu/news-perspective/2017/06/who-reports-3-saudi-hospital-mers-clusters-new-cases-uae-qatar

Thursday, 26 January 2017

WHO sets the table....and lays it with MERS-CoV details

This just made my day. A Tweet from scientist and program manager at the World Health Organization (WHO), Dr Embarek. In the tweet he noted that Middle East Respiratory syndrome coronavirus (MERS-CoV) data will now be presented by WHO in an easy-to-access Mirosoft Excel table...


An example is in this latest update.[1]

Excerpt of new MERS-CoV data from [1]
This will make data collection for scientists, public health teams and researchers looking to follow what's happening with this camel-borne virus as it spills over to humans so much easier. I've been painstakingly entering data from several sources since 2013 - and this will really streamline the process.

Thanks to those at the WHO for making this happen.

Now, could you please also do this for all the other pathogens you keep track of....different influenza viruses (H7N9, H5N6, H5N1), zika virus, dengue virus, yellow fever virus....and make it retrospective....

References...
  1. http://www.who.int/csr/don/26-january-2017-mers-saudi-arabia/en/


Saturday, 17 September 2016

MERS is a disease we spread...

There is little doubt now that Middle East respiratory syndrome  (MERS) disease outbreaks are triggered by sporadic zoonotic transmission of the MERS coronavirus (MERS-CoV) from an infected camel to a susceptible human. 

Little doubt to anyone who has followed the story of MERS at all, anyway.

But that's just the tip of the iceberg. 

The majority of human cases that have contributed to those steep rises in the cumulative MERS-CoV detection graph below are there because humans have infected other humans while in or associated with a healthcare facility. A telling picture when you consider that MERS-CoV is not a great transmitter. We've done much to make something from what should have been nothing.

Can we vaccinate against lapses in infection prevention and control?


Thursday, 15 September 2016

Middle East respiratory syndrome coronavirus (MERS-CoV) hotzone map gets a paint job..

A slightly updated MERS-CoV map adding in some camel detection sites in Africa and changing up the colours.

27 countries have been visited - 13 have had local transmission.

And there have been 2 humans in Kenya found to harbour antibodies to MERS-CoV. This helps address the question of why we hadn't seen human MERS cases in Africa despite countries harbouring MERS-CoV infected dromedary camels. The answer of course is, we hadn't looked.

Click on image to enlarge

Sunday, 4 September 2016

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]

Friday, 2 September 2016

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

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Tuesday, 17 May 2016

27 countries have seen a MERS-CoV case with Bahrain's addition...

13 of those 27 have had local transmission.

The Bahrain-diagnosed infection was likley acquired from a camel in his dromedary camel farm in Saudi Arabia.

Click to enlarge.

Monday, 11 April 2016

Colombia...no recent confirmed Zika virus positives or reporting lag or...?

UPDATE #1: 24APR2016
Okay. Let me rephrase an issue I had from one of my posts yesterday-the one looking over the Colombian data. The relevant text was...


"I'm still not clear how the tally of confirmed cases is rising, but not showing up on the Colombian NIH graph (the red bars; the grey ones are clinical suspected cases). 
I've excised and posted the Colombian NIH graph to the left. 458 cases this week should show up clearly using that axis - it was the second biggest tally, just below Week No. 8 (also missing?) and 1.6X bigger than Week No. 4 which has been plotted and shows up clearly. I'm just assuming that the graph person has forgotten but would love to know if there is something else going on."

Below I've excised the relevant graphs from the most recent epidemiology report (Week No. 13 [2]) and also the one that first plotted confirmed alongside suspected Zika virus (ZIKV) cases (Week No. 11 [1]).

You can in fact see that the red bars have grown over the 3 week period - but that none of the 700 confirmed cases reported over that time have visibly made it into a bar after Week No. 5. So my question is whether that means:

  1. no newly confirmed ZIKV cases have been detected/become ill during the past 8 epidemiology weeks (keeping in mind that Week No. 13's report only reports data to 02APR2016)
  2. there is an 8-week lag in getting lab data into these reports?
  3. Someone forgot to update the graphs
  4. Colombia is no longer testing for ZIKV

 ..or perhaps something else altogether?


Week No. 11.
Data from [1]

Week No. 13.
Data from [2]
The lag seems to be the leading theory so far (see Tweet below)...but that's quite a lag. 

I find it strange that no-one seems to be critical of the testing lag here and yet it was the topic du jour for MERS in the Kingdom of Saudi Arabia. 

Is it simply about the perception of resources - the Americas are perceived as resource-poor and the Saudis as resource abundant? 

In the area of lab testing, I'm not at all convinced that the Saudis were at all resource rich though. I don't think they were in any better position at the start of their outbreaks. Especially if the resource we measure is understanding about testing to understand the aetiology of an emerging infectious disease.

References...
  1. Added a new 3rd option which was not carried over from the orginal post 10APR2016  - and pushed the previous 34rd to 4th

Tuesday, 22 March 2016

SNAPDATE: MERS by the years...

When it comes to Middle East respiratory syndrome coronavirus (MERS-CoV) infections, the years  and the comorbidities - really do take a toll. 

The graph below helps to highlight how the median and average ages of MERS-CoV positive cases and deaths are distinct from the median age of the total Saudi Arabian population - among whom most MERS-CoV infections have been reported. ...although there is the issue of expatriate workers who also get infected - do they contribute to the Kingdom's median age?

Click on image to enlarge.

SNAPDATE: MERS-CoV around the world...

A quick snap update to show how the Middle East respiratory syndrome coronavirus (MERS-CoV has been travelling around the world in the pat 4 years, using a cumulative curve.


Click on image to enlarge.

Friday, 18 March 2016

Back to the bats for MERS-CoV...

It's a smoking bat. Get it? Hmm.
In late February Munster and a team of United States' researchers infected bats with MERS-CoV. 

The aim here was to seek out information about a possible origin for MERS-CoV in bats and perhaps find an animal source from which camels may have first been infected. This path is suspected because of the genetic similarities between MERS-CoV and other bat coronaviruses which make bats an attractive reservoir for MERS-CoV...or an earlier form of MERS-CoV.

It's worth reinforcing that there is as yet no "smoking bat" - no bat species has been found to harbour infectious MERS-CoV in the wild or more than a diagnostic PCR fragment's worth of genetic material. To date.

The team used a bat species called Artibeus jamaicensis - the Jamaican fruit bat. 

They first tested whether the bat's version of the molecular known to be the human MERS-CoV receptor,  dipeptidyl peptidase 4 (DPP4), could act in that role. To do this they cloned the relevant bat sequence and introduced it into some some cells that usually didn't permit MERS-CoV to infect and replicate wihtin them. When the introduced DPP4 material was expressed, the cells permitted MERS-CoV infection and replication; Jamaican fruit bat DPP4 could act as the MERS-CoV receptor, just like human DPP4 does.

From the Histology Lecture Image Gallery at Yale
Medical Cell Biology.[3]
Next the team infected 10 A.jamaicensis bats via the nose and body cavity; none showed signs of disease, lost weight or were found to have a rise in their temperature but 8 shed virus - moreso from their respiratory than their gastrointestinal tracts.

When the bats were killed at different times and examined, the lower respiratory tract was found to contain the highest level of virus, but MERS-CoV was also found throughout the bodies of the bats, possibly spread via a blood-borne path since viral RNA was detected in the blood 2 and 4 days after inoculation. 

Signs of mild tissue damage could only be found in 2 bats - both in the respiratory tract with signs that virus infected Type I pneumocytes. Type I pneumocytes form part of the alveolar gas exchange barrier. In humans, Type II pneumocytes were identified as MERS-CoV targets in the only human autopsy conducted to date.[2] Type II pneumocytes are responsible for secreting surfactant which helps stop the lung's air sacs from sticking to themselves, they metabolize drugs, move water across epithelium (tissues that line the body's hollow cavities in this case) and repair injured alveoli.[4]

Only 1 bat developed a MERS-CV a specific antibody response.

The discussion had some interesting points including....
  • A.jamaicensis may be a good model system for studies of how bats and their coronaviruses co-exist
  • MERS-CoV "maintains the ability to efficiently replicate" in bats which the authors take to support the hypothesis that bats are the ancestral reservoir for MERS-CoV. Or maybe its ancestor?
  • Because bat coronaviruses are usually bat gut pathogens, but MERS-CoV was a bat respiratory pathogen, this might suggest MERS-CoV evolved to be so in camels. Orrrr...it might not.
  • In the absence of disease, a detectable antibody response may not occur in humans as was found in bats, or it may be delayed in humans as has been previously reported. 
  • In most bats and bat tissues, MERS-CoV RNA could not be detected beyond a 2 week period after inoculation - but in 1 bat, the small intestine was still positive at day 28

I'll get back onto the camel literature reviews next.

References...
  1. Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis)
    http://www.nature.com/articles/srep21878
  2. Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014
    http://ajp.amjpathol.org/article/S0002-9440(15)00647-1/abstract
  3. http://medcell.med.yale.edu/medcell.php#
  4. http://www.ncbi.nlm.nih.gov/pubmed/3285521

Monday, 14 March 2016

Middle East respiratory syndrome coronavirus kicks off...

Click on it.
It gets bigger!
The next wave of MERS-CoV cases is well underway in the Kingdom of Saudi Arabia (KSA). 

Since 2012, 1,702 MERS-CoV detections have been reported in humans from 26 countries around the world.


Click to expand.
Graph captured from [3]
The first reported MERS cases appeared on our radar via an eMail to ProMED sent September 20th 2012.[1] That person became ill in April 2012 and some others, found later, were ill in March 2012 [2] - so we're smack dab into our 4th "disease onset birthday" right now. 

Each year we news and number watchers, wonder aloud about the course that MERS-CoV might plot. We don't predict it though - that would be dumb. No-one can know where things may go because that's all based on human behaviours, oversights and mistakes. And who knows how, how many, how often, why or when those will occur?

MERS-CoV is very much a human problem - it's a particularly opportunistic virus which causes it's biggest impact when we create the conditions for it to spread among vulnerable people in health care settings.  Whether or not that whole process will play out again in 2016 is anyone's guess. As I noted in my last post, it has already happened to some degree in Buraidah in the Al Quassim province of KSA. The KSA is - if you are new to MERS-CoV - the country in which 80.4% of infection have been acquired. Word oen the Tweet is that the outbreak is under control now.

I've updated my graphs, tallies and charts with the latest numbers now, so feel free to click on the MERS-CoV tab above to see where we're at.

And don't forget - an outbreak of an infectious disease in one country has the potential to be an outbreak in any country. Just add human behaviour.

References...
  1. http://www.promedmail.org/direct.php?id=20120920.1302733
  2. http://www.zeit.de/wissen/2014-05/mers-fall-2012-paper.pdf
  3. http://virologydownunder.blogspot.com.au/2014/08/mers-cov-daily-monthly-and-cumulative.html

Tread carefully when MERS-CoV stirs in hospitals as it can spiral out of control quickly..

In 2014 a stepwise increase in Middle East respiratory syndrome coronavirus (MERS-CoV) cases preceded the largest healthcare facility outbreak of MERS to date. 

If you look at the most recent daily Kingdom of Saudi Arabia (KSA) Ministry of Health report below,[1] you could be forgiven for thinking that there is currently a threatening rise in cases which could easily spiral out of control once again unless it is quickly stepped on.

Adding fuel to the fire is the fact that in Buraidah, in the province of Al Quassim , there has clearly been a healthcare-associated outbreak ticking over since November 2015 - patients, healthcare workers and relatively little camel contact make for a pretty clear picture.
When these fires are let smoulder in this way, they can quickly spread embers across the region and then cases fly out to other ports.
A week ago there were 8 cases reported in a day. That's far from the biggest reporting day we've seen in 3 MERS years (around 31 cases in a day n April '14), but it's still high. There have been 11 consecutive days with 2 -8 cases reported each day. The region in the map above has been the hotspot, but in the 12-March report there were 4 cases, each in a different city

There have also been an usually high number of camel mentions so far this MERS season. We do not usually see so many consecutive cases reported to have some form of camel contact. These are from cases across the KSA but also from United Arab Emirates- and Oman-acquired cases too. Is this because of a better understanding and acceptance of the role of camels in spreading MERS-CoV to humans, after research really hammered home the facts, or is it that more camels are infected, or there are more infected herds this season, are other animals becoming infected, or is it that, for some unknown reason, there is more contact between humans and infected camels/other animals this season?

There have been no viral gene or genome sequences from 2016 arriving on the interwebs yet, so we are left with a few of the old questions...again
  • is this all normal or is something different this time around?
  • has this season's MERS-CoV undergone a significant genetic change(s), affecting stability, tropism or transmission?
  • has infection control and prevention slipped again?
  • is there more contact with infected camels this year?
  • are increased camel descriptions an indication of better surveillance and questioning about camel contact?

Time to start watching and plotting MERS-CoV again.

References...

Friday, 8 January 2016

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



Tuesday, 15 December 2015

One man has a lot of MERS on his mind....

Professor Christian Drosten heads a sizable, very friendly and diverse team of scientists seeking to understand all aspects of the Middle East respiratory syndrome coronavirus (MERS-CoV). 

And not just understand, but also to detect, educate, vaccinate and generally interrupt MERS-CoV transmission in camels and to and between humans. 

That's a heckuva lot to think about.

From the First WHO-EMRO Training Workshop on MERS-CoV Laboratory Diagnostics in cooperation with the Central Veterinary Research Laboratory (CVRL). 

Saturday, 5 December 2015

The season of the MERS...is mainly whenever the infection control fails

I still only see a "seasonality" to MERS and human MERS-CoV detections that is made up of the times when hospital outbreaks spread cases due to missed opportunity to control and prevent infection wihtin their walls. In other words - no real season at all. 

MERS-CoV is an opportunistic virus - which includes making the most of the frequent opportunities we humans provide for it to spread.

Data from public sources up until December 3rd 2015.
Click on image to enlarge.

Any true seasonality is in that small percentage of cases that are the result of a primary, sporadic infection from an infected and infectious camel. Those cases may be related to times of camel calf weaning when young camels acquire their first infection, or it might just be whenever a particular herd has MERS-CoV raging though it.


MERS-CoV: Saudi Arabia still tops the chart..by a long way

A quick reminder that MERS and the MERS-CoV remain a thing of the Kingdom of Saudi Arabia from where 80% of detections have been reported.

South Korea's hospital outbreak comprises 11% of all reported detections.


Sunday, 22 November 2015

Updating the animal "to-do" list...

I have a couple of talks coming up, so I'm making graphics again. And I like to share those. 

This one is an update on some of the creatures that could also be considered suspects in the hunt for sources of MERS-CoV infection of humans.

Of course, camels are the ones we know to be a true risk for infection and there was that 1 bat that was positive for a very small diagnostic PCR product. Cattle contact was also recently listed, with little detail, as a significant risk factor among those acquiring MERS-CoV infection and we also know that cells from camels, horses, alpacas, cattle and goats can be infected and host genome or virus replication of MERS-CoV in the lab, or have the MERS-CoV cellular receptor, DPP4, on their surface.[1,2]

I heard that there will be more bat testing in the future, but we haven't read of any MERS-CoV targeted bat studies since 2013.

So here is the long laundry list of animal testing that needs more work - many of which have been tested in small numbers over limited time periods already - in a graphical form.

Click on image to enlarge.
You can also access this from Figshare.[3]
References...

  1. http://www.ncbi.nlm.nih.gov/pubmed/25656066
  2. http://wwwnc.cdc.gov/eid/article/22/1/15-1340_article
  3. http://figshare.com/articles/Creatures_of_interest_to_how_humans_acquire_a_MERS_CoV_infection/1609604

Thursday, 5 November 2015

Updating the very model of a modern mammal-camel....

The new findings from the case-control study out of the Kingdom of Saudi Arabia (and US CDC) deserve an update of my old model of how one might become infected with MERS-CoV after exposure to an infected camel.[1,2]

Some of the possible ways in which MERS-CoV may be spread from an infected
camel to a human in direct or close contact with the camel or with surfaces
onto which MERS-CoV-laden camel excretions or secretions have been deposited.
The major change is the removal of the ingestion options. As readers of this blog will know, I've never been a "believer" in that route of infection, and the new study would seem to support that gut feeling with some facts.

As ever, the distinction between direct contact and being close enough to be exposed to droplets that are inhaled, has not been possible and wasn't attempted. The word "droplet" does not appear anywhere in the paper. In fact, animal contact and droplet-producing processes are all rolled together in the new study under the direct contact banner - so I have retained droplets among the possible risks shown in the figure.

References...

  1. http://virologydownunder.blogspot.com.au/2015/11/it-was-camel-in-library-with-mers-cov.html
  2. http://virologydownunder.blogspot.com.au/2014/05/camels-at-centre-aerosol-all-around.html