USGS: Genetic Analysis Of North American Reassortant H5N1 Virus From Washington State

How viruses shuffle their genes (reassort)

# 9896

 

Last fall, when the recently emerged Asian H5N8 avian flu virus arrived in North America (presumably via migratory birds), it encountered a wide range of North American avian influenza viruses that circulate in native species.  As avian viruses are sometimes wont to do - they simultaneously inhabited a number of hosts - and through reassortment produced at least a couple of hybrid viruses.

 

The reassortment that has done the best so far has been HPAI H5N2, which has now spread to at least 13 states, and has been plaguing commercial turkey operations across the Midwest (see APHIS: H5N2 Confirmed In South Dakota, 4th Farm Hit In Minnesota).

 

In January, in OIE: New Reassortant HPAI H5N1 In North America, we learned that an HPAI H5N1 subtype had also been generated, which was discovered in an an American green-winged teal in Whatcom County, Washington.   Three weeks later a similar virus was detected in a backyard flock in British Columbia (see  OIE Notification On Canadian H5N1 Detection).

 

While sharing the same subtype identifier (H5N1) with  the infamous – and often deadly – Eurasian H5N1 virus, this was a new reassortant that carried some – but not all – of the Eurasian avian H5N1 genes, mixed with genetic contributions from North American (AM) avian viruses. 

 

In other words, a new version of H5N1.

 

The good news is, that unlike its Eurasian cousin, we’ve seen no evidence that this version of H5N1 is pathogenic to humans.  Human exposure has likely been limited and the virus continues to evolve, so the CDC has cautiously advised:

 

The appearance of newly detected avian influenza A H5 viruses in North America may increase the likelihood of human infection with these viruses in the United States. Because these newly identified avian influenza A H5 viruses are related to avian influenza A viruses associated with severe disease in humans (e.g., highly pathogenic Asian-lineage avian influenza A (H5N1) virus), they should be regarded as having the potential to cause severe disease in humans until shown otherwise

 

Yesterday the journal Genome Announcements published a genetic analysis of this first North American H5N1 reassortant, produced by the USDA and the USGS.   First a link, and some excerpts from the study, followed by a USGS press release, after which I’ll return with a little more:

 

Novel H5 Clade 2.3.4.4 Reassortant (H5N1) Virus from a Green-Winged Teal in Washington, USA

Mia Kim Torchetti^a, Mary Lea Killian^a, Robert J. Dusek^b, Janice C. Pedersen^a, Nichole Hines^a, Barbara Bodenstein^b, C. LeAnn White^b, Hon S. Ip^b

ABSTRACT

Eurasian (EA)-origin H5N8 clade 2.3.4.4 avian influenza viruses were first detected in North America during December 2014. Subsequent reassortment with North American (AM) low-pathogenic wild-bird-origin avian influenza has generated at least two reassortants, including an EA/AM H5N1 from an apparently healthy wild green-winged teal, suggesting continued ongoing reassortment.

GENOME ANNOUNCEMENT

(EXCERPT)

This novel EA/AM H5N1 reassortant virus contains 4 EA H5N8 and 4 AM-origin RNA segments. The Eurasian polymerase basic 2 (PB2), hemagglutinin (HA), nucleoprotein (NP), and matrix (MA) genes have the closest similarities (99%) to those of the A/gyrfalcon/Washington/41088-6/2014 (H5N8) and A/crane/Kagoshima/KU1/2014 (H5N8) viruses from Japan. The hemagglutinin protein has a multibasic protease cleavage site sequence of PLRERRRKR/GLF that is characteristic of the HPAIV H5 clade 2.3.4 (5). The 4 AM low-pathogenic wild-bird-lineage segments have 99% similarities to the AM AIV segments of wild-bird origin, as follows: PB1, A/bufflehead/California/3118/2011 (H4N8); polymerase acidic (PA), A/American green-winged teal/Wisconsin/11OS3425/2011 (H12N5); neuraminidase (NA), A/blue-winged teal/Texas/AI12-909/2012 (H7N1); and nonstructural (NS), A/northern shoveler/California/HKWF392sm/2007 (H10N7).

Earlier in 2014, the EA-H5N8 HPAIV circulating in South Korea was found to have diverged into two groups (A and B) (6). The group A viruses have now been detected across multiple countries, with evidence of regional diversification (intercontinental group A, subgroups 1 to 3 [icA1-3; D. Lee, M. Torchetti, K. Winkler, H. Ip, C. Song, D. Swayne, unpublished data]). Two icA2 reassortant viruses (EA/AM H5N2 and EA/AM H5N1) have now been detected in Washington; however, no reassortants have been detected to date in any of the other icA subgroups.

The introduction of the icA2-H5 clade 2.3.4.4 virus initially into the Pacific Flyway in 2014 with subsequent detection of at least two reassortants with North American low-pathogenic AIV by early 2015 suggests the potential for further reassortment events as the icA2-H5 viruses continue to circulate among wild birds. Further work to monitor for such reassortments and an evaluation of these viruses are warranted. During the preparation of this paper, a nearly identical H5N1 virus was found in a backyard flock in Chilliwack, BC, Canada.

Nucleotide sequence accession numbers.The genome sequence of A/American green-winged teal/Washington/195750/2014 (H5N1) virus is deposited in GenBank under accession numbers KP739418 to KP739425.

 

 

Circulation of Highly Pathogenic Avian Flu in North American Birds

Viral Changes Make Current Situation More Complex
Released: 4/2/2015 11:45:00 AM

Highly pathogenic avian influenza (HPAI) H5 viruses of Eurasian origin continue to circulate and evolve in North American wild birds.

The U.S. Geological Survey and U.S. Department of Agriculture published the genetic analysis of a mixed-origin HPAI H5N1 avian flu virus in the journal Genome Announcements today. This novel virus was discovered in a green-winged teal in Washington State that was sampled at the end of 2014. It is a mixed-origin virus containing genes from the Eurasian HPAI H5N8 and genes from North American low pathogenic avian influenza from wild birds. This H5N1 virus is different from the well-known Asian H5N1 HPAI virus that emerged in 1996.

This new publication follows a recent article describing the introduction of Eurasian HPAI H5N8 into North America at the end of 2014 and the detection of a different mixed-origin virus (HPAI H5N2) in wild birds. In March 2015, the HPAI H5N2 virus was detected in commercial turkey flocks in Minnesota, Missouri and Arkansas, in a backyard flock of mixed poultry in Kansas and in a wild bird in Wyoming.

“Such findings are not unexpected and might continue as the Eurasian lineage H5 circulates in the United States,” said co-author Mia Kim Torchetti, a USDA Animal and Plant Inspection Service scientist.

<SNIP>

Each mixed-origin virus might carry different risks and surveillance of circulating HPAI viruses is ongoing. The USGS and USDA scientists continue to monitor Eurasian H5 lineage viruses and provide stakeholders with timely information for management purposes.

 

The most recent Wild Bird Findings confirmed by USDA’s National Veterinary Services Laboratories (dated 3/27/2015) list 50 detections of HPAI H5 viruses across a dozen western states, and this tally continues to grow. 

 

It is likely that these viruses are already present in more states than surveillance has revealed, and that their geographic range will continue to expand. AS that happens they are likely to encounter additional native avian flu subtypes, and new opportunities for reassortment may occur. 

 

For now, all of this is primarily a concern for the nation’s poultry farmers - but novel influenza viruses are spectacularly unpredictable - and so we watch these developments with considerable interest.

EID Journal: Novel Eurasian HPAI A H5 Viruses in Wild Birds – Washington, USA

Major Global Migratory Flyways – Credit FAO

 

# 9727

 

Just over 13 months ago, the HPAI H5N8 virus appeared at poultry farms  – and in wild and migratory birds – in South Korea, and over the next couple of months managed to spread to more than 3 dozen farms.   More than a year later, Korean poultry producers are still fighting skirmishes with this emerging virus.

50 day Spread of H5N8 - Map Credit Japan’s MAFF

 

Until November of last year, H5N8 stayed pretty much an `Asian’ problem.  It turned up briefly in Japan, carried by migratory birds last spring (and again in the fall), was reported in North Eastern China - and has more recently produced a massive outbreak in Taiwan - but had not strayed outside of the far northern half of the East Asian Flyway.

 

At least, not until early November when it surprised everyone by showing up at a German poultry farm (see Germany Reports H5N8 Outbreak in Turkeys), which was quickly followed by reports in the Netherlands, the UK, and eventually even Italy. 

 

Remarkably, H5N8 had travelled farther in a matter of a few months than the H5N1 virus had managed to do over several years. A history we looked at three months ago in  H5N8: A Case Of Deja Flu?

 

It was only few weeks later that British Columbia reported an outbreak of HPAI H5N2 (see Fraser Valley B.C. Culling Poultry After Detecting H5 Avian Flu), followed two weeks later by the announcement from OIE/APHIS: HPAI H5N8 & H5N2 Detected In Washington State Wild Birds.

This upstart H5N8 virus had done in ten months what its predecessor – HPAI H5N1 – had not been able to do in over ten years;  it had crossed oceans and made it to the Americas.

And once here, it had managed to successfully reassort with North American (NA) avian influenza viruses, producing new, highly pathogenic subtypes. In short order wild and migratory birds in six western states (Washington, California, Oregon, Idaho, Utah & Nevada) were discovered to be carrying these viruses (see Oregon Quarantines Another Backyard Flock Over HPAI).

 

Although only two commercial poultry producers (in California) have been hit with this virus, several smaller backyard flocks have been affected, and the virus constitutes a new, and potentially serious threat to our domestic poultry producers.

 

The good news is, thus far, we’ve seen no evidence of a serious threat to human health from these viruses, but the CDC remains cautious (see CDC Interim Guidance For Testing For Novel Flu).

 

All of which serves as prelude to a dispatch in the CDC’s EID Journal, that looks at the arrival, reassortment, and potential impact of these HPAI H5 viruses in the Pacific Northwest.

 

Volume 21, Number 5—May 2015

Dispatch

Novel Eurasian Highly Pathogenic Influenza A H5 Viruses in Wild Birds, Washington, USA, 2014

Hon S. Ip¹, Mia Kim Torchetti¹ , Rocio Crespo, Paul Kohrs, Paul DeBruyn, Kristin G. Mansfield, Timothy Baszler, Lyndon Badcoe, Barbara Bodenstein, Valerie Shearn-Bochsler, Mary Lea Killian, Janice C. Pedersen, Nichole Hines, Thomas Gidlewski, Thomas DeLiberto, and Jonathan M. Sleeman

Abstract

Novel Eurasian lineage avian influenza A(H5N8) virus has spread rapidly and globally since January 2014. In December 2014, H5N8 and reassortant H5N2 viruses were detected in wild birds in Washington, USA, and subsequently in backyard birds. When they infect commercial poultry, these highly pathogenic viruses pose substantial trade issues.

The novel Eurasian lineage clade 2.3.4.4 highly pathogenic avian influenza (HPAI) A(H5N8) virus (http://www.who.int/influenza/gisrs_laboratory/h5_nomenclature_clade2344/en/) spread rapidly and globally during 2014, substantially affecting poultry populations. The first outbreaks were reported during January 2014 in chickens and domestic ducks in South Korea and subsequently in China and Japan (1–4), reaching Germany, the Netherlands, and the United Kingdom by November 2014 and Italy in early December 2014 (5). Also in November 2014, a novel HPAI H5N2 virus was reported in outbreaks on chicken and turkey farms in Fraser Valley, British Columbia, Canada (5). This H5N2 influenza virus is a reassortant that contains the Eurasian clade 2.3.4.4 H5 plus 4 other Eurasian genes (polymerase acidic protein subunit, matrix protein, polymerase basic protein subunit [PB] 2, nonstructural protein) and 3 North American wild bird lineage genes (neuraminidase [NA], nucleoprotein, PB1) (5). Taiwan has recently reported novel reassortants of the H5 clade 2.3.4.4 with other Eurasian viruses (H5N2, H5N3).

The appearance of highly similar Eurasian H5N8 viruses in Asia, Europe, and now the United States suggests that this novel reassortant may be well adapted to certain waterfowl species, enabling it to survive long migrations (6). These appearances also represent a major change in Eurasian H5 virus circulation. After the reported spread of HPAI H5N1 virus in Asia, a large, interagency avian influenza virus (AIV) surveillance effort was implemented throughout the United States during April 2006–March 2011 (7). Of nearly 500,000 wild bird samples tested, none harbored Eurasian subtype H5 AIV. The overall prevalence of AIV was ≈11%, and most viruses (86%) were detected in dabbling ducks (family Anatidae) (8). Although H5N8 subtype viruses have been detected previously in the United States, all have been low pathogenicity AIV of North American wild bird lineage.

<SNIP>

Phylogenetic analysis of the H5 clade 2.3.4.4 viruses detected in the United States resulted in 3 major findings (Figures 1, 2; Technical Appendix[PDF - 1.71 MB - 7 pages]). First, the Eurasian lineage avian H5N8 clade 2.3.4.4 virus survived introduction into North America in its entirety. Second, introduction of Eurasian H5N8 virus into North America appears to be independent from introductions of the virus into Europe. Third, the duration of circulation of H5N8 virus in the Pacific flyway (California, Idaho, Nevada, Oregon, Utah, and Washington, USA) is unknown, but it was sufficient for reassortment with low pathogenicity North American lineage wild bird AIV (Figure 1).

Conclusions

The ongoing circulation of these Eurasian HPAI H5 viruses in wild birds considerably alters the potential risks and subsequent consequences for US poultry and wildlife rehabilitation centers. Detection of HPAI H5N8 virus in apparently healthy common teal (A. crecca), Eurasian wigeon (A. penelope), mallard, spot-billed duck (A. poecilorhyncha), and tundra swans (C. columbianus) (3,5) suggests that wild birds may contribute to further spread of this HPAI H5 lineage in North America. However, culling and otherwise disturbing wild birds or their habitats has not been shown to be beneficial in the control of avian influenza (10). The scientifically supported management action (10) is to enhance biosecurity to minimize contacts between poultry, wild birds, and their fomites (10). In addition, hunters should be cognizant of risks from handling potentially infected carcasses (http://www.aphis.usda.gov/animal_health/birdbiosecurity/downloads/USDA_HntrCd_Hi.pdf).

Examination of wild bird surveillance samples collected before December 2014 may provide further insight into the timing and route of introduction of the Eurasian clade 2.3.4.4 H5N8 virus into North America. In addition, enhanced and ongoing influenza surveillance in wild birds and poultry will contribute to a better understanding of the geographic distribution and species involved in the spread of these HPAI H5 viruses. Together, these data may enable waterfowl managers and poultry producers to better assess and manage disease risks. Human infections have not been associated with either virus; however, H5 clade 2.3.4 H5N1 virus has caused human death, so caution is warranted. During preparation of this article, H5N8 was reported in wild birds and poultry along the Pacific flyway; novel H5N2 virus was detected in Idaho, Oregon, and Washington; and another novel reassortant H5N1 was detected in Washington and British Columbia (5). These detections have had major effects on US poultry trade (11).

H5N1 Detected In B.C. Backyard Flock

 

 

# 9686

On January 15th of this year we learned of the first detection of a reassorted HPAI EA/AM H5N1 virus in North America, when this emerging subtype was detected in a green-winged teal in Whatcom County, Washington (see OIE: New Reassortant HPAI H5N1 In North America).

 

While carrying the same HA/NA designations as its more infamous Asian cousin -  this subtype is comprised of gene segments from the Eurasian (EA) H5N8 virus, along with genetic contributions from North American (AM) avian viruses. 

In other words, a new version of H5N1.

 

The OIE described it as:

This H5N1 subtype is different from strain circulating in Asia.

The gene constellation is as follows:

• Eurasian lineage genes (PB2, H5, NP, MP >99% identical to A/gyrfalcon/WA/41088/2014 H5N8);
• North American lineage genes (PB1 {98% identical to A/Northern pintail/Washington/40964/2014 H5N2}, PA, N1, NS of North American LPAI wild bird lineage.

The HA cleavage site is compatible with strains that are highly pathogenic. This novel HPAI EA/AM H5N1-reassortant virus has NOT been found in commercial poultry anywhere in the United States.

 

Although this reassortant was discovered in only one bird last month, the implications are that it is probably spreading in other wild and migratory  birds as well, and so it isn’t terribly surprising that it would turn up again in the Pacific Northwest.

 

After a couple of days of rumors and  media reports, yesterday Canada’s CFIA posted the following  notice of the detection of this new virus in a “non-commercial’ flock in Chilliwack, BC.

 

CFIA confirms presence of H5N1 virus in British Columbia and removal of quarantines from three farms

February 7, 2015

The Canadian Food Inspection Agency (CFIA) is continuing its investigation into an outbreak of avian influenza in British Columbia's Fraser Valley. The CFIA has confirmed the presence of a high pathogenic H5N1 avian influenza virus on a non-commercial farm in Chilliwack, BC. The infected premises is under quarantine, depopulation of the affected birds has been completed and disposal measures are underway.

This is the first time the H5N1 strain of the virus has been detected during the current avian influenza outbreak in British Columbia's Fraser Valley. The other affected farms in BC were infected by the H5N2 strain.

The H5N1 strain was found in wild birds in Washington State in January 2015.

(Continue . . .)

 

This notification provides us with very little actual information beyond the requisite assurances that `Avian influenza viruses do not pose risks to food safety when poultry and poultry products are properly handled and cooked.’  

 

We are even left to assume that this H5N1 virus is a match for the Washington state finding (likely so, but not stated implicitly).

While some of their official nonchalance may be forced, it is absolutely true that so far we’ve not seen any evidence that reassorted HPAI H5 viruses descended from the recently emerged Eurasian H5N8 subtype (H5 clade 2.3.4.4) have the ability to infect humans. 

These are, however, early days. 

And as new reassortants appear, and evolve, their behaviors and properties can sometimes change. Something our own CDC took notice of a little over a week ago, when they published interim guidance (see here and here) on testing and managing individuals potentially exposed to novel (H5 or H7) avian flu.  They wrote:

The appearance of newly detected avian influenza A H5 viruses in North America may increase the likelihood of human infection with these viruses in the United States. Because these newly identified avian influenza A H5 viruses are related to avian influenza A viruses associated with severe disease in humans (e.g., highly pathogenic Asian-lineage avian influenza A (H5N1) virus), they should be regarded as having the potential to cause severe disease in humans until shown otherwise

 

Of course, it is perfectly possible that H5N8 derived viruses – like the H5N2 viruses we’ve seen in the past – pose very little threat to human health.  But to assume such based on a very a limited track record would be folly.   The reason that H5 and H7 avian viruses are reportable to the OIE is because of their track record of quickly changing as they passage through birds.

For now, however, the big risk is to poultry operations. 

 

Unlike in Asia and the Middle East, which have endured heavy avian flu losses for more than a decade, North American poultry producers have not had to deal with these highly pathogenic H5 viruses.  If one or more of these subtypes (or future reassortants from them) manages to become endemic in North American birds - and that may already be happening -  the risks to the industry will only escalate.

OIE: New Reassortant HPAI H5N1 In North America

 

# 9608

Yes, you read the title right;  H5N1.  

 

Not the same H5N1 as has been rife in Asia for the past decade, and is currently making trouble in Egypt - but a cousin - a new reassortant H5N1 with genetic components derived from both the Eurasian H5N8 virus (including the H5 HA) and by North American avian viruses. 

 

A more complete description is provided in the OIE report below, after which I’ll be back with more.

 Epidemiology

Source of the outbreak(s) or origin of infection

• Contact with wild species

As part of the increased AI surveillance of wild birds (performed by testing hunter harvested birds), another Eurasian H5 clade 2.3.4.4 virus has been identified through whole genome sequencing of the virus isolate. Introduction of the Eurasian (EA) H5N8 virus into the Pacific Flyway sometime during late 2014 has allowed mixing with North American (AM) lineage viruses and generated new combinations with genes from both EA and AM origin (or “reassortant” viruses) such as the EA/AM H5N2-reassortant detected in Canada and the United States.

Such findings are not unexpected as the EA-H5N8 virus continues to circulate. A novel EA/AM H5N1-reassortant clade 2.3.4.4 was isolated from an American green-winged teal in Whatcom County, Washington.

This H5N1 subtype is different from strain circulating in Asia. The gene constellation is as follows: Eurasian lineage genes (PB2, H5, NP, MP >99% identical to A/gyrfalcon/WA/41088/2014 H5N8); North American lineage genes (PB1 {98% identical to A/Northern pintail/Washington/40964/2014 H5N2}, PA, N1, NS of North American LPAI wild bird lineage. The HA cleavage site is compatible with strains that are highly pathogenic. This novel HPAI EA/AM H5N1-reassortant virus has NOT been found in commercial poultry anywhere in the United States.

 

H5N8 continues to impress in its ability not only to travel rapidly across continents and oceans on the wings of migratory birds, but in the number of viable reassortant viruses it has managed to  spawn along the way.  Last spring, in EID Journal: Describing 3 Distinct H5N8 Reassortants In Korea, we saw early indicators of this virus’s growing diversity, while just last week Taiwan reported two `new’ reassortant viruses (H5N2 & H5N3).

 

Right now we don’t know anything about how this new reassortant virus will behave in poultry (other than being HPAI), or in non-avian species (including humans).  I would posit that there is a good deal of testing & research going on right now to determine that. 

Whether this turns out to be a flash in the avian flu pan, or an early glimpse of a new emerging threat, this report does remind us that influenza viruses are capable of rapid evolution, particularly through reassortment.

 

The number of new avian viruses that have appeared over the past couple of years (H7N9, H5N8, H5N6, H5N5, H5N3, H5N2, H10N8, etc.) illustrate that nature’s laboratory is open 24/7, and one that can easily throw us a nasty curve ball at any time.

Updating The New York H5N? Report

Photo Credit – FAO

 

# 6856

 

Two days ago in (Presumably) LPAI H5N1 Found In New York, I blogged on a report from National Chicken Council’s Washington Report indicating that (presumably Low Pathogenic) H5N1 avian influenza had been detected at a New York live bird market, resulting in a halt of poultry exports to Japan & Taiwan.

 

Since then, a lot of people have been trying to track down details on this story, with very little success.

 

At least until this afternoon, when Sharon Sanders of FluTrackers managed to get responses from two members of the National Chicken Council who informed her that:

 

The USDA notified them of a laboratory confirmed low pathogenic H5N1 trace picked up from routine surveillance from a live market in one of the boroughs of New York City. This occurrence was approximately 2 weeks ago and they characterized this market as some type of neighborhood venue that sells non-commercially grown poultry i.e. not from a large commercial grower.

 

They also further clarified that the test came back positive for H5, but the N1 component was not detected.

 

Shortly after 5pm today, the USDA’s APHIS (Animal and Plant Health Inspection Service) forwarded the following information to Flutrackers and ProMed Mail  (along with a number of other recipients).

 

On behalf of Veterinary Services, APHIS, US Dept of Agriculture, I’d like to provide the following additional information on the 12Jan13 posting “PRO/AH/EDR> Avian influenza (H5N1:low path) - USA: (NY) poultry, RFI”:

· A Muscovy duck from a Brooklyn, NY Live Bird Market tested positive by rRT-PCR specific for the hemagglutinin H5 gene and negative for the neuraminidase N1 gene of avian influenza virus.

· Virus isolation is pending and we do not have an N-type at this time.

· The amino acid sequencing at the hemagglutinin protein cleavage site is compatible with North American low pathogenic avian influenza.

·  The market underwent an immediate sell down, closure and cleaning and disinfection (C&D). The C&D was completed on 1/11/13.

· Tracing and testing of the source flocks is underway.

 

 

To read how this whole detective story has unfolded over the past 48 hours, I would invite you to read this thread on FluTrackers. 

Kudos to the entire FluTrackers Team for staying on top of this story.

 

As I wrote on Saturday, the discovery of LPAI H5N1 in the United States is neither terribly unusual, nor is it a public health concern.  But as LPAI viruses can be progenitors of more virulent HPAI strains, steps will have to be taken to contain and eradicate this virus.

(Presumably) LPAI H5N1 Found In New York

Photo Credit – FAO

 

# 6851

 

On Friday a small news item appeared in the National Chicken Council’s Washington Report indicating that (presumably Low Pathogenic) H5N1 avian influenza had been detected at a New York live bird market, resulting in a halt of poultry exports to Japan & Taiwan.

 

Avian Influenza Found in New York Live Bird Market; Japan and Taiwan Halt Poultry Exports from New York

On January 11, 2013, in Avian Influenza

USDA’s National Veterinary Services Laboratories has confirmed H5N1 (presumably low pathogenic) from a live bird market in New York . . .

 

While quite common in other countries, many Americans may be surprised to know that there are more than 90 live bird markets in and around New York (cite Cornell University).  Live markets can also be found in other states as well.

 

The newshounds at FluTrackers have been all over this story since early yesterday (see thread), but there’s been nothing new reported over the weekend.  Sharon Sanders put in a call to the National Chicken Council yesterday, unfortunately their offices are closed until Monday.

 

ProMed Mail issued an alert overnight AVIAN INFLUENZA, H5N1, LPAI - USA: (NEW YORK) POULTRY, REQUEST FOR INFORMATION, from a news item submitted by Gert van der Hoek at FluTrackers.

 

As you might expect, there is a certain degree of frustration in Flublogia this weekend over the lack of details available on this story.

 

There are two broad categories of avian influenza; LPAI (Low Pathogenic Avian Influenza) and HPAI (Highly Pathogenic Avian Influenza).

 

• LPAI viruses are quite common in wild birds, cause little illness, and only rarely death.  They are not considered to be a serious health to public health. The concern is (particularly with H5 & H7 strains) that LPAI viruses have the potential to mutate into HPAI strains.
• HPAI viruses are more dangerous, can produce high morbidity and mortality in wild birds and poultry, and can sometimes infect humans with serious result. The type of bird flu scientists have been watching closely for the past decade has been HPAI H5N1 (and to a lesser extent HPAI H7s & H9s).

 

Before the middle of the last decade, there was no uniform requirement to report or track LPAI infections.  That changed in 2006 when the OIE made reporting of LPAI H5 & H7 viruses mandatory.

 

LPAI H5N1 has been detected before across North America, and a partial list (from the USDA Release No. 0296.06) Includes:

 

LPAI H5N1 ("North American" H5N1)

LPAI, or "low path" AI, commonly occurs in wild birds. In most cases, it causes minor sickness or no noticeable signs of disease. It is rarely fatal in birds. LPAI strains are not a human health concern. This includes LPAI H5N1.

 

Evidence of LPAI H5N1 has been found in wild birds in the United States in recent years and is not closely related to the more severe HPAI H5N1 circulating overseas. Examples of historical reports of LPAI H5N1 received by USDA include:

 

• 1975 - LPAI H5N1 was detected in a wild mallard duck and a wild blue goose in Wisconsin as part of routine sampling, not as a result of noticeable illness in the birds
• 1981 and 1985 - the University of Minnesota conducted a sampling procedure in which sentinel ducks were monitored in cages placed in the wild for a short period of time and LPAI H5N1 was detected in those ducks in both years.
• 1983 - LPAI H5N1 was detected in ring-billed gulls in Pennsylvania.
• 1986 - LPAI H5N1 was detected in a wild mallard duck in Ohio as part of routine sampling, not as a result of noticeable illness in the birds.
• 2002 - LPAI H5N1 antibodies were detected in turkeys in Michigan but the virus could not be isolated; therefore this detection could not be confirmed.
• 2005 - LPAI H5N1 was detected in ducks in Manitoba, Canada.
• 2006 - LPAI H5N1 was confirmed in two Michigan mute swans and mallard ducks; Maryland resident wild mallard ducks, and Pennsylvania wild mallard ducks; and Delaware green-winged teals, all sampled as part of USDA's expanded avian influenza surveillance.  

 

Another, more current list, is available on FluTrackers, with nearly 20 LPAI detections reported between 2006-2013 in the United States.

 

The discovery of LPAI H5N1 in the United States is neither unusual, nor is it a public health concern.  But as LPAI viruses can be progenitors of more virulent HPAI strains, steps will have to be taken to contain and eradicate this virus.

 

Hopefully we’ll get more information on the location and extent of this detection, and some details on the steps being taken to contain it over the coming days. While I’ll update this story, the latest news is likely to be found on this FluTrackers thread first.

North American Flu Surveillance: Week 7

 

 

# 5340

 

 

Influenza activity in the United States remains elevated, while in Canada – where levels had been declining for several weeks -  the number of new influenza cases is on the rise again.

 

A few excerpts from week 7’s data (ending Feb 19th) -pulled from the latest CDC’s FluView and PHAC’s  FluWatch  surveillance reports.

 

In Canada:

 

Summary of FluWatch Findings for the Week ending February 19, 2011

• In week 07, there was an increase in overall influenza activity level, with 62.5% (35/56) of regions reporting localized influenza activity. There was a substantial increase in the number of outbreaks reported this week. The proportion of positive influenza detections overall decreased slightly, though the ILI consultation rate remained similar to the previous week.
• Since the beginning of the season, 86.3% of the subtyped positive influenza A specimens have been influenza A/H3N2. In week 07, pandemic H1N1 2009 detections increased to 8% of positive influenza detections while the proportion of influenza B detections remained stable at 10%.

Overall Influenza Summary – Week 7 (February 13 to February 19, 2011)

In week 07, 35 regions reported localized activity (in all provinces except PE), 15 regions reported sporadic activity (in all provinces and territories except YK) and 6 regions presented no activity (see Activity level Map).

Compared to the previous week (week 06), 15 regions reported an increased level of influenza activity, 5 regions reported decreased activity, and 33 regions maintained a stable level of influenza activity (sporadic or higher).

Fifty-one new ILI/influenza outbreaks were reported: 26 in long-term care facilities (LTCF) in BC(2), SK (5), ON(4), QC(7), NB (2) and NS(6); 20 school outbreaks in AB(2), NB(15), NS(1) and NL(2); 1 hospital outbreak in ON; and 4 outbreaks in other facilities in SK(1), ON(2) and NL(1).

 

 

From the CDC, a few excerpts from this week’s FluView report.

 

 

2010-2011 Influenza Season Week 7 ending February 19, 2011

Synopsis

During week 7 (February 13-19, 2011), influenza activity in the United States remained elevated.

• Of the 9,154 specimens tested by U.S. World Health Organization (WHO) and National Respiratory and Enteric Virus Surveillance System (NREVSS) collaborating laboratories and reported to CDC/Influenza Division, 2,866 (31.3%) were positive for influenza.
• The proportion of deaths attributed to pneumonia and influenza (P&I) was above the epidemic threshold for the fourth consecutive week.
• Six influenza-associated pediatric deaths were reported bringing to season total to 41. Three of these deaths were associated with an influenza B virus, one was associated with an influenza A (H3) virus, one was associated with a 2009 influenza A (H1N1) virus, and one was associated with an influenza A virus for which the subtype was not determined.
• The proportion of outpatient visits for influenza-like illness (ILI) was 4.9%, which is above the national baseline of 2.5%. All 10 regions reported ILI above region-specific baseline levels. Twenty-one states experienced high ILI activity; six states experienced moderate ILI activity; New York City and 16 states experienced low ILI activity; seven states experienced minimal ILI activity, and the District of Columbia had insufficient data.
• The geographic spread of influenza in 44 states was reported as widespread; four states reported regional influenza activity; the District of Columbia reported local influenza activity; Puerto Rico, the U.S. Virgin Islands, and two states reported sporadic influenza activity, and Guam reported no influenza activity.

U.S. Virologic Surveillance:

WHO and NREVSS collaborating laboratories located in all 50 states and Washington D.C. report to CDC the number of respiratory specimens tested for influenza and the number positive by influenza type and subtype. The results of tests performed during the current week are summarized in the table below.

Pneumonia and Influenza (P&I) Mortality Surveillance

During week 7, 8.3% of all deaths reported through the 122-Cities Mortality Reporting System were due to P&I. This percentage was above the epidemic threshold of 8.0% for week 7 and is the fourth consecutive week in which P&I has been above the epidemic threshold.

Influenza-Associated Pediatric Mortality

Six influenza-associated pediatric deaths were reported to CDC during week 7. Three of these deaths were associated with an influenza B virus, one was associated with an influenza A (H3) virus, one was associated with a 2009 influenza A (H1N1) virus, and one was associated with an influenza A virus for which the subtype was not determined. Forty-one deaths from 21 states (Arizona, Colorado, Florida, Georgia, Illinois, Indiana, Louisiana, Michigan, Nevada, New Jersey, New Mexico, New York, North Carolina, North Dakota, Oklahoma, Pennsylvania, Texas, Utah, Virginia, West Virginia, and Wisconsin) and New York City have been reported during this influenza season.

Sixteen of the 41 deaths reported were associated with influenza B viruses, 10 deaths reported were associated with influenza A (H3) viruses, eight were associated with 2009 influenza A (H1N1) viruses, and seven were associated with an influenza A virus for which the subtype was not determined.

North America Influenza Surveillance - Week 4

 

 

 

# 5290

 

While the flu season appears to have peaked in Canada, the numbers in the United States continue to climb in the latest surveillance reports.

 

We’ve also fresh report in this week’s MMWR and CDC FluView  on another novel H3N2 swine flu virus detection in Pennsylvania dating back to last September.

 

As you will recall, last year the US saw 4 other cases, and last month China reported a case as well (see China: Single Novel Swine Flu Infection Reported).

 

First some details on this latest novel virus detection, then a brief look at the latest surveillance numbers from Canada and the United States.

 

The following comes from this week’s FluView report. I’ve bolded some of the highlights.

 

 

Novel Influenza A Virus:

One case of human infection with a novel influenza A virus was reported by the Pennsylvania Department of Health. The patient was infected with a swine origin influenza A (H3N2) virus. The patient reported contact with pigs in the week preceding symptom onset on September 6, 2010, did not require hospitalization, and has since fully recovered.

Initial testing of the specimen indicated a seasonal influenza A (H3N2) virus and the specimen was submitted to CDC as a routine surveillance sample. The delay from onset to detection occurred because attempts to culture the virus were unsuccessful. RT-PCR testing confirmed swine-origin influenza A (H3N2). Six other human infections with swine origin influenza A (H3N2) viruses have been identified in the United States during 2009 through 2010, including one other case from Pennsylvania in week 44 of 2010.

 

No epidemiologic links between this case and any of the other cases of swine-origin H3N2 infection have been identified and the viruses from all seven cases have genetic differences indicating different sources of infection.

 

There is no evidence of human-to-human transmission with this virus; however, early identification and investigation of all human infections with novel influenza A viruses is critical to evaluate the extent of the outbreak and possible human-to-human transmission. Surveillance for human infections with novel influenza A viruses continues year round.

 

For more on the potential threats posed by novel swine viruses, you wish to revisit my recent blog The (Swine) Influenza Reassortment Puzzle.

 

Moving on to Canada’s FluWatch report:

 

Summary of FluWatch Findings for the Week ending January 29, 2011

• Overall influenza detections appear to have peaked, with most regions across the country continuing to show a decline in the percentage of positive influenza detections, with the exception of the Atlantic provinces. Other indicators of influenza activity have either decreased or remained similar to the previous week.
• Since the beginning of the season, 88.9% of the subtyped positive influenza A specimens were influenza A/H3N2.In week 04, detections of pandemic H1N1 2009 decreased slightly as a proportion of subtyped influenza A specimens, while influenza B virus detections increased slightly. The proportion of positive tests for RSV continued to increase.

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Moving on to the United States FluView report:

 

010-2011 Influenza Season Week 4 ending January 29, 2011

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Synopsis:

During week 4 (January 23-29, 2011), influenza activity in the United States increased.

• Of the 6,209 specimens tested by U.S. World Health Organization (WHO) and National Respiratory and Enteric Virus Surveillance System (NREVSS) collaborating laboratories and reported to CDC/Influenza Division, 2,044 (32.9%) were positive for influenza.
• One human infection with a novel influenza A virus was reported.
• The proportion of deaths attributed to pneumonia and influenza (P&I) was above the epidemic threshold.
• Six influenza-associated pediatric deaths were reported. Four of these deaths were associated with influenza B viruses, one of these deaths was associated with an influenza A (H3) virus, and one was associated with a 2009 influenza A (H1N1) virus.
• The proportion of outpatient visits for influenza-like illness (ILI) was 4.0%, which is above the national baseline of 2.5%. Seven of the 10 regions (Regions 1, 2, 3, 4, 5, 6, and 7) reported ILI at or above region-specific baseline levels. Seventeen states experienced high ILI activity; three states experienced
• moderate ILI activity; New York City and 10 states experienced low ILI activity; the District of Columbia and 19 states experienced minimal ILI activity, and one state had insufficient data.
• The geographic spread of influenza in 30 states was reported as widespread; 15 states reported regional influenza activity; the District of Columbia and one state reported local influenza activity; Puerto Rico, the U.S. Virgin Islands, and four states reported sporadic influenza activity, and Guam reported no influenza activity.

Pneumonia and Influenza (P&I) Mortality Surveillance

During week 4, 8.5% of all deaths reported through the 122-Cities Mortality Reporting System were due to P&I. This percentage was above the epidemic threshold of 7.9% for week 4.

Outpatient Illness Surveillance:

Nationwide during week 4, 4.0% of patient visits reported through the U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet) were due to influenza-like illness (ILI). This percentage is above the national baseline of 2.5%.

North America: Flu Surveillance Week 3

 

 

 

# 5266

 

 

The weekly surveillance numbers from Canada and the United States were released yesterday and some interesting trends are beginning to emerge.

 

In Canada, the peak of the flu season may have been reached, although some indicators are up while others are down – while in the United States influenza activity is picking up pretty much across the board.

 

Interestingly, while the H3N2 virus remains the dominant influenza A strain detected in the United States, after several months of low activity, levels of H1N1 have risen 3 weeks in a row.

 

We’ll start with Canada’s weekly FluWatch report.

 

January 16 to January 22, 2011 (Week 03)

Summary of FluWatch Findings for the Week ending January 22, 2011

• Overall influenza detections appear to have peaked, with most regions across the country now showing a decline in the percentage of positive influenza detections, except BC and the Atlantic provinces. Paediatric and adult hospitalizations have decreased this week, however, some indicators have increased including the number of regions reporting widespread and localized influenza/ILI activity, the number of outbreaks, and the ILI consultation rate.  
• Since the beginning of the season, 89.5% of the subtyped positive influenza A specimens were influenza A/H3N2.In week 03, detections of pandemic H1N1 2009 increased slightly to 16.9% of all subtyped influenza A specimens, compared to 15.5% in week 02. The overall proportion of positive tests for RSV has increased from 9.6% to 12.5% in week 03.

Percent positive influenza tests, compared to other respiratory viruses, Canada, by reporting week, 2010-2011

 

Moving south, the CDC’s  FluView system paints a picture of a flu season still gaining speed.  While it varies from year-to-year, February is usually the the height of the influenza season in the United States.

 

 

2010-2011 Influenza Season Week 3 ending January 22, 2011

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

Synopsis:

During week 3 (January 16-22, 2011), influenza activity in the United States increased.

• Of the 5,823 specimens tested by U.S. World Health Organization (WHO) and National Respiratory and Enteric Virus Surveillance System (NREVSS) collaborating laboratories and reported to CDC/Influenza Division, 1,754 (30.1%) were positive for influenza.
• The proportion of deaths attributed to pneumonia and influenza (P&I) was below the epidemic threshold.
• Three influenza-associated pediatric deaths were reported. Two of these deaths were associated with influenza A (H3) virus infection and one was associated with an influenza B virus.
• The proportion of outpatient visits for influenza-like illness (ILI) was 3.6%, which is above the national baseline of 2.5%. Six of the 10 regions (Regions 2, 3, 4, 5, 6, and 7) reported ILI above region-specific baseline levels. Nine states experienced high ILI activity, eight states experienced moderate ILI activity, New York City and nine states experienced low ILI activity, 24 states experienced minimal ILI activity, and data were insufficient from the District of Columbia.
• The geographic spread of influenza in 25 states was reported as widespread; 16 states reported regional influenza activity; the District of Columbia and four states reported local influenza activity, Puerto Rico, the U.S. Virgin Islands, and four states reported sporadic influenza activity, Guam reported no influenza activity, and one state did not report.

U.S. Virologic Surveillance:

WHO and NREVSS collaborating laboratories located in all 50 states and Washington D.C. report to CDC the number of respiratory specimens tested for influenza and the number positive by influenza type and subtype. The results of tests performed during the current week are summarized in the table below.

All 50 states and the District of Columbia have reported laboratory-confirmed influenza this season.

Pneumonia and Influenza (P&I) Mortality Surveillance

During week 3, 7.5% of all deaths reported through the 122-Cities Mortality Reporting System were due to P&I. This percentage was below the epidemic threshold of 7.9% for week 3.

(click for interactive map)

 

 

 

For more on all of this, Lisa Schnirring at CIDRAP news has an excellent summary of this week’s flu reports.

 

US flu picking up pace; global activity mixed