Wednesday, 9 April 2014

Ebola virus disease and lab testing...

Virology Down Under's latest Ebola virus case case chart.
Click on chart to enlarge.
Maia Majumder has posted a nice concise comment on her blog. In her latest post [1] she notes that we shouldn't be too surprised that the number of Ebola virus disease (EVD) cases with a lab confirmation (conf) represent a relatively low proportion of the total cases we hear about. 

Currently (see the chart above), 35.3% are lab confirmed. That's 59 confirmed among 167 cases; the remainder are suspected [susp] or probable [prob] cases.[3]

What might contribute to the speed of laboratory confirmation in this and other EVD outbreaks? 

Some thoughts below:
  • Obtaining a specimen. If a body has already been hidden, buried or otherwise disposed off before a sample can be collected. Sampling may have been refused by next of kin-although I am not at all sure if that is a "thing"  during an EVD outbreak
  • The need to work under enhanced safety conditions to prevent laboratory-acquired infections. BSL4/PC4 not strictly available to the field labs (although they are setup to work with those pathogens; see Tweet below), but increased care and awareness still slows down the diagnostic process compared to testing for a much less fatal virus
  • The generally tough conditions for doing precise and careful lab work in a mobile laboratory; work that is often resource-, temperature- and power-sensitive not to mention fiddly and in need of well-controlled experimental conditions
  • Distance from the site of collection to qualified lab and the quality of sample once it reaches that lab. A sample that sat around in the sun or was accidentally frozen, lost, broken, sent to the wrong place, may be falsely or weakly negative requiring further testing
  • The case is positive for a different virus but one that causes similar signs and symptoms. This may also require additional testing to identify. Other virus testing may be run in parallel..or may not
  • You could argue that previous outbreaks used older and often much slower diagnostic methods. That's true, if you compare them side-by-side in a results race. In practice, PCR-based testing comes with lots of extra "bits" that can slow down the production of a final result. The process is still faster than things used to be, quite possible more  sensitive too, but still not as fast as we'd all like. Apples and oranges though.

What defines a suspected case requiring testing anyway? 

Pretty much the same things that define this for any outbreak; a suspected case is a person with the appropriate signs and symptoms of disease, who was in the right place at the right time to have come into contact with a known infected human or animal in such a way that they may have exposed themselves to virus, but they have not yet received a lab confirmation that they have that virus. It may be that a case never receives that confirmation because of a lack of positive specimens (don't have specimen or cannot get a positive result) in which case the person becomes a probable case if they meet the clinical criteria but cannot be confirmed. 

Why would a sample not be collected? 

As noted above, perhaps the next of kin did not allow samples to be collected, perhaps the body was disposed of before sampling could be achieved or perhaps the lab testing failed. To safeguard against the latter, PCR-based testing (not the only method) usually involves multiple assays, running replicates of each sample, and using several assays, each preferably targeted to a spatially different region of the viral genome to overcome the negative impact of any genetic changes in relying on a single site. Such viral genetic change may be an issue during a new outbreak. We haven't seen much by way of sequence analysis from any viral detections to date, but very early on in this outbreak the species was confirmed using genetic sequence determination, to be a strain of the species Zaire ebolavirus.

The numbers are constantly changing.

After all that, even a probable case may still get be discarded after lab test results are in; it may have been a suitably relevant disease, but caused by infection with a completely different virus.

While I think many of us understand that the numbers do change, I also think some of the interest we have in wanting to see them is to understand which way the trends are changing; up, down, steep, flat etc. There has been a fair bit of cautioning about the numbers. In my own defence, these numbers are real. They are collected by people on the ground. They are a much better metric to watch, changeable or not, than the many headlines and blogs and Tweets that may be more aimed at attracting readers and followers, or just be ill- or uninformed.

So the numbers change. What does that mean? As it stands, the Sierra Leone cases have now been taken off the Ebola tally because they were confirmed as haemorrhagic fevers due to a completely different virus; Lassa virus. A suspected EVD case in a child tested negative in Ghana. 2/6 suspected cases from Mali have also tested negative for the Zaire ebolavirus. The Liberian hunter thought to be an isolated EVD acquisition [8,9,10] not linked to Guinea, has now tested negative for the virus. So the numbers change quickly. That's your proof and it confirms what WHO's Gregory Haertl has been saying since Day 1 of this outbreak. These changes have effects too.

The fatal case percentage may rise despite more cases testing negative.

Not as strange as it sounds.

If the number of susp/prob cases drops as some are discarded because the lab confirms they are not EVD, the proportion of cases that are confirmed and died due to EVD will "look" larger-it will be a bigger percentage. The proportion of fatal cases currently sits around 63% of all susp/prob/conf cases now (up from a lowest point of 59%, down from a high of 72%). If the denominator (total susp/prob) cases should shrink while the numerator (fatal EVD cases) remains steady, or grows, the ratio will grow. Be prepared for that and the accompanying headlines or poorly informed Tweets and comments that will scream "the virus is mutating" blah blah blah. It probably isn't. It probably won't. But you may not get that message from using Google alone (try the links below and work your way up).

This EVD outbreak is proving especially challenging.

The term "challenging" seems to have become an agreeable descriptive for both the WHO and MSF, at last, as of yesterday's WHO virtual press conference[5]

The challenges that differentiate this Ebola outbreak from previous mostly seem to be about the wide spread of cases around the countries of both Guinea and Liberia, complicated by the presence of other pathogens that cause clinically similar diseases. More usual problems for tracking, identifying and confirming EVD cases are listed above including working under the requirements of enhanced safety and the need to bring in many essential resources. Careful and accurate confirmation of cases by the lab is a time-consuming process but one that must be given that time in order to ensure it gets the right result. False-negative results or lab-acquired infections would be a very bad outcome at any time but especially if resulting from an unnecessarily rushed testing process. False-positive results have an arguably larger negative impact on the entire situation. Timeliness is a very subjective thing. But lab confirmation is most definitely not like making a cup of coffee.

Can we see the forest for the trees yet?

The most recent EVD susp/prob/conf cases became symptomatic on 06-April-14, but no new healthcare workers were among them and some cases are now being discharged .[4] Some good news there.

We're obviously not out of the woods yet (pardon the pun) in terms of transmission chains. The WHO suggests it will be "some months" before we stop seeing cases. But the recent WHO virtual media conference stressed that while EVD is a serious disease it is one that can be controlled and the risk of infection is low, when the right precautions are in place.[5]

See the latest WHO-AFRO Ebola in Western Africa Situation Update also. It's got totals and charts!! Bloomberg quicktake webpage [6] and the US CDC webpages [7] have lots of digestible information too.

References...
  1. #Ebola2014: On the Topic of Lab-Confirmation
    http://maimunamajumder.wordpress.com/2014/04/08/ebola2014-on-the-topic-of-lab-confirmation/
  2. WHO-AFRO Ebola virus disease (EVD), West Africa Situation Report 07-Apr-14.
    http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4089-dashboard-ebola-virus-disease-in-west-africa-07-april-2014.html
  3. WHO GAR DON Ebola virus disease (EVD), West Africa Update 07-Apr-14
    http://www.who.int/csr/don/2014_04_07_ebola/en/
  4. SUCCESSES AND CHALLENGES IN RESPONSE TO GUINEA EBOLA EPIDEMIC
    Médecins Sans Frontières Press Release 08-Apr-2014
    http://www.msf.org.au/media-room/press-releases/press-release/article/successes-and-challenges-in-response-to-guinea-ebola-epidemic.html
  5. Audio file for WHO virtual press Conference
    http://terrance.who.int/mediacentre/presser/WHO-RUSH_Ebola_outbreak_Guinea_presser_08APR2014.mp3
  6. Bloomberg's QuickTake on Ebola
    http://www.bloomberg.com/quicktake/ebola/
  7. The US Centers for Disease Control and Prevention on Ebola in West Africa, 2014
    http://www.cdc.gov/vhf/ebola/outbreaks/guinea/
  8. Liberia reports suspected Ebola outbreak unconnected to Guinea
    http://news.yahoo.com/liberia-reports-suspected-ebola-outbreak-unconnected-guinea-130714958.html
  9. LIBERIA: Ebola Deaths Rise In Liberia, Health Minister Confirms
    http://www.gnnliberia.com/articles/2014/04/05/liberia-ebola-deaths-rise-liberia-health-minister-confirms
  10. Liberia: An isolated Ebola case
    http://crofsblogs.typepad.com/h5n1/2014/04/liberia-an-isolated-ebola-case.html