VDU's blog: lab testing

Showing posts with label lab testing. Show all posts

Monday, 11 April 2016

Colombia...no recent confirmed Zika virus positives or reporting lag or...?

UPDATE #1: 24APR2016

Okay. Let me rephrase an issue I had from one of my posts yesterday-the one looking over the Colombian data. The relevant text was...

"I'm still not clear how the tally of confirmed cases is rising, but not showing up on the Colombian NIH graph (the red bars; the grey ones are clinical suspected cases).

I've excised and posted the Colombian NIH graph to the left. 458 cases this week should show up clearly using that axis - it was the second biggest tally, just below Week No. 8 (also missing?) and 1.6X bigger than Week No. 4 which has been plotted and shows up clearly. I'm just assuming that the graph person has forgotten but would love to know if there is something else going on."

Below I've excised the relevant graphs from the most recent epidemiology report (Week No. 13 [2]) and also the one that first plotted confirmed alongside suspected Zika virus (ZIKV) cases (Week No. 11 [1]).

You can in fact see that the red bars have grown over the 3 week period - but that none of the 700 confirmed cases reported over that time have visibly made it into a bar after Week No. 5. So my question is whether that means:

no newly confirmed ZIKV cases have been detected/become ill during the past 8 epidemiology weeks (keeping in mind that Week No. 13's report only reports data to 02APR2016)
there is an 8-week lag in getting lab data into these reports?
Someone forgot to update the graphs
Colombia is no longer testing for ZIKV

..or perhaps something else altogether?

Week No. 11.
Data from [1]

Week No. 13.
Data from [2]

The lag seems to be the leading theory so far (see Tweet below)...but that's quite a lag.

@MackayIM @INSColombia graph reflects adjusted reported cases per wk. not #s on table. "New" confirmed may be old. Wk12 only 1,100 on graph
— Gabby Molinolo (@gabby_molinolo) April 10, 2016

I find it strange that no-one seems to be critical of the testing lag here and yet it was the topic du jour for MERS in the Kingdom of Saudi Arabia.

Is it simply about the perception of resources - the Americas are perceived as resource-poor and the Saudis as resource abundant?

In the area of lab testing, I'm not at all convinced that the Saudis were at all resource rich though. I don't think they were in any better position at the start of their outbreaks. Especially if the resource we measure is understanding about testing to understand the aetiology of an emerging infectious disease.

References...

Updates...

Added a new 3rd option which was not carried over from the orginal post 10APR2016 - and pushed the previous 34rd to 4th

Sunday, 27 March 2016

Zika virus is a testing problem for science...

Edited by Katherine E Arden, Ph.D.
UPDATE #1: 30MAR2016
UPDATE #2: 08APR2016
UPDATE #3: 30MAY2016

I need to get this off my curmudgeonly chest.

I've watched the Zika virus (ZIKV) "event" since January 2016, back when I said this...

I think Zika might be my 2016 virus.
— Ian M Mackay, PhD (@MackayIM) January 3, 2016

...and wrote a small overview while on holiday.[1]

Since then I've been, on an almost daily basis, alternately and in no particular order disgusted, amazed, shocked, horrified, stunned, disappointed and flabbergasted by the quality, type and amount of detailed information available, about the discussion around that information as it comes out, about the language used and the assumptions underpinning the discussions that have occurred. In short - too many assumptions, too little virus testing data and too many people impatiently rushing to conclude that correlation is the same as causality.

The communication of being sure, or unsure...

There was a confusing comment from the Director General of the World Health Organization, Dr Margaret Chan. Keeping in mind that this is the organization that suggests how to communicate risk to the community in their document Risk communication and community engagement for Zika virus prevention and control: A guidance and resource package for country offices for coordination, planning, key messages and actions.[2]

Dr Chan: Though the #Zika-fetal malformations association is not yet scientifically proven, the circumstantial evidence is now overwhelming
— WHO (@WHO) March 22, 2016

So we are overwhelmed by non-evidence, despite the evidence not being available yet? How far from actual evidence is that?

Before this, WHO has been good at saying "looks like something different is happening with ZIKV but we don't know much more yet. In the meantime we're doing things that facilitate reducing the known vector, the mosquito, and bites from them, we're ramping up the testing and the science and we're moving things along on the vaccine front, but we're not putting all our eggs into one basket just yet."

Why are so many so hell-bent on jumping the gun on ZIKV?

WHO's science meeting reviewed evidence linking ZIKV infection with foetal malformations and neurological disorders and advised that the implication from the evidence was that the link between microcephaly and ZIKV was looking real.

Dr Chan said "If this pattern is confirmed beyond Latin America and the Caribbean, the world will face a severe public health crisis" - absolutely true.[22] But this still remains an "IF" for now.

Lab testing and reporting from Brazil needs work...

Among the 6,671 suspected diagnoses of microcephaly in Brazil - the rapid rise for which WHO called a Public Health Emergency of International Concern (PHEIC) - just 122 (1.8%) have any current laboratory evidence identifying that ZIKV infection - past or present - occurred. If there are more laboratory testing data from Brazil to fill this huge gap, they need to be talked about.

Brain injuries...

Microcephaly diagnoses and congenital brain malformations, which are rare diagnoses overall, have been occurring worldwide for a long time.[4] I don't know for how long - perhaps throughout human history? So if the epidemic of ZIKV is actually driving a sudden rise in microcephaly and foetal brain deformity diagnoses, plus meningitis and Guillain-Barre syndrome cases, those diagnoses should be higher in number than what is normal for Brazil.

Finding a baseline on which to base the official line...

The rate at which microcephaly diagnoses have been reported in Brazil still awaits some type of overall agreement.[13] In the north east, individual reports quote doctors, such as the van der Lindens, who have personal experience in seeing dozens more examples of microcephaly and brain malformations from August 2015 onwards than they had been used to seeing.[11,12,26,27]

This widely reported evidence is hard to deny despite being anecdotal-the doctors and their collaborators are yet to publish their observations.[25] NB: New paper describing 105 microcephaly diagnoses infants born in Pernambuco State, Brazil was released after this post, including a van der Linden as author, but has no ZIKV testing.[29] A second study with a van der Linden finds ZIKV IgM in 7/23 microcephaly diagnoses.[30]

In this extrapolation, 2 and 12 are the limits of the

range of microcephaly diagnoses

reported by the US CDC.[24]

Publications still appear which use the initial rates of ~150 microcephaly diagnoses in Brazil per annum - about 0.005% of 2.9 million annual live births.[5] This is despite data and others' analyses suggesting that these may not be realistic rates. [6,7,8,9,10,14]

The reported 'spike' in diagnoses might not be above, or as drastically above, normal figures for Brazil, or certain regions of Brazil, as at first thought. But even this fundamental knowledge remains unclear.

The vector in Brazil is probably something...

No mosquito species in Brazil has yet been identified as a carrier of ZIKV.[3] Testing is being done but no report of a mosquito testing positive for ZIKV have emerged as yet.[3]

It's not clear whether this extra information would have any impact on the more general mosquito-reduction measures that have been rolled out - spraying, fogging and poisoning.

However, might this knowledge gap have an impact on some species-specific anti-mosquito measures, such as those involving interfering with mosquito mating or reproduction?

We assume that the Brazil vector is Aedes aegypti because that's what's been the culprit elsewhere and because they can ingest and become infected by ZIKV.[17,18,19,20,21] Other Aedes species also stand accused, as does Culex quinquefasciatus.[23] So this too remains unclear.

Some clarity falls out from between the gaps...

From among all these gaps has recently fallen an article that makes sense.[15]

No, it didn't support any causal link between ZIKV presence and any sort of brain damage in foetuses.

It just describes the genetic findings from analysing 7 ZIKV genome sequences from 4 human cases and made a modelled estimate suggesting that ZIKV was in Brazil from May-December 2013. This may sink the canoe hypothesis.[28]

That date could still change if other sequences are found of course - such as older ones in stored specimens. But it's a nice estimate for now. It may also explain why microcephaly diagnoses were predicted to have been high prior to 2015 according to the Mattos report,[6] if ZIKV is indeed a new and sizeable cause of the burden of these diagnoses. While this paper tells its story with lots of dense detail - as befits a paper in the journal Science - it takes a little bit of extra time and space to clearly and plainly state what the data do not mean (see the quote above).

This sort of extra detail is so very important. It shows that the authors have thought through their work and placed it in a bigger picture and it helps those who may be looking to paraphrase the study to see that it has limitations that should be mentioned.

This really shouldn't be something to praise - it should be the norm - but in many of the Zikaglyphs put into print this year, care has not been taken, too many assumptions have been made and too little thought has gone into the complexities of trying to associate the presence of a pathogen with a disease that is occurring at the same time, or some days, weeks or months later on.

So maybe there is still some hope to be had that science and the media will start talking more frequently and clearly about what we don't know, what we haven't looked for and what other possibilities exist, instead of what we almost know.

"Yes, Zika infection during pregnancy can lead to brain-related birth defects in a fetus".[16]

Or maybe not quite yet.

In summary...

We do not yet have definitive scientific evidence of a causal link between increased microcephaly diagnoses, brain malformations and ZIKV infection.

That is not to say there is no such link, just that we have not yet gathered the evidence to confirm one.

Given the potentially severe consequences of the link being real, it is entirely appropriate that measures are being taken now to reduce exposures to ZIKV by potential parents of either sex.

Until data show otherwise, it remains possible that ZIKV is not to blame and so we need to keep an open mind, keep searching and keep carefully examining strong evidence, because if the cause is not ZIKV alone, or it is ZIKV working alongside some other factor(s), we are missing the boat and failing in our duty to help halt a severe public health crisis.

References...

Updates...

Added reference to a van der linden publication [29]
Added a reference to a second Dr van der Linden publication [30]
Repaired typos to Crawford Kilian's name

Sunday, 21 February 2016

508 confirmed microcephaly diagnoses in Brazil...let's just say they're all Zika virus related because...belief?

This comes from the 13th Brazil Ministry of Health's (MOH) Health Portal epidemiological reports on microcephaly [1] which spans from when microcephaly diagnoses began sometime during 2015, to the 13th of February 2016.[2]

With the aid of Google translate, the report states that 5,820 suspected diagnoses have been logged to 13FEB2016 of which 1,345 (25.5%) have been finalised as:

508 confirmed (37.7% of the finalised suspects)
837 discarded (62.2%)
60.1% were recorded in 2015 and 39.9% are from 2016 so far
The previous MOH report noted that 41 of the then 462 confirmed microcephaly diagnoses were somehow (mum or foetus or baby?) laboratory confirmed as being aligned with a Zika virus infection [4]

Geographic distribution of 508 confirmed microcephaly cases from 2015 and 2016.
Data and graphic from the Brazil Ministry of Health.[2]

But what absolutely flummoxes me is this translated text (highlights added by me) from the end of the report,[2] found in a big red "Heads up" box. In particular that highlighted in yellow:

The Ministry of Health believes that there was infection zika virus mostly mothers who had babies whose final diagnosis was "microcephaly and / or changes in the central nervous system, suggestive of infection congenital ".

Therefore clarifies that from this Report Epidemiological No. 13 concerning the epidemiological week 06, 2016, will disclose these confirmed cases, without specifying the laboratory diagnosis to Zika virus, because these data do not adequately represent the number of observed cases (magnitude).

Furthermore, from that moment, consider that all confirmed cases are related to congenital infection Zika virus.

All cases are individually assessed and submitted to a laboratory set of diagnostic tests and imaging (ex .: ultrasound transfontanellar etc.). A very small proportion of these cases, after monitoring and Specific analysis is confirmed for other causes, but they are so few children that does not change the assessment the trend (increase or decrease) the number of cases (magnitude). It is important to inform that the Ministry of Health participates in and supports the entire national effort directly and international for better understanding of this new disease and that every effort is being made to improve diagnostic methods and strengthen assistance to children and families affected.

I'm presuming this is because the MOH cannot get any samples from earlier diagnoses and thus cannot test them. Or perhaps they were negative and it has a "feeling" that they should have been positive.

No idea.

I have felt nothing but unease about the way Zikacephaly has been settled on via a process of accusation, summary judgement and instant public conviction during 2016 - via instances in both the media and the scientific literature.

I'm now in complete disbelief that a national MOH is relying on a 'belief' without further data or discussion, to officially communicate a message about the cause of a severe disease.

Why not rely on a careful analysis of extensive testing data? Do such data exist? Are they bottled up in the publication pipeline? Why not employ a more reasoned public engagement strategy whereby careful and balanced description of the the risks and all the knowledge gaps, is communicated to a rightfully worried community? And to the world, because no outbreak or epidemic affects the host country in isolation any more.

The battle to cull the mosquito vector and avoid bites was under way quickly, so why the need to point the finger so urgently when nothing additional can be done right now anyway? So we can get a vaccine underway? What if...heretical at this point I know, but what if Zika virus is not the cause of the surge in microcephaly cases? Gasp!! What a gigantic waste of resources and public faith in science we will have burned through because-belief?

Wouldn't it be better to undertake a more careful investigation and analysis before putting any more eggs in the single, lonely Zika virus basket?

Just to be clear, I don't for second discount that Zika virus could be the cause of microcephaly - but I'm not just going to put that in a text book until the studies have been done. Those studies have not been done yet and neither have any studies been done that discount anything.

As we can see in red above, there are clearly other causes of microcephaly being found in Brazil. Presumably these are some of the better known causes like in utero or at birth infections by the Toxoplasma gondii parasites, Treponema pallidum bacteria, rubella virus, herpes simplex virus, cytomegalovirus and human immunodeficiency virus or due to chemical exposures in the mum, including to arsenic, mercury, alcohol, radiation, and smoking or perhaps genetic abnormalities including Down syndrome or even severe malnutrition during development. Even if in small numbers-one or more of those things (which were not detailed by the MOH report) are clearly present and though to be acting.

Everything is still on the table as a cause of microcephaly in the north east of Brazil-as it always has been since probably much earlier than October of 2015.[3]

References...

Monday, 12 May 2014

VDU Quote for the night...

From:

Z.A. Memish et al.

Screening for Middle East respiratory syndrome coronavirus infection in hospital patients and their healthcare worker and family contacts: a prospective descriptive study.

Clinical Microbiology and Infection, 2014.

"Surveillance studies also help in defining and monitoring transmission rates, case load, and epidemic risk assessment, and assist in instituting infection control measures with new diagnostic methods and treatments."

Thursday, 8 May 2014

Pressure testing...

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...

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.
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.
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.
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?
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.
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.
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.
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.
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...

http://news.sciencemag.org/health/2014/05/mers-virologists-view-saudi-arabia
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
http://www.nccid.ca/files/Evidence_Reviews/NCCID_H1N1_impact_04.pdf

Sunday, 27 April 2014

If this is what MERS-CoV detections look like with more testing...what is the "normal" community level of virus?? [UPDATED]

The bar along the top depict how much time passed between each 100 cases.
Click on chart to enlarge.

For a virus that is chugging along without the aid of any new genetic changes, and perhaps showing up more often (a) because of enhanced testing and/or (b) because of a large-scale breakdown in infection prevention and control (IPC), this curve sure does depict the possibility that we had no idea how much MERS-CoV was transmitting among the population. Still a poor transmitter compared to an influenzavirus, because we have seen a few larger MERS-CoV studies than show few to no MERS-CoV positives, but still more people positive than we thought.

Can we really lay this rate of climb at the feet of poor IPC alone? Wouldn't that also mean that every other respiratory virus would do this too? Perhaps not if MERS-CoV was the only one capable of causing acute pneumonia. It isn't. So shouldn't all hospitals always be full of acute pneumonia and respiratory disease among older males with comorbidities? These are modern hospitals after all. Also modern doctors with great training and skills acquired from all over the world. Perhaps poor IPC plus enhanced testing is an option? Maybe. Probably most likely when combined with an outbreak that starts in April for an unknown reason.

What about this option, which focusses on testing alone? Better levels of testing are at last showing it like it really is in the Arabian peninsula? This options proposes that we've been underestimating the ability of MERS-CoV to travel from person-to-person, all along. An underestimation driven by testing only the "tip of the iceberg" of disease and just watching the rest of the iceberg from a distance? What if severe disease is only found in already ill older males and most (granted, not all) of the rest get milder or unnoticeable disease but do get infected? Yes, in the past 2 weeks 5,000 samples have been tested in the Kingdom of Saudi Arabia (KSA) to yield ~140 MERS-CoV detections (~3%). After the 2012 Hajj, 154 pilgrims were tested by Gautret et al and, despite a high proportion with respiratory symptoms (83%), none were found positive for MERS-CoV. At 3% in Jeddah, testing of the Hajjis should have yielded ~4 detections among this cohort if the distribution of MERS-CoV was at this level all the time. In screening 5,065 cases and their contacts (family and healthcare workers) over a year from 1st-Oct-2012, Memish et al reported 106 detections (~2%) and no significant rise in case detection rates over that year. So a very similar proportion of positive cases, and both Jeddah and this larger study have similar numbers and a roughly similarly broad population being tested. Of course, even endemic human CoVs are not always detectable every year at the same site. Some have a biennial periodicity.

So perhaps 2-3% prevalence, similar to endemic CoVs, is the magic number for MERS-CoV positivity? Which just leaves the question, why weren't more Hajjis positive last year? Or was that just a testing thing too?

Just wondering out loud here.

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.

#Ebola samples now tested locally in #Conakry and Guéckédou, #Guinea http://t.co/oOYsd1PPGW [PHOTOS] #AskEbola pic.twitter.com/2UfehauCs7
— WHO (@WHO) April 5, 2014

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]

Dr Fukuda: We expect to continue seeing #Ebola cases for some months, to go through several incubation periods. Premature to say decreasing
— WHO (@WHO) April 8, 2014

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...

#Ebola2014: On the Topic of Lab-Confirmation
http://maimunamajumder.wordpress.com/2014/04/08/ebola2014-on-the-topic-of-lab-confirmation/
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
WHO GAR DON Ebola virus disease (EVD), West Africa Update 07-Apr-14
http://www.who.int/csr/don/2014_04_07_ebola/en/
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
Audio file for WHO virtual press Conference
http://terrance.who.int/mediacentre/presser/WHO-RUSH_Ebola_outbreak_Guinea_presser_08APR2014.mp3
Bloomberg's QuickTake on Ebola
http://www.bloomberg.com/quicktake/ebola/
The US Centers for Disease Control and Prevention on Ebola in West Africa, 2014
http://www.cdc.gov/vhf/ebola/outbreaks/guinea/
Liberia reports suspected Ebola outbreak unconnected to Guinea
http://news.yahoo.com/liberia-reports-suspected-ebola-outbreak-unconnected-guinea-130714958.html
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
Liberia: An isolated Ebola case
http://crofsblogs.typepad.com/h5n1/2014/04/liberia-an-isolated-ebola-case.html

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