Friday, April 03, 2015

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 Reassortant (H5N1) Virus from a Green-Winged Teal in Washington, USA

Mia Kim Torchettia, Mary Lea Killiana, Robert J. Dusekb, Janice C. Pedersena, Nichole Hinesa, Barbara Bodensteinb, C. LeAnn Whiteb, Hon S. Ipb


Eurasian (EA)-origin H5N8 clade 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.



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 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.


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.

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