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MERS-CoV in camels... [CORRECTED]

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The top pie chart shows the distribution
of all human cases containing the word 
"camel" in their case notes, by the site where
the human was likely to have acquired their 
MERS-CoV infection. The bottom bar 
graph shows those data in terms of the
 proportion of cases at that site for which
"camel" contact was possible.
Click on chart to enlarge.
Thanks very much to Nicholas Evans (@neva9257 via Twitter) for asking me to back up my gut feeling about there having been more camel-links among MERS-CoV cases outside the Kingdom of Saudi Arabia (KSA) compared to inside.

I live to serve and so using those data I have to hand I've made a couple of charts. I'll keep these updated from now on too. 

I'd be grateful if anyone wanted to shout out human cases where camel contact was mentioned. I currently have 8 in total on my list of 201 lab confirmed MERS-CoV cases. (see the figure up there for where my cases are sourced). There may be many I have missed though.

One obvious question arising from the bottom bar graph is why does such a low proportion of camel-associated cases occur in the KSA but not elsewhere? 

For the sake of simplicity, I'll exclude the possibility that MERS-CoV jumps off its camel hosts at a border. Because the latest 68M from UAE may well have acquired his infection while visiting his camels in the KSA I have now listed him as a KSA acquisition...until I hear differently). We also know that camels in the KSA get actively infected (see earlier posts, listed below, on these findings [1,2,4]). 

So do these charts, by highlighting that so few camel links are to be found in the KSA (site of >80% of MERS-CoV human cases), discount camels as a source of infection? I don't think so. We have some very compelling evidence for camels hosting MERS-CoV [4], for camels being present in mass gatherings [5], and nothing but an absence of epidemiology to counter their role as a host and source.

I suspect the graph shows that MERS cases in the KSA won't admit to camel contact. Alternatively, perhaps contact, in its many possible direct and indirect forms is not being adequately sought or listed in case reports and in "gumshoe epidemiology" efforts (Ian Lipkin's comment, [6]). But why would camel contact not be listed, reported or collected? Perhaps it is seen as a bad thing? There may be stigma associated with acquiring an illness from a camel. Or perhaps stigma attached to the way in which that illness was acquired.

Perhaps it is a simpler explanation. There is likely to be fear, or a real risk, of social and economic fall-out of "naming and-shaming" camels as a major source of infection/disease. Camels fill many important and significant roles in the lives of those around the Arabian peninsula; from food, drink, religion to tourism and fun. But not identifying camel links in the spread of MERS-CoV, if indeed more links do exist, won't stop KSA's locals from acquiring infection and MERS. 

If there is a deficit in reporting camel exposures in the KSA, for whatever reason, it does one thing particularly well; it delays the understanding of how to protect people and reduce their exposure to MERS-CoV. I think that understanding is probably inevitable, so it may be better for the KSA Ministry of Health to get out in front of the issue; be proactive in finding the source of infections and openly discuss and plan for the implications. But I may be seen as living in a world of unicorns and fairies (again) to suggest that will eventuate. My cynicism is based on 2-years and 201 cases of a virus that's been very well virologically and molecularly detected and characterised outside the KSA, while its basic aetiology and epidemiology inside the KSA has left much to be desired.

I would very much like some locals to weigh in on this topic. Here (in the comments below) or by email or on Twitter. The bar graph simply highlights a discrepancy that could be cleared up with a better understanding (perhaps just by me) of what may  underlie the difference in the apparent roles for camels among countries sharing borders.

References...

  1. Dromedary camels are a host of MERS-CoV...
    http://newsmedicalnet.blogspot.com.au/2013/12/middle-east-respiratory-syndrome.html
  2. Middle East respiratory syndrome coronavirus (MERS-CoV): camels, camels, camels!
    http://newsmedicalnet.blogspot.com.au/2014/02/dromedary-camels-are-host-of-mers-cov.html
  3. MERS in the UAE....[UPDATED]
    http://newsmedicalnet.blogspot.com.au/2014/03/mers-in-uae.html
  4. Dromedary camels are a host of MERS-CoV...
    http://newsmedicalnet.blogspot.com.au/2014/02/dromedary-camels-are-host-of-mers-cov.html
  5. Middle East respiratory syndrome coronavirus (MERS-CoV) cases rise in march: Festival-related?
    http://newsmedicalnet.blogspot.com.au/2014/03/middle-east-respiratory-syndrome.html
  6. Receptor for new coronavirus found: Virus might have many animal reservoirs.
    http://www.nature.com/news/receptor-for-new-coronavirus-found-1.12584


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MERS in Kuwait...

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It's a "MERS-in.." kinda day. 

The World Health Organization todayannounced a fatal case of confirmed MERS-CoV infection diagnosed in Kuwait [1].

Summary of the case details:
  1. The infected person was a 60-year old male
  2. A Syrian national
  3. Hospitalised 13-Feb-2014
  4. Died 6-Mar-2014
  5. Lab confirmed 9-Mar-2014
  6. He had comorbidities
A few things here worth noting I think:
  • There was quite a gap (24-days) between being hospitalised (not sure when the case started showing signs of illness) and having a laboratory confirmation (also 3-days after death)
  • While this is the 3rd case identified within Kuwait, it seems to be the first case that could be nailed down as having been acquired in Kuwait. I tend to try and list my numbers and maps by where the case was acquired rather than where they were diagnosed. Two previous MERS-CoV cases (FluTrackers #158 and #159; includes 1 case with camel contact noted) diagnosed in Kuwait had travelled outside Kuwait blurring the ability to see where they had picked up the virus


References...
  1. WHO Disease Outbreak Notification 20-Mar-2014
    http://www.who.int/csr/don/2014_03_20_mers/en/
  2. FluTrackers thread on Kuwait MERS-CoV case #1
    http://www.flutrackers.com/forum/showthread.php?p=514258#post514258
  3. FluTackers on Kuwait MERS-CoV case #2
    http://www.flutrackers.com/forum/showthread.php?p=528694#post528694




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MERS in the UAE....[UPDATED]

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For the second time this month, there has been a case of Middle East respiratory syndrome coronavirus (MES-CoV) infection confirmed in the United Arab Emirates (UAE; Abu Dhabi to be precise). 

What added to my confusion (as you'll know if you were following me on Twitter this morning) was that both cases, apart from being from Abu Dhabi, were also 68-year old males and both have had camel contact. 

Today's 68M UAE case frequently visited his camel farm in the Kingdom of Saudi Arabia (KSA; had just returned from there 5-days earlier, thus in my mind making this a likely KSA acquisition) while the earlier 68M UAE case owns his farm in the UAE where he contacted animals including camels which he breeds.

This raises another question from me; why do we see proportionately more camel contact outside the KSA than we do inside the KSA (I haven't done the maths so this may just me my unfounded gut feeling)? Is it something simple like better epidemiological investigations conducted by Qatari and UAE investigators or are things, yet again, different somehow inside the KSA than they are outside the KSA? 

Surely there are some clues in there for investigators to use either to either improve how the epidemiology investigations are conducted or to look beyond camels in the KSA at other sources of acquisition?
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Any differences in the sex of avian influenza A(H7N9) virus cases in different areas of China?

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a) Male (blue) and female (lavender) lab-confirmed H7N9 human cases broken into the Province or Municipality of likely acquisition. b) The proportion of total H7N9 positives at each site of acquisition that are female (lavender).  The proportion of females in Wave 1 (Range of weeks beginning 18-Feb-13 to 20-May-12) and Wave 2 (07-Oct-13:current) are also shown as a horizontal line for comparison.
Click on chart to enlarge.









This new chart idea was just a look-see at whether there is anything out of the ordinary about the sex distribution of H7N9 human cases in the different areas of China. These are total numbers from both Waves of H7N9 season.

I've included case numbers in Part a) as well as proportion of females in part b) to show that a value of 100% must be place in context of only 1 POS!

Nothing much to see here folks.


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MERS-CoV: sex, age and accumulating death

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

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

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

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

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

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

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

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

Yet another reason for every State to test its population for respiratory viruses I suppose, because then one has a baseline for the known viruses which can help judge the impact of newly identified or emerging viruses.
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Influenza viruses in Queensland, Australia: 03-Mar-2014:09-2014.

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Map of Queensland's Hospital and Health service
areas. Adapted from
http://www.health.qld.gov.au/maps/hhs_facilities.pdf.
Click on image to enlarge.
Sure enough, as promised on the 12-Mar, the new Queensland flu numbers are out (I post a week after the next new numbers come out publicly; its just the deal I have). So this follows on from last Wednesday.

This is the next week's numbers which follow on from my earlier post on the increased number of influenza cases and the media reports of influenza A(H1N1)pdm09 virus  predominance.

The Queensland Health Statewide Communicable Disease Surveillance Report for the week 03-Mar:09-Mar has some extra detail, this week. The extra detail outlines that most (860; 94%) of this year's 918 influenza notifications (2.3X the 5-year year-to-date mean value) to date are located in the following Hospital Health Service (HHS) areas (see the map above):
  • Metro South: 192 (21%)
  • Metro North: 176 (19%)
  • Gold Coast: 110 (12%)
  • Cairns and Hinterland: 106 (12%)
  • Townsville: 73 (8%)
  • Darling Downs: 52 (6%)
  • Sunshine Coast: 50 (5%)
  • Cape York: 46 (5%)
  • West Moreton: 28 (3%)
  • Mackay: 27 (3%)
The median age of cases is 41-years and 50% are male. The highest rate of notifications is in the 50-59-year age group at 24.8/100,000.

Percentages represent the proportion of all 80 
notifications for this reporting period.IFAV-Influenza A virus; IFBV-Influenza B virus.
Click on image to enlarge.
This report also has some typing (Flu A or B) and subtyping data (H3N2 or H1N1).

These data are very much appreciated  since this is ahead of the traditional "flu season" reports. 

Many thanks to all associated with the Communicable Diseases Unit, Queensland Health, for adding this detail in. 

The chart above makes it very clear that H1N1 dominates the Qld influenza landscape so far. Specifically...
  • 80 notifications with signs and symptoms during the reporting period
  • 68 were typed as influenza type A viruses (85%)
    • 13/14 were subtyped as H1N1 (pdm09 I presume; 93% of the FluAs that were subtyped)
    • 1/14 H3N2
  • 12 were typed as influenza type B viruses
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Respiratory viruses: the viruses we detect in the human respiratory tract

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A list of the viruses we can and do detect in the (mostly upper) human respiratory tract.

The standard testing panel/diagnostic menu comprises the influenza A and B viruses, parainfluenza viruses 1-3, respiratory syncytial virus, human metapneumovirus and the adenoviruses.

Some caveats:
  • I make no claims to there being a link between cause-and-detect here. Because these viruses are mostly detected using polymerase chain reaction-based methods (PCR, RT-PCR mostly in a real-time format), virus may be detected before, during or after a symptomatic period. Virus may also be found when there are no symptoms at all; an asymptomatic infection. 
  • In some instances the virus types included in this list are taken from a larger number of viruses grouped within a genus, for example the genus Enterovirus or the genus Mastadenovirus. My selection is based on our lab's multi-year, PCR-based studies since it can be hard to find decent data for a list like this using the scientific literature. Yes, I should write & publish faster, I know. 227 may well be an underestimate. For example viruses that may cause symptoms of gastroenteritis and central nervous system disease like the Saffold cardioviruses or the parechoviruses (HPeV) may begin their journey towards those diseases as a respiratory infections or involve the respiratory tract in the transmission process in some way.
  • Other viruses including the newer polyomaviruses (WUPyV and KIPyV) are also detected in the airways but I have not listed them here.
In short, take this figure as a guide, but a pretty good one, of the approximately 227 viruses that comprise the pool from which we get infected each year. 

Also keep in mind that most if not all viruses seem capable of being associated with a spectrum of clinical disease; from no symptoms at all (yes, even influenza) to mild and short-lived acute respiratory diseases (common colds), severe colds, bronchiolitis, wheeze in the absence of asthma, cough, sore throat, middle ear infection, pneumonia, exacerbating asthma and chronic obstructive pulmonary disease and preceding bacterial secondary infections. These viruses often circulate in seasons some of which overlap and some of which are exclusive. They can also co-occur in the same person at the same time, regardless of season.

We can vaccinate against influenza virus; but it's worth remembering that a vaccine does not stop the virus entering our nose/throat. An effective immunization stops the severe form of the disease which can result from that infection. We may still test positive in a laboratory test after we have been vaccinated, but we are unlikely to be experiencing the full form of the disease (unless the vaccine did not "take" or there was a vaccine mismatch with the intended virus that we got infected by etc). 

Specific antiviral drugs among the respiratory viruses are rare; most infections are self-limiting (you recover from them yourself) and short-lived [1]. Influenza virus is again an exception in that we have useful drugs to apply after we get infected. A specific monoclonal antibody treatment for respiratory syncytial virus (RSV) has also been successfully used for some years [2] and the broader acting ribavirin is licensed for use in humans [3].

One question that is often posed when discussing testing for some/all of the list above is: why bother? If determining the virus won't lead to applying a treatment/cure and is of no use in prevention (if a patient is currently positive for that virus), then why expend time and money to sort it all out? Four very good reasons (from reference  #4) plus some of mine (with some overlap), are listed below. 

We test to...
  • Provide information about disease occurrence [4]
  • Monitor trends in disease prevalence [4]
  • Guide public health efforts to prevent and control diseases [4]
  • Allow timely detection of outbreaks to facilitate their management and control [4]
  • Inform parents of ill children (clients in some areas of health-speak) who deserve to know what their children are infected with because from that information Doctors can provide a measure of the prognosis (how long they will be like this, how bad it might get etc)
  • Inform the drug researchers about the importance of each virus
  • Cohort patients with certain viral infections when they are in hospitals, to keep the same viruses together and away from other susceptible but uninfected patients
  • Know when one seasonal virus is on the rise (RSV) or decline (rhinoviruses) because that may inform us about when another (influenza virus) is about to take off
  • Know which virus is causing disease currently as that may affect hospital resource allocations; being able to identify a bigger influenza season may trigger increased purchasing of antivirals, masks, certain supportive care equipment or consumables or drive the updating of procedures and plans
  • Look for sign that an outbreaks has occurred because of a change in the virus or its "behaviour". These changes can also trigger the State to make available new funding for targeted research
These are the viruses that we interact with all the time; some more often than others at certain times of the year. Over a few years, we're likely to have fended them all off, or succumbed to the signs and symptoms of an infection by them, at one time or another. 

Great to have an immune system huh? 

Reference..

  1. Antiviral Drugs for Viruses Other Than Human Immunodeficiency Virus
    http://www.ncbi.nlm.nih.gov/pubmed/21964179
  2. Monoclonal antibody for reducing the risk of respiratory syncytial virus infection in children.
    http://www.ncbi.nlm.nih.gov/pubmed/23633336
  3. Respiratory syncytial virus infection in adult populations.http://www.ncbi.nlm.nih.gov/pubmed/22335500
  4. Queensland Government's Queensland Health Notifiable Conditions Page
    http://www.health.qld.gov.au/ph/cdb/sru_data.asp
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Middle East respiratory syndrome coronavirus (MERS-CoV) cases rise in march: Festival-related?

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It's been nearly 3-weeks since my last update so I'm well overdue to look at what's changed.
Click on image to enlarge.

A quick post first up showing the accumulating cases by the region in which the person probably caught their infection and the week in which they became ill - or the week in which the case was publicly reported by a Ministry if no onset date was provided.

Why the recent uptick in cases; ~9 reported this month so far? 

There have been a few things going on in Riyadh (a city of 6 million, in which 10/11 most recent cases have been acquired) that might link people with camels (the likely intermediate or primary host of MERS-CoV in the region). 

I have listed a few other events listed that may also be pertinent for MERS-CoV acquisition &/or transmission, from whatever source, in a post 29-Jan [5]. To add to that there is this:
  • The 17-day long 29th annual Janadriyah Festival kicked off Feb-12. It showcases the national heritage and culture of the Saudi lifestyle. Includes camel rides and racing [3,4] and is visited by millions of people from all over the Kingdom of Saudi Arabia (1.4mil by 26-Feb) [2][3]. But not just locals; tourists come from all other regions of the Arabian peninsula too, including the UAE which a "guest of honor" this year. Of note: the recent 68-year old male UAE MERS-CoV case had exposure to animals from his own farm and is not noted as having traveled.
References...
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