Wednesday, 16 August 2017

This little MERS-CoV infected piggy had RNA, but that little piggy with indirect contact had none...


Back in April, a Spanish/Dutch collaborative study came out looking at whether pigs deliberately infected with Middle East respiratory syndrome coronavirus (MERS-CoV) might be able to transmit that virus to other pigs.[1] Turns out they can, but so weakly that the authors concluded pigs are unlikely to be a source of virus in the wild.

Alpacas have been use for transmission studies in the past - these furry four legs do seem to be able to host and transmit MERS-CoV once infected, and in the wild, and may have a role in keeping the virus alive among animals. They may also be a source for spillover into humans on occasion; check out MERS-CoV: alpacapalooza for a reminder.[2]

But what did this new study do?

First up they infected a  group of 5 pigs (P1, P2, P3, P4, P5) with a fair whack (107 TCID50 (50% tissue culture infectious doses) of the HCoV-EMC/2012 MERS-CoV virus variant by shooting 1.5ml of virus in saline up each nostril of the pig's noses. None of the pigs showed any measurable signs of illness - no temperature rise or respiratory signs. That result alone shows that otherwise healthy walking bacon is not a model of  MERS (the disease).

After 2 days, 5 uninfected pigs were added to the same cage to permit direct contact (touching snouts and other stuff that pigs do to each other when in the same space); P6-P10. This group were called 'direct contacts'. They represents your Mum & Dad - the ones who keep kissing you while you're in hospital with MERS (not that kids often get sick with MERS-CoV!).

A third group of piggies were housed in a separate pen, 30cm away, and called 'indirect contacts'. They represent that cousin who came to visit you in the hospital, but just sat in the corner playing PokemonGo on their tablet because they didn't really like you anyway but got dragged along by your Uncle.

A lot of different samples were taken from the pigs from before inoculation and at various intervals up until 26 days afterwards. The results from testing these samples break down as follows:

  1. Cell culture studies found that only the MERS-CoV inoculated pigs shed infectious virus and developed an antibody response to MERS-CoV spike protein (measured by S1 ELISA) or that were capable of neutralizing MERS-CoV in cell culture experiments.
    Neither of the 2 contact groups shed detectable infectious virus or mounted an immune response. 
  2. Sensitive molecular methods (RT-PCR [3]) found that the inoculated pigs all shed MERS-CoV RNA from day 1 after inoculation; 3 stopped shedding after day 7. 3 of 5 direct contact pigs shed MERS-CoV RNA between day 3 and day 5. These pigs entered the infected pig's pen at day 2-were they being infected by residual inoculum?
    A sample of virus left on the bench for a week and a portion tested each day in cell culture and by RT-PCR would have been useful to assure us that infectious virus from the original inoculum wasn't the only thing being detected in this study
  3. Some viral RNA was detected in air samples collected between the two pens and from some wall/surface swabs - but infrequent and in very small amounts
So, the study concluded that infected pigs may transmit MERS-CoV but that if they do, it's a pretty inefficient process. 

It's not clear to me whether the initial P1-P5 were successfully infected by MERS-CoV at all. The piggies had virus given to them, sure. But did that virus enter cells and replicate within those cells to assemble new viruses? If it did, were those new viruses infectious? Did new viruses release from the infected cells and infect new cells and the other pigs, or was this all detection of eh original inoculating virus? 

The immune responses detected only in the inoculated pigs may have been the response to inoculum, without MERS-CoV replication. The very small amounts of viral RNA detected in indirect contacts and in the air and on some surfaces could also be leftover inoculum spread from the noses of P1-P5. Without knowing how long MERS-CoV in saline remain infectious or detectable under their conditions, we cannot answer that. We do know that MERS-CoV can remain infectious for 2 days and be detected by RT-PCR methods for at least 5 days.[4,5] 

So all in all, the main contribution of this study to the furthering of MERS knowledge is its ability to rule out pigs as a useful animal model for disease or transmission.

References...
  1. Middle East respiratory syndrome coronavirus experimental transmission using a pig model
    https://www.ncbi.nlm.nih.gov/pubmed/28653496
  2. MERS-CoV: alpacapalooza
    http://virologydownunder.blogspot.com.au/2016/09/mers-cov-alpacapalooza.html
  3. Reverse transcription polymerase chain reaction (RT-PCR)...a primer
    http://virologydownunder.blogspot.com.au/2015/05/reverse-transcription-polymerase-chain.html
  4. Middle East respiratory syndrome coronavirus: how tough is it?
    http://virologydownunder.blogspot.com.au/2013/10/middle-east-respiratory-syndrome.html
  5. Korea contamination: Middle East respiratory syndrome coronavirus in the room..
    http://virologydownunder.blogspot.com.au/2016/09/korea-contamination-middle-east.html

Saturday, 15 July 2017

900 words on some general stuff about viruses and those other bugs...


We (Dr @kat_arden and I) were invited to contribute one part to a four-part series in The Conversation this week - and after a lot of no...yes/no/yes from yours truly (I do that a lot these days), we put this piece together.

If I was still a researcher this might be classified 'public service' - but as a simple scientist these days, it's simply science communication. 😀

Now. Back to trying to get back into blogging about viruses. Or writing the MERS review. Or writing up my own old data... 😱

Sunday, 9 July 2017

Ebola virus disease over in the DRC....

Another year, another outbreak of Ebola virus disease (EVD) overcome in the Democratic Republic of the Congo with the help of a mix of expert local skill and knowledge, isolation and rapid global response.

The World Health Organization have summed up the end of an outbreak in which 4 died, 5 cases were lab confirmed and there were a total of 8 likely EVD cases.


References...

  1. http://www.afro.who.int/en/media-centre/pressreleases/item/9744-who-declares-an-end-to-the-ebola-outbreak-in-the-democratic-republic-of-the-congo.html

Sunday, 2 July 2017

Editor's Note #27: Anakin Fencewalker joins the Force...

After 19 years, our furry family member had to leave us this Wednesday. His quality of life was decreasing and he had stopped eating - he made the call and he let us know.

He is missed enormously and remembered daily by his human family, for many things.

He saw two PhDs completed; he sat through the writing of 70+ papers, a book, 14 chapters, 11 reviews (all had late night writing components that required pats and scratches), he watched over the growth of two babies and has been with them all their lives; he lived in the two houses my family have known; he was a constant companion to my wife and he kept me (and my keyboard) company while I wrote many pieces for this blog.

Anakin Fencewalker.
12SEPT1998-28JUL2017
Thankyou Anakin.

May the Fence be with you.

Saturday, 24 June 2017

Another canary in the same coalmine - mild MERS may be bad news...

Sometimes, the Middle East respiratory syndrome coronavirus (MERS-CoV) is detected in a person who is not ill. 

Weird huh? 

Not really. This is the result of laboratory testing of contacts of a known and infected person during the process of containing a potential outbreak.


For me personally, this is one big question about new or emerging viral infections or infections we are still learning about - like new influenza viruses, MERS-CoV, ebolaviruses and Zika virus. Do we really know how often a laboratory-confirmed infected person with mild or no illness can spread virus to a new person - an uninfected potential host? Are our tools up to the job of detecting what's happening and are we using them properly?

Conventional wisdom is that truly asymptomatic but virus infected people do not infect others around them, or if they do, it's a pretty rare event. Because the risk is seen as low, studies around this issue are often down the list of research priorities.

The importance of this issue lies in whether mild or asymptomatic people need to be more closely considered as having a role in spreading virus and contributing to community or hospital outbreaks.

Emerging from the 2015 South Korean MERS-CoV outbreak, a recent report described the findings from laboratory testing of 82 contacts of an asymptomatic healthcare worker.[1] No other person became MERS-CoV positive. I have some issues with the fact that the nurse herself does not seem to have been tested to show that she developed antibodies to MERS-CoV and there also isn't a lot of discussion about how the PCR testing for MERS-CoV can be a bit "flaky" when sampling once from the upper respiratory tract. Although, there aren't any sampling details in this paper either (I'll blog about this paper another day)!

But I digress. 

I've plotted the all the publicly available mentions of asymptomatic MERS-CoV infections, by week, in the graph below (the bottom panel). 

Click on image to enlarge.
The yellow peaks show that cases without illness usually correlate with healthcare workers in the graph above, during hospital and healthcare facility outbreaks (see my previous post describing the pink graph in the top panel).[2] 

This isn't too surprising. The majority of disease associated with MERS-CoV infection arises in older males who already have an underlying disease including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions. Healthcare workers however are usually younger and do not have, or have not yet developed, such comorbidities. 

MERS-CoV is often a shown to be a bit of a bully when challenged by a healthy younger host's immune system. Although, when hit with a larger primary dose of virus from an infected camel, even the healthy can get hit very hard.

Healthcare workers can be the 'canary in the coalmine', except singing about a healthcare outbreak rather than a gas leak. Similarly, laboratory confirmed MERS-CoV infection manifesting with only mild or no signs and symptoms of disease, also serve this role as a sentinel of hospital, rather than camel-to-human, transmission of MERS-CoV.

References...

Tuesday, 20 June 2017

Working for health can make you sick....

Below is a quick look at the percentage of total Middle East respiratory syndrome coronavirus (MERS-CoV) cases reported each week that are listed as being healthcare workers (HCWs).



The sources of the numbers used in this graph.

These data are curated by me for this blog in my spare time and are compiled from the Kingdom of Saudi Arabia'a Ministry of Health (MOH) daily reports, the World Health Organization (WHO) disease outbreak notifications (and relatively new line lists) and from the FluTrackers line list

I use the same numbering as FluTrackers use in an attempt to produce at least two lists that agree on numbering and content. 

Some other things to note about this graph..

Each of the pink "spikes" is a percentage calculated by dividing the number of MERS-CoV laboratory confirmed HCW by ALL of the MERS-CoV laboratory-confirmed cases that were reported in that same week... 
Sometimes there might be just 1 HCW and 1 patient - which would give a pretty big looking 50% positive (1 divided by 2). But clearly, it is just 1 HCW. 

So proportion (%) alone is not a whole lot of use sometimes. One needs to know the denominator (the bottom number of a fraction) to get a gauge of how big the problem really is. 

The current June hospital outbreak in Saudi Arabia includes three facilities in Saudi Arabia according to the WHO and the MOH.[1,2] From the 47-year old male reported on the 1st June as an index case in one facility, there have been about 44 secondary MERS-CoV detections (cases) in Riyadh. 

Of the 44 MERS cases, 26 are listed as HCWs; 18 of 25 HCW MERS cases occurring in a single week (week beginning 5th June) and accounting for the 72% spike seen at the end of the graph above. 

Just to confuse things, there were 3 distinct hospital outbreaks that occurred previously,  in April and May, but it's not clear whether they contribute any cases to the June tally.[3]

Why can't we have nice things?

There has been no other successful effort, by anyone, to produce a single public MERS case list with a universally agreed upon numbering scheme that contains useful but deidentified case detail, that everyone could refer to and use. The same applies to the influenza A (H7N9) virus as well. This has only been achieved by public volunteer bloggers; FluTrackers and this blog. Pretty poor when you think on it.

References...

  1. http://www.cidrap.umn.edu/news-perspective/2017/06/who-details-saudi-mers-clusters-outbreak-grows
  2. http://www.who.int/csr/don/13-june-2017-mers-saudi-arabia/en/
  3. http://www.cidrap.umn.edu/news-perspective/2017/06/who-reports-3-saudi-hospital-mers-clusters-new-cases-uae-qatar

Sunday, 18 June 2017

Climate and science denial....

I'm in a reading and watching phase at the moment - not much time for writing. Two videos I've recently come across are so good that I've embedded them below; they are just so good at describing their topics.

Yes, I know this is not directly abort virology - but climate change (CC) and science denial very much does indirectly impact on the fields of virology - some example include

  • virus transmission
  • imported infection disease
  • mass gatherings and disease
  • virus vaccines
  • viral immnuology
  • emerging virus diseases
  • viral zoonoses
  • seasonal viruses


These two vids are also just important science communication tools for all of our everyday lives. Show your kids. So I've bookmarked them as much for my own future reference as for yours.

1. Why reducing carbon emissions matters. 

This was lifted from an article at The Conversation.[1]


  

2. Denial 101x: five characteristics of science denial.

This was also lifted from a longer article in The Conversation.[2]



References...

  1. https://theconversation.com/the-three-minute-story-of-800-000-years-of-climate-change-with-a-sting-in-the-tail-73368?utm_source=twitter&utm_medium=twitterbutton
  2. https://theconversation.com/one-nations-malcolm-roberts-is-in-denial-about-the-facts-of-climate-change-63581

Sunday, 21 May 2017

Ebola in the DRC: list of border-checking countries at seven...

Starting from WHO Regional Office for Africa Ebola Virus Disease (EVD) Situation Report No. 2,[1] there have been an increasing number of countries that are screening ill-looking people for EVD at their ports of entry. Currently [7] there are 7 and they are:

  • Kenya
  • Nigeria
  • Rwanda
  • South Africa
  • United Republic of Tanzania
  • Zambia
  • Zimbabwe 

Quite a few more than I listed yesterday. 

Latest EVD figures form the DRC.
Click on image to enlarge.
No borders are closed to travellers from, or who have travelled through, the Democratic Republic of the Congo, which is good news.

Screenshot from SitRep No.5.[1]
Click on image to enlarge.
Presumably this screening relies on the appearance of signs of illness, questionnaires and perhaps thermal camera images to identify feverish people.

As I alluded to yesterday, these efforts are not very effective at actually picking up EVD cases from among a milieu of other febrile illness that stumble through a port of entry.

Studies - some of which are summed up in this Canadian review [2] - are usually not supportive of any practical benefit from using fever as a screening tool to pick out a single disease in passing travellers.[3,4,5] 

However, these screening efforts do play a role in making citizens and politicians feel better and more useful. The precautions may also be helpful in keeping travel flowing.[6] Whether the continued flow of travel during an epidemic that may leak from a hotzone is a good thing or not will no doubt (once again) be dissected after a more more transmissible pathogen sweeps across the world I expect.

References....

  1. http://apps.who.int/iris/bitstream/10665/255463/1/EbolaDRC-1652017-eng.pdf?ua=1
  2. https://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0071254/
  3. http://afludiary.blogspot.com.au/2011/05/study-thermal-scanners-pandemic.html
  4. http://afludiary.blogspot.com.au/2014/11/eid-journal-evaluating-border-entry.html
  5. http://afludiary.blogspot.com.au/2014/10/why-airport-screening-cant-stop-mers.html
  6. https://www.ncbi.nlm.nih.gov/pubmed/27390092
  7. http://www.afro.who.int/index.php?option=com_docman&task=doc_download&gid=10836&Itemid=2593

Saturday, 20 May 2017

Ebola virus disease in the DRC: first graphs...

The World Health Organization have apparently found an outlet for their Ebola virus disease (EVD) reports for 2017's Democratic Republic of the Congo outbreak.

It's not the Disease Outbreak News site. It's not the WHO media page. It's not any of the past EVD outbreak pages on the central WHO site.

Turns out the Situation Reports (SitReps) are to be found on a new page on the WHO African site.[1] Okay. Why not? Found it eventually. I've plotted the first 4 (they started from 15th of May) below. Not much to say about trends at this early stage obviously!

Click on image to enlarge.
Don't go expecting to find how we got to the totals shown on the 15th - those may well be lost details. Or they may come out later. We'll have to wait and see. Outbreaks viewed from the public point of view are very much about patience and trying not to leap to any dramatic conclusions - like those decisions taken by at least one country in Africa to start screening passengers for signs of EVD.[2] It's your budget guys - spend up if it makes you feel safe. At this stage, and perhaps ever, its a pretty wasteful exercise though; apart from your citizens seeing you doing something.

Back to numbers. I'm pretty impressed with the WHOAfro SitRep - the 4th Report carries a detailed table of cases, deaths and locations and also a timeline graphic (below) which is fantastic. 

Click on image to enlarge.This image is part of SitRep No.4.[3]
And to wrap up, just for a glimpse of what has come before and where we are now (and because I promised @kristindownie I would!), I've also added an updated "EVD through time" bar graph. Where we are with the current outbreak total is highlighted using a red arrow and the towering totals of West Africa are indicated by yellow arrows.

Click on image to enlarge.


References...

  1. http://www.afro.who.int/en/ebola/ebola-situation-reports.html
  2. http://www.premiumtimesng.com/news/231328-ebola-nigeria-intensifies-screening-at-airports.html
  3. http://apps.who.int/iris/bitstream/10665/255526/1/EbolaDRC-1852017-eng.pdf?ua=1

Saturday, 13 May 2017

Ebola returns to the Democratic Republic of the Congo (DRC): Zaire...

UPDATE No.1 14MAY2017 AEST
UPDATE No.2 15MAY2017 AEST
UPDATE No.3 17MAY2017 AEST
UPDATE No.4 18MAY2017 AEST
 UPDATE No.5 18MAY2017 AEST
The World Heath Organization alerted the world on May 12th [1] to an outbreak of Ebola virus disease (EVD) in Likati, a remote region in the Bas-Uele province of the Democratic Republic of the Congo (DRC).[4] The news had been communicated to them on the 11th May by the DRC Ministry of Heath.[6]

This is the 8th recorded outbreak in the DRC and it is hoped that their expertise, together with a range of rapidly mobilised outside expertise, will contain this one quickly and with a minimal loss of life.[5]

It reportedly took 10 days for the first samples to reach the lab in Kinshasa for testing.[8] Google estimates about 47 hours  to travel the ~3,000km from Kinshasa to Aketi (about 50km beyond Likati via Google's inland suggested route - doesn't account for off the 'main' road and forest parts) - it doesn't give estimates for Likati direct. The WHO explained...

See thread here if you use Twitter.
The journey to Likati is not an easy one.[16] Planes and helicopters are being used and there are questions around how secure the area is.[18] While remoteness is anecdotally beneficial for containing the spread of an outbreak, there are 2 clusters of illness and death outside of Bas-Uele, marked on the Ebola SitRep maps, which may test this theory.[17]

There are reportedly 300,000 (GAVI/Merck emergency stockpile [13])-700,000 doses of the  rVSV-ZEBOV vaccine which has been reported to be highly effective at preventing EVD.[3,9,10]

Early numbers were a bit confusing [2] - as often happens in the fog of announcement of an outbreak - but since 22nd April there seem to have been:
  • 20 suspected and confirmed cases in total [17]
    • 3 fatal cases (proportion of fatal cases: 15%)
    • 1 of 5 samples was initially laboratory confirmed (PCR) at Institut National de Recherche Biomédicale (INRB) in Kinshasa - it tested positive for Zaire ebolavirus
    • a 2nd case has since been Zaire ebolavirus lab confirmed [12]; 3 have tested negative [17]
    • at least 6 cases hospitalised [7]
    • ≧416 contacts being traced [17]
    • 1st case - 45 year old (or 39yo) male (45M) transported by taxi; died on arrival [11]
      • driver fell ill and died
      • carer of 45M fell ill and died (=25 contacts) 
    • Nambwa health district has notified the greatest number of the earliest cases: 13 in all, with 2 deaths (case fatality: 15%).[15]
 

References...

  1. https://twitter.com/WHO/status/863022054223773697 
  2. https://www.theatlantic.com/science/archive/2017/05/a-new-ebola-outbreak-in-the-democratic-republic-of-congo/526506/ 
  3. http://www.npr.org/sections/thetwo-way/2017/05/12/528124232/ebola-death-confirmed-in-democratic-republic-of-congo 
  4. https://www.wired.com/2017/05/ebola-returns-central-africas-virus-hunters-ready/ 
  5. https://foreignpolicy.com/2017/05/12/ebola-returns-in-congo-a-test-of-next-time/ 
  6. www.minisanterdc.cd 
  7. http://www.who.int/csr/don/13-may-2017-ebola-drc/en/ 
  8. http://www.mysanantonio.com/news/local/article/New-Ebola-case-reported-in-Democratic-Republic-of-11143890.php?cmpid=twitter-tablet 
  9. http://www.sciencemag.org/news/2017/05/will-vaccine-help-curb-new-ebola-outbreak-drc 
  10. http://www.nature.com/news/ebola-vaccine-could-get-first-real-world-test-in-emerging-outbreak-1.21989 
  11. http://www.afro.who.int/en/media-centre/pressreleases/item/9609-dr-moeti-in-kinshasa-to-discuss-reponse-to-ebola-outbreak.html 
  12. http://www.reuters.com/article/us-health-ebola-congo-idUSKCN18A0ZP
  13. https://www.newscientist.com/article/2131131-ebola-once-again-on-the-prowl-as-emergency-teams-stand-ready/
  14.  http://reliefweb.int/report/democratic-republic-congo/ebola-virus-disease-democratic-republic-congo-external-situation-0
  15. http://www.afro.who.int/en/media-centre/pressreleases/item/9631-drc-response-to-the-ebola-virus-disease-outbreak-in-bas-uele.html
  16. http://www.radiookapi.net/2017/05/15/actualite/sante/ebola-en-rdc-defis-et-chances-dun-lointain-enclavement 
  17. http://apps.who.int/iris/bitstream/10665/255486/1/EbolaDRC-1752017-eng.pdf?ua=1 
  18. http://www.healio.com/infectious-disease/emerging-diseases/news/online/%7Bf835f3ce-da12-4ae7-9c8c-0e0f3d6ef8f3%7D/extent-of-ebola-outbreak-in-drc-may-not-be-known-for-weeks

Maps used to help place Likati and Bas-Uele...
      Updates...
      1. Fixed spelling mistakes in Likati, added detail about sampling delays
      2. Added references 10-12; noted 2 cases now confirmed, 19 suspect cases in total 
      3. Update on where the 300,000 vaccines come from [13]
      4. Update on contacts and ReliefWeb and WHO references
      5. New SitRep from WHOAfro - altered case & testing numbers