Tuesday, 30 June 2015

Ebola mysteriously returns to Liberia...[UPDATED]

v2-1JULY2015 AEST
In a gut-wrenching, but not wholly unexpected event, a new case of Ebola virus disease (EVD) has popped up in a town called Nedowein (or Nedowian [8]), about 50km south west of Liberia's capital, Monrovia.

Liberia had been declared a country free of EVD on 9-May-2015 - 52 days ago, or 1 month, 21-days, or 1248 hours.  

The 17 year old male (17M) died on Wednesday (about 6 days ago) and has already been buried by all accounts. Samples from his corpse tested positive at least twice.[3]

It's not an unexpected event because both Guinea and Sierra Leone, adjoining countries, continue to struggle with EVD and have been unable to stop the disease from spreading, even though in relatively small numbers compared to what was occurring in 2014. 

What makes this new case in Liberia a little mysterious is that 17M died far from the border with either of these countries; approximately 150km from Sierra Leone's south-eastern border and about 200km from the nearest Guinean border. Sure, these are not insurmountable distances to travel while incubating an Ebola virus infection, but it would have been a simpler call that this was an imported case if it had occurred on or nearer to the border of one of the two countries with ongoing disease. However, it seems the young man did not travel outside Liberia.[8]

Hopefully the contact tracing and investigations that are going on now will find that 17M simply made contact with someone who had traveled from outside of Liberia, perhaps to Nedowein, which is described as the home town of 17M.[2,7] If this is not an imported case then one is left to wonder about various other scenarios including:

  1. sexual or other less common transmission of Ebola virus from an as yet undiscovered convalescent EVD case
  2. contact with an unknown case who had traveled across the border from a country with EVD
  3. a new zoonotic acquisition of a different Ebola virus variant
  4. there may still be clusters of EVD within Liberia that have been smouldering on without the knowledge of any authorities

Time and further hard work will no doubt tell.

UPDATE: A second  case, associated with 17M ("Abraham") has been diagnosed.[9] Some discussion is evolving around the consumption of dog meat by 17M,[11] however, the same questions around how a dog would become infected (no record of the detection of active replication in a dog have been recorded to date, although antibodies have suggested the possibility in earlier outbreaks) will apply.

Further reading...

  1. http://www.frontpageafricaonline.com/index.php/news/5660-ebola-back-in-liberia-1-month-20-days-after-free-declaration
  2. http://www.bbc.com/news/world-africa-33323664
  3. http://www.ibtimes.com/ebola-liberia-corpse-tests-positive-deadly-virus-weeks-after-liberia-declared-ebola-1989248
  4. http://bigstory.ap.org/article/581e523aeb1144f68aa1a1629b0e9252/liberian-official-says-corpse-tests-positive-ebola
  5. http://news.yahoo.com/liberia-announces-return-ebola-one-death-094057018.html
  6. http://www.nytimes.com/2015/06/30/world/africa/liberia-new-ebola-death-is-reported.html
  7. http://newsworldmap.com/ebola-returns-to-liberia-but-health-minister-tells-public-no-need-to-panic-washington-post/ 
  8. http://news.sciencemag.org/africa/2015/06/liberias-puzzle-how-did-new-ebola-patient-become-infected 
  9. http://www.nytimes.com/2015/07/01/world/africa/liberia-ebola-epidemic.html?partner=rss&emc=rss&smid=tw-nytimesscience&_r=0  
  10. http://frontpageafricaonline.com/index.php/health-sci/5667-ebola-mystery-dog-meat-story-eclipses-border-lapse-theory
Version history..
  1. New links added; town name variation added from Science report; hypothesis of contact with another imported case - #2; note on lack of travel outside of Liberia; announcmene tof a 2nd case

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.

Saturday, 20 June 2015

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

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

  1. Excel version, Office 2010
    https://drive.google.com/open?id=0B5sEcTjB5Aila3c5WXI4bzlkLWc&authuser=0
  2. MS DOS CSV file
    https://drive.google.com/open?id=0B5sEcTjB5AilTHRub1FRZnhpQmM&authuser=0
  3. Original WHO PDF
    https://drive.google.com/open?id=0B5sEcTjB5AilWlo0UDZwVzRpdVE&authuser=0
Its taken a week to get these data, and its unclear why detail data dried up from the 12th June to the 19th, or why the data have appeared now, but they are here at last and that's great.

Saturday, 13 June 2015

Middle East respiratory syndrome (MERS) coronavirus: Outbreak in South Korea

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

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


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



.
References...

2. The Korean Broadcasting System's News websites
http://dj.kbs.co.kr/resources/2015-06-08/ &
http://dj.kbs.co.kr/resources/2015-06-04/
3.  World Health Organization pages
Main landing page on MERS and MERS-CoV (includes link to WHO line list under General Information)
http://www.who.int/emergencies/mers-cov/en/
Disease Outbreak News pages
http://www.who.int/csr/don/don_updates/en/
 
News on the current situation
http://www.wpro.who.int/outbreaks_emergencies/wpro_coronavirus/en/
Summary of Korean statistics-rapidly updated

http://www.wpro.who.int/outbreaks_emergencies/summary.of.MERS.stats/en/

Translating from the Korean for MERS epidemiology...

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

But processes, time money and stuff...

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

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

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

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

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

Wednesday, 10 June 2015

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

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

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

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

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

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

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

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

References...

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

Monday, 8 June 2015

MERS-CoV and opportunity to spread...

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

So what?

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

But MERS-CoV ain't no measles virus. 

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

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

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

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

References..

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

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

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

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

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

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

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

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

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

References..

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