Ebola update: some additional numbers for Guinea & Liberia from 20-April, WHO-AFRO update

Click on image to enlarge.

The case curves are flattening which is a good sign that he 2014 West African Zaire ebolavirus outbreak is being brought under control. 

Nothing new is happening in Sierra Leone-no new case onsets have occurred there since 6-Apr. Nothing has tested positive in Mali.

The previous SitRep [2] seemed to have lowered the Liberia case numbers but they have popped back up again - perhaps part of the "cleaning" of case data there - and that has made it "look" like a jump (contributing to the grey bar), when it may have been a more gradual rise.

The most recent activity is in Guinea, where the last cases isolated were on 20-Apr.

Finally, despite all the Tweets flying around about the virus having spread to Europe and "broken containment", that would not seem to be the case from the latest report. Oh and the lack of any credible source for that.

Source...

1. http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4106-ebola-virus-disease-west-africa-22-april-2014.html
2. http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/sitreps/4102-sitrep-2-ebola-virus-disease-west-africa-17-april-2014.html

A situation well in control....?

Click on image to enlarge.

Is the slowly-spreading epidemic of MERS-CoV changing gears or are the vastly shortened times required to reach each 100 cases just a blip?

I don't know but here's a chart that tells a story of speed.

Ebola update: some additional numbers for Guinea from 17-April, WHO-AFRO update

These numbers slightly change the numbers I last posted from 18-April. 

A small uptick in deaths and lab confirmations and a change to the most recent illness onset which is now 17-Apr. The clock is still waiting to start on the 2-incubation periods required, without new cases, before the region will be declared free of Zaire ebolavirus.

18 healthcare workers are lab confirmed with Ebola virus disease, 6 are probables (24 in total) of which 15 have died (11 are lab confirmed).

Source..

1. http://www.afro.who.int/en/clusters-a-programmes/dpc/epidemic-a-pandemic-alert-and-response/outbreak-news/4104-ebola-virus-disease-west-africa-19-april-2014.html

MERS-CoV cases and deaths by month and growing tallies: a look at the impact of 2 clusters on a "slowly growing epidemic"

The yellow star are to highlight that the 
y-axis (left-hand side values) in 2014
is set to a higher maximum value
than for 2012/2013.
Click on image to enlarge.

The 2 healthcare-associated clusters (paramedic cluster and Jeddah cluster) are the driving factors underpinning the case number spike in April. Cases in other regions are either linked or relatively few in number.

Click on image to enlarge.

With a dozen new cases noted by the United Arab Emirates (UAE) early this morning (my time) I've updated the case and epidemic curve chart below as well, again. This makes UAE the clear second place hotzone for MERS-CoV cases. 

Whether these cases, all asymptomatic, are liked to the paramedic cluster or just the result of enhanced testing (there was mention of contacts in the media release though) is unknown and awaits clarification as do more details on most of the recent 90 cases .

Click on image to enlarge.

And lastly for this post, a chart I last updated 18-Mar when there were fewer then 200 cases. Ahh the good old days. How a month and a couple of healthcare outbreaks change things. This shows the total cases, obviously driven by the Kingdom of Saudi Arabia, but adds on those from the UAE and Yemen as well. A very interesting feature here is the current proportion of fatal cases. The PFC sits at 32.7%; the lowest proportion of fatal cases in the history of MERS-CoV. Why? Because the denominator in that equation (total case numbers) has sky-rocketed without an accompanying rise in fatal cases. While some of the recent cases may yet succumb to severe MERS, the spike we've seen in cases without any disease or with only mild disease, who probably won't die, will offset that and the PFC looks to remain lowered. I would very much like someone to tell me whether these increased numbers of mild cases are due to a change in the approach to testing (contact me!) of people; more testing and less watching and waiting to see if contact and other become obviously sick. Either way - this is great to see.

So this last chart really hammers home one good reason to include asymptomatic cases in the tallies; we get to see the full spectrum of disease from MERS-CoV infection, including no disease at all. 

Knowing that gives us some much needed context when we see a headline that reads "killer virus spreads". 

Now if we just knew whether asymptomatic cases spread infectious virus either through occasional coughs or sneezes or by contaminating their environments. Baby steps.

Where the Guinea ebolaviruses hang in the jungle of the genus Ebolavirus

The 3 complete genomes from the NEJM article are boxed in pink.
Viruses that belong to the species Zaire ebolavirus, are boxed in blue
(including the Gueckedou and Kissidougou isolates).
With my thanks to Dr Stephan Gunther for providing these 3
genome sequences for this tree. Alignments were made using Geneious v6.1.6.
Neighbor-joining tree with 500 bootstraps made using Mega 6.06.
GenBank accession numbers are shown for each entry. Two representatives of the genus Marburgvirus are also included at the bottom of the tree.
Click on image to enlarge.

References...

1. Emergence of Zaire Ebola Virus Disease in Guinea — Preliminary Report
   http://www.nejm.org/doi/pdf/10.1056/NEJMoa1404505

Naming the new Zaire ebolavirus variants

The recent NEJM paper [1,2] on the Guinea Ebola outbreak listed 3 full genome sequences (detected from infected people using standard "Filioviridae-specific RT-PCR assays" and published "real-time RT-PCR assays targeting the glycoprotein (GP) or nucleoprotein (NP) gene".

My thanks to Dr Stephen Gunther for answering my email and giving permission to list these names. They should be on Genbank now he tells me (I have not found them as yet). We now know that these virus variants of the species Zaire ebolavirus are called:

• Ebola virus H.sapiens-wt/GIN/2014/Gueckedou-C05
  GenBank accession number: KJ660346, KJ660347 or KJ660348
• Ebola virus H.sapiens-wt/GIN/2014/Gueckedou-C07
  GenBank accession number: KJ660346, KJ660347 or KJ660348
• Ebola virus H.sapiens-wt/GIN/2014/Kissidougou-C15
  GenBank accession number: KJ660346, KJ660347 or KJ660348

See more one the way the Filioviridae Study Group prefers to name ebolaviruses in a recent post here.[2]

On the issue of whether these variants can still be detected using published diagnostic PCRs, the answer is yes they can (they were detected using them after all!). To look more closely at that, I aligned the 3 new full genomes and also the primer sequences for 2 diagnostic reverse-transcription real-time polymerase chain reaction (RT-rtPCR) assays mentioned in the NEJM article by Baize and colleagues [3,4]. They target the nucleoprotein (NP; [4]) region of the genome and the glycoprotein (GP; [3])

The two PCR assay regions targeting GP and NP PCR oligonucleotides
(primers and fluorogenic probes) primers. The yellow stars in the NP assay
highlight a 2 nucleotide mismatches between the forward primer or probe
(T in oligo, A in genome) and the 3 genomes. These shouldn't decrease
assay sensitivity too much at all.
Click on image to enlarge.

References...

1. Emergence of Zaire Ebola Virus Disease in Guinea — Preliminary Report
   http://www.nejm.org/doi/pdf/10.1056/NEJMoa1404505
2. http://virologydownunder.blogspot.com.au/2014/04/update-on-ebola-virus-disease-evd-case_17.html
3. Development and Evaluation of a Fluorogenic 5 ' Nuclease Assay To Detect and Differentiate between Ebola Virus Subtypes Zaire and Sudan | Gibb and colleagues | J Clin Microbiol. 2001 p4125-30
   http://jcm.asm.org/content/39/11/4125.full.pdf+html
4. Rapid detection of filoviruses by real-time TaqMan polymerase chain reaction assays.| Huang and colleagues | Virologica sinica 2012 p273-7
   http://www.ncbi.nlm.nih.gov/pubmed/23001480

Editor's Note #19: An indication of the level of interest in MERS?

I know this is just a little blog and one tat is pretty nichey, but if it's visitor numbers are any guide, interest in the Middle East respiratory syndrome coronavirus (MERS-CoV) is at a fever pitch. This past week (13th-19th of April-2014) was the biggest week, in terms of site visits and views, for Virology Down Under, since the VDU blog came into being.

Countries from which visits to VDU have originated
between 30-Mar and 19-Apr 2014. USA 1st. 2nd most
visiting country; the Kingdom of Saudi Arabia.
Thanks to @AB_Algaissi for asking.

13 of the 18 posts in the past week were MERS-CoV themed and each drew between 80 and 652 views. Yesterday most of those users were new visitors. So why don't you come back??? Oh well, I'll keep a light on ;)

The light is slowly dawning among researchers, that the many messages of science can be so much better conveyed through social media platforms than through scientific papers. And the public seem to be enjoying this slow moving change.

Apart from being stodgily written or sometimes incoherent, even to other scientists, such papers can be placed behind a paywall which cannot be accessed unless you have links to a University. Scientific papers are also frequently slow to emerge (reviewing and copy-editing and layout and such can take weeks, depending on the journal) and are aimed towards only a very select few; at least unless you have results that make it into a luxury journal like Science or Nature. The sloth like turnaround time is in start contrast to the emergence of an infectious disease outbreak and so the public, and many professional too,  must look elsewhere if they want to know the facts behind the latest "Killer virus mutates" media banner. Many big organisations have resources and professionals devoted to providing those answers; sometimes they are hard to wade through too, sometimes not.

If our research findings are good enough to be if interest to the scientific media, we may get a much wider pickup for our message. The trick then is being able to convey that message in understandable chunks. Ever been to a accountant/lawyer/banker/statistician? Then you know that half of what they say slips into their own tech-terminology. Yeah, we  scientists do that a lot too. Its a hard habit to break out of. We just get used to using that language in our day-to-day dealings even though it may confound (see?) others. But don't put up with convoluted tech-speak; ask for clarification. 

Realistically though, most submissions to luxury journals get rejected. Unfortunately, media attention can often be drawn to work appearing in those luxury journals rather than some journal with a lower impact factor. Yes, impact factors still get used in the real world at many levels from grant review panels to fellowship panels to contract renewals to attracting media attention. Why? Because your work has been deemed by some to be interesting and important enough to get there in the first place. 

And so the circle of scientific life goes on.

Thanks to all who read and visit. I hope its been worth your average 1min 29sec visit. ;)