VDU's blog

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

UPDATE No.6 10MAY2018 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...

Maps used to help place Likati and Bas-Uele...

Updates...

Fixed spelling mistakes in Likati, added detail about sampling delays

Added references 10-12; noted 2 cases now confirmed, 19 suspect cases in total
Update on where the 300,000 vaccines come from [13]
Update on contacts and ReliefWeb and WHO references
New SitRep from WHOAfro - altered case & testing numbers
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

https://marchforscienceaustralia.org/

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 https://marchforscienceaustralia.org/ 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 :

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.
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

References...

Friday, 24 February 2017

H7N9 numbers....no-one agrees...

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

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https://virologydownunder.com/h7n9-numbers-no-one-agrees/

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...

https://virologydownunder.com/h7n9-virus-in-humans-in-china-just-how-big-is-this/

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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.

References...

Updates...

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.

Friday, 10 February 2017

Science needs to talk more but I know many scientists who don't...

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Friday, 27 January 2017

H7N9 is having a big season...Happy New Year!

My how things can change in 5 weeks.

If you look back a few posts you'll see that in late December, the data suggested avian influenza A(H7N9) virus was having a wimpy season - its slowest to date.

Well, thanks to 100+ cases in China which have been bulk reported by the ever vigilant Hong Kong Centre for Heath Protection (CHP) - and captured and listed by FluTrackers - the situation has changed dramatically.

Never take your eye off influenza virus - especially during its favourite season. And this season is a particularly active one for avian influenza all over the world.[4]

H7N9 is an avian influenza virus (hence the "bird flu" moniker) that to date has been localised to China - especially but not exclusively to its eastern coast provinces - and it's a flu virus that doesn't make the birds it infects noticeably sick.

These "low pathogenic" influenza viruses can sneak silently through poultry flocks because infections are mild - they don't cause infected birds to get sick or die.

Data on human infections with avian influenza A(H7N9) virus. Data from [1]
Click on image to enlarge.

The H5 avian influenza viruses on the other hand - H5N1, H5N8, H5N5 or H5N6 for example - are called "high pathogenicity" avian influenza viruses because they kill off infected birds. Thankfully, H5N1 is the only H5 avian influenza that has caused a sizable number of human infections. H5N6 is gaining some ground though. The other H5s do not reportedly cause much impact in humans. Whether this is because they are not found or not sought in humans who have had contact with infected animals is unclear.

Disease in an H5-infected flock can serve as a sentinel for an outbreak of the virus.

With H7N9 though, it's humans falling ill that set of the alarm that H7N9 (or another influenza virus) is in the house...or the market. And there are a sizable number of deaths among those - often male - who already have some sort of underlying illness and then acquire an H7N9 infection.

Most human cases of H7N9 result from contact with a "wet" market, also called a live bird market (LBM) in which chickens and ducks can be chosen, killed and dressed to provide a super-fresh meal. These tasty treats are especially in demand around this time of year as Chinese New Year is upon us.

Chinese New Year is also a time when we observe the largest seasonal migration of humanity in the world. [2] Loved ones travel across a massive country to visit each other, share stories, traditions, meals - and the occasional respiratory virus like influenza.

From [3].

In the coming weeks, as the gatherings disperse, it will be very interesting to see whether the current spike in human H7N9 infections is reflected by a steep rise in human cases acquired during the New Year celebrations - some of which include contact (direct or indirect) with infected poultry in backyard farms or LBMs.

Stay tuned. And don't forget to wash your hands often and cough/sneeze into the crook of your elbow.

References...

Static pages

Saturday, 13 May 2017

Sunday, 16 April 2017

Monday, 27 March 2017

Tuesday, 14 March 2017

Sunday, 5 March 2017

Friday, 24 February 2017

Tuesday, 21 February 2017

Sunday, 19 February 2017

Friday, 10 February 2017

Friday, 27 January 2017