Monday, September 25, 2017

#NatlPrep: The Gift Of Preparedness 2017

Note: This is day 25 of National Preparedness Month . Follow this year’s campaign on Twitter by searching for the #NatlPrep hash tag.
This month, as part of NPM17, I’ll be rerunning some edited and updated older preparedness essays, along with some new ones. 


Ten years and more than 11,500 blogs ago, in Hickory Farms Will Hate Me For This, I began promoting the idea that - instead of gifting cheese platters, fruitcakes and ugly sweaters - we should be giving our loved ones preparedness items for holidays, birthdays, and anniversaries.
As the CDC graphic above illustrates, nearly half of all Americans families don't even have the basics to deal with a short term emergency, much less a major disaster.
This was driven home for me a little over two weeks ago when Hurricane Irma was bearing down on Florida, and I saw thousands of Floridians going from store to store, desperately seeking flashlights, bottled water, and batteries.   
Over the past decade I’ve made it a point - in addition to securing my own preparedness items - to give water filters, LED lanterns, NWS weather radios, MREs, batteries, first aid kits, and emergency stoves to friends and family.
Things that most people know they should have, but will rarely go out and buy for themselves until a threat appears on the horizon - and then it may be too late.
Most of these items are inexpensive - many under $20 - but are invaluable when you really need them.
Products mentioned or pictured below are to provide a general idea of the type of gift, and should not be viewed as an endorsement of one brand over another. I often find these gifts on sale in discount stores, bargain basements, and flea markets, and stock up whenever I come across a good deal. 
Sometimes I make the gifts myself, as when several years back I put together some first aid kits, and distributed them to a number of friends and relatives. You can either put one together yourself, or purchase one already assembled. 

Trust me, there is no substitute for having a well stocked first aid kit when you really need one.

A couple of years ago I also bought several 5 gal. buckets (with lids) from a home improvement store, along with mylar bags and oxygen absorbers from Amazon, and put together some long-term food storage buckets for friends.  

Cost per bucket?  About $30.  But enough food to keep two people going for ten days or more in an emergency.  I keep a couple on hand (one for me, one for the cat), myself.

Anyone who knows me knows that I have a particular interest in (ok, its more of a fetish for) LED flashlights and lanterns. Probably because I lived so many years aboard a sailboat in the tropics with hot, smelly kerosene lanterns.
LEDs are far preferable to many other light sources because they run a very long time on batteries, they don't pose the fire hazard of candles or kerosene, and they don't produce heat or fumes.
A couple of years ago I ran across a display of LED light sticks, with three modes of light, and a built in whistle. The button batteries promise 200 hrs of running, but even if they last half that, at $3 each they were a bargain.

I bought 5 to test out.  One for my car, one for my bug out bag, and three for stocking stuffers.   Since then, I've bought several more.

My collection of LED lights continues to grow, and the best part is none of the items pictured below cost me more than $5 each.  My local Walmart has LED flashlights for $1 apiece in the sporting goods section; cheap but serviceable and a great stocking stuffer.

High on the list of things to have is a way to make water potable.

Although (unscented) bleach will work, it requires measuring, and imparts a taste to the water many dislike.  An option that has gotten a lot less expensive in recent years are filtration systems, like the LifeStraw ®.

At just 2 ounces, this personal water filter will reportedly filter 1000 liters down to .2 microns. Not bad for around $20.  I've recently added the Sawyer Mini-Filter to my preps, again about $20.

Speaking of water, having a way to store enough water for three days (1 gal/person/day) is essential. A family of 4 will need at least 12 gallons for 72 hours.   Personally, I keep enough on hand for a couple of weeks.
While there are plenty of `free options’ – like rinsed and recycled 2-liter plastic soda bottles or other food-safe plastic jugs – you can also buy collapsible 5 gallon containers.
I also picked up a few single burner Propane stove units on sale for $10 each. Add a couple of 1 pound propane cylinders (about $3 each) and you can cook for a week.

Every home should have a battery operated radio (with NWS weather band), yet many do not.  Some are available with crank or solar charging.  In any event, you'll want something which can pick up the NOAA NWS Emergency Broadcaster in you region.

As I’ve described in  Preparedness: Solar Power On A Budget, it is a relatively easy task to set up a simple solar charging system.
No, you won’t keep the A/C or refrigerator running on a budget system, but you can keep your LED lantern batteries, cell phone, iPod or iPad, or notebook computer running.
In recent years I'm seeing reasonably priced `briefcase’ solar panels – often for between $50 and $80 – that, when unfolded, can charge a 12 volt storage battery with up to 13 watts of power. Add a $20 inverter (converts 12 volt battery power to 120v AC), and you can do a heck of a lot.

12 volt inverter

Last week I ordered an inexpensive USB solar charger/powerbank - along with a USB fan - which I'll be testing out before gifting to a friend for Christmas. For roughly $40 for the pair, I don't expect miracles, but I'm very interested to see how well it does.

Something as simple, and as utilitarian, as a multifunction `Swiss’ army knife, a`Multi-tool’, a `plug in' auto 12 volt USB charger (see below), or even a good first aid manual, makes a great preparedness gift.

A walk through any camping supply or hardware store will provide plenty of inspiration. Just ask yourself . . . what would you want if the power and water were out for a week or longer, and the stores were closed?  Buy first for yourself, and then for a friend or a loved one.
We need to cultivate a culture of preparedness in this country, and around the world. 
And we can start doing that, one gift at a time.

Maryland Dept. of Ag.: 11 Pigs At Frederick County Fair Test Positive For Influenza A

CDC Safety Poster


Yesterday, in Updating The Maryland Swine Variant H3N2v Outbreak, we looked at reports from the Maryland Health Department that the number of human H3N2v infections reported since the middle of last week had increased to 10, and a media report that a Sick Pig and Child Causes Shut Down Of Frederick Co. Fair Pig Exhibit.

While the child's illness has yet to be identified as swine variant influenza, 11 pigs have at the Frederick County Fair have tested positive for influenza A (subtype pending), and their hog barn has been put under quarantine.
Since the influenza subtypes that commonly circulate in swine (H1, H2 & H3) are also the same HA subtypes as have caused all of the human pandemics going back 130 years (see Are Influenza Pandemic Viruses Members Of An Exclusive Club?), swine influenza viruses are watched carefully for signs of jumping to humans.

Up until about six years ago the CDC only received 1 or 2 swine variant human infection reports each year. In 2010, that number jumped to 8, and in 2011 to 12. In 2012 we saw more than 300 casesmostly mild - and nearly all associated with exposure to pigs at state and local agricultural fairs.
This year - up until a week ago - 20 cases had been reported, mostly over the summer from Ohio. 
Since then Maryland has reported 10 presumptive positive cases, and the epidemiological investigation - and testing - continues. At this point we only have confirmed human infections linked to the Charles County Fair.

While more details will likely emerge over the next 24 to 48 hours, late yesterday the Maryland Department of Agriculture posted the following statement.

Influenza A Detected in Swine Exhibited at The Great Frederick Fair 

September 24, 2017

ANNAPOLIS, MD – The Maryland Department of Agriculture, Maryland Department of Health and the Frederick County Health Department are investigating 11 cases of influenza in pigs recently exhibited at The Great Frederick Fair. Preliminary tests show that the pigs are infected with influenza A, but it is not yet known if this strain is potentially transmissible to humans. Additional testing and investigation is underway by the Department of Agriculture.

All swine at the Frederick County fairgrounds are under a quarantine order from the Department of Agriculture and will not be released until seven days after the last pig shows signs of influenza illness. To report sick pigs, or if you have questions about pigs and influenza, please call the Department of Agriculture at 410-841-5810 or after hours at 410-841-5971.

It is rare for influenza viruses that normally infect pigs – often called “swine flu” – to spread to people, but it is possible. Most commonly, human infections with swine flu occur in people who have been exposed to infected pigs (e.g., children handling pigs at agricultural fairs or workers in the swine industry). Limited human-to-human spread of swine flu has been detected previously, but no sustained or community spread has been identified.

The symptoms of swine flu in humans are similar to non-swine influenza and can include fever, cough and sore throat. Prescription influenza antiviral drugs can treat swine flu infections in people, especially when started early. Health officials recommend that people with influenza-like illness contact their healthcare provider and inform them if they have had pig contact within the past seven days. Providers are advised to contact their local health departments if they suspect swine flu in their patients to coordinate appropriate testing with their local health department. The Frederick County Health Department can be reached at 301-600-1733.

In accordance with the Secretary of Agriculture’s Hold Order (September 19, 2017), all swine exhibitions and any other activities involving swine will remain closed at the St. Mary’s and Calvert county fairs. All other movement or activities involving swine, including slaughter and butchering can proceed as usual.

Influenza viruses do not affect the safety of properly cooked pork. As with any raw meat, pork should always be properly handled and cooked to eliminate a range of food safety concerns.

The CDC's Risk Assessment on H3N2v and other swine variant viruses reads:
CDC Assessment
Sporadic infections and even localized outbreaks among people with variant influenza viruses may occur. All influenza viruses have the capacity to change and it's possible that variant viruses may change such that they infect people easily and spread easily from person-to-person. The Centers for Disease Control and Prevention (CDC) continues to monitor closely for variant influenza virus infections and will report cases of H3N2v and other variant influenza viruses weekly in FluView and on the case count tables on this website

For more information on swine variant viruses, and how to protect yourself when in contact with farm animals, the CDC provides the following guides.

Sunday, September 24, 2017

J. Infect. Diseases: Human Clusters Of H7N9 In China - March 2013 to June 2015


Although the vast majority of H7N9 infections have been attributed to direct or indirect contact with infected birds - particularly at live bird markets - we've seen scattered reports of small clusters where human-to-human transmission has been considered a possibility. 
Details on these clusters, often provided in WHO updates, have been slim - particularly since early in 2015 when China abruptly stopped detailed reporting on cases (see H7N9: No News Is . . . . Curious).
While reporting from China has gotten considerably better since January of this year, we still aren't seeing the kind of epidemiological case detail we were seeing during the first two epidemic waves (2013-2014). 
Although a record number of cases have been reported during this 5th Epidemic wave (n=766), only the `sickest of the sick' are hospitalized and tested, and so the actual number of human infections is believed to be much larger. 
All of which brings us to a new study, published this past week in the Journal of Infectious Diseases, which examined the known details on 21 H7N9 clusters (involving 22 contacts) from the first three waves, and found that at least 12 infections were likely the result of human-to-human transmission, another 4 were considered `possible', while 6 were determined to be unlikely.

First the abstract and link to the study (which, alas, is behind a paywall) then I'll return with a bit more.

J Infect Dis. 2017 Sep 15;216(suppl_4):S548-S554. doi: 10.1093/infdis/jix098.

Clusters of Human Infections With Avian Influenza A(H7N9) Virus in China, March 2013 to June 2015.
Liu B1, Havers FP2, Zhou L1, Zhong H3, Wang X4, Mao S5, Li H6, Ren R1, Xiang N1, Shu Y7, Zhou S8, Liu F9, Chen E10, Zhang Y1, Widdowson MA2, Li Q1, Feng Z11.

Author information


Multiple clusters of human infections with novel avian influenza A(H7N9) virus have occurred since the virus was first identified in spring 2013. However, in many situations it is unclear whether these clusters result from person-to-person transmission or exposure to a common infectious source.
We analyzed the possibility of person-to-person transmission in each cluster and developed a framework to assess the likelihood that person-to-person transmission had occurred. We described 21 clusters with 22 infected contact cases that were identified by the Chinese Center for Disease Control and Prevention from March 2013 through June 2015.
Based on detailed epidemiological information and the timing of the contact case patients' exposures to infected persons and to poultry during their potential incubation period, we graded the likelihood of person-to-person transmission as probable, possible, or unlikely. We found that person-to-person transmission probably occurred 12 times and possibly occurred 4 times; it was unlikely in 6 clusters. Probable nosocomial transmission is likely to have occurred in 2 clusters.
Limited person-to-person transmission is likely to have occurred on multiple occasions since the H7N9 virus was first identified. However, these transmission events represented a small fraction of all identified cases of H7N9 human infection, and sustained person-to-person transmission was not documented.

Some of these cases have been previously discussed in this blog, including:
EID Journal: Nosocomial Co-Transmission Of H7N9 & H1N1pdm09 
Study: Probable Nosocomial Transmission Of H7N9 In China
It is worth noting that since 2015, the H7N9 virus has undergone significant changes, both genetically, and in its behavior. In 2015's EID Journal: The Transmission Potential Of A(H7N9) In China, the authors found that while no evidence of sustained transmission was detected, they noted:
  • `evidence of a small but significant amount of transmission between humans in the first and second waves’
  • `evidence of increased transmission potential in the second wave
While in May of 2016, in EID Journal: Human Infection With H7N9 During 3 Epidemic Waves - China, researchers found patients hospitalized in the 2nd and 3rd wave with severe H7N9 tended to be younger, and from more rural areas, than those from the 1st wave.
They also found that the risk of death among hospitalized patients was greater in the second and third waves, although that varied between provinces.
Earlier this month, in the MMWR's  Update: Increase in Human Infections with Novel Asian Lineage Avian Influenza A(H7N9) Viruses During the Fifth Epidemic — China, October 1, 2016–August 7, 2017, the authors wrote about more recent changes in the virus:
During the fifth epidemic, mutations were detected among some Asian H7N9 viruses, identifying the emergence of high pathogenic avian influenza (HPAI) viruses as well as viruses with reduced susceptibility to influenza antiviral medications recommended for treatment. Furthermore, the fifth-epidemic viruses diverged genetically into two separate lineages (Pearl River Delta lineage and Yangtze River Delta lineage), with Yangtze River Delta lineage viruses emerging as antigenically different compared with those from earlier epidemics.
Because of its pandemic potential, candidate vaccine viruses (CVV) were produced in 2013 that have been used to make vaccines against Asian H7N9 viruses circulating at that time. CDC is working with partners to enhance surveillance for Asian H7N9 viruses in humans and poultry, to improve laboratory capability to detect and characterize H7N9 viruses, and to develop, test and distribute new CVV that could be used for vaccine production if a vaccine is needed.
While H7N9 hasn't managed to adapt well enough to human physiology to transmit efficiently, the CDC's IRAT system ranks the newly emerged Yangtze River Delta lineage along with the original Pearl River Delta Lineage (see Updating the CDC's IRAT (Influenza Risk Assessment Tool) Rankings) at the top of their list of viruses with the greatest pandemic potential.

Updating The Maryland Swine Variant H3N2v Outbreak


On Thursday, in Maryland DOH: 7 Fairgoers Test Positive For Swine Variant H3N2v, we learned of an outbreak of swine variant influenza among attendees of the Charles County Fair, and the decision to close the swine venues at two upcoming county fairs (Calvert County & St. Mary's).

The CDC describes Swine Variant viruses in their Key Facts FAQ.
What is a variant influenza virus?
When an influenza virus that normally circulates in swine (but not people) is detected in a person, it is called a “variant influenza virus.” For example, if a swine origin influenza A H3N2 virus is detected in a person, that virus will be called an “H3N2 variant” virus or “H3N2v” virus.
Over the past dozen years we've seen just over 420 swine variant cases (H1N1v, H1N2v, H3N2v) reported by the CDC with 307 coming in just one year (2012). Last year we saw an uptick in cases (see  MMWR: Investigation Into H3N2v Outbreak In Ohio & Michigan - Summer 2016), as we have again this summer.   

The 7 cases reported on Thursday have not yet been added to the CDC's total, and a brief notice posted on the Maryland Health Department website now indicates the number of presumptive cases has risen to 10.
Influenza A (H3N2) Variant Virus


The Maryland Department of Health has presumptively identified the influenza virus strain H3N2v (variant flu) in Maryland residents who had close contact with pigs at the Charles County Fair. None of the infected individuals has developed serious illness or been hospitalized. 

Influenza is an infection caused by the influenza virus which can affect people and other animals, including pigs and birds. Symptoms for the H3N2v strain are the same as seasonal flu and include fever and respiratory symptoms, such as sore throat and cough. Historically, there is limited human to human transmission from this strain of variant flu. The treatment recommendations for this strain of influenza are the same as for seasonal flu. 

It is recommended that people with influenza-like illness contact their healthcare provider and inform them if they have had pig contact within the past seven days. Providers are advised to contact their local health departments if they suspect variant flu in their patients to coordinate appropriate testing with their local health department. For local health department contact information, visit:​​

Maryland Cases (as of September 22, 2017)
10 presumptive positive cases
In an attempt to better quantify the size of this outbreak, the Maryland Department of Health has issued a letter to clinicians with guidance for testing and reporting. An excerpt from the letter describes when testing is appropriate:
When to suspect variant influenza virus 
Variant influenza virus infection cannot be distinguished by clinical features from seasonal influenza virus infection, or from infection with other respiratory viruses that can cause influenza-like illness (fever and either cough or sore throat). Therefore, the key to suspecting variant virus infection in an ill patient is to elicit an epidemiological link to recent swine exposure in the 7 days prior to illness onset,specifically:
  • Direct contact with swine (e.g., showing swine, raising swine, feeding swine, or cleaning swine waste); or
  • Close contact (within 2 meters or approximately 6 feet) with an ill person who had recent swine exposure or is known to be infected with a variant virus.
A weaker epidemiological link would be:
  • Indirect exposure to swine (e.g., visiting a swine farm or walking through a swine barn), especially if swine were known to be ill
We've seen studies in the past suggesting that only a fraction of cases are ever identified  (see CID Journal: Estimates Of Human Infection From H3N2v (Jul 2011-Apr 2012), and while H3N2v is viewed as having only low to moderate pandemic potential, the CDC is always keen to investigate whenever a zoonotic virus like swine H3N2 jumps species.
While both local and state health departments are reporting no serious illnesses or hospitilzations, several local media outlets are reporting on an 8-year-old girl hospitalized with swine flu after attending Charles County Fair, mother says.
Normally mild or moderate infections, serious illness and even deaths have occasionally been reported with swine variant viruses (see here, here, and here). Despite a long history of exposure to seasonal H3N2 flu viruses, research has shown only limited community immunity to these variant strains (see CIDRAP: Children & Middle-Aged Most Susceptible To H3N2v).

Although it may or may not be related to swine variant influenza (tests are pending), late yesterday another fair in Maryland closed their pig barn due to the discovery of a sick pig, and reports of a child hospitalized with flu-like symptoms with prior exposure.

This report from the CBS-TV affiliate (WJZ) in Baltimore.
Sick Pig and Child Causes Shut Down Of Frederick Co. Fair Pig Exhibit 

September 23, 2017 11:15 PM

BALTIMORE (WJZ) — The swine barn at The Great Frederick Fair was shut down Saturday after state inspectors found at least one pig with a 106-degree fever.

The Frederick News-Post reports that state veterinarian Michael Radebaugh said that a pig at the fair was showing signs of illness, with swine flu as a possible cause.

The Animal Health section of the Maryland Department of Agriculture closed the barn within an hour of symptoms.

A sick child at Frederick Memorial Hospital was also reportedly showing flu-like symptoms and the fair board was alerted.

The child’s parents told doctors that they had been at the fair and around pigs.
(Continue . . . )
We should know more about this incident, and whether it is related to a swine variant virus, in the next few days. While the evidence is still circumstantial, Maryland officials are obviously operating with an abundance of caution. 
With state and county fair season continuing into the fall, it would not be unexpected to see additional, scattered reports of swine variant infection from around the nation.
H2N2v is the most common swine variant virus reported in the United States, but is far from the only swine flu virus of concern. Co-circulating in North America are also H1N1 and H1N2 swine viruses, along with occasional reassortants like H3N1 (see J. Virol: Novel Reassortant Human-like H3N2 & H3N1 Influenza A Viruses In Pigs). 
Globally the picture becomes even more complicated, with reports of other swine flu variants coming from Europe, South America, and Asia. As surveillance and testing is spotty at best, the constellation of of swine flu viruses in circulation is likely much larger and more complex than we know.
A few recent blogs on other swine flu threats include:
Virology: Detection & Characterization Of Avian H4N6 In Midwestern Swine (2015)
J. Virology: A Single Amino Acid Change Alters Transmissability Of EAH1N1 In Guinea Pigs

I&ORV: Triple-Reassortant Novel H3 Virus of Human/Swine Origin Established In Danish Pigs
Emerg. Microbes & Inf.: Pathogenicity & Transmission Of A Swine Influenza A(H6N6) Virus - China

Sci Rpts:Reassorted H9N2:pH1N1 Virus Transmission After Serial Passage In Swine

Saturday, September 23, 2017

#NatlPrep: Disaster Preparedness For Kids

Note: This is day 23 of National Preparedness Month . Follow this year’s campaign on Twitter by searching for the #NatlPrep hash tag.
This month, as part of NPM17, I’ll be rerunning some edited and updated older preparedness essays, along with some new ones. 

Despite a widespread, albeit naive belief that the United States is relatively immune to large scale disasters, over the past 30 days we've seen three major hurricanes (Texas, Florida & Puerto Rico) which have impacted millions of American lives. 
Millions have been forced to evacuate from their homes, and hundreds of thousands have returned to homes only to find them badly damaged, and made uninhabitable by wind and rising waters.  
Beyond the trauma of evacuating, staying in shelters, and living without power for days or weeks, many families have lost nearly everything, often finding themselves either uninsured or under insured. The economic and emotional pain of these three hurricanes will be with these communities for years to come.
As traumatic as all of this has been for adults (see Post Disaster Stress & Suicide Rates) imagine how difficult all of this has been for kids. 
As parents, we all want to spare our children this sort of experience, but in truth, natural disasters are beyond our control and the best we can hope for is to prepare our kids to deal with them.

Growing up on the west coast of Florida during the tropically active 1960s, I got used to the `drill' of preparing for hurricanes at a very early age.  The first storm I really remember was Hurricane Donna in 1960 - which put a large tree limb across our roof as it crossed the state and ran up the East Coast.

During my `formative years’  a lot of named storms crossed my path (I spent most of that time living in the green circle around Tampa Bay), and like most kids in Florida, I kept a hurricane tracking map on my bedroom wall to monitor their progress.


I knew their strength, forward speed, and direction of movement, and dutifully updated the map every 6 hours. Call it therapeutic. But I took comfort in knowing where these storms were, where they were likely headed, and knowing when they posed a potential threat - and more importantly – when they didn’t. 
I was involved, and so I felt in control.
When you add in cold war jitters, the 1962 Cuban Missile Crisis, constant school duck & cover drills and evacuations, CONELRAD alerts on TV, and films like Survival Under Atomic Attack and `Bert the turtle’ PSAs in elementary school, you’d think you’d have a recipe for night terrors and phobias.

But surprisingly, most of us just took it in stride. In large part, I believe, because we were encouraged at a very young age to participate in disaster preparedness. The lesson was that threats were something you prepared for, not worried about.
Fortunately, disaster preparedness – particularly for kids - has come a long way from the grim messaging of the cold war.
Today, our concerns are focused more on natural disasters, like floods, hurricanes, and earthquakes.  Scenarios that are far more survivable than an all-out nuclear attack, and that can be approached in a more `kid-friendly’ fashion. 
Still, the core message – that disasters happen, and we should all be prepared – hasn’t changed.’s kid friendly preparedness page contains games and activities for kids along with information for parents and educators on how to teach simple, but effective preparedness lessons.

Many states have their own preparedness site for kids, such as Florida Division of Emergency Management’s Kids Get A Plan page, which provides an excellent interactive introduction to preparedness for children.
Most of these programs are designed for younger kids, so I was pleased last year to find an online disaster preparedness game more suitable for older kids; the ISDR: The `Stop Disasters’ Simulation Game.  The game has five scenarios, with three levels of difficulty in each, to choose from.  Earthquake, tsunami, hurricane, wildfire or flood.
For more ideas on teaching kids to be disaster and earthquake resilient SHAKEOUT.ORG has a long list of educational resources divided up by suitable school grade brackets (K-6, 7-12).
Although most parents want to protect their kids from undo worry - when a disaster threatens, it threatens all of us – regardless of our age. 

Helping kids to understand more about emergency preparedness and community resilience will help them cope (and perhaps, even help) in the event they, or their community, are caught up in a disaster.

Friday, September 22, 2017

Virology: Five Distinct Reassortants of HPAI H5N6 In Japan - Winter 2016–2017


While it seems longer, it was just over ten months ago that HPAI H5N6 broke out from its original range of China/Laos/Vietnam and turned up - first in South Korea - followed days later in Japan (see Japan: H5N6 Virus Detected At Izumi, Kagoshima).
South Korea was hardest hit, but within three weeks Japan had reported 53 separate detections (of one or more) HPAI positive wild birds across 11 Prefectures, along with several poultry outbreaks.  Numbers that would steadily grow over the winter.
Like its more famous cousin H5N8, the evidence suggested that HPAI H5N6 was expanding its geographic horizons via enhanced carriage by wild and migratory birds (see map above).  While H5N1 spread around the globe in a similar fashion, both clade H5N8 and H5N6 have moved farther and faster than any HPAI virus previously seen.  
As these viruses have conquered new territories, they've encountered a variety of other Avian Influenza (AI) viruses along the way, and being both promiscuous and out on a spree, have generated a large number of reassortants. 
Influenza A viruses are broadly categorized by two proteins they carry on their surface; their HA (hemagglutinin) and NA (neuraminidase), producing subtypes like H5N1, H7N9, or H5N6.  There are currently 18 known HA subtypes and 11 known NA subtypes.

So, when we talk about a subtype, we're aren't necessarily just talking about a single viral threat, but often an expanding array of related viruses sharing the same (or similar) HA and NA genes.

Within each HA subtype there can be genetic groupings called clades, and often within each clade - subclades. Within each of these, many minor variants may exist. Add in the ability to mix-and-match internal genes, and you can come up with literally dozens of genotypes for each subtype.
Each can have different properties (virulence, transmissibility, host range, etc.), and each is on its own evolutionary path. 
Last December, in Cell Host Microbe: Genesis, Evolution and Prevalence of HPAI H5N6 In China, we saw a report that found that H5N6 had become the dominant HPAI H5 virus in Chinese ducks (replacing H5N1), with 34 distinct H5N6 genotypes, including 4 that have infected people.

When H5N6 invaded South Korea last winter, reports suggested continual evolution of the virus (see Korea H5N6: New Genetic Analysis & Investigating Its Rapid Spread), with researchers reporting no fewer than 5 new genotypes during the first month.

We've a new report this week in the journal Virology that finds similar rapid evolution took place with the H5N6 virus during its foray into Japan last winter.  The full report is available via PDF, and is well worth reading in its entirety.

Five distinct reassortants of H5N6 highly pathogenic avian influenza A viruses affected Japan during the winter of 2016–2017
Under a Creative Commons license
open access
Download PDF


•    H5N6 HPAIVs affected poultry and wild birds in Japan during the winter of 2016–2017.
•    HA genes of the Japanese H5N6 strains belonged to the clade
•    Existence of 3 distinct AIV-derived PA genes in the Japanese H5N6 HPAIVs was evident.
•    NS genes of the Japanese H5N6 HPAIVs originated from 2 distinct Chinese H5N6 HPAIVs.
•    Five distinct genotypes among the Japanese H5N6 HPAIVs were found.


To elucidate the evolutionary pathway, we sequenced the entire genomes of 89 H5N6 highly pathogenic avian influenza viruses (HPAIVs) isolated in Japan during winter 2016–2017 and 117 AIV/HPAIVs isolated in Japan and Russia. 

Phylogenetic analysis showed that at least 5 distinct genotypes of H5N6 HPAIVs affected poultry and wild birds during that period. 

Japanese H5N6 isolates shared a common genetic ancestor in 6 of 8 genomic segments, and the PA and NS genes demonstrated 4 and 2 genetic origins, respectively. Six gene segments originated from a putative ancestral clade H5N6 virus that was a possible genetic reassortant among Chinese clade H5N6 HPAIVs. In addition, 2 NS clusters and a PA cluster in Japanese H5N6 HPAIVs originated from Chinese HPAIVs, whereas 3 distinct AIV-derived PA clusters were evident.

These results suggest that migratory birds were important in the spread and genetic diversification of clade H5 HPAIVs.

 (Continue . . .  )

The H5N6 virus has caused at least 17 human infections in China, with a high fatality rate, but thus far we've seen no reports of human infection out of South Korea, Japan (or later Taiwan and the Philippines).  The following passage from the study's discussion addresses this:
From May 2014 through December 2016, 17 human cases of clade H5N6 HPAIV infection were reported in China (Jiang et al., 2017). Our analysis indicated that amino acid substitutions responsible for adaptation to mammalian hosts (Bussey et al., 2010; Hatta et al., 2001; Min et al., 2013; Steel et al., 2009; Yamada et al., 2010) were missing from the Japanese H5N6 isolates.
The T160A mutation in the HA protein is linked to the acquisition of binding specificity for α2,6- linked sialic acid receptors, which are predominant in the human upper respiratory tract (Gu et al., 2017; Wang et al., 2010); however, some clade H5Nx HPAIVs that carry the T160A mutation show limited binding specificity for α2,6-linked receptors (Guo et al., 2017; Kaplan et al., 2016). Additional studies are needed to definitively understand the effect of T160A on the receptor specificity of clade H5N6 HPAIVs.
In addition, to our knowledge, no human cases resulting from a G1.1.9 H5N6 HPAIV that is a potential progenitor of Japanese H5N6 HPAIVs have been reported. Thus, the zoonotic potential of Japanese H5N6 HPAIVs is considered to be low.

As we've discussed before, even small changes in a virus can either enhance, or reduce, its virulence, transmissibility, or host range  (see Differences In Virulence Between Closely Related H5N1 Strains).  
While it has been a stroke of good fortune that recent strains of H5N6 have - at least temporarily -  evolved away from mammalian adaptation, there are no guarantees how long that trend will continue.
The take away from all of this is that H5N6, like its H5N8 cousin, are rapidly spreading, multifaceted, and continually evolving avian flu threats. What we can say about their behavior and threat to public health today may not hold true tomorrow.

For more on the rapid evolution of clade  H5 viruses, you may wish to revisit:

J. Virulence : Altered Virulence Of (HPAI) H5N8 Reassortant Viruses In Mammalian Models
J Vet Sci: Evolution, Global Spread, And Pathogenicity Of HPAI H5Nx Clade
Study: Virulence Of HPAI H5N8 Enhanced By 2 Amino Acid Substitutions

J. Virology: Molecular Evolution and Emergence of Avian H5N6