Friday, December 19, 2014

USDA/APHIS: H5N8 Detected In Oregon Backyard Flock



# 9465


While not making huge headlines, one of the big stories of the week has been the encroachment of HPAI H5N8 (and HPAI H5N2) into the Pacific Northwest, likely carried in via migratory birds.


Just above the border in British Columbia, North America’s first outbreak of HPAI H5 (see CFIA: 11th Poultry Operation Identified With H5N2) - which began nearly 3 weeks ago - continues to plague poultry operations.


Today it was announced (h/t Sharon Sanders on FluTrackers) that Oregon is now the second state this week to detect the arrival of these highly pathogenic avian flu viruses (see Tuesday’s OIE/APHIS of HPAI H5N8 & H5N2 Detected In Washington State Wild Birds).   


At this point no U.S. commercial poultry operations have been affected, and the risk to human health from these viruses is considered low.  First stop, the Animal and Plant Health Inspection Service (APHIS) release on this latest detection:


H5N8 Found in Backyard Poultry in Oregon; Virus not found in commercial poultry in U.S. - No public health concern at this time

 Dec. 18, 2014— The United States Department of Agriculture’s (USDA) Animal and Plant Health Inspection Service (APHIS) confirmed the presence of highly pathogenic (HPAI) H5N8 avian influenza in guinea fowl and chickens from a small backyard poultry flock in Winston, Oregon. The flock of approximately 100 birds has access to the outdoors. A pond and a marsh on the premises are frequented by migratory birds. The H5N8 virus has NOT been found in commercial poultry anywhere in the United States. There is no immediate public health concern, as the H5N8 virus has been found in birds in other parts of the world and has not caused any human infection to date.

Surveillance for avian influenza is ongoing in commercial poultry operations, live bird markets, and in migratory wild bird populations. Additionally, commercial poultry producers follow strict biosecurity practices and raise their birds in very controlled environments. Birds from the affected backyard flock will not enter the food chain. All poultry, poultry products and wild birds are safe to eat as long as they are properly handled and cooked to a temperature of 165 degrees Fahrenheit. The finding in Oregon was quickly reported and identified due to increased awareness of avian influenza in light of the HPAI H5 findings in wild birds in Washington State earlier this week. This H5N8 virus is the same virus that was found in the Washington State gyrfalcons.

Oregon State officials and USDA are working jointly to respond to this detection, following existing HPAI response plans. The State of Oregon quarantined the affected premises, and APHIS will assist the State in depopulating the remaining birds to prevent the spread of the disease. Additional surveillance of poultry around the infected premises will be conducted as outlined in the response plans. USDA notified the World Organization for Animal Health (OIE) of this detection today as required by the OIE. USDA expects trading partners to respond to this reported detection according to OIE’s science-based standards. USDA is working with trading partners to minimize trade impacts on poultry and poultry products as much as possible.

All bird owners, whether commercial producers or backyard enthusiasts, are encouraged to practice good biosecurity, prevent contact between their birds and wild birds, and to report sick birds or unusual bird deaths to State/Federal officials, either through your state veterinarian or through USDA’s toll-free number at 1-866-536-7593. Additional information on biosecurity for backyard flocks can be found at USDA is coordinating closely with its partners, including Washington and Oregon State officials, the U.S. Department of the Interior and the U.S. Department of Health and Human Services, on avian influenza surveillance, reporting, and control.


Meanwhile, the State of Oregon has released the following statement:


News release: Oregon activates avian influenza response plan

News release, Plants, Animals, Insects

December 19th, 2014


The State of Oregon has activated a multi-agency response plan following the confirmation of highly pathogenic H5 avian influenza in domestic birds in Douglas County. The Oregon Department of Agriculture is the lead state agency responding to the incident, working closely with the Oregon Department of Fish and Wildlife, and Oregon Health Authority. The US Department of Agriculture’s Animal Plant Health Inspection Service (USDA-APHIS) will play a key role in the response as well.

There is no immediate public health concern due to the avian influenza virus detected in Oregon. H5N8 virus has been found in other parts of the world and has not caused any human infection to date. Avian influenza does not affect poultry meat or egg products, which remain safe to eat. As always, both wild and domestic poultry should be properly cooked.

The H5N8 avian influenza virus was confirmed by USDA in guinea fowl and chickens from a small backyard poultry flock in Winston, Oregon. The flock of approximately 100 birds has access to the outdoors. A pond and a marsh on the premises are frequented by migratory birds. The virus has not been found in commercial poultry anywhere in the US. Surveillance for avian influenza is ongoing in commercial poultry operations, live bird markets, and in migratory wild bird populations.

The finding in Oregon was quickly reported and identified due to increased awareness of avian influenza in light of the high path avian influenza findings in wild birds in Washington earlier this week. This H5N8 virus is the same virus that was found in a Washington captive gyrfalcon.

ODA is advising commercial poultry growers and backyard flock owners to be vigilant with biosecurity measures and surveillance.

“Steps are being taken to contain the disease and we have not diagnosed avian influenza elsewhere in Oregon’s domestic poultry population, but the presence of the virus in migratory waterfowl poses a potential risk to our backyard poultry,” says ODA’s State Veterinarian Dr. Brad LeaMaster. “This event underscores the importance of biosecurity for backyard bird owners. We strongly encourage owners to take biosecurity measures to reduce the risk of spreading the disease. That includes preventing contact between their birds and wild birds. We also want them to monitor their flock closely and report sick birds.”

Backyard flock owners can report sick birds to the State Veterinarian’s office at 1-800-347-7028 or can call USDA toll free at 1-866-536-7593.

Oregon’s commercial poultry industry has a robust avian influenza testing program and ODA conducts weekly surveillance testing and health inspections at the state’s only live bird market in Woodburn. In addition, wild bird mortality surveillance is routinely conducted by the Oregon Department of Fish and Wildlife. Wild bird deaths can be reported to the ODFW toll-free line at 1-866-968-260

Introducing The Bifurcated Needle Blog

 From: CDC Image Library

From: CDC Image Library


# 9464


My thanks to Matt Watson (@BioAndBaseball) senior analyst and Communications Specialist at UPMC Center for Health Security for the head’s up on a new blog called The Bifurcated Needle, self described  as `featuring views and insights from the diverse group of professionals at the UPMC Center for Health Security.

In just the first week there are already 8 posts (listed below) which live up to that description, including an explanation for the rather enigmatic blog name.  


Take-aways from the National Academies’ “Gain of Function” Meeting

December 17, 2014  By Tom Inglesby

The Growth and Future of Healthcare Emergency Preparedness Coalitions

December 17, 2014 By Eric Toner

Aren't we Prepared Yet?

December 15, 2014 By Tom Inglesby

Is virus gain-of-function research a security risk?

December 15, 2014 By Gigi Gronvall


Collateral Benefits of Nuclear Power Plant Preparedness

December 10, 2014 By Tara Kirk Sell

Smallpox’s State of Affairs

December 10, 2014 By Amesh Adalja

Cleaning Up is Hard to Do

December 10, 2014 By Crystal Boddie

Origin Story 

December 10, 2014 By Tom Inglesby & Anita Cicero


I’ve added a link in my sidebar, and based on the topics and authors represented during this first week, fully expect to add this blog to my short list of `must-visits’ every day.


Welcome to the blogosphere one and all.  


Now . . . .  I’ve got a lot of reading to catch up on.

FluView Week 50


# 9463


Earlier this week, in It’s Beginning To Look A Lot Like . . . Flu Season, I wrote about the recent media reports on school absences (and some closures) due to influenza.  You’ll also find some advice in that blog on the home treatment of flu, and when to seek medical care, from the CDC.


Although the CDC numbers, and maps, lag about a week behind current conditions - they clearly show that this year’s flu season is well underway across much of the middle of the nation.  


With an overwhelmingly H3N2 dominant flu season so far – and a `mismatched’ strain reducing this year’s vaccine’s efficiency – the CDC has warned Early Data Suggests Potentially Severe Flu Season ahead.  While the numbers don’t show us there yet – we are still below the `epidemic threshold’ for P&I Mortality – we are seeing steady week-to-week increases in flu activity.


Some excerpts from this week’s FluView report, then I’ll be back with a footnote.


2014-2015 Influenza Season Week 50 ending December 13, 2014

All data are preliminary and may change as more reports are received.


During week 50 (December 7-13, 2014), influenza activity continued to increase in the United States.

  • Viral Surveillance:Of 20,064 specimens tested and reported by U.S. World Health Organization (WHO) and National Respiratory and Enteric Virus Surveillance System (NREVSS) collaborating laboratories during week 50, 5,200 (25.9%) were positive for influenza.
  • Pneumonia and Influenza Mortality: The proportion of deaths attributed to pneumonia and influenza (P&I) was below the epidemic threshold.
  • Influenza-associated Pediatric Deaths:Four influenza-associated pediatric deaths were reported.
  • Influenza-associated Hospitalizations: A cumulative rate for the season of 6.2 laboratory-confirmed influenza-associated hospitalizations per 100,000 population was reported.
  • Outpatient Illness Surveillance: The proportion of outpatient visits for influenza-like illness (ILI) was 3.7%, above the national baseline of 2.0%. Nine of 10 regions reported ILI at or above region-specific baseline levels. Puerto Rico and 13 states experienced high ILI activity; six states experienced moderate ILI activity; New York City and five states experienced low ILI activity; 26 states experienced minimal ILI activity; and the District of Columbia had insufficient data.
  • Geographic Spread of Influenza: The geographic spread of influenza in Guam and 29 states was reported as widespread; Puerto Rico and 14 states reported regional activity; the District of Columbia, the U.S. Virgin Islands and five states reported local activity; and two states reported sporadic activity.


Influenza Virus Characterization*:

CDC has characterized 248 influenza viruses [10 A (H1N1)pdm09, 209 A (H3N2), and 29 influenza B viruses] collected by U.S. laboratories since October 1, 2014.

Influenza A Virus [219]

  • A (H1N1)pdm09 [10]: All 10 H1N1 viruses tested were characterized as A/California/7/2009-like, the influenza A (H1N1) component of the 2014-2015 Northern Hemisphere influenza vaccine.
  • A (H3N2) [209]: Sixty-four (30.6%) of the 209 H3N2 viruses tested have been characterized as A/Texas/50/2012-like, the influenza A (H3N2) component of the 2014-2015 Northern Hemisphere influenza vaccine. One hundred forty-five (69.4%) of the 209 viruses tested showed either reduced titers with antiserum produced against A/Texas/50/2012 or belonged to a genetic group that typically shows reduced titers to A/Texas/50/2012. Among viruses that showed reduced titers with antiserum raised against A/Texas/50/2012, most were antigenically similar to A/Switzerland/9715293/2013, the H3N2 virus selected for the 2015 Southern Hemisphere influenza vaccine. A/Switzerland/9715293/2013 is related to, but antigenically and genetically distinguishable, from the A/Texas/50/2012 vaccine virus. A/Switzerland-like H3N2 viruses were first detected in the United States in small numbers in March of 2014 and began to increase through the spring and summer.


Influenza-Associated Pediatric Mortality:

Four influenza-associated pediatric deaths were reported to CDC during week 50. Two deaths were associated with an influenza A (H3) virus and occurred during week 49 (week ending December 6, 2014). One death was associated with an influenza A virus for which no subtyping was performed and occurred during week 50 (week ending December 13, 2014), and one death was associated with an influenza B virus and occurred during week 49.

A total of 11 influenza-associated deaths have been reported during the 2014-2015 season from six states (Florida [2], Minnesota [2], North Carolina [2], Nevada [1], Ohio [2], and Texas [2]).
Additional data can be found at:

Click on image to launch interactive tool

(Continue . . .)

If you are looking for good news, none of the viruses this season have tested as being resistant to our two main antiviral drugs – Oseltamivir and Zanamivir. 


This time last year, we were seeing nearly 2% of viruses showing signs of resistance.

While expected, and on a less positive note, the percentage of `drifted’ H3N2 viruses continues to climb, with apparently none of the (admittedly small number) of H3N2 viruses tested last week (n=12) matching the vaccine strain.  In the week 49 FluView, of 84 viruses sequenced, less than 20% were a match.


As we often see Influenza B become more dominant towards the end of the flu season, this year’s flu shot may still offer you some welcome protection next spring, and the CDC suggests it might still provide some protection against this drifted strain. 


For now, whether you got the shot or not, with holiday gatherings upon us our focus should be on practicing good flu hygiene.  The CDC suggests:

  • Try to avoid close contact with sick people.
  • If you are sick with flu-like illness, CDC recommends that you stay home for at least 24 hours after your fever is gone except to get medical care or for other necessities. (Your fever should be gone without the use of a fever-reducing medicine.)
  • While sick, limit contact with others as much as possible to keep from infecting them.
  • Cover your nose and mouth with a tissue when you cough or sneeze. Throw the tissue in the trash after you use it.
  • Wash your hands often with soap and water. If soap and water are not available, use an alcohol-based hand rub.
  • Avoid touching your eyes, nose and mouth. Germs spread this way.
  • Clean and disinfect surfaces and objects that may be contaminated with germs like the flu.

Saudi MOH Reports 1 MERS Case In Al-Kharj


# 9462


In November we saw 5 cases of MERS reported from Al-Kharj, but have not heard anything in several weeks. Today we’ve another case from that region, of a 53 year old male with reported animal exposure.


CFIA: 11th Poultry Operation Identified With H5N2


Credit CFIA


# 9461


Overnight a new farm was added to the CFIA’s  Infected Premises List,  a second chicken farm in the Langley, B.C. area very near Vancouver.



Meanwhile, just south of the Canadian border - in Washington State – at least two wild birds have tested positive for HPAI H5 avian viruses (see OIE/APHIS: HPAI H5N8 & H5N2 Detected In Washington State Wild Birds), although no poultry farm infections have been reported.


The state department of Agriculture is advising poultry raisers to stay alert.



Study: H5 Clade Receptor Binding


# 9460



Unlike in mammals, where influenza viruses generally produce a respiratory infection, influenza in birds is a gastrointestinal malady. The virus attaches to - and replicates in – the avian gut,  and is spread primarily through infected droppings.


As you might imagine, avian flu viruses are well adapted to attack the kind of cells found within the avian intestinal tract; α2,3-linked sialic acid  avian receptor cells.


Humans, and many (but not all) mammals have very few α2,3 receptor cells in their upper airway (but do have some deep in the lungs), making it difficult for avian flu viruses to easily attach to, and infect, non-avian species


When they do jump to humans, it usually results in a serious deep lung infection (pneumonia).

Human, or mammalian adapted flu viruses bind preferentially to a different type of cell - α2,6 receptor cells -  which are abundant in their upper respiratory systems. They are also adapted to replicate in the 5 to 10 degree cooler environment of the upper airway, compared to the intestinal tract of birds.

For an avian influenza virus to successfully jump species and to become a human pandemic threat, these receptor binding and temperature tolerance issues are believed to be two of the biggest hurdles.  There are likely others, but these two appear to top the list.


As avian viruses jump (even tentatively) to other species, it gives them a chance to produce host adaptations;  mutations that favor survival in their new environment. The more jumps, the more opportunities the virus has (through trial and error)  to `figure out’  what evolutionary changes are needed to make the new species a suitable host.


Viruses also change slowly through antigenic drift, even in their native hosts, and can abruptly change through antigenic shift – or reassortment.  Shift occurs when two flu viruses inhabit the same host at the same time, swap genetic material, and produce a `hybrid’ strain.  


Birds, swine, humans . . .  in fact almost any flu susceptible species – can act as a mixing vessel.  While pandemic viruses are rare, as any virologist will tell you . . . Shift happens.


While we are justifiably concerned over the recently emerged H7N9 virus given its track record over the past couple of years, the avian flu virus with the longest resume and greatest diversity is H5N1 and its recently emerged cousins; H5N8, H5N6, H5N3.  This virus has been around for 18 years, and has gone from a single clade discovered in 1996 to a diverse, and growing constellation of clades, sub-clades, and variants within sub-clades.


The following chart from the World Health Organization hints at just how much diversity the virus acquired over its first 15 years..


(click to load larger image)  (Note: Chart only goes through 2011)


Until a year or so ago, most H5N1 clades were classified by 3 digit identifiers, such a clade 2.3.4.

But in 2013, researchers reported on Novel Variants of Clade 2.3.4 Highly Pathogenic Avian Influenza A(H5N1) Viruses, China, and suggested that `these groups should be assigned new fourth-order clades of,, and to reflect the wide divergence of clade 2.3.4 viruses.’


In short order, we saw the emergence of several new H5 subtypes (through reassortment), all carrying the newly identified H5 clade HA gene segment, including the recent high flying H5N8 and H5N6 subtypes. The graphic below (produced before H5N8 showed up in Europe and North America) illustrates their recent geographic spread in Asia comes from the November FAO-EMPRES Report On The Emergence And Threat Of H5N6).



While there are a lot of H5 clades out there, and more will invariably appear, right now clade is making a lot of noise.   So the open access study, published this week in the Journal Veterinary Research, that looks at the receptor binding qualities of this new clade is of particular interest.


While many will want to read the entire report, I’ve excepted some highlights below.


In short, they determined that this new clade binds to both avian α2,3  and mammalian α2,6 receptor cells, and that at least one (of 4 tested) strains replicated well, and transmitted efficiently, in test guinea pigs.


Novel H5 clade viruses with both α-2,3 and α-2,6 receptor binding properties may pose a pandemic threat

Qunhui Li1, Xuan Wang1, Min Gu12, Jie Zhu1, Xiaoli Hao1, Zhao Gao1, Zhongtao Sun1, Jiao Hu12, Shunlin Hu12, Xiaoquan Wang12, Xiaowen Liu12 and Xiufan Liu12*


The emerging H5 clade viruses of different NA subtypes have been detected in different domestic poultry in China. We evaluated the receptor binding property and transmissibility of four novel H5 clade subtype highly pathogenic avian influenza viruses. The results show that these viruses bound to both avian-type (α-2,3) and human-type (α-2,6) receptors. Furthermore, we found that one of these viruses, GS/EC/1112/11, not only replicated but also transmitted efficiently in guinea pigs. Therefore, such novel H5 subtype viruses have the potential of a pandemic threat.



Historically, changes in the receptor binding protein of influenza virus, HA, have been implicated in the initiation of a pandemic. It has been established for the H1N1 (1918), H2N2 (1957) and H3N2 (1968) pandemic viruses that a change in HA protein from a preference for α-2,3-linked sialic acids (avian receptor) to a preference for α-2,6-linked sialic acids (human receptor) is a prerequisite for efficient transmission of avian viruses to humans [10].

H5 HPAIV pose a serious pandemic threat due to their virulence and high mortality in humans, and their increasingly expanding host reservoir and significant ongoing evolution could enhance their human-to-human transmissibility. Recently, novel clade H5 HPAIV with various NA subtypes (H5N1, H5N2, H5N6, and H5N8) were reported in Eastern China and South Korea [2]-[7],[9],[15].

Here, we evaluated their receptor specificity and transmission in guinea pigs. The results show that the viruses bound to both avian-type (α-2,3) and human-type (α-2,6) receptors. In humans, the α-2,6 receptor is expressed mainly in the upper airway, while the α-2,3 receptor is expressed in alveoli and the terminal bronchiole [16].

A virus with good affinity to both α-2,3 and α-2,6 receptors may especially be harmful, as it could infect efficiently via its binding to α-2,6 receptors in the upper airway and simultaneously cause severe infection in the lung via its binding to α-2,3 receptors. And this hypothesis is supported by the fact that one of the two well-characterized HA genes from the H1N1 1918 pandemic virus binds efficiently to both α-2,3 and α-2,6 receptors [17]. In addition, previous studies showed that the human-infecting novel H7N9 and the latest reassortant H10N8 avian influenza viruses yet have substantial affinity to both avian-type (α-2,3) and human-type (α-2,6) receptors [18],[19].

Sequence analysis showed that novel H5 (HPAIV) clade simultaneously carry a T160A mutation which results in the lack of an oligosaccharide side chain at 158–160 of HA, and it is critical for the H5 subtype influenza viruses tested to bind to human-like receptors and to transmit among a mammalian host [20],[21]. Whether this T160A variation affects the receptor-binding property deserves further investigation.

Previous studies showed that some H5 subtype influenza viruses can transmit efficiently in guinea pigs [21]. In this study, we also found that one of these viruses, GS/EC/1112/11, not only replicated but also transmitted efficiently in guinea pigs. These findings emphasize that continued circulation of these viruses may pose health threats for humans. Therefore, we need to intensify our effort to detect such viruses as early as possible.

(Continue . . .. )



Although there are likely other inhibiting factors stopping this H5 clade strain (and others) from sparking a pandemic, this dual binding ability would appear to move this particular clade a little closer towards it becoming a potential global health threat.  


That said, it should be noted that in 2013 we saw a similar finding with the H7N9 virus (see NEJM Journal Watch: Characteristics of H7N9), but that virus still has not displayed the ability to spread efficiently from human-to-human.

Despite our continual gains in knowledge regarding influenza viruses, we obviously don’t know all of the factors involved in turning an avian influenza virus into a `humanized’ one.  But studies like this one may help us recognize an impending threat, and give us enough warning time to prepare our defenses (i.e. vaccines, antivirals, etc.).

For more on the evolution of H5 and H7 viruses, you might wish to revisit:


Nature Comms: Host Adaptation Of Avian Influenza Viruses
EID Journal: Potential Human Adaptation Mutation of Influenza A(H5N1) Virus, Canada
PLoS: Human-Type H5N1 Receptor Binding In Egypt