Showing posts with label World Health Organisation. Show all posts
Showing posts with label World Health Organisation. Show all posts

Saturday, 23 April 2016

On Zika and microcephaly: causality, consensus and checklists....

Over the past month the World Health Organization (WHO) and then the United States Centers for Disease Control and Prevention (CDC) have associated infection of by Zika virus (ZIKV) with cases of microcephaly and central nervous system disease (M&CD).[1]
The first WHO statement cited a scientific consensus identified at a meeting called to examine the evidence linking ZIKV infection with foetal malformations and neurological disorders.[1] Later in March the WHO pointed to case studies as the origin for that scientific consensus.[2] I've talked about my views on gaps in some of these studies before - for example here and here.

The CDC based their much stronger comments on a review of the literature and its application to address historically robust checklists - Shepard's criteria and the Bradford Hill criteria - that have heretofore proven themselves useful to identify teratogens (causes of embryonic malformation).[3] The CDC authors of this paper note that there is no "smoking gun" at this point and Dr Tom Frieden, CDC Director said it could take years before answers to other questions are found.[12] But not about ZIKV causing microcephaly. That question is answered according to two of the world's leading public health agencies. 

Checking the checklists.

The checklists CDC used were applied to resolve the questions around the cause of an apparent surge of M&CD diagnoses - the so-called congenital Zika syndrome.[4,5] To date this has been almost exclusively occurring in north east Brazil. Some instances have been reported in other countries with current - or past - ZIKV epidemics, but the numbers are small enough for questions to linger about whether these represent part of "normal" M&CD figures, perhaps brought to attention because of the enhanced focus on congenital deformities in 2015 and 2016 or ZIKV-caused disease.

Shepard noted in 1994 that..

"the rare malformation/rare exposure 
or case report method is far easier, 
less expensive, and more common than 
full epidemiologic studies."

He described "Examples of this rare defect/rare exposure "proof" (or better stated strong association)"[sic] including the virus driven congenital rubella. I'm not sure about rare in terms of ZIKV infection tough. While data are near on-existent from Brazil, we've been told that over a million people have been infected with ZIKV.[19] That seems to be a much less stringent use of Shepard's criteria than that of the CDC's "no longer any doubt".[12] Shepard's criteria have gone on to be used in legal definitions [7] which also take a broader view on causality in the study of teratology..

"causation is demonstrated between an 
exposure and an outcome if the outcome 
would not have occurred but for the exposure. 
The but-for test is typically modified by a 
substantial factor test, that is, the 
exposure was a substantial factor in 
bringing about the outcome, or by 
consideration of the exposure as a 
contributory cause"

The other checklist was the tabulated criteria of Bradford Hill, described in 1965 in his occupational medicine-focussed paper, The Environment and Disease: Association or Causation? which sought to relate sickness, injury and conditions of work.[18] I find Bradford Hill's comments in the Experiment section of his criteria interesting as they discuss whether a preventative action in fact reduces the frequency of the event...

"Here the strongest support for the
causation hypothesis may be revealed."

The CDC interpret this wholly in relation to an animal model.[3] Perhaps this meaning has evolved in subsequent analyses that I admittedly haven't read, but I see this criterion differently. To me it is addressing the need to wait and watch for any impact on reduced mosquito breeding and presence either because of seasonal variation or human interventions; a long wait.

In a statement similar to Koch's about his postulates, Bradford Hill stresses that none of these criteria can be used as if they were set in stone and none bring indisputable evidence for or against a cause-and-effect hypothesis. They are intended to..

"help us to make up or mins on the fundamental 
question - is there any other way of 
explaining the set of facts before us, is 
there any other answer equally, or more, 
likely than cause and effect?"

This seems - to me at least - at odds with the CDC's strident use of these criteria to define causality here.

Neither checklist necessarily hits the mark perfectly for what we're seeing in Brazil but, as with Koch's original postulates, these have been "matured" and tuned over time to fit the need of the moment-presence of a common virus infection causing a rare syndrome. 

Is the strong language essential to a response?

But let's back quietly out of the courtroom and return to the world of science, research and causality. We don't have a smoking gun but that has not prevented some important triggers being pulled. Principal among these was that the WHO called a Public Health Emergency of International Concern (PHEIC) on the 1st of February 2016.[8] Well before the need to use stronger language in March 2016, the PHEIC generated recommendations [9] for...
  • To interrupt ZIKV transmission using enhanced surveillance, diagnostics, risk communication, vector control measures, counselling and more
  • research and develop vaccines, therapeutics and diagnostics and increases  relevant services in affected areas
  • provide uptodate advice on travel to affected areas, disinfection of aircraft but do not restrict travel or trade
  • ensure rapid and timely reporting and sharing of information of public health importance relevant to the PHEIC
Obviously those things are expensive. We know from recent experience that the WHO struggled to get the pledged funds they'd requested to mount for an effective Ebola virus disease reposes fast enough and to match the requested spend. Perhaps stronger language is intended to free up the purse strings.[10,11] The main sigh of relief outcome from making such a strong statement by the CDC was...

"Now that we've determined the causal the 
relationship, we can use this information to 
redouble our efforts to prevent Zika, more 
narrowly focus our research and communicate
 even more directly about the risks of Zika."

And herein lies one of my concerns. Narrowed research, by definition, could miss things that have contributed to congenital Zika syndrome. Things that might include...
  • other viruses - rubella and cytomegalovirus are teratogenic viruses that are sometimes sought and not often found but that search can use a hodgepodge of methods. But what about new viruses and new variants of existing viruses? 
  • the impact of chemicals or toxins - the pesticide issue has not gone away [13]
  • the very complex immune responses that to date have mostly been a topic for discussion as a problem for antibody detection in the lab, but may be a part of the process [14,16] although did not seem to play a role in Guillain-Barre syndrome [15]
But all those things may still be included in a narrowed research focus. Those things aside we do know that ZIKV loves to grow in epithelial cell-derived neural stem cells; there is a lot of IgM antibody to ZIKV in babies born with microcephaly [20] and ZIKV has been found in the brain tissues of foetuses with disease.[21]

Devil's advocate - what other things might we consider?

We have not yet addressed whether ZIKV is just as harmless as we used to think it was and whether it is found in these tissues as a passenger and not a pathogen. 

Might it also be in the brain tissues of ZIKV-infected foetuses who do not develop any congenital anomalies? There has been little or no exploration of controls in most papers to date. Mostly - this would be unethical, but there might be other reasons for related tissues to be sampled which could then be leveraged fro important testing. Its important yet missing information.

Excerpted from WHO Zika virus microcephaly
and Guillain-Barre syndrome situation report. [17]
There is also the Colombian elephant in the room. 

This week saw the number of M&CD diagnoses in Colombia double...okay, from 2 to 4... having decreased the week before. This might be normal and part of the 140 annual cases reported in Colombia annually-that's an average of 2.6 per week. 

More time has now passed in Colombia than had in Brazil before Brazil reported its first concerns - and 141 M&CD diagnoses - over ZIKV and M&CD, after it identified local ZIKV transmission. As I've discussed previously, there could be many reasons for that difference - and a rise in cases in Colombia this week may herald that the starting line has been crossed indicating the beginning of some important supporting evidence for ZIKV causing M&CD. Or we might just be seeing normal levels of M&CD that also happen to be ZIKV infected-during an epidemic of ZIKV.

To my mind, the studies used to check off the lists leave some important things unanswered. Patience might have been advisable since the previous announcement of a PHEIC mean that there was no obvious need for the issue to be forced. Or perhaps this is more about the politics of finding a better way to secure the funding needed to address congenital Zika syndrome, and avoid the pitfalls of funding gaps dug during the fight to contain Ebola virus syndrome.

Only time will tell whether such strong WHO and CDC language was needed, helped or even hindered the response and understanding of congenital Zika syndrome. 


References...

  1. WHO Director-General briefs the media on the Zika situation
    http://www.who.int/mediacentre/news/statements/2016/zika-update-3-16/en/
  2. Zika situation report 31-March 2016
    http://who.int/emergencies/zika-virus/situation-report/31-march-2016/en/
  3. Zika Virus and Birth Defects — Reviewing the Evidence for Causality
    http://www.nejm.org/doi/full/10.1056/NEJMsr1604338
  4. http://www.bbc.com/news/world-latin-america-35763232
  5. http://annals.org/article.aspx?articleid=2498549
  6. "Proof" of Human Teratogenicity
    http://onlinelibrary.wiley.com/doi/10.1002/tera.1420500202/pdf
  7. Causation in Teratology-Related Litigation
    https://www.teratology.org/pubs/Causation_Ter-Rl_Litigation.pdf
  8. http://www.who.int/mediacentre/news/statements/2016/emergency-committee-zika-microcephaly/en/
  9. http://www.who.int/mediacentre/news/statements/2016/1st-emergency-committee-zika/en/
  10. http://www.globalissues.org/news/2016/02/01/21800
  11. http://www.oxfam.org.uk/media-centre/press-releases/2016/01/international-community-fails-west-africa-yet-again-ebola
  12. http://www.cdc.gov/media/releases/2016/t0414-zika-update.html
  13. https://peerj.com/preprints/1959/
  14. http://www.sciencemag.org/news/2016/03/qa-scott-halstead-zika-will-subside-5-years-max
  15. http://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(16)00562-6.pdf
  16. https://www.statnews.com/2016/02/17/zika-dengue-infections/
  17. http://apps.who.int/iris/bitstream/10665/205505/1/zikasitrep_21Apr2016_eng.pdf?ua=1
  18. The Environment and Disease: Association or Causation?
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1898525/pdf/procrsmed00196-0010.pdf
  19. http://www.reuters.com/article/us-health-zika-brazil-exclusive-idUSKCN0VA331
  20. http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(16)30253-7/fulltext?rss=yes
  21. http://www.nejm.org/doi/full/10.1056/NEJMe1601862?af=R&rss=currentIssue

Sunday, 21 June 2015

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

Update #1 27JUNE2015
Update #2 28JUNE2015
Sometimes people work from different playbooks.
Figure 1. MERS in South Korea. Most cases now plotted
on graph using their dates of illness onset.
An outbreak in decline. This is up-to-date - 3 new cases
from 21JUN2015 added (column at right hand side -
onset dates unknown)
Click on graph to enlarge

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

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



Embedded image permalink
Figure 2. What the graph above looked like before
we had dates of illness onset. Many cases
were 'moved' to earlier time points because
report dates always follow onset of illness dates
and they can follow by varying periods of time -
sometimes a day, sometimes a week or more.
Two file formats are in the folder I've linked to below. This is my first attempt - yes, it is a work in progress - to match up the new WHO case list from the 19th June which includes the highly prized date of illness onset (DOOs) for most cases - with that of the South Korean (SK) Health Authority. They do differ. Quite a bit. And in several ways. For example, the numbering scheme is off by one or more, SK69 seems to be missing from the WHO list, there is a question mark hanging over SK152 & SK156 and the WHO data seem to have a number of different ages from the SK data- mostly differing by one year (presumably someone is rounding up or down). 

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

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


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

  1. Google Drive folder with MERS data files
    https://drive.google.com/open?id=0B5sEcTjB5Ailfm1PcU1oNDF6M2hiaDduUDgzQUdxNlZxeHBkU0FHeVBRRFJkbHIxTmdjX3c&authuser=0
Updates...
  1. With the help of FluTrackers updated line list to cross check against, the first half of my list has been updated - some bugs fixed. 
  2. After about 5 hours - on and off - FluTrackers helped me sort out a few errors and the latest version of my list has been uploaded into the the folder linked above. Some typos corrected.

Thursday, 10 July 2014

Ebola virus disease (EVD) cases, clusters and outbreaks mapped out...

The West African region epidemic (top map), including countries with imported cases and the totals from past Ebola virus disease outbreaks and the few imported monkey cases (the US & Philippines [hence zero human cases]) plotted by total numbers and country (bottom map).

These maps are best viewed alongside my Ebola virus disease numbers page found here.


The WHO create multi-page Situation Reports [2] and brief Situation Summaries.[3] They are currently presented on Wednesday and "additional updated figures" will be posted "as they become available any day of the week" (via eMail to journalists from WHO).

My totals include all countries that have hosted a case in, or sourced from, a West African nation. Countries include Guinea, Liberia, Sierra Leone, Nigeria (now EVD-free), Senegal (now EVD-free), the United States of America, Spain and Mali.

This is a static page but as of 21-Jan-2015 (AEST) I have copied the maps to the bottom of my main EVD EBOV|Makona (west African Zaire ebolavirus variant) outbreak page at:  http://virologydownunder.blogspot.com.au/2014/07/ebola-virus-disease-evd-2014-west.html


A note about the proportion of fatal cases (PFC): 
On these graphs, my PFC calculations for West African countries and the DRC are based on dividing the total number of suspect/probable/confirmed deaths by the number of total suspect/probable/confirmed cases for the same date. This is crude and may be a sizable underestimate of the true PFC.

It may be better to use the deaths at the most recent date divided by the total cases from 9-16-days  earlier (this number is not precisely known) to better account for the lag in time between presenting to a treatment facility and dying (for those who do not recover). 


Some estimates suggest the true PFC may be closer to 70%-80%. I don't have enough data (or smarts) to be able to calculate the lag for now so please be aware that the PFC above is likely an underestimate.


  • The figure above, as with all on VDU, is made for general interest only. It is also freely available for anyone's use, just cite the page and me (Dr. Ian M Mackay, PhD) please. It may be that I have misinterpreted the language in the reports (sometimes a little tricky to wade through) or miscalculated some totals based on the way data have been presented. 
  • Sometimes there are very country-specific differences in what gets presented to/via the World WHO DONs/SitReps which make this process less clear than it could be. I recommend you have a read and compare the data from each of the countries for yourself to understand these issues. 
  • As I've talked about previously,[1] these numbers are all volatile for a variety of reasons, some Ebola-specific, so regard this chart for its trends only.
  • I am only able to plot what is publicly available. To date, this does not include granular data with dates of onset, or daily data of any kind. The WHO have these data and you will see them become more available through their Situation Reports found here http://www.who.int/csr/disease/ebola/situation-reports/en/
References... 
  1. Ebola virus disease and lab testing...
    http://virologydownunder.blogspot.com.au/2014/04/ebola-virus-disease-and-lab-testing.html
  2. Ebola virus disease outbreak Situation Reports (SitRep)
    http://www.who.int/csr/disease/ebola/situation-reports/en/
  3. Ebola virus disease outbreak Situation Summaries (SitSumm)
    http://apps.who.int/gho/data/view.ebola-sitrep.ebola-summary-latest?lang=en

Sunday, 1 June 2014

The International Health Regulations (IHR) 2005...

I've heard a lot about the IHR but I have not read the entire document. 

This post is just to note which States are considered to be a party to them and what they mean in general terms.

 A blog-friendly reformatted excerpt from the Foreward (highlighting is mine)...

"The purpose and scope of the IHR (2005) are “to prevent, protect against, control and provide a public health response to the international spread of disease in ways that are commensurate with and restricted to public health risks, and which avoid unnecessary interference with international traffic and trade.” The IHR (2005) contain a range of innovations, including: 

  • (a) a scope not limited to any specific disease or manner of transmission, but covering “illness or medical condition, irrespective of origin or source, that presents or could present significant harm to humans”; 
  • (b) State Party obligations to develop certain minimum core public health capacities; 
  • (c) obligations on States Parties to notify WHO of events that may constitute a public health emergency of international concern according to defined criteria; 
  • (d) provisions authorizing WHO to take into consideration unofficial reports of public health events and to obtain verification from States Parties concerning such events; 
  • (e) procedures for the determination by the Director-General of a “public health emergency of international concern” and issuance of corresponding temporary recommendations, after taking into account the views of an Emergency Committee; 
  • (f) protection of the human rights of persons and travellers; and 
  • (g) the establishment of National IHR Focal Points and WHO IHR Contact Points for urgent communications between States Parties and WHO."


This was taken from the PDF of the IHR2005 [1]

References...

  1. International Health Regulations 2005
    Second Edition
    http://whqlibdoc.who.int/publications/2008/9789241580410_eng.pdf?ua=1

Saturday, 4 May 2013