Avian Influenza Genomics

By sequencing low pathogenic avian influenza (LPAI) genomes sampled from wild birds, ASC researchers gather information on how likely migratory bird species are to carry influenza genes between the Eastern and Western Hemispheres. To date the highly pathogenic strain of H5N1 has not been detected in North America, nor has any avian influenza virus (AIV) genome of completely Eurasian origin. However, occasionally some gene segments of Eurasian origin mix with gene segments from North America by a process known as reassortment. Our understanding of where this reassortment takes place is limited, but geneticists at the ASC have detected Eurasian LPAI genes in North America suggesting that intercontinental movement of AIV genes does occur.

Understanding what happens to Eurasian gene segments once they arrive in North America is an important area of research under continuous investigation. It would appear, however, that the establishment and persistence of these Eurasian genes in the North American gene pool is rather rare.

By calculating the prevalence of reassortment events between host species and between geographic locations genetic research identifies species of important geographic locations as likely routes of avian influenza movements, further enhances surveillance efforts by targeting sampling efforts near such sites.

Genetic evidence for intercontinental movement of avian influenza genes found in Northern Pintails (Anas acuta)

Northern Pintails are one of the most common waterfowl breeding in Alaska. They are highly migratory and satellite telemetry data coupled with banding data suggests many North American pintails travel to eastern Asia where they interact with Eurasian waterfowl including other pintails increasing the potential for contact with HPAI H5N1. Furthermore, genetic sequencing of LPAI viruses sampled from North American pintails found multiple instances of Eurasian gene segments reassorting with North American LPAI genes. The prevalence of such reassortment events appears to be higher in Northern Pintails than in other birds studied. Ongoing research continues to provide support for maintaining Northern Pintails as a species of great interest in HPAI H5N1 surveillance efforts.

Ramey, A. M., J. M. Pearce, P. L. Flint, H. S. Ip, D. V. Derksen, J. C. Franson, M. J. Petrula, B. D. Scotton, K. M. Sowl, M. L. Wege and K. A. Trust. 2010. Intercontinental reassortment and genomic variation of low pathogenic avian influenza viruses isolated from northern pintails (Anas acuta) in Alaska: Examining the evidence through space and time. Virology 401(2): 179-189.

Flint, P. L., K. Ozaki, J. M. Pearce, B. Guzzetti, H. Higuchi, J. P. Fleskes, t. Shimada and D. V. Derksen. 2009. Breeding-Season Sympatry Facilitates Genetics Exchange Among Allopatric Wintering Populations of Northern Pintails in Japan and California. The Condor 111(4):591–598.

Pearce, J. M., A. M. Ramey, P. L. Flint, A. V. Koehler, J. P. Fleskes, J. C. Franson, J. S. Hall, D. V. Derksen, and H. S. Ip. 2009. Avian influenza at both ends of a migratory flyway: Characterizing viral genomic diversity to optimize surveillance plans for North America. Evolutionary Applications 1752-4571; 1-12.

Koehler, A. W., J. M. Pearce, P. L. Flint, J. C. Franson and H. S. Ip. 2008. Genetic evidence of intercontinental movement of avian influenza in a migratory bird: the northern pintail (Anas acuta). Molecular Ecology 17(21): 4754-4762.

Contact: John Pearce

Shorebirds display regional differences in prevalence and levels of inter-continental movement of avian influenza viruses across North America

Shorebirds have long been considered a reservoir of avian influenza viruses and are intercontinental and trans-hemispheric migrants, often crossing large distances in a single flight. As many as 20 shorebird species that visit North America in summer have migratory routes through, and share staging areas within, countries in which outbreaks of the H5N1 highly pathogenic avian influenza have occurred. Thus, from a migratory perspective shorebirds constitute an important taxonomic group for avian influenza (AI) surveillance sampling in North America. Few shorebirds have tested positive for AI on the west coast of North America, in stark contrast to the Atlantic coast of the continent where prevalence is especially high in the spring. On-going research is exploring alternatives to intensive surveillance to identify epidemiological patterns for influenza virus infection in shorebirds.

Pearce, J. M., A. M. Ramey, H. S. Ip and R. E. Gill Jr. 2010. Limited evidence of trans-hemispheric movement of avian influenza viruses among contemporary North American shorebird isolates. Virus Research 148(1-2): 44-50.

Contact: John Pearce

Comparison of LPAI viruses found within two Alaskan host species, Northern Pintails (Anas acuta) and Mallard (Anas platyrhynchos): Analyzing influenza viruses from hosts with different migratory behaviors but similar and shared breeding habitats

The movement and transmission of avian influenza viral strains via wild migratory birds may vary by host species as a result of migratory tendency and sympatry with other infected individuals.  To examine the roles of host migratory tendency and species sympatry on the movement of Eurasian low pathogenic avian influenza (LPAI) genes into North America, we characterized migratory patterns and LPAI viral genomic variation in mallards (Anas platyrhynchos) of Alaska in comparison to LPAI diversity of northern pintails (Anas acuta).  A 50-year band recovery data set suggests that unlike northern pintails, mallards rarely make trans-hemispheric migrations between Alaska and Eurasia.  Concordantly, fewer (14.5%) of 62 LPAI isolates from mallards contained Eurasian gene segments compared to those from 97 northern pintails (35%), a species with greater inter-continental migratory tendency.  Aerial survey and banding data suggest that mallards and northern pintails are largely sympatric throughout Alaska during the breeding season, promoting opportunities for interspecific transmission.  Comparisons of full genome isolates confirmed near-complete genetic homology (>99.5%) of seven viruses between mallards and northern pintails.  This study found viral segments of Eurasian lineage at a higher frequency in mallards than previous studies, suggesting transmission from other avian species migrating inter-hemispherically or the common occurrence of endemic Alaskan viruses containing segments of Eurasian origin.  We conclude that mallards are unlikely to transfer Asian origin viruses directly to North America via Alaska, but that they are likely infected with Asian origin viruses via interspecific transfer from species with regular migrations to the Eastern Hemisphere.

Pearce, J.M., A.R. Reeves, A.M. Ramey, J.W. Hupp, H.S.Ip, M. Bertram, M.J. Petrula, B.D. Scotton, K.A. Trust, , B.W. Miexell, J.A. Runstadler. 2010.  Interspecific exchange of avian influenza virus genes in Alaska: the influence of trans-hemispheric migratory tendency and breeding ground sympatry. Molecular Ecology. doi: 10.1111/j.1365-294X.2010.04908.x

AIV persistence in arctic and subarctic environments

Migratory waterfowl are presumed to be the dominant reservoir of avian influenza viruses. However, it remains unclear if abiotic reservoirs, such as lakes and ponds, play a role in the persistence of influenza viruses overwinter. Ongoing efforts are underway to sample water and sediment from Alaskan wetlands to help to unravel how AIVs are maintained in wild migratory birds and their habitats throughout the year.

Contact: Paul Flint

Comparisons of intercontinental LPAI movement among multiple hosts in the Yukon-Kuskokwim Delta: A community wide analysis of a large sub-arctic breeding ground

Research indicates that avian influenza viruses differ genetically between and within some groups of wild bird hosts (i.e. waterfowl, gulls, and shorebirds). The Yukon National Wildlife Refuge is a major breeding ground of global significance for many species, including several species of priority for HPAI H5N1 surveillance. Because of the close contact these bird species have during the breeding season, this ecosystem provides a unique opportunity to study influenza ecology across a large community of multiple host species by sequencing and comparing influenza viruses isolated within the refuge. Data collected from this project will be used to gain insight into the movement, transmission and evolution of avian influenza viruses.

Contact: John Pearce

Genetic diversity and reassortment of avian influenza viruses on St. Lawrence Island, Alaska

St. Lawrence Island is located in the Bering Sea between Alaska and Russia. Genetic sequencing of viruses from wild migratory birds sampled at this location indicates frequent exchange of virus genes originating from Asia and North America. Genomic analyses also demonstrate transmission of nearly identical viruses between birds of different species. Results from this project suggest that marine birds warrant additional investigation as vectors of influenza viruses.

Ramey, A.M., J.M. Pearce, C.R. Ely, L.M. Sheffield Guy, D.B. Irons, D.V. Derksen and H.S. Ip. 2010. Transmission and reassortment of avian influenza viruses at the Asian - North American interface. Virology, 406:352-359.

Contact: Andrew Ramey