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...

1. http://virologydownunder.blogspot.com.au/2014/11/influenza-ah7n9-virus-detection-numbers.html
2. https://www.nytimes.com/2017/01/26/world/asia/chinese-new-year-home-lunar.html?_r=0
3. https://www.cdc.gov/flu/protect/covercough.htm
4. http://news.trust.org/item/20170126150919-05z2c/

WHO sets the table....and lays it with MERS-CoV details

This just made my day. A Tweet from scientist and program manager at the World Health Organization (WHO), Dr Embarek. In the tweet he noted that Middle East Respiratory syndrome coronavirus (MERS-CoV) data will now be presented by WHO in an easy-to-access Mirosoft Excel table...

An example is in this latest update.[1]

Excerpt of new MERS-CoV data from [1]

This will make data collection for scientists, public health teams and researchers looking to follow what's happening with this camel-borne virus as it spills over to humans so much easier. I've been painstakingly entering data from several sources since 2013 - and this will really streamline the process.

Thanks to those at the WHO for making this happen.

Now, could you please also do this for all the other pathogens you keep track of....different influenza viruses (H7N9, H5N6, H5N1), zika virus, dengue virus, yellow fever virus....and make it retrospective....

References...

1. http://www.who.int/csr/don/26-january-2017-mers-saudi-arabia/en/

Snapdate: influenza H7N9 cases in humans, by the numbers...

An updated chart.
[SNAPDATE'S are snap updates that don't have lots of detail and chat...although they almost always end up having lots of chat!]

A summary of the monthly, weekly and daily data graphing human avian influenza A(H7N9) virus infections in humans reported from the hotzone, China.

Daily weekly and monthly H7N9 numbers, taken from the
FluTrackers curated line list [1] and the World Health
Organization disease outbreak news reports.
Click on image to enlarge.

References...

1. http://www.flutrackers.com/forum/showthread.php?t=202713
2. http://www.who.int/csr/don/en/

H7N9:2016 has been the most quiet year to date...

Influenza A(H7N9) virus, or 'H7N9', has had a quiet year when compared to past outbreaks.

All human cases to date have been linked to China. The majority of human cases have had some link with poultry - chickens or ducks - although we do hear of human-to-human transmission, this seems to be limited. H7N9 has been found in poultry from backyard farms and in live poultry markets (LPMs) in China - sometimes in the company of other influenza viruses, like H9N2.[1]

Cases and deaths each month over the 4 years we have known
about human cases of H7N9 infection.
Click on image to enlarge.

Despite the slow year,the 2016 graph above shows the usual December uptick in human cases. It will be what happens next that matters. Will be see a big January surge as in 2014, or a later Feb-April surge as in 2013 and 2015? Will live LPMs be quickly closed, disinfected, the animals destroyed and any outbreaks in 2017 squashed or will they remain open allowing more human cases as the virus spreads among market animals?

Time, and testing data - which China generates lots of but does not seem to enjoy publicly reporting - will tell.

In 2016 - 2 new regions were added for the first time - Tianjin municipality and Liaoning province - both in the north-eastern coastal region of China. 

In 2013, no sustained human-to-human transmission had been reported [2] - this remains true up until today.

References...

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911810/pdf/nihms749408.pdf
2. http://www.nature.com/news/mapping-the-h7n9-avian-flu-outbreaks-1.12863

Happy Festive Season to all who read this....

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

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https://virologydownunder.com/happy-festive-season-to-all-who-read-this/

Please adjust your bookmarks.

Apologies for any inconvenience.

Get off my lawn you 2016....!

Zika virus-positive microcephaly in Colombia...

The latest epidemiological report (epidemiological week 47) from Colombia, which includes data on Zika virus (ZIKV) disease (ZVD; 20NOV2016-26NOV2016), has been produced by the Colombian National Institute for Health team.[1]

NOTE: While these data were reported the past epidemiological week (EW), they may not be from that week. See earlier post about possible reporting lag.

As of this report, 60 (+0 from last EW) live births have been diagnosed with congenital ZIKV syndrome (CZVS; microcephaly/central nervous system disorder), confirmed as being ZIKV positive. That represents 1.0% of all confirmed ZIKV positive mothers-a slowly but steadily rising proportion.

The change in confirmed ZIKV infection numbers when detected in
association with a microcephaly diagnosis, Colombia, compared to the
preceding week's total (yellow bars, right-hand axis). Those diagnoses still in question and under investigation are shown as yellow dots (left-hand axis).
Data are from [1]. Click on graph to enlarge.

It has now been 415 days, or 1 year, 1 month and 18 days, since ZIKV was first confirmed in Colombia on 16th October 2015.[5] Keep in mind that when talking about microcephaly - we have to think back in time to what insult or infection might have occurred during pregnancy. The counts of ZIKV occurring this week will have zero impact on what happened back then. Also keep in mind that Colombia may be reporting things differently from Brazil.[3]

The cumulative curve of confirmed ZVD cases
(green circles, left-hand axis) and the change in confirmed ZVD case
numbers when compared to the preceding week's total
(green bars, right-hand axis). Data from [1].
Click on graph to enlarge.

No new laboratory confirmed ZIKV detections have been reported in Colombia for eh 20th week (green graph, above).

Brazil first reported positive (but unconfirmed) laboratory tests for ZIKV disease on 29th April 2015. Brazil then started to report a rise in foetal anomalies (an initial 141), in the form of microcephaly on 30th October 2015. This was 184 days - or about 6 months later.[4] However, the genetic analyses suggest ZIKV was in Brazil from around 2013. It had a lot longer to get established. Perhaps this is the difference between Brazil and Colombia, given reports a growing 2,180 ZIKV congenital syndrome diagnoses [2] compared to Colombia's 60.

References...

1. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/2016%20Bolet%C3%ADn%20epidemiol%C3%B3gico%20semana%2047.pdf
2. http://www.paho.org/hq/index.php?option=com_docman&task=doc_view&Itemid=270&gid=37143&lang=en
3. http://virologydownunder.blogspot.com.au/2016/06/the-elephant-squeaked.html
4. http://www.paho.org/hq/index.php?option=com_docman&task=doc_view&gid=35139&Itemid=270&lang=en
5. http://www.nejm.org/doi/full/10.1056/NEJMoa1604037#t=article

The reality of the post-truth world's impact on science communication...

So:

 We tweet 2each other. 

We write 4each other. 

We're considered elite. 

We don't understand our community. 

We can't reach them. 

Cool. [sarcasm]

P.S.
Post-truth is now defined by the Oxford dictionary...

ADJECTIVE

Relating to or denoting circumstances in which objective facts are less influential in shaping public opinion than appeals to emotion and personal belief:

‘in this era of post-truth politics, it's easy to cherry-pick data and come to whatever conclusion you desire’


‘some commentators have observed that we are living in a post-truth age’

Another virus found to remain infectious on hard surfaces...

That headline doesn't bring in the readers. But - as far as we can tell having not been to the Nov 13-17 conference at which the preliminary data were presented during a seminar- it sums up the main finding of a new study on Zika virus (ZIKV).[1,2,4]

A 2016 Puerto Rico strain of the Asian lineage of ZIKV added to blood or a salt/protein solution was dried onto hard, solid surfaces. 

ZIKV was able to be recovered from those surfaces up to 8 hours later when in the presence of blood, but not the salty solution. 
Blood protected the virus. 

ZIKV recovery was achieved after rehydrating the dried material and adding dilutions to cells in culture (Vero E6 cells). There was no news on infectivity at warm temperatures or on cloth, tissues or other porous surfaces on which enveloped viruses like ZIKV usually don't do so well. By the way, when I say "recovered", I mean virus coudl be grown using lab conditions, producing more infectious virus. So the findings show that enough ZIKV remained infectious (or that it retained some infectivity) to start a new infection in lab cultures, despite being held outside the host cells it needs to replicate. 

Can ZIKV virus "live for hours" on surfaces? It's a virus - so it doesn't do much of anything outside of the living cell it completely depends upon for energy and raw materials ("dietary requirements"!). 

The main takeaway is not that the study defined a new route of ZIKV transmission to add to mosquitoes, sex, intrauterine transmission and transfusion.[11] This might have been your interpretation if you'd read...

.."The Zika virus is able to infect people even after sitting out on a counter for several hours, according to new research" [6]..

The study is really about the observations that some disinfecting agents (bleach and peracetic acid) may not work well when the virus is spilt onto these surface in the presence of blood. Isopropyl alcohol and quaternary ammonium/alcohol agents were still effective though.[3] West Nile virus (WNV) and bovine viral diarrhoea virus (BVDV) responded similarly. This is not a new finding for viruses in general, but it's a good one to have. This can be used as a reference for risk assessments for a lab that works with ZIKV or for healthcare facilities that may be dealing with ZIKV infected patients and needing to know how to effectively clean up spills or contaminated rooms.

Should we worry about this new finding?

Does the finding that a ZIKV spill can remain infectious on surfaces add new knowledge to our understanding of the risks of acquiring ZIKV infection? Not as far as we know because we have very limited evidence that ZIKV can infect a human through their epithelial surfaces (mucous membranes) - like we did have for Ebola virus for example. Such a route of infection - from surface to mucous membrane -is the the implied risk here. In other words, getting enough of those spilt infectious viruses into your eye, mouth or onto/into your nether regions. Its possible, but not likley and we have little evidence that its happens. 

We also have little evidence that ingesting something contaminated with infectious ZIKV or breathing it in can result in an infection. 

As ever, little evidence does not equate to zero evinced - we just have few actual data either because theses are such rare events or because we really haven't looked much (my bet).

Rare ZIKV transmission events do happen...

We have seen documented some unusual/infrequent ZIKV transmission events. Laboratory acquired infections [5,12] for example and that case of a severely immunocompromised/chronically ill adult passing ZIKV to his healthy adult son, perhaps via mucous membrane exposure to a high ZIKV load.[8,9] 

Infection of Dengue virus following exposure of a healthcare worker's mucous membranes to an infected IgM-positive patient's blood has also been described previously.[10] 

This route of transmission is certainly in need of some serious study. That said, transmission was not what this study was investigating. 

Infectious fluids such as blood, saliva, breast milk, urine or semen may come into contact with epithelial surfaces in a range of ways. 

Studies that do set out to focus on this interaction and measure how often an infection results from this contact, are needed. 


References...

1. Research finds Zika virus can live for hours on hard, non-porous surfaces
   https://www.eurekalert.org/pub_releases/2016-11/aaop-rfz111116.php
2. Zika virus can survive on hard surfaces for hours, researchers say
   http://www.upi.com/Health_News/2016/11/15/Zika-virus-can-survive-on-hard-surfaces-for-hours-researchers-say/9781479267969/
3. Study: Zika virus can linger on hard surfaces
   http://www.cidrap.umn.edu/news-perspective/2016/11/study-zika-virus-can-linger-hard-surfaces
4. Inactivation of Zika Virus on a Hard Non-porous Surface
   https://annual.aapsmeeting.org/event/member/309446
5. http://www.achd.net/pr/pubs/2016release/060916_zika.html
6. Zika can survive for hours on hard, nonporous surfaces
   http://www.cnbc.com/2016/11/15/zika-can-survive-for-hours-on-hard-nonporous-surfaces.html
7. Zika virus can live for hours on hard, non-porous surfaces
   https://www.sciencedaily.com/releases/2016/11/161115164220.htm
8. Scientists just documented the first case of Zika spreading through physical contact
   http://www.sciencealert.com/scientists-just-documented-the-first-case-of-zika-spreading-through-physical-contact
9. Fatal Zika Virus Infection with Secondary Nonsexual Transmission
   http://www.nejm.org/doi/full/10.1056/NEJMc1610613?query=featured_home&
10. Transmission of Dengue Virus without a Mosquito Vector: Nosocomial Mucocutaneous Transmission and Other Routes of Transmission
    http://cid.oxfordjournals.org/content/39/6/e56
11. Zika Virus Disease Cases - 50 States and the District of Columbia, January 1-July 31, 2016.
    https://www.ncbi.nlm.nih.gov/pubmed/27631604
12. http://www.cdc.gov/zika/transmission/

Time to pick ourselves up, learn from our mistakes and do better...

We've all learned some hard lessons in the past 24 hours. We've seen something happen that we can't really comprehend. But such is life. Life is always teaching, always surprising. And we should always be learning from it, from others and from ourselves. We should teach others - both the good and the bad.

Most who read this will be lucky people. Never forget the luck you were born into-nor deny it. Others are not so lucky and they wake up to that every day. 

Don't blame others for the place we find ourselves in. Be a better person yourself. Teach your children to be good people, to be accepting, forgiving and giving people. Be inclusive. Study, be kind. Don't give in to anger and hatred - they are easy to sow but hard to repair and in the end make nobody happy.

Make the world a better place and remember to bring everyone along with you. Boy, girl, any colour, shade, height, nationality or belief. Help others see the things you see and learn to appreciate what they see and share with you. Understand the patterns and changes in their lives and help them view our global community for the joys its tribes can bring - we share many things.

But do rage against the threats to progress and social justice that we now face all over the world. Do not stop calling out that which harkens back to darker days and ways of life otherwise we will find ourselves waking into those days.

We can be better than this and we should always strive to be.