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Snapdate: MERS-CoV by date 20-Apr:08-May [UPDATED]

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With the addition of a new country, Lebanon, the 18th to host an imported or locally acquired laboratory confirmed MERS-CoV-positive, I've updated the world map below. 
Click on map to enlarge. It needs it!
I've also had a quick look at cases per day for some (but not all) recent detections of the MERS-CoV, based on the dates we have to work with. 

It certainly looks like case numbers are dropping slowly. 


Click on image to enlarge.
Having more dates of onset has helped to re-assign when people actually became ill, an important piece of the transmission puzzle for tracking the Jeddah-based outbreak. Onset is my date of choice - when it's available. 

We no longer know, or can't calculate using public data;

  1. When a death/recovered person is first identified. The Kingdom of Saudi Arabia (KSA) Ministry of Health (MOH) reports do not include any deliberate link between age/location of death/recovery they now note, and date the case was originally reported/became ill/was hospitalized. Any of those would be a Rosetta stone to decode the link. Apart from a "total dead/recovered" tally, having only partial information on death/recovery is another missed opportunity to be clear.
  2. Profession of the infected person. Just in broad categories, as we saw from China for H7N9 earlier on (not so much now). Healthcare worker detail has disappeared with no communication about whether this is due to an actual drop in such cases or not. Some assume it means we're just no longer being told this information. But a recent Filipino HCW (h/t @lisaschnirring) was reported back home as having died, yet HCW does not seem to have been listed on relevant KSA MOH report supporting the worries of the some.
  3. Homeland.  Is the infected person a KSA citizen, expatriate worker, pilgrim for umrah (or hajj later this year) a traveler for business or for pleasure?
  4. Links for contacts. We get told of contacts with previous cases but no linkage detail is provided.
  5. Respiratory symptoms may be mentioned as a reason for hospitalization (which is dated) but the date of onset (DOO) of these symptoms is sometimes not provided. DOO is the currency of good basic epidemiology in my opinion. Its gold, diamonds and platinum. It's chocolate (okay, that's just my currency). This data will occur for some cases but not for others, even within a single MOH announcement.
  6. Animal contact. No longer to we get mentions about exposure (be that to airborne or ingested virus) to camels/animals/farms. Add festivals to that.
  7. Date of laboratory testing. This isn't available for prodromal/asymptomatic people. They would be best identified using the date of testing - but since the MOH doesn't tell us the date of testing, I use the date of reporting. That might be anywhere from 1-day to 2-weeks after actual testing. 
  8. Nosocomial (hospital-acquired) MERS-CoV infection. Reliable dates would help identify these. This is available sometimes, but inconsistently. Relates to both #5 and #7 This is also confounded by the recent removal of hospital names, presumably to avoid panic and save face by not broadcasting the names of facilities with continued poor control of MERS-CoV spread.
I know that by saying "providing half-baked data is tantamount to providing no data at all", the intent could be changed and instead used to say "okay, then lets provide no data at all". Hopefully charts like mine and others and our commentaries do not serve to focus the MOH gaze on what to remove from the data that have draw our ire, but instead provide a service to help hone the message by stopping up data gaps and oversights. 

Endemic communication timidity and inconsistencies have been a hallmark of the emergence of MERS and the MERS-CoV. They only serve to promote anxiety and attempts by talking heads (like myself) to fill such information voids with guesses, the overuse of CAPITAL LETTERS and just plain vacuous garbage.

As ProMED put it in an email to its membership today in relation to Polio (and in seeking some funds to keep running which you can help with by donating here)..
"...the notion that gathering data and sharing it freely is in the best interests of everyone's health. Vigilant surveillance remains the best strategy for rapid response.."
'Nuff said.

Thanks to @HelenBranswell for further additions.
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Avian influenza A(H7N9) virus found in more than half of wet markets in Guangdong...

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It comes as no surprise to me, but is still a very welcome piece of data, that Guangzhou's ongoing live bird markets and concurrent continued cases of H7N9 in people, are also happening in a an environment of 60% of market stalls tested positive for the virus in April.

A report in the South China Morning Post noted 
"Upon conclusion of the trial on September 30, the city government proposes gradually extending the ban, covering chickens, ducks, geese and pigeons, to other parts of the metropolis. The ban is expected to be implemented citywide by 2024."

"Currently, it affects 298 live poultry stalls at 82 wet markets in Yuexiu district, and in parts of Tianhe, Liwan and Panyu districts, where vendors will sell centrally slaughtered chickens that will be provided by three designated suppliers."
This is welcome news and a positive step towards stopping not just H7N9, but a raft of other influenza viruses that jump to us from, and mix to create new virus within, birds.

Source...
  1. http://www.scmp.com/news/china/article/1505389/guangzhou-begins-trial-ban-live-poultry
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Pressure testing...

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Comments in the recent ScienceInsider article (a great read by the way [1]) interview with Prof Christian Drosten got me to thinking.

What follows is a stream of consciousness around the need, or not, to expand laboratory testing capacity during times of an acute rise in cases such as during a viral cluster / outbreak / pandemic situation (COP; just made that up-it's not an official acronym or anything).

During a COP, the workload in a diagnostic virology/microbiology/pathology laboratory is dramatically increased. More samples, more often. And this is due to the testing of just 1 added virus. Often, the biggest impact on service delivery comes from the need to add a new test for this virus which may not have been part of any existing testing menu or panel; it adds to the number of tests already being run. In one major Australian laboratory, routine diagnostic testing for non-influenza-related diseases runs at ~1,000 tests/day.[2] In winter, Australia's peak season for influenza, this lab (Victorian Infectious Diseases Laboratory or VIDRL) would normally test ~100 samples per day for that 1 pathogen, but during the influenza A(H1N1)pdm09 pandemic, one day saw 1,401 tests done for it alone.[2] Impressively, these guys kept to their usual result turnaround time (TAT).

Such a response requires coping with extra paperwork, quality control, and the creation and implementation of new protocols, perhaps overcoming special specimen reception issues and specimen handling requirements. There may be delays in getting specimens to the lab and a need to enrol other (previously quality assured) COP assistance laboratories to cope with the load. Less urgent testing and research may be halted and even expanded lab space may be sought in adjoining areas. This all create some real impact. It can affect other results, it may impact on the TAT for a lab (although prior planning is aimed at coping with the strain of COPs and keeping the result TAT in check as happened in the example above). A COP strains nucleic acid extraction robots, centrifuges, bio-hazard safety cabinets, labelling machines, pipettes and thermal cyclers - all of which break down when you least need them to. Reagents may become rare and if not stockpiled could create a bottleneck in assay performance - basic PCR assay reagents may be hard to come by or slow to receive, especially during a global and/or sustained outbreak or pandemic. And very importantly, there is a real toll on staff and managers. Hours may be extended, tiredness and stress will set in and a shortage of expertise may be an issue for maintaining quality and TAT...and sanity

In other words, test results don't magically appear and diagnostic labs are nowhere near as automated as you might think.

All this adds up to a system that can reach its capacity and thereafter shows signs of stress. The influenza A(H1N1)pdm09 pandemic did this. Now we hear of that MERS-CoV may be creating a similar circumstance in the Kingdom of Saudi Arabia (KSA). Why is the KSA Central Laboratory, which does all the PCR testing for MERS-CoV, under such stress now? According to Prof Drosten, it's because of changes in the testing which may be a driving factor underpinning April's Jeddah surge of viral detection.
Something dramatic changed, and that is the case definition.
Prof. Drosten to ScienceInsider

This change led to a jump in testing from 459 samples for all of 2014 prior to the outbreak, to 4,629 in just 1 month. As the number of MERS-CoV tests being performed in each (daily) report of new cases is no longer part of the KSA Ministry of Health's (MOH) message, a thumbnail sketch is that 154 sample per day are being tested for that month (divided by 30 days). And then there was this comment..
"The question of whether there is a mild, short-lived infection in some people is scientifically interesting. But in cities like Jeddah, it is bringing the health system close to collapse. That is the big problem. So many samples are being tested that the lab capacity won�t suffice for the real cases."
Prof. Drosten to ScienceInsider

An entirely fictional map of MERS-CoV spread including
severely ill, mild/moderately ill and prodromal /
asymptomatic infections. Simply intended to be
something to think about when discussing the
impacts of limiting PCR testing. Reduced PCR
testing should not happen until until we know which
parts of this map are real, and which are a load of rubbish.
With this background and these comments in mind I have some thoughts and questions...


  1. I know almost nothing about the KSA's pathology laboratory testing capacity generally nor its approach to respiratory virus testing in particular. I do know that the KSA is are a country of around 29 million people while Australia has around 23 million. I refer to the numbers above when I say that 4,629 samples in a month, for what has become an epidemic that seems to have exposed major flaws in infection control across multiple hospitals around the west, south and central regions of a wealthy country, should not be threatening the KSA's testing capacity unless it did not exist in the first place.
  2. Why wouldn't pathology testing which is robustly designed to cope with a worse-case-pandemic, not exist in the KSA? I don't know. Does testing exist for standard virus screening and if so what sort of throughput is the norm? The KSA healthcare systems seems to be laden with western-influenced medicine, and with that influence comes our compulsive need to create protocols and preparedness plans and to learn for the misfortune of others. The WHO have all this sort of information publicly available and always seem available for a chat.
  3. The reality is, and I am not on the ground to see whether this is a real factor in the KSA, laboratory capacity needs to be such that it can cope with a surge in cases such as that during a COP. It also needs to manage other endemic respiratory virus testing and whatever is coming next. It seems highly likely to me that the same at-risk older male population with kidney and heart disease, diabetes and obesity issues that get hit so hard by MERS, is also suffering badly from influenza and other viral infections. Back in August we heard about additional laboratories coming on line. It looks like they may not have. They need to.
  4. Am I especially naive (probably) to expect wealthy countries to make sure something as important as pathology testing is not in danger of falling over when it's particularly needed? We expect our electricity to be quickly reconnected after a storm, out SUVs to be easily refuelled no matter what wars or disaster befall the worlds, we take for granted that water is just there and we'd riot if our shop were not stocked with food 24/7. Why would testing your population to make sure you have a real-time knowledge of the pathogens infecting them, not be given an equal measure of attention and support? Especially if that pathogen has never been seen before, is transmitting without your understanding and is killing 1:4 of those it infects?
  5. Prof. Drosten noted that he has been working to get good MERS-CoV antibody testing in place within the KSA to get a better idea of how widespread prior exposures to MERS-CoV is. That will be a very helpful piece of knowledge to have. But it will not tell the MOH what is happening now in Hospital X (an apt name since we no longer know names of the hospitals where cases are being treated; that dropped off the new MOH messaging format last night). We're not even sure MERS-CoV antibodies are produced if the PCR-positive person only had a mild or asymptomatic case. PCR testing must remain in place until the MOH or whomever it looks to for advice, can be sure they have seen all the faces of MERS and the MERS-CoV. We're some way off seeing that yet I believe.  Don't get me wrong - an antibody test is great and we should roll it out alongside PCR. But in context - it will tell us information about the status of the KSA population in terms of how many have been exposed to MERS-CoV. And then it will have done its job as a research tool. Routinely, we need to test with the gold standard; PCR. And I think we should keep testing widely. 
  6. Prof Drosten also suggested that instead of continued PCR testing of contacts (the source of asymptomatic cases presumably), the KSA should consider a home isolation approach. Would that be  for up to 2-weeks, away from work, school - away from family too? Seems like a lot of hassle and disruption for the sake of a PCR test. Perhaps a shorter period once we know more about the dynamics and shedding during the diseases prodrome or from asymptomatic people. That will require PCR to define a person was initially MERS-CoV positive in order to study whether virus is shed.
  7. Let's also keep in mind that antibody testing is labour-intensive too. Perhaps not as intensive as PCR, but it would still increase the workload on a pathology laboratory.  It's a new tool not a better one.
  8. Why do I think the KSA should keep testing widely? Because if we don't we might be missing mild and asymptomatic or prodromal cases which may (and we have no data to support the argument in either direction right now, so its much better to be safe and test as the World Health Organization advise) contribute to the spread of MERS disease. Who knows how much virus an already old ill male needs to become severely ill? Perhaps much less than a healthy young nurse with lots of previous exposures to other viruses, including some that may provide cross-protective immunity I suspect. 
  9. If the KSA had not switched gear and accelerated into more testing, we would still only know the face of MERS that is pneumonia and death. It is clearly a lot more than that-as are all respiratory viruses. It would be a great shame in my opinion, to do things the way they were done with SARS, just...because. We always need to look afresh with the knowledge and tech we have to hand on the day.
Now more than ever with new measures being instigated to educate the KSA public (a bit more anyway), reduce camel exposures (although it's clear many don't see a link to camels as justified) and improve hospital infection control (too late for the majority of MERS cases that seem to have occurred in linkage with healthcare facility outbreaks) and hospital triage of MERS cases, testing efforts must not wane.

And while that goes on in the background, it really is past time to sort out some transmission details. How is the virus spread (a) from and between camels and (b) to and between people? These are fundamental questions and all risk reduction hinges on their answers. 

At least now that we know the virus hasn't changed, we shouldn't be seeing any more cases during the upcoming multi-million person Hajj pilgrimage, than we saw last year. Right? Last month was all about an infection prevention and control breakdown that can be fixed before October. Yes? And the few instances of Umrah pilgrims that seem to be popping up positive this year that we didn't see in 2013 and the bunch of single export cases? Just increased testing? Yup. Some of that even kinda fits in with what I wrote about Umrah 2013. 

Oh look. 10 new cases tonight, just like on 2013. Oh wait. No it wasn't like tat in 2013. We didn't have any 10-detections/day days in 2012 or 2013. Guess these will be because of all the pesky asymptomatic people? Let's see...ICU, hospitalised, ICU, symptomatic but home isolated, ICU, ICU, asymptomatic, ICU, asymptomatic, hospitalised oh and in two most likely unlinkable previous cases: death, death. 2 out of 10 with no symptoms. 

Definitely keep up the testing guys. MERS isn't SARS but then 2014 isn't 2013 either.

Sources...
  1. http://news.sciencemag.org/health/2014/05/mers-virologists-view-saudi-arabia
  2. Reality Check of Laboratory Service Effectiveness during Pandemic (H1N1) 2009, Victoria, Australia | Emerging Infectious Diseases. 2001. 17(6):963-
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358210/pdf/10-1747_finalS.pdf
  3. http://www.nccid.ca/files/Evidence_Reviews/NCCID_H1N1_impact_04.pdf
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Just the right height for a kiss....

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..lick, slobber, spit....

At least working out transmission routes isn't a big issue here!


From minujbe: http://www.minube.com/fotos/rincon/2174724/7509277












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MERS-CoV in Australian camels? The search is underway...

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I have been asked a few times about whether Australia is testing its large feral camel population (approx 300,000 animals [3,6,7]; Australia also exports camels [5]) for the Middle East respiratory syndrome coronavirus (MERS-CoV). 

I put that specific inquiry to Mr Gary Crameri, the Stream Leader for Emerging Zoonotic Disease at the Commonwealth Scientific and Industrial Research Organisation's (CSIRO) Australian Animal Health Laboratory (AAHL)[1]. You can also see a little more about Gary and MERS-CoV here [2]

And, as per comments below, it looks like Australia is now in a good position to study many aspects of the MERS-CoV. 
We are indeed the lab doing this work MERS is one of the many viruses we research and is of particular interest to us given its relationship to SARS and our global role as a WHO Collaborating Centre for SARS. We are currently investigating MERS as part of our national mission to research and understand the processes by which new diseases emerge and spread.
Some background on CSIRO AAHL.[1]

AAHL has a national responsibility to protect Australia�s animals and people by delivering science that will further our understanding and management of infectious diseases. This work includes diagnostic and surveillance activities, which currently includes MERS in bats and camels. Our research also includes comparative immunology and genome sequencing to study the evolution and transmission pathways of new viruses to help us manage the risks such viruses pose to both animals and people.
AAHL officially opened a new biosecure immunology laboratory yesterday [4] and work has begun there on the MERS virus to study how different hosts� immune system responds to the virus.
More information about what and how and why will follow in the future.

References...
  1. http://www.csiro.au/aahl
  2. http://theconversation.com/sars-mers-preparing-for-the-next-coronavirus-pandemic-16359
  3. http://www.abc.net.au/news/2013-11-21/feral-camel-culling-report/5105884
  4. http://www.csiro.au/en/Portals/Media/New-antivirals-closer-with-opening-of-new-laboratory.aspx
  5. http://news.bbc.co.uk/2/hi/middle_east/2038834.stm
  6. http://www.australian-information-stories.com/camels-in-australia.html
  7. http://www.paddymchugh.com/camels.html
  8. http://www.abc.net.au/landline/stories/s584460.htm
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Snapdate; MERS-CoV and the thickening age/sex pyramid..

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Click on image to enlarge.
No, it's not the title for an epidemiologist's detective novel. It's a comparison of my previsou and my latest age/sex pyramids.

And it really looks like MERS needs to go on a diet. Its "waist" has broadened quite a bit as a sign of younger cases becoming part of the rogue's gallery of infected, if not afflicted, people. 

Also note the axis along the bottom has changed a lot between mid-April and now. So we have more total numbers but also more detections of virus in the under-50s age band.

And as always, males predominate in MERS-world.


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Healthcare for All at Hospital San Carlos, Altamirano, Chiapas, Mexico

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With the incredible nuns of Hospital San Carlos.
The evening prior to my departure from Altamirano, the Hospital San Carlos nuns invited me to join them for dinner in their community.  As I mentioned in my prior entry, they are a truly incredible group of women.  Each has unique and important responsibilities in the daily functions of the hospital.  Among them include: Sor Rosario, determined hospital director and fearless leader; Sor Edith, wise clinical supervisor and xray technician; Sor Genoveva, director of nursing and nursing education; Sor Paz, pharmacist; Sor Consuelo, near to my heart, head pediatric nurse; Sor Rosaura, head medicine nurse; and Sor Anita, the most senior of the group, tireless nurse anesthetist.  Though each came to Catholic sisterhood through distinct paths, they all share a deeply religious and loving dedication to the poor and marginalized.  A story they shared that evening highlights the irreplaceable role that they and the Hospital play in providing care to so many families throughout Chiapas amidst a sea of barriers:
During a weekend when I had taken a respite to visit the Mayan ruins in Palenque, a gravely ill five year old girl was carried through the doors of the hospital by her parents in the middle of the night.  She was in severe respiratory distress, with a fever, and a concerning murmur, likely decompensating from pneumonia superimposed on a previously undiagnosed congenital heart disease.  Francisco, one of the several new physicians spending his year of social service at the Hospital, immediately called Carlos, an outstanding family medicine physician from Spain who has served as the hospital pediatrician for several years. The patient was rapidly stabilized and survived the 3-4 hour long journey to the pediatric subspecialty hospital in Tuxtla Gutierrez, where she was intubated and placed on a ventilator. Francisco formed a special bond with the family, who, like him, spoke the indigenous language of Tzotzil.  Later the following week, he received a phone call from the parents, informing him that their daughter had died after several days of medical care. They had been profoundly impacted and upset by a question that a Tuxtla provider had asked them, �Why did you take so long to bring your daughter to the hospital?�  Perhaps a sign of a provider having trouble coping with the injustice of losing a young life, or perhaps willful ignorance with regards to daily injustices, including poverty and discrimination, faced by the indigenous communities of Chiapas.
Hospital San Carlos serves as a safe, accessible, and culturally sensitive and acceptable provider of inpatient, outpatient, medical, surgical, pediatric, and OB/GYN care for indigenous as well as autonomous communities throughout much of the state of Chiapas.  Of course, resources are limited.  Plain films and basic labs (which do not include cultures) are available during the day as well as at night in the case of emergencies. Bedside ultrasound skills are acquired by some of the physicians over time.  Outpatient subspecialty referrals can be challenging, whether due to lack of patient resources or long wait lists.  Inpatient transfers, such as for neonates who may need CPAP or intubation, are at times refused by the referral hospital due to lack of beds. 

One segment of the infant and toddler's unit.
Caring for patients in both the inpatient and outpatient pediatric units was truly an excellent clinical experience.  In addition to a handful of newborns, we typically had somewhere between 3 and 7 inpatient pediatric patients.  Admission diagnosis were reflective of two the top five killers of children under five globally, acute respiratory tract infection and acute diarrheal illness.  Probably about a third of infants and toddlers were admitted with bronchiolitis, pneumonia, and a surprisingly high proportion of bronchodilator-responsive bronchospasm, perhaps secondary to indoor air pollution from firewood use.  Another third were admitted with dehydration in the setting of viral gastroenteritis, dysentery, and parasitosis.  These diagnoses certainly have parallels with those that most commonly lead to admission to MGHfC; however, the superimposed stunting and/or wasting among most of the patients clearly demonstrated how chronic and acute malnutrition might contribute to 50% of under-five mortality around the world. 

I learned a number of infectious disease-related clinical pearls during my month: one should assume that all children with severe acute malnutrition have a severe bacterial infection whether or not they have signs or symptoms such as fever; iron repletion for anemia should be deferred until treatment of bacterial infections (e.g. infectious enteritis, see: BMJ 2002;325:1142) has been completed, as there is a theoretical risk of worsened infection; congenital tuberculosis exists (see: N Engl J Med 1994; 330:1051-1054); and the management of fever without a source in well-appearing newborns/infants in the absence of culture data can rely significantly on clinical suspicion. 

Abnormal L5
The remaining one third of admissions encompassed an interesting mix of subspecialty issues. These included: a 12 year old boy with anasarca, ascities, pericardial effusion, and pleural effusions secondary to nephrotic syndrome; a 3 year old girl with >50% partial and full thickness second degree scald burns, one week out from injury, who was transferred AMA from government hospital; a 7 month old boy with tachypnea since birth and failure to thrive, without murmur, but certainly with a yet undetermined congenital heart defect, admitted with worsened respiratory distress; a 3 month old girl with severe stunting, presenting with vomiting since birth, found to have hemoglobin of 4 and guaiac positive stools; an 18 year old boy admitted after intentional ingestion of Gramaxone (aka Paraquat), an almost universally fatal herbicide without effective treatment nor antidote; and a full term, newborn boy with perinatal asphyxia, low apgars, who developed clinical seizures on day two of life, requiring phenobarbital.  I also encountered a good deal of developmental delay, including a 2 year old boy who presented to clinical with a URI and who apparently could not walk, stand, nor really sit appropriately.  He had bilateral ankle clonus, lower extremity spasticity, bilateral Babinski, and these apparent findings on physical exam and plain film:

Violaceous mass over lower lumbar spine.


Hospital de Especialidades Pediatricas - Tuxtla, Gutierrez
I was frequently left with the desire to teleconsult my MGHfC attendings and fellows and, in fact, did speak with one of our wonderful cardiologists, Dr. Manuella Lahoud-Rahme regarding one of our CHD patients.  Wait times for consultations with subspecialists at Hospital de Especialidades Pediatricas are often prolonged, and the prospect of enduring the costs and opportunity costs of travel make the trip all the way to Tuxtla Gutierrez prohibitively expensive for many families.  Performing an echocardiogram while Dr. Lahoud-Rahme watches via Skype, is just one example of the potential for telemedicine to advance access to subspecialty pediatric care at Hospital San Carlos.



Helping Babies Breathe - Workshop 1
In addition to the clinical and community-oriented aspects to my trip, I spent some time working in the realm of formal medical education and quality improvement.  I gave a chalk-talk on a variety of neonatal health issues for the physicians during one of the biweekly morning conferences.  This was perhaps more of a learning experience for me, as my audience helped me grasp the many adaptations necessary to take care of newborns in a low resource setting. Continuing with the theme of neonatal health, Dr. Jennifer Kasper and I prepared an abbreviated Helping Babies Breathe� training for nurses, nursing students, and auxiliary staff at Hospital San Carlos, in collaboration with Sor Genoveva. 
Nursing students at their capping ceremony.
There were 42 participants who attended one of two, two-hour sessions that focused on the Golden Minute of life and practicing scenarios with NeoNatalie newborn mannequins. About 3 weeks later, I was able to schedule a follow-up refresher session, and while this landed at the tail end of vacation week for the nursing students, 31 learners participated in the workshop, including 10 new participants.  While I had intended to perform OSCEs to evaluate effectiveness of the first workshop measuring retention of knowledge and skills, this was ultimately not feasible in light of time and resource constraints.  Subjectively, the students expressed that they very much appreciated the opportunity to reinforce and practice their skills.  I could see that many were more prepared to revive their mock newborn patients, and to do so within the first minute of life.  The second session also gave me the opportunity to fine-tuning practices that I had observed in the delivery room during my month, for example: not delaying bag mask ventilation to attach oxygen to the self-inflating ambu bag and acting upon an emergency plan (i.e. calling Carlos) at the first sign of trouble, whether fetal distress or difficulty with ventilation. 

Carlos (pediatrician in-charge) and I.
Lastly, I worked with one of the hospital administrators and Carlos to create a self-evaluation tool for the pediatrics unit that could be used to highlight and select priority issues for quality improvement.  Drawing from hospital standards from the WHO, the Mexican General Health Council, and other resources, the tool asks doctors and nurses to respond to questions relating to seven themes using Likert scales: professional communication, medications and errors, rights of the hospitalized child, involvement and education of families, evaluation and treatment of pain, hygiene and prevention of infection, personnel and equipment, and trainees and continuing medical education.

I truly hope that I will have an opportunity to return to Chiapas and to Hospital San Carlos.  My upcoming fellowship program in pediatric emergency medicine is affiliated with two hospitals, UCSF and Highland, who send attendings and residents to San Carlos.  Now that I�ve had a chance to reflect on my trip, it�s time to get busy thinking of next steps.  Next steps in strengthening the Hospital�s referral capabilities, perhaps via telemedicine � next steps in ongoing capacity-building in skills such as neonatal resuscitation and pediatric ultrasound.  I�m so grateful to all my new, amazing colleagues in Chiapas, the sisters of Hospital San Carlos, Dr. Jennifer Kasper, Dr. Juan Manuel Canales, and Doctors for Global Health, who together made this experience as enriching as it was.  Many thanks as well to MGHfC Pediatric Residency Program and the Partners Center of Expertise in Global and Humanitarian Health without which this incredible experience would not have been possible.

Ashkon Shaahinfar, MD, MPH
MassGeneral Hospital for Children
Pediatrics, PGY3








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MERS-CoV by sex, week and age...

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Two quick charts on the Middle East respiratory syndrome coronavirus (MERS-CoV; which I verbalize as "murrs coronavirus" just fyi )data.

The first chart shows a rise in the proportion of females (pinked dashed line; right-hand axis) during the Jeddah outbreak over recent weeks. But this does not change the fact that males still make up the majority of humans positive for MERS-CoV. For camels - I don't know sex, but juveniles seem to more often have RNA detected and less often have MERS-CoV antibodies present.

It's interesting that a similar rise in the proportion of positive females occurred in April-2013 when there was another healthcare-related outbreak around Al-Ahsa.

It would be nice to know what the sex breakdown is when comparing index cases to non-index cases. Does human-to-human spread involve more females as it goes along than does acquisition from camels - these presumably being a more common source for the sporadic cases that trigger each smaller cluster? Could a rise in the proportion of females be useful as a marker for an impending extended outbreak? Do men have most of the contact with camels? A few question marks there.


The sex distribution, by week, of MERS-CoV positive people and the proportion of those,
each week, who are female (shown using a 6-day moving average).
Click on image to enlarge.

The second chart plots the average age each week (an orange dot) and plots a 10-day moving average. The moving average continues to show the cyclical pattern I alluded to in my last post of this chart - whatever it means or doesn't mean. 

During the Jeddah outbreak, the average age appears to have dropped compared to prior to just the outbreak. But there is a lot of movement in the average age over time. Although, there does seem to be a downward trend after the Apr-2013 outbreak as well and another after something happened in October. Do we know of an outbreak in Oct-2013? Could this mark one that occurred but that we didn't hear about? Am I wearing my tinfoil hat again? So many questions.

Age drops among the tested population may be another marker of the wider or differently composed population that is being infected during human-to-human spread compared to when cases are sporadic and perhaps more closely camel-contact related. 

The average age, each week, of MERS-CoV positive people and a trend shown 
using a 6-day moving average.
Click on image to enlarge.

Or it may be nothing but noise from the incomplete data we have to play with here.
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Snapdate: MERS-CoV detections near 500...

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MERS-CoV detection by day; Jeddah outbreak.
Click on image to enlarge.
Welcome to the beginning of MERS-CoV's 112th week (2.15 years). We sit at 497 cases (probably over 500 if the United Arab Emirates would confirm their cases with some extra data that made them more identifiable and "real". For now, I'm not including them after the recent issue around theUAE12. For now my count says at 497 with ~131 deaths (26.3%).

Judging by tonight's announcement of only 3 cases (only 1 with an onset date which was 24-Apr), let's hope this is the week where the Jeddah outbreak gets put to bed.

MERS-CoV detection by week 2012-present.
Click on image to enlarge.
Also, make this the week that the Kingdom of Saudi Arabia's(KSA) Ministry of Health adds some consistency to its releases. They've been doing a 100% improved job in the past weeks, adding much more detail, but it needs to be the same detail for every case, every day. And the listing of deaths and recovered cases is also great; but is currently not able to be linked to the original announcements so we don't know where they these people were from, comorbidities, HCWs etc as there are often 2 or more people from the same region with the same age. A date of affliction is needed to permit the linkage between original announcement and death/recovery. Just 1 more variable guys. Pleeease.

Nonetheless the dailies seem to be slowing, although the cumulative average still strolls upwards but in a linear, not exponential manner.

We stay tuned.


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Ebola virus disease (EVD) West Africa update for 02-May, WHO-AFRO update...

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Click on image to enlarge.
Thankfully the latest World Health Organisation update includes figures for Liberia. The last West Africa update did not, so I didn't post a chart.

Summary..

Total suspected/probable/confirmed cases: 244
Total suspected/probable/confirmed deaths: 162 (66.4%)
Total lab confirmations: 133 (54.5% of 227)

These figures are very important for two reasons...

Firstly they show a drop in suspect/probable cases after data scrubbing by the Liberian Ministry of Health and Social Welfare. This reinforces that the outbreak is being well controlled.;The date of isolation of the most recent confirmed cases is 30-April from Conakry and Guekedou (Guinea).

Secondly there has been a concomitant rise in the proportion of fatal cases of EVD due toZaire ebolavirus (see the percentages above the orange line in the chart). This is not because the numbers have jumped, it's because the denominator has shrunk for the relevant calculation:
No. EVD fatalities/No. total susp/prob/conf cases.
We've known this rise in proportion was coming because it was highly likely that case numbers would change as the dust settles and the susp/prob EVD patient numbers get discarded because they are found to be infected by something else; clinically similar disease, but not because of infection with Zaire ebolavirus. I've written about it previously if you'd like some background.

With the use of more antibody testing, the numbers will continue to change, as they always do in outbreaks.

This will be my last update on this outbreak linked to the WHO-AFRO announcements unless anything major happens.

A reminder - the chart above is made for general interest. It may be that I have misinterpreted the language in the report (sometimes a little tricky to wade through these reports) but the trends should still be informative even if a number or data point is out of place.


Sources...

  1. http://www.who.int/csr/don/don_updates/en/
  2. http://reliefweb.int/report/liberia/unicef-liberia-ebola-virus-disease-sitrep-20-2-may-2014
  3. http://newsmedicalnet.blogspot.com.au/2014/04/ebola-virus-disease-and-lab-testing.html
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MERS-CoV by month, now with added camels and hospital outbreaks...

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Weekly case tallies for 20012-4 (blue-surviving 
and fatal cases; red-fatal cases). Also indicated 
are the season in which camels give birth (I've
noted "birthdays" because it seems to be 1-year
old or older camels that are usually positive for
MERS-CoV. Past and future Hajj pilgrimage 
dates are also shown as is 1 of several
large camel events in the KSA.
Click on image to enlarge.
While the World Health Organization is yet to produce confirmed case data for the majority of the MERS-CoV outbreaks' biggest month, some of those data and extra information are being provided by the Kingdom of Saudi Arabia Ministry of Health v2.0. 

And it's very welcome and much appreciated. There still remain some vagaries and data gaps that make consistency an issue. But further information is not forthcoming so let look at some charts of what we have. 

For now, we can see in the daily graph, 4-days into May, that cases are still being announced but at what looks like a slower rate. We are seeing cases reported with a lag of approximately a week from when they became ill/were hospitalised (when those dates are present).

A plot of cases per day. Many (?most) are based on dates of reporting although
more dates of illness onset have emerged lately and I am working through them. This means that the specific peaks may chop and change a little as dates are assigned. Nonetheless, the trend seems to be one of decreasing numbers per day and
the cumulative average may be suggesting a peaked for this KSA outbreak.
Click on image to enlarge.
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