Saturday, 2 September 2017

VDU has moved house....

If you're looking for new posts about viruses and virus-related stuff (which could be anything really!), from now on please go over to the new site with its easy-to-remember address...

Hope to see you there!


Wednesday, 16 August 2017

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

This post has been moved to the new Virology Down Under platform on Wordpress.

You can get to this specific post by clicking on the link below...

Please adjust your bookmarks.

Apologies for any inconvenience.

Saturday, 15 July 2017

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

This post has been moved to the new Virology Down Under platform on Wordpress.

You can get to this specific post by clicking on the link below...

Please adjust your bookmarks.

Apologies for any inconvenience.

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.



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.
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.


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.



Sunday, 18 June 2017

Climate and science denial....

This post has been moved to the new Virology Down Under platform on Wordpress.

You can get to this specific post by clicking on the link below...

Please adjust your bookmarks.

Apologies for any inconvenience.

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.



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.



Saturday, 13 May 2017

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

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 Biom├ędicale (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]



Maps used to help place Likati and Bas-Uele...
      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
      6. Replaced maps to add in the correct population!

      Sunday, 16 April 2017

      March...for Science...this Saturday 22nd April...

      Hi All,

      Reprinted with permission from
      I hope you can make some time this coming Saturday 22nd April to get to your local March for Science venue, wave a sign and listen to some talks. 

      Check out the Australian website for details and RSVP to help the organisers understand how many will be attending.

      It would be great to see as many scientists and members of the science-supporting public turn up to support the ongoing need for science in our everyday lives. 

      As the local Australian supporters page details, the March for Science aims to celebrate that scientific knowledge delivers...
      • community knowledge and understanding about the world(s) around us
      • information about new disocveries that is clearly communicated for eveyone to understand
      • facts to underpin public policies that guide our way of life
      • results that are deserving of ongoing long-term funding

      I'm not involved in the march organisation but I hope to be at my local Brisbane march - along with my science loving family. 

      After cleaning our teeth with toothpaste and fluoridated water - both of which have scientific data to prove their effectiveness - we'll probably drive there in a car fabricated, assembled, painted, tested, fuelled and imbued with safety devices that have all resulted from scientific advances. 

      We'll drive to the city on roads and bridges designed and made thanks to scientific achievements. We'll be singing along to the Moana soundtrack - a digital download copied onto a CD  from a movie we saw - every step of which was made possible thanks to a slew of scientific innovations and with storytelling bolstered by scientifically accurate research. 

      We'll be wearing clothes made possible by scientific advances in fabric design, machining and colouring, assembled by people using machines that were produced from numerous individual scientific breakthroughs. We'll have applied sunscreen of a formulation that has been proven to reduce skin burning while we stand in Queensland's high ultraviolet midday sun. Sunburn has been shown through medical research (science!) to increase the risk of developing skin cancer later in life. One of my son's will be actively and safely mounting an immune response to his recent HPV vaccine - a development that will reduce his risk of some cancers, and reduce the risk of him passing along the virus that may cause such cancer in others.

      I'll also be wearing a machined cap to protect my head from burning. It will be embroidered with a computer-designed rhinovirus logo. Thank goodness for a vast array of scientific advances that that lead to computers, communication networks, financial transaction systems, broadband cabling and the internet via which I write this very blog (while consuming too much chocolate - which medical science tells me is overly laden with sugar and fat so as to be bad for me if I consume it regularly while continually sitting on this chair).

      There's a good chance I'll have taken some pain relief for a headache caused by a (probably rhino-)virus-induced common cold. The drug and the knowledge of the virus were all generated by medical doctors, chemists, physiologists, virologists, epidemiologists and other researchers generating and using science in a whole range of ways over decades.

      Later we'll grab some lunch from a vendor that has made and stored the food in ways that mean we won't end up with food poisoning later (we hope) - because of lessons learned about microbes and food storage through the application of the scientific method and ongoing scientific checks. 

      And that's just a sampling of the science that will permeate our lives during this one day.

      Science is everywhere and we are wholly dependant upon it in our big city and suburban lifestyles. Science makes us safe. It allows us to work and to travel and to communicate (reading this on a mobile device much?) more effectively. 

      Science permeates our life in ways we already know and in ways we have yet to understand. Imagine what continuing the support for science will lead to in the near and distant future.

      We will March for Science because science has mostly made our lives better. 

      Monday, 27 March 2017

      Happy 4th birthday...

      This blog!

      I'm sure somene one said that a year in social media equates to 7 cat years. Maybe it 9.

      Anyhoo, I'll be hunting down a cake for us all today - or maybe a muffin at the canteen.

      My heartfelt thanks to those who have made writing for this blog so much fun. 

      I hope we all keep learning about viruses together. Anything is worthwhile if you learn something from it. ...and have a reference to prove it was based on data...and cite that reference...and it gets cited by others...and peer reviewed....

      Happy 4th!!

      Tuesday, 14 March 2017

      SNAPDATE: H7N9 by map...

      With the latest numbers out from Hong Kong's Centre for Health Protection, Week 10 marks the second week of around a dozen human spillover cases - likley to be poultry to human infections.

      Click on image to enlarge.
      While the number of cases at each geographic location within China is small given the millions living in each region, this week's cases are spread across 10 provinces or municipalities. A huge area. 

      Guangxi province is adjacent to Vietnam. It's always worth remembering that an outbreak anywhere can turn into a threat everywhere

      From these numbers, there is no obvious escalation of human cases to suggest anything has changed in the way H7N9 infections are acquired; they remain relatively rare and from animal-to-human close contact.

      While the cases are still coming, the totals (see weekly and daily bars below) shows a levelling off - at last suggesting a slowing of this season's epidemic. But stay tuned.

      Numbers of human H7N9 cases.
      Image taken from the VDU static H7N9 graphs and numbers page.
      Click on image to enlarge.

      Sunday, 5 March 2017

      Avian influenza A(H7N9) virus in humans: lay of the land...

      I'm getting a little more of a grip on the H7N9 numbers thanks to the data from the Hong Kong Centre for Health Protection (CHP) [1] - which have been a solid source in 2017.

      Keep in mind that these numbers :

      1.  are imperfect because they are reported inconsistently by those who have the data and because they only contain partial detail - death details are impossible to come by.  Please keep in mind that there is no global, running-tally of H7N9 cases presented to the public, by any public health entity. There is a great line list from the citizen-run FluTrackers list, ([2]my usual go-to) but in 2017 they got swamped by these unsatisfactory data.
      2. will only represent those cases that have been lab tested. Any people who have met the criteria for being a "Case" [pick from 3-6] - which in most instance means being sick. In some instances a cases is identified because diligent doctors have followed up those people who had contact with a known case - which is called contact tracing. Sometimes these contacts may virus positive by only mildly ill or have no illness at all.
      I've graphed these wrangled data using one of my older formats - to show which province, municipality or autonomous region is contributing to the peaks as the site of origin for an H7N9 case.

      Sometimes where a case has been detected may not be where they were infected. I prefer to talk about where a case "acquired" their infection. 

      Click on image to enlarge.
      Data for this graph can be downloaded from my static H7N9 graphs page, here.[9]
      We can see - perhaps - that the major contributors to the peaks in January and February's 5th Wave are Jiangsu province (green circles) followed by Zhejiang province (orange circles) then Guangdong (brown circles), Anhui (purple circles), Hubei (red squares) and a range of smaller contributor regions.

      Guangdong and Zhejiang are familiar to H7N9 watchers as being hotspots for human spillover and while Jiangsu has always had a presence in the outbreaks, it has had a very big season this time around.

      It remains to be seen whether a range of market live poultry market (LPM) closures has cut the flow of virus into these markets and to their many, many visitors. These closures have been in response to cases rather than to prevent the outbreaks but no obvious nationwide coordination is apparent. It seems likely that spread of infected fowl will continue until more markets close, the source is contained or the seasons for influenza spread (winter and colder shoulders) is over.

      Stay tuned to the CHP update this week - last week's tally was lower than previous weeks; a blip or a trend? 

      A few things about this graph.
      • It mirrors the FluTracker's line list numbering scheme up until FT816. From entry No. 817 it uses data from the CHP reports. These are PDFs but as they helpfully told me by email this week - you can extract the data yourself using Adobe Acrobat Pro. If you don't have that - I've already done that extraction and am happy to share an Excel version of it with you. Shoot me an email, leave a message or Tweet me @MackayIM.
      • The Outbreak numbering - or waves - is based on when cases appeared or stopped. Its imperfect too. There are published schemes but they also differ from each other [e.g. 7,8]. This isn't life or death - you get the idea from the obvious peaks and troughs. FYI - this year I've updated my numbering for previous outbreaks.
      • Market closures include long term or short term shutdowns or rotating closures for one or more days for disinfection followed by restocking. Each province is a populous place. Often markets are closed here or there but not everywhere in a province and certainly not all provinces at once. 
      • Data are plotted by week of illness onset (hard data to come by) or when the case was reported. The grey peaks indicate totals from all provinces for that week

      Friday, 24 February 2017

      H7N9 agrees...

      This post has been moved to the new Virology Down Under platform on Wordpress.

      You can get to this specific post by clicking on the link below...

      Please adjust your bookmarks.

      Apologies for any inconvenience.

      Tuesday, 21 February 2017

      H7N9 virus in humans in China: just how big is this?

      This post has been moved to the new Virology Down Under platform on Wordpress.

      You can get to this specific post by clicking on the link below...

      Please adjust your bookmarks.

      Apologies for any inconvenience.

      Sunday, 19 February 2017

      H7N9 in humans - biggest ever season in humans - most poorly reported as well

      UPDATE: No.1 20FEB2017
      Below is the best I can do to plot avian influenza H7N9) virus cases in humans against month.

      And just to be clear - it's a very big underestimation. WHO is reporting 1,222 cases in humans [3] - but patchy public data exist for about 1,000.

      Click on image to enlarge.
      NOTE: This is a big underestimate as it only includes cases
      with public detail available to identify them. There are 
      approximately 200 cases missing. 
      Ideally the charts above woudl be based on the month that illness onset occurred - when each person became ill. But those details just are not publicly forthcoming from China's massive human and animal influenza surveillance and testing system. 

      I'm sure the data are to hand internally, and they may be on hand at the World Health Organization (WHO) - but you wouldn't know it by looking for them publicly. 

      The WHO used to be helpful with providing H7N9 data but it seems their latest efforts to provide more detail on MERS cases has exhausted them.

      Hong Kong's Centre for Health Protection (CHP) has been valiantly chipping away, but they also fail to provide sufficient detail to link cases with media or other reports. What they do provide are summary totals.

      As for fatal outcomes from H7N9 infection - forget understanding who dies when and why. Those numbers have been frankly a pathetic mess for four years.

      This week marked the fourth anniversary of our knowledge of H7N9 in humans - the first case became ill February 18th 2013 in as part of a Shanghai family cluster. Since then we've seen less and less detail on cases. And by "detail" I don't mean their names and addresses - just case age, sex, date of illness onset/hospitalization/death, linkage between case and death, poultry or human contact and place infection was likely acquired. Basic and standard stuff.

      Meanwhile the mainstream media report every bolus of data that are dumped as if these were new cases and deaths that have just occurred. In reality, the huge January spike below may include many cases and deaths from a month or more earlier. It may mis many cases that have not been detected.

      We're definitely having a huge H7N9 season in 2016/17 (n=176 human cases using public case data, but over 400 based on announced totals[3]). We had bigger detailed tallies in 2014 (n=326) and 2015 (n=220), but never a season as big as these totals make it out to be now. 

      This is the largest H7N9 season ever recorded.

      In media interviews over the past weeks, I've put the current season down to lethargy in closing live bird markets as cases and deaths have mounted. The response has been faster in previous years.[1,2] Poultry is a big deal in China.[2] Perhaps the poultry lobby has won out over human life this season. 

      1. Amended to indicate the scale of the case numbers, based on totals, not individual detailed cases, in the 2016/17 seasons. The largest season of H7N9 in humans...on record.