Multiple gene segment reassortment between Eurasian and American lineages of influenza A virus (H6N2) in Guillemot (Uria aalge)

Global distribution, receptor binding, and cross-species transmission of H6 influenza viruses: risks and implications for humans

The H6 subtype of avian influenza virus (AIV) is a pervasive subtype that is ubiquitously found in both wild bird and poultry populations across the globe. Recent investigations have unveiled its capacity to infect mammals, thereby expanding its host range beyond that of other subtypes and potentially facilitating its global transmission. This heightened breadth also endows H6 AIVs with the potential to serve as a genetic reservoir for the emergence of highly pathogenic avian influenza strains through genetic reassortment and adaptive mutations. Furthermore, alterations in key amino acid loci within the H6 AIV genome foster the evolution of viral infection mechanisms, which may enable the virus to surmount interspecies barriers and infect mammals, including humans, thus posing a potential threat to human well-being. In this review, we summarize the origins, dissemination patterns, geographical distribution, cross-species transmission dynamics, and genetic attributes of H6 influenza viruses. This study holds implications for the timely detection and surveillance of H6 AIVs.

A systemic review on medicinal plants and their bioactive constituents against avian influenza and further confirmation through in-silico analysis

Background

Avian influenza or more commonly known as bird flu is a widespread infectious disease in poultry. This review aims to accumulate information of different natural plant sources that can aid in combating this disease. Influenza virus (IV) is known for its ability to mutate and infect different species (including humans) and cause fatal consequences.

Methods

Total 33 plants and 4 natural compounds were identified and documented. Molecular docking was performed against the target viral protein neuraminidase (NA), with some plant based natural compounds and compared their results with standard drugs Oseltamivir and Zanamivir to obtain novel drug targets for influenza in chickens.

Results

It was seen that most extracts exhibit their action by interacting with viral hemagglutinin or neuraminidase and inhibit viral entry or release from the host cell. Some plants also interacted with the viral RNA replication or by reducing proinflammatory cytokines. Ethanol was mostly used for extraction. Among all the plants Theobroma cacao, Capparis Sinaica Veil, Androgarphis paniculate, Thallasodendron cillatum, Sinularia candidula, Larcifomes officinalis, Lenzites betulina, Datronia molis, Trametes gibbose exhibited their activity with least concentration (below 10 μg/ml). The dockings results showed that some natural compounds (5,7- dimethoxyflavone, Aloe emodin, Anthocyanins, Quercetin, Hemanthamine, Lyocrine, Terpenoid EA showed satisfactory binding affinity and binding specificity with viral neuraminidase compared to the synthetic drugs.

Conclusion

This review clusters up to date information of effective herbal plants to bolster future influenza treatment research in chickens. The in-silico analysis also suggests some potential targets for future drug development but these require more clinical analysis.

Reassortment and Persistence of Influenza A Viruses from Diverse Geographic Origins within Australian Wild Birds: Evidence from a Small, Isolated Population of Ruddy Turnstones

Australian lineages of avian influenza A viruses (AIVs) are thought to be phylogenetically distinct from those circulating in Eurasia and the Americas, suggesting the circulation of endemic viruses seeded by occasional introductions from other regions. However, processes underlying the introduction, evolution and maintenance of AIVs in Australia remain poorly understood. Waders (order Charadriiformes, family Scolopacidae) may play a unique role in the ecology and evolution of AIVs, particularly in Australia, where ducks, geese, and swans (order Anseriformes, family Anatidae) rarely undertake intercontinental migrations. Across a 5-year surveillance period (2011 to 2015), ruddy turnstones (Arenaria interpres) that "overwinter" during the Austral summer in southeastern Australia showed generally low levels of AIV prevalence (0 to 2%). However, in March 2014, we detected AIVs in 32% (95% confidence interval [CI], 25 to 39%) of individuals in a small, low-density, island population 90 km from the Australian mainland. This epizootic comprised three distinct AIV genotypes, each of which represent a unique reassortment of Australian-, recently introduced Eurasian-, and recently introduced American-lineage gene segments. Strikingly, the Australian-lineage gene segments showed high similarity to those of H10N7 viruses isolated in 2010 and 2012 from poultry outbreaks 900 to 1,500 km to the north. Together with the diverse geographic origins of the American and Eurasian gene segments, these findings suggest extensive circulation and reassortment of AIVs within Australian wild birds over vast geographic distances. Our findings indicate that long-term surveillance in waders may yield unique insights into AIV gene flow, especially in geographic regions like Oceania, where Anatidae species do not display regular inter- or intracontinental migration.IMPORTANCE High prevalence of avian influenza viruses (AIVs) was detected in a small, low-density, isolated population of ruddy turnstones in Australia. Analysis of these viruses revealed relatively recent introductions of viral gene segments from both Eurasia and North America, as well as long-term persistence of introduced gene segments in Australian wild birds. These data demonstrate that the flow of viruses into Australia may be more common than initially thought and that, once introduced, these AIVs have the potential to be maintained within the continent. These findings add to a growing body of evidence suggesting that Australian wild birds are unlikely to be ecologically isolated from the highly pathogenic H5Nx viruses circulating among wild birds throughout the Northern Hemisphere.

Ecology of Influenza A Viruses in Wild Birds and Wetlands of Alaska

Alaska represents a globally important region for the ecology of avian-origin influenza A viruses (IAVs) given the expansive wetlands in this region, which serve as habitat for numerous hosts of IAVs that disperse among four continents during the annual cycle. Extensive sampling of wild birds for IAVs in Alaska since 1991 has greatly extended inference regarding intercontinental viral exchange between North America and East Asia and the importance of Beringian endemic species to IAV ecology within this region. Data on IAVs in aquatic birds inhabiting Alaska have also been useful for helping to establish global patterns of prevalence in wild birds and viral dispersal across the landscape. In this review, we summarize the main findings from investigations of IAVs in wild birds and wetlands of Alaska with the aim of providing readers with an understanding of viral ecology within this region. More specifically, we review viral detections, evidence of IAV exposure, and genetic characterization of isolates derived from wild bird samples collected in Alaska by host taxonomy. Additionally, we provide a short overview of wetland complexes within Alaska that may be important to IAV ecology at the continental scale.

The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status

Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV+ and IAV- cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV- ducks than IAV+ ducks, and the effect size of host species on the microbiome was three times higher in IAV- birds than IAV+ birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level.IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual's microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent "flu-like" microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.

First Characterization of Avian Influenza Viruses from Greenland 2014

In late February 2014, unusually high numbers of wild thick-billed murres (Uria lomvia) were found dead on the coast of South Greenland. To investigate the cause of death, 45 birds were submitted for laboratory examination in Denmark. Avian influenza viruses (AIVs) with subtypes H11N2 and low pathogenic H5N1 were detected in some of the birds. Characterization of the viruses by full genome sequencing revealed that all the gene segments belonged to the North American lineage of AIVs. The seemingly sparse and mixed subtype occurrence of low pathogenic AIVs in these birds, in addition to the emaciated appearance of the birds, suggests that the murre die-off was due to malnutrition as a result of sparse food availability or inclement weather. Here we present the first characterization of AIVs isolated in Greenland, and our results support the idea that wild birds in Greenland may be involved in the movement of AIV between North America and Europe.

A Bird's Eye View of Influenza A Virus Transmission: Challenges with Characterizing Both Sides of a Co-Evolutionary Dynamic

In nature, wild birds and influenza A viruses (IAV) are continually co-evolving, locked into a back-and-forth of resistance and conquest that has approached a stable equilibrium over time. This co-evolutionary relationship between bird host and IAV may appear stable at the organismal level, but is highly dynamic at the molecular level manifesting in a constant trade-off between transmissibility and virulence of the virus. Characterizing both sides of the host-virus dynamic has presented a challenge for ecologists and virologists alike, despite the potential for this approach to provide insights into which conditions destabilize the equilibrium state resulting in outbreaks or mortality of hosts in extreme cases. The use of different methods that are either host-centric or virus-centric has made it difficult to reconcile the disparate fields of host ecology and virology for investigating and ultimately predicting wild bird-mediated transmission of IAV. This review distills some of the key lessons learned from virological and ecological studies and explores the promises and pitfalls of both approaches. Ultimately, reconciling ecological and virological approaches hinges on integrating scales for measuring host-virus interactions. We argue that prospects for finding common scales for measuring wild bird-influenza dynamics are improving due to advances in genomic sequencing, host-tracking technology and remote sensing data, with the unit of time (months, year, or seasons) providing a starting point for crossover.

Optimizing Surveillance for South American Origin Influenza A Viruses Along the United States Gulf Coast Through Genomic Characterization of Isolates from Blue-winged Teal (Anas discors)

Relative to research focused on inter-continental viral exchange between Eurasia and North America, less attention has been directed towards understanding the redistribution of influenza A viruses (IAVs) by wild birds between North America and South America. In this study, we genomically characterized 45 viruses isolated from blue-winged teal (Anas discors) along the Texas and Louisiana Gulf Coast during March of 2012 and 2013, coincident with northward migration of this species from Neotropical wintering areas to breeding grounds in the United States and Canada. No evidence of South American lineage genes was detected in IAVs isolated from blue-winged teal supporting restricted viral gene flow between the United States and southern South America. However, it is plausible that blue-winged teal redistribute IAVs between North American breeding grounds and wintering areas throughout the Neotropics, including northern South America, and that viral gene flow is limited by geographical barriers further south (e.g., the Amazon Basin). Surveillance for the introduction of IAVs from Central America and northern South America into the United States may be further optimized through genomic characterization of viruses resulting from coordinated, concurrent sampling efforts targeting blue-winged teal and sympatric species throughout the Neotropics and along the United States Gulf Coast.

Potential Intercontinental Movement of Influenza A(H7N9) Virus into North America by Wild Birds: Application of a Rapid Assessment Framework

A critical question surrounding emergence of novel strains of avian influenza viruses (AIV) is the ability for wild migratory birds to translocate a complete (unreassorted whole genome) AIV intercontinentally. Virus translocation via migratory birds is suspected in outbreaks of highly pathogenic strain A(H5N1) in Asia, Africa and Europe. As a result, the potential intercontinental translocation of newly emerging AIV such as A(H7N9) from Eurasia to North America via migratory movements of birds remains a concern. An estimated 2.91 million aquatic birds move annually between Eurasia and North America with an estimated AIV prevalence as high as 32.2%. Here, we present a rapid assessment to address the likelihood of whole (unreassorted)-genome translocation of Eurasian strain AIV into North America. The scope of this assessment was limited specifically to assess the weight of evidence to support the movement of an unreassorted AIV intercontinentally by migratory aquatic birds. We developed a rapid assessment framework to assess the potential for intercontinental movement of avian influenzas by aquatic birds. This framework was iteratively reviewed by a multidisciplinary panel of scientific experts until a consensus was established. Our assessment framework identified four factors that may contribute to the potential for introduction of any AIV intercontinentally into North America by wild aquatic birds. These factors, in aggregate, provide a framework for evaluating the likelihood of new forms of AIV from Eurasia to be introduced by aquatic birds into North America. Based on our assessment, we determined that the potential for introduction of A(H7N9) into North America through aquatic migratory birds is possible, but the likelihood ranges from extremely low to low.

Diverse inter-continental and host lineage reassortant avian influenza A viruses in pelagic seabirds

Avian influenza A viruses (AIVs) often infect waterfowl, gulls and shorebirds, but other bird groups including pelagic seabirds also serve as hosts. In this study, we analyzed 21 AIVs found in two distant breeding colonies of Common Murre (Uria aalge) in Newfoundland and Labrador, Canada, during 2011. Phylogenetic analyses and genotype assignments were performed for the 21 Common Murre viruses together with all Common and Thick-billed Murre (Uria lomvia) AIV sequences available in public sequence databases. All fully characterized viruses from the Common Murres in 2011 were H1N2 subtype, but the genome sequences revealed greater diversity and the viruses belonged to four distinct genotypes. The four genotypes shared most segments in common, but reassortment was observed for PB2 and M segments. This provided direct genetic data of AIV diversification through segment reassortment during an outbreak of AIV infection in high-density breeding colonies. Analysis of the total collection of available murre viruses revealed a diverse collection of subtypes and gene lineages with high similarity to those found in viruses from waterfowl and gulls, and there was no indication of murre-specific AIV gene lineages. Overall, the virus gene pool in murres was predominantly made up of AIV lineages associated with waterfowl, but also featured considerable gull lineage genes and inter-continental reassortments. In particular, all but one of the 21 Common Murre viruses from 2011 in Newfoundland contained 1 or 2 Eurasian segments and 16 contained 1 gull lineage segment. This mosaic nature of characterized murre AIV genomes might reflect an under-recognized role of these pelagic seabirds in virus transmission across space and between bird host taxa.

Phylogenetic studies of H3 low pathogenic avian influenza viruses isolated from wild mallards in Poland

In order to study the variation of low pathogenic avian influenza viruses (AIV) of H3 subtype in the natural reservoir, partial genetic characterisation of four AIV isolates of H3 subtype, recovered from wild mallards in Poland in 2006-2010, was performed. Phylogenetic analysis clearly confirms that there is a constant flow of AIV H3 between wild birds in Eurasia and Africa, and, to a limited degree, to North America (Alaska), with an occasional spill-over to poultry. The analysis of the PA gene of one isolate from 2010 suggests that it is closely related to several HPAI H5N1 viruses belonging to clade 2.3.2 and that, therefore, a reassortment event has occurred recently between low pathogenic and H5N1 highly pathogenic AIV.

Host restrictions of avian influenza viruses: in silico analysis of H13 and H16 specific signatures in the internal proteins

Gulls are the primary hosts of H13 and H16 avian influenza viruses (AIVs). The molecular basis for this host restriction is only partially understood. In this study, amino acid sequences from Eurasian gull H13 and H16 AIVs and Eurasian AIVs (non H13 and H16) were compared to determine if specific signatures are present only in the internal proteins of H13 and H16 AIVs, using a bioinformatics approach. Amino acids identified in an initial analysis performed on 15 selected sequences were checked against a comprehensive set of AIV sequences retrieved from Genbank to verify them as H13 and H16 specific signatures. Analysis of protein similarities and prediction of subcellular localization signals were performed to search for possible functions associated with the confirmed signatures. H13 and H16 AIV specific signatures were found in all the internal proteins examined, but most were found in the non-structural protein 1 (NS1) and in the nucleoprotein. A putative functional signature was predicted to be present in the nuclear export protein. Moreover, it was predicted that the NS1 of H13 and H16 AIVs lack one of the nuclear localization signals present in NS1 of other AIV subtypes. These findings suggest that the signatures found in the internal proteins of H13 and H16 viruses are possibly related to host restriction.

Molecular and epidemiological characterization of avian influenza viruses from gulls and dabbling ducks in Norway

Background

Wild aquatic birds constitute the natural reservoir for avian influenza viruses (AIVs). Separate Eurasian and American AIV gene pools exist. Here, the prevalence and diversity of AIVs in gulls and dabbling ducks in Norway were described. The influence of host species and temporal changes on AIV prevalence was examined. Five AIVs from Norway, including three from common gull (Larus canus), were analyzed along with 10 available AIV genomes from gulls in Eurasia to search for evidence of intracontinental and intercontinental reassortment of gene segments encoding the internal viral proteins.

Methods

Swabs collected from 2417 dabbling ducks and gulls in the south-west of Norway during five ordinary hunting seasons (August-December) in the period 2005–2010 were analyzed for presence of AIV. Multivariate linear regression was used to identify associations between AIV prevalence, host species and sampling time. Five AIVs from mallard (Anas platyrhynchos) (H3N8, H9N2) and common gull (H6N8, H13N2, H16N3) were full-length characterized and phylogenetically analyzed together with GenBank reference sequences.

Results

Low pathogenic AIVs were detected in 15.5% (CI: 14.1–17.0) of the samples. The overall AIV prevalence was lower in December compared to that found in August to November (p = 0.003). AIV was detected in 18.7% (CI: 16.8–20.6) of the dabbling ducks. A high AIV prevalence of 7.8% (CI; 5.9–10.0) was found in gulls. A similar temporal pattern in AIV prevalence was found in both bird groups. Thirteen hemagglutinin and eight neuraminidase subtypes were detected. No evidence of intercontinental reassortment was found. Eurasian avian (non H13 and H16) PB2 or PA genes were identified in five reference Eurasian gull (H13 and H16) AIV genomes from GenBank. The NA gene from the Norwegian H13N2 gull isolate was of Eurasian avian origin.

Conclusions

The similar temporal pattern in AIV prevalence found in dabbling ducks and gulls, the relatively high virus prevalence detected in gulls and the evidence of intracontinental reassortment in AIVs from gulls indicate that gulls that interact with dabbling ducks are likely to be mixing vessels for AIVs from waterfowl and gulls. Our results support that intercontinental reassortment is rare in AIVs from gulls in Eurasia.

Molecular surveillance of low pathogenic avian influenza viruses in wild birds across the United States: inferences from the hemagglutinin gene

A United States interagency avian influenza surveillance plan was initiated in 2006 for early detection of highly pathogenic avian influenza viruses (HPAIV) in wild birds. The plan included a variety of wild bird sampling strategies including the testing of fecal samples from aquatic areas throughout the United States from April 2006 through December 2007. Although HPAIV was not detected through this surveillance effort we were able to obtain 759 fecal samples that were positive for low pathogenic avian influenza virus (LPAIV). We used 136 DNA sequences obtained from these samples along with samples from a public influenza sequence database for a phylogenetic assessment of hemagglutinin (HA) diversity in the United States. We analyzed sequences from all HA subtypes except H5, H7, H14 and H15 to examine genetic variation, exchange between Eurasia and North America, and geographic distribution of LPAIV in wild birds in the United States. This study confirms intercontinental exchange of some HA subtypes (including a newly documented H9 exchange event), as well as identifies subtypes that do not regularly experience intercontinental gene flow but have been circulating and evolving in North America for at least the past 20 years. These HA subtypes have high levels of genetic diversity with many lineages co-circulating within the wild birds of North America. The surveillance effort that provided these samples demonstrates that such efforts, albeit labor-intensive, provide important information about the ecology of LPAIV circulating in North America.

Oseltamivir (Tamiflu(®)) in the environment, resistance development in influenza A viruses of dabbling ducks and the risk of transmission of an oseltamivir-resistant virus to humans - a review

The antiviral drug oseltamivir (Tamiflu(®)) is a cornerstone in influenza pandemic preparedness plans worldwide. However, resistance to the drug is a growing concern. The active metabolite oseltamivir carboxylate (OC) is not degraded in surface water or sewage treatment plants and has been detected in river water during seasonal influenza outbreaks. The natural influenza reservoir, dabbling ducks, can thus be exposed to OC in aquatic environments. Environmental-like levels of OC induce resistance development in influenza A/H1N1 virus in mallards. There is a risk of resistance accumulation in influenza viruses circulating among wild birds when oseltamivir is used extensively. By reassortment or direct transmission, oseltamivir resistance can be transmitted to humans potentially causing a resistant pandemic or human-adapted highly-pathogenic avian influenza virus. There is a need for more research on resistance development in the natural influenza reservoir and for a prudent use of antivirals.

Phylogeographic analysis of avian influenza viruses isolated from Charadriiformes in Belgium confirms intercontinental reassortment in gulls

Nine influenza viruses isolated from gulls and shorebirds in Belgium (2008-2010), including H3N8, H5N2, H6N1, H11N9, H13N6, H13N8, and H16N3 subtypes, were targeted using random amplification and next-generation sequencing. The gene segments of these viruses segregated into three phylogeographic lineage types: (1) segments circulating in waterfowl in Eurasia with sporadic introduction in other species and in the Americas ("Eurasian avian"), (2) segments circulating in American waterfowl with sporadic introduction to other species and regions ("American avian"), and (3) segments circulating exclusively in gulls and shorebirds and having increased connectivity between the two hemispheres ("Charadriiformes specific"). Notably, an H6N1 and an H5N2 isolated from L. argentatus had mainly Eurasian avian genes but shared a matrix segment of American avian origin (first documentation in European gulls of transhemispheric reassortment). These data support the growing evidence of an important role of Charadriiformes birds in the dynamic nature of avian influenza ecology.

Genetics, evolution, and the zoonotic capacity of European Swine influenza viruses

The European swine influenza virus lineage differs genetically from the classical swine influenza viruses and the triple reassortants found in North America and Asia. The avian-like swine H1N1 viruses emerged in 1979 after an avian-to-swine transmission and spread to all major European pig-producing countries. Reassortment of these viruses with seasonal H3N2 viruses led to human-like swine H3N2 viruses which appeared in 1984. Finally, human-like swine H1N2 viruses emerged in 1994. These are triple reassortants comprising genes of avian-like H1N1, seasonal H1N1, and seasonal H3N2 viruses. All three subtypes established persistent infection chains and became prevalent in the European pig population. They successively replaced the circulating classical swine H1N1 viruses of that time and gave rise to a number of reassortant viruses including the pandemic (H1N1) 2009 virus. All three European lineages have the capacity to infect humans but zoonotic infections are benign.

Extensive geographic mosaicism in avian influenza viruses from gulls in the northern hemisphere

Due to limited interaction of migratory birds between Eurasia and America, two independent avian influenza virus (AIV) gene pools have evolved. There is evidence of low frequency reassortment between these regions, which has major implications in global AIV dynamics. Indeed, all currently circulating lineages of the PB1 and PA segments in North America are of Eurasian origin. Large-scale analyses of intercontinental reassortment have shown that viruses isolated from Charadriiformes (gulls, terns, and shorebirds) are the major contributor of these outsider events. To clarify the role of gulls in AIV dynamics, specifically in movement of genes between geographic regions, we have sequenced six gull AIV isolated in Alaska and analyzed these along with 142 other available gull virus sequences. Basic investigations of host species and the locations and times of isolation reveal biases in the available sequence information. Despite these biases, our analyses reveal a high frequency of geographic reassortment in gull viruses isolated in America. This intercontinental gene mixing is not found in the viruses isolated from gulls in Eurasia. This study demonstrates that gulls are important as vectors for geographically reassorted viruses, particularly in America, and that more surveillance effort should be placed on this group of birds.

Interspecific exchange of avian influenza virus genes in Alaska: the influence of trans-hemispheric migratory tendency and breeding ground sympatry

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 with 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.

Transmission and reassortment of avian influenza viruses at the Asian-North American interface

Twenty avian influenza viruses were isolated from seven wild migratory bird species sampled at St. Lawrence Island, Alaska. We tested predictions based on previous phylogenetic analyses of avian influenza viruses that support spatially dependent trans-hemispheric gene flow and frequent interspecies transmission at a location situated at the Asian-North American interface. Through the application of phylogenetic and genotypic approaches, our data support functional dilution by distance of trans-hemispheric reassortants and interspecific virus transmission. Our study confirms infection of divergent avian taxa with nearly identical avian influenza strains in the wild. Findings also suggest that H16N3 viruses may contain gene segments with unique phylogenetic positions and that further investigation of how host specificity may impact transmission of H13 and H16 viruses is warranted.

The genome sequence of an H11N2 avian influenza virus from a Thick-billed Murre (Uria lomvia) shows marine-specific and regional patterns of relationships to other viruses

Influenza A viruses infect a range of host species, including various mammals and more than 100 species of birds. For avian influenza viruses (AIV), prevalence varies between different groups of birds, with waterfowl showing the highest prevalence. We have sequenced the complete genome of A/Thick-billed Murre/Newfoundland/031/2007(H11N2), an AIV identified in the pelagic seabird, Thick-billed Murre (Uria lomvia). This represents the first complete genome sequence of an AIV from this host species, and only the second complete genome sequence from a seabird in the alcid group. All of the virus segments fall within the American avian lineage. Several of the segments show a close relationship to AIV identified in other marine host species, and also a strong geographic association with other AIV sequences from the northeastern coast of North America from recent years. The identification of this virus, and the growing number of AIV identified in seabird species, indicates these marine birds could be underappreciated host species. This has potential consequences for global influenza dynamics because of the seasonal distributions and migratory patterns of this group of birds.

Surveillance and characterization of low pathogenic H5 avian influenza viruses isolated from wild migratory birds in Korea

Migratory waterfowls are the natural reservoir of influenza A viruses. However, interspecies transmission had occasionally caused outbreaks in various hosts including humans. To characterize the genetic origins of H5 avian influenza viruses isolated from migratory birds in South Korea, phylogenetic analysis were conducted. A total of 53 H5 viruses were isolated between October 2005 and November 2008. Full genetic characterization indicated that most of these viruses belong to the Eurasian-like avian lineage. However, some segments of the AB/Korea/W235/07 and the AB/Korea/W236/07 isolates were clustered with North American lineage viruses rather than those of the Eurasian lineage, suggesting the occurrence of reassortment between these two avian virus lineages. Phylogenetic analysis further demonstrated that the H5N2 and H5N3 virus isolates were of the low pathogenicity H5 phenotype. The H5 viruses appear to be antigenically similar to each other, but could be distinguished from a recent HPAI H5N1 (EM/Korea/W149/06) virus by hemagglutinin inhibition (HI) assays. Experimental inoculation of representative viruses indicated that certain isolates, particularly AB/Korea/W163/07 (H5N2), could be detected in trachea and lungs of chickens but none could be transmitted by direct contact. Furthermore, all of the viruses could be detected in mice lung without prior adaptation which is indicative of their pathogenic potential in a mammalian host. Overall, our results emphasize the important role that migratory birds play in the perpetuation, transport, and reassortment of avian influenza viruses stressing the need for continued surveillance of influenza virus activity in these avian populations.

Gene segment reassortment between Eurasian and American clades of avian influenza virus in Italy

All genes of avian influenza A viruses are phylogenetically distinguished into two large clades, namely the American and Eurasian clade. Reassortments among the gene segments of influenza viruses belonging to the two distinct clades are rare events and have never been described in poultry in Europe and Asia before. This study presents the genetic characterization of two influenza viruses isolated from domestic mallards in Italy in 2004 and 2005. Phylogenetic analysis of the entire genome showed that these viruses contain mixed gene segments belonging to the American and Eurasian clades.

Gene flow and competitive exclusion of avian influenza A virus in natural reservoir hosts

Geographical separation of host species has shaped the avian influenza A virus gene pool into independently evolving Eurasian and American lineages, although phylogenetic evidence for gene flow and reassortment indicates that these lineages also mix on occasion. While the evolutionary dynamics of the avian influenza gene pool have been described, the consequences of gene flow on virus evolution and population structure in this system have not been investigated. Here we show that viral gene flow from Eurasia has led to the replacement of endemic avian influenza viruses in North America, likely through competition for susceptible hosts. This competition is characterized by changes in rates of nucleotide substitution and selection pressures. However, the discontinuous distribution of susceptible hosts may produce long periods of co-circulation of competing virus strains before lineage extinction occurs. These results also suggest that viral competition for host resources may be an important mechanism in disease emergence.

Avian influenza at both ends of a migratory flyway: characterizing viral genomic diversity to optimize surveillance plans for North America

Although continental populations of avian influenza viruses are genetically distinct, transcontinental reassortment in low pathogenic avian influenza (LPAI) viruses has been detected in migratory birds. Thus, genomic analyses of LPAI viruses could serve as an approach to prioritize species and regions targeted by North American surveillance activities for foreign origin highly pathogenic avian influenza (HPAI). To assess the applicability of this approach, we conducted a phylogenetic and population genetic analysis of 68 viral genomes isolated from the northern pintail (Anas acuta) at opposite ends of the Pacific migratory flyway in North America. We found limited evidence for Asian LPAI lineages on wintering areas used by northern pintails in California in contrast to a higher frequency on breeding locales of Alaska. Our results indicate that the number of Asian LPAI lineages observed in Alaskan northern pintails, and the nucleotide composition of LPAI lineages, is not maintained through fall migration. Accordingly, our data indicate that surveillance of Pacific Flyway northern pintails to detect foreign avian influenza viruses would be most effective in Alaska. North American surveillance plans could be optimized through an analysis of LPAI genomics from species that demonstrate evolutionary linkages with European or Asian lineages and in regions that have overlapping migratory flyways with areas of HPAI outbreaks.

Gene segment reassortment between American and Asian lineages of avian influenza virus from waterfowl in the Beringia area

Since prehistoric times, the Bering Strait area (Beringia) has served as an avenue of dispersal between the Old and the New Worlds. On a field expedition to this area, we collected fecal samples from dabbling ducks, geese, shorebirds, and gulls on the Chukchi Peninsula, Siberia, and Pt. Barrow, Alaska, and characterized the subtypes of avian influenza virus present in them. Four of 202 samples (2%) from Alaska were positive for influenza A virus RNA in two independent polymerase chain reaction (PCR)-based screening assays, while all shorebird samples from the Chukchi Peninsula were negative. Subtypes H3N8 and H6N1 were recorded once, while subtype H8N4 was found in two samples. Full-length sequences were obtained from the three unique isolates, and phylogenetic analysis with representative sequences for the Eurasian and North American lineages of influenza A virus showed that one HA gene clustered with the Eurasian rather than the North American lineage. However, the closest relative to this sequence was a North American isolate from Delaware described in 2002, indicating that a H6 spillover from Asia has established itself in North America.

Genetic evidence of intercontinental movement of avian influenza in a migratory bird: the northern pintail (Anas acuta)

The role of migratory birds in the movement of the highly pathogenic (HP) avian influenza H5N1 remains a subject of debate. Testing hypotheses regarding intercontinental movement of low pathogenic avian influenza (LPAI) viruses will help evaluate the potential that wild birds could carry Asian-origin strains of HP avian influenza to North America during migration. Previous North American assessments of LPAI genetic variation have found few Asian reassortment events. Here, we present results from whole-genome analyses of LPAI isolates collected in Alaska from the northern pintail (Anas acuta), a species that migrates between North America and Asia. Phylogenetic analyses confirmed the genetic divergence between Asian and North American strains of LPAI, but also suggested inter-continental virus exchange and at a higher frequency than previously documented. In 38 isolates from Alaska, nearly half (44.7%) had at least one gene segment more closely related to Asian than to North American strains of LPAI. Additionally, sequences of several Asian LPAI isolates from GenBank clustered more closely with North American northern pintail isolates than with other Asian origin viruses. Our data support the role of wild birds in the intercontinental transfer of influenza viruses, and reveal a higher degree of transfer in Alaska than elsewhere in North America.

Phylogenetic analysis of the non-structural (NS) gene of influenza A viruses isolated from mallards in Northern Europe in 2005

BACKGROUND

Although the important role of the non-structural 1 (NS) gene of influenza A in virulence of the virus is well established, our knowledge about the extent of variation in the NS gene pool of influenza A viruses in their natural reservoirs in Europe is incomplete. In this study we determined the subtypes and prevalence of influenza A viruses present in mallards in Northern Europe and further analysed the NS gene of these isolates in order to obtain a more detailed knowledge about the genetic variation of NS gene of influenza A virus in their natural hosts.

RESULTS

A total number of 45 influenza A viruses of different subtypes were studied. Eleven haemagglutinin- and nine neuraminidase subtypes in twelve combinations were found among the isolated viruses. Each NS gene reported here consisted of 890 nucleotides; there were no deletions or insertions. Phylogenetic analysis clearly shows that two distinct gene pools, corresponding to both NS allele A and B, were present at the same time in the same geographic location in the mallard populations in Northern Europe. A comparison of nucleotide sequences of isolated viruses revealed a substantial number of silent mutations, which results in high degree of homology in amino acid sequences. The degree of variation within the alleles is very low. In our study allele A viruses displays a maximum of 5% amino acid divergence while allele B viruses display only 2% amino acid divergence. All the viruses isolated from mallards in Northern Europe possessed the typical avian ESEV amino acid sequence at the C-terminal end of the NS1 protein.

CONCLUSION

Our finding indicates the existence of a large reservoir of different influenza A viruses in mallards population in Northern Europe. Although our phylogenetic analysis clearly shows that two distinct gene pools, corresponding to both NS allele A and B, were present in the mallards populations in Northern Europe, allele B viruses appear to be less common in natural host species than allele A, comprising only about 13% of the isolates sequenced in this study.

Evolutionary mechanisms involved in the virulence of infectious salmon anaemia virus (ISAV), a piscine orthomyxovirus

Infectious salmon anaemia virus (ISAV) is an orthomyxovirus causing a multisystemic, emerging disease in Atlantic salmon. Here we present, for the first time, detailed sequence analyses of the full-genome sequence of a presumed avirulent isolate displaying a full-length hemagglutinin-esterase (HE) gene (HPR0), and compare this with full-genome sequences of 11 Norwegian ISAV isolates from clinically diseased fish. These analyses revealed the presence of a virulence marker right upstream of the putative cleavage site R267 in the fusion (F) protein, suggesting a Q266-->L266 substitution to be a prerequisite for virulence. To gain virulence in isolates lacking this substitution, a sequence insertion near the cleavage site seems to be required. This strongly suggests the involvement of a protease recognition pattern at the cleavage site of the fusion protein as a determinant of virulence, as seen in highly pathogenic influenza A virus H5 or H7 and the paramyxovirus Newcastle disease virus.

Influenza in migratory birds and evidence of limited intercontinental virus exchange

Migratory waterfowl of the world are the natural reservoirs of influenza viruses of all known subtypes. However, it is unknown whether these waterfowl perpetuate highly pathogenic (HP) H5 and H7 avian influenza viruses. Here we report influenza virus surveillance from 2001 to 2006 in wild ducks in Alberta, Canada, and in shorebirds and gulls at Delaware Bay (New Jersey), United States, and examine the frequency of exchange of influenza viruses between the Eurasian and American virus clades, or superfamilies. Influenza viruses belonging to each of the subtypes H1 through H13 and N1 through N9 were detected in these waterfowl, but H14 and H15 were not found. Viruses of the HP Asian H5N1 subtypes were not detected, and serologic studies in adult mallard ducks provided no evidence of their circulation. The recently described H16 subtype of influenza viruses was detected in American shorebirds and gulls but not in ducks. We also found an unusual cluster of H7N3 influenza viruses in shorebirds and gulls that was able to replicate well in chickens and kill chicken embryos. Genetic analysis of 6,767 avian influenza gene segments and 248 complete avian influenza viruses supported the notion that the exchange of entire influenza viruses between the Eurasian and American clades does not occur frequently. Overall, the available evidence does not support the perpetuation of HP H5N1 influenza in migratory birds and suggests that the introduction of HP Asian H5N1 to the Americas by migratory birds is likely to be a rare event.

Influenza surveillance in wild migratory birds has been done at two sites in North America: 1) in Alberta, Canada, for the past 31 years, and 2) along Delaware Bay, United States, for the past 22 years. These studies support the concept that wild migratory birds are the reservoirs of all influenza A viruses and that the influenza viruses in the world can be divided into two distinct superfamilies, one in Eurasia and the other in the Americas. From time to time these viruses spread to domestic poultry and to humans and cause pandemics of disease. Many investigators have expanded these studies particularly in Europe, Asia, and the Americas. The emergence of highly pathogenic H5N1 in Asia a decade ago and the continuing evolution and spread of these H5N1 viruses to the whole of Eurasia is a continuing problem for veterinary and human public health. The available evidence from Eurasia is that migratory birds can be infected and may be involved in local spread of the highly pathogenic H5N1 virus. The question addressed in the present study is why the highly pathogenic H5N1 influenza virus has not yet reached the Americas despite the overlap in migratory bird pathways, particularly in Alaska. Genomic analysis of influenza viruses from our repository failed to provide evidence of influenza viruses with their whole genome originating from Eurasia. However, we found occasional influenza viruses from North America with single or multiple genes that originated in Eurasia. Our interpretation is that while influenza viruses do exchange between the two hemispheres, this is a rare occurrence. Regardless, enhanced surveillance should be continued in the Americas in case this rare event occurs.

A polar system of intercontinental bird migration

Studies of bird migration in the Beringia region of Alaska and eastern Siberia are of special interest for revealing the importance of bird migration between Eurasia and North America, for evaluating orientation principles used by the birds at polar latitudes and for understanding the evolutionary implications of intercontinental migratory connectivity among birds as well as their parasites. We used tracking radar placed onboard the ice-breaker Oden to register bird migratory flights from 30 July to 19 August 2005 and we encountered extensive bird migration in the whole Beringia range from latitude 64 degrees N in Bering Strait up to latitude 75 degrees N far north of Wrangel Island, with eastward flights making up 79% of all track directions. The results from Beringia were used in combination with radar studies from the Arctic Ocean north of Siberia and in the Beaufort Sea to make a reconstruction of a major Siberian-American bird migration system in a wide Arctic sector between longitudes 110 degrees E and 130 degrees W, spanning one-third of the entire circumpolar circle. This system was estimated to involve more than 2 million birds, mainly shorebirds, terns and skuas, flying across the Arctic Ocean at mean altitudes exceeding 1 km (maximum altitudes 3-5 km). Great circle orientation provided a significantly better fit with observed flight directions at 20 different sites and areas than constant geographical compass orientation. The long flights over the sea spanned 40-80 degrees of longitude, corresponding to distances and durations of 1400-2600 km and 26-48 hours, respectively. The birds continued from this eastward migration system over the Arctic Ocean into several different flyway systems at the American continents and the Pacific Ocean. Minimization of distances between tundra breeding sectors and northerly stopover sites, in combination with the Beringia glacial refugium and colonization history, seemed to be important for the evolution of this major polar bird migration system.

Spatial, temporal, and species variation in prevalence of influenza A viruses in wild migratory birds

Although extensive data exist on avian influenza in wild birds in North America, limited information is available from elsewhere, including Europe. Here, molecular diagnostic tools were employed for high-throughput surveillance of migratory birds, as an alternative to classical labor-intensive methods of virus isolation in eggs. This study included 36,809 samples from 323 bird species belonging to 18 orders, of which only 25 species of three orders were positive for influenza A virus. Information on species, locations, and timing is provided for all samples tested. Seven previously unknown host species for avian influenza virus were identified: barnacle goose, bean goose, brent goose, pink-footed goose, bewick's swan, common gull, and guillemot. Dabbling ducks were more frequently infected than other ducks and Anseriformes; this distinction was probably related to bird behavior rather than population sizes. Waders did not appear to play a role in the epidemiology of avian influenza in Europe, in contrast to the Americas. The high virus prevalence in ducks in Europe in spring as compared with North America could explain the differences in virus–host ecology between these continents. Most influenza A virus subtypes were detected in ducks, but H13 and H16 subtypes were detected primarily in gulls. Viruses of subtype H6 were more promiscuous in host range than other subtypes. Temporal and spatial variation in influenza virus prevalence in wild birds was observed, with influenza A virus prevalence varying by sampling location; this is probably related to migration patterns from northeast to southwest and a higher prevalence farther north along the flyways. We discuss the ecology and epidemiology of avian influenza A virus in wild birds in relation to host ecology and compare our results with published studies. These data are useful for designing new surveillance programs and are particularly relevant due to increased interest in avian influenza in wild birds.

Significant gaps in our knowledge of the ecology of avian influenza in wild migratory birds have become apparent during recent outbreaks of H5N1 highly pathogenic avian influenza, in particular in relation to the risk of virus spread by wild birds. An eight-year surveillance study, which included more than 36,000 wild birds tested for low pathogenic avian influenza, provides new information on host species, prevalence, and temporal and geographical variation of avian influenza in wild migratory birds in Europe. Dabbling ducks harbored nearly all known influenza virus subtypes, with the exception of H13 and H16, which were found primarily in gulls. In contrast to American studies, waders did not play a role in the epidemiology of avian influenza in Europe. This study provides important information on the ecology and epidemiology of avian influenza A virus and could assist in the design of new surveillance studies for high and low pathogenic avian influenza in wild birds.

Genetic reassortment of infectious bursal disease virus in nature

Infectious bursal disease virus (IBDV), a double-stranded RNA virus, is a member of the Birnaviridae family. Four pathotypes of IBDV, attenuated, virulent, antigenic variant, and very virulent (vvIBDV), have been identified. We isolated and characterized the genomic reassortant IBDV strain ZJ2000 from severe field outbreaks in commercial flocks. Full-length genomic sequence analysis showed that ZJ2000 is a natural genetic reassortant virus with segments A and B derived from attenuated and very virulent strains of IBDV, respectively. ZJ2000 exhibited delayed replication kinetics as compared to attenuated strains. However, ZJ2000 was pathogenic to specific pathogen free (SPF) chickens and chicken embryos. Similar to a standard virulent IBDV strain, ZJ2000 caused 26.7% mortality, 100% morbidity, and severe bursal lesions at both gross and histopathological levels. Taken together, our data provide direct evidence for genetic reassortment of IBDV in nature, which may play an important role in the evolution, virulence, and host range of IBDV. Our data also suggest that VP2 is not the sole determinant of IBDV virulence, and that the RNA-dependent RNA polymerase protein, VP1, may play an important role in IBDV virulence. The discovery of reassortant viruses in nature suggests an additional risk of using live IBDV vaccines, which could act as genetic donors for genome reassortment.

Towards improved influenza A virus surveillance in migrating birds

The last decade has seen a marked increase in highly pathogenic avian influenza (HPAI) outbreaks around the world. This increase and the zoonotic potential of some of the HPAI viruses are of great concern to animal and public health as well as biodiversity. It is now well recognized that global influenza virus surveillance in wild birds can play a key role in the early recognition of and preparation for these threats. Here we summarize the most important results from our wild bird surveillance studies in Northern Europe over the last 8 years and conclude that surveillance studies in wild birds are indeed useful to generate prototypic vaccine candidates and to design and evaluate diagnostic tests, prior to the occurrence of outbreaks in animals and humans. Through this 8-year experience we also identified gaps in our knowledge on influenza A viruses and their natural hosts which may help to assist in the design of improved surveillance studies. This is particularly relevant if wild bird surveillance studies are used as an "early warning system" for the arrival of the H5N1 HPAI virus in a country or region and to assess the risk posed by these viruses in general.

Genotype turnover by reassortment of replication complex genes from avian influenza A virus

Reassortment among the RNA segments of Influenza A virus caused the two most recent human influenza pandemics; recently, reassortment has generated viral genotypes associated with outbreaks of avian H5N1 influenza in Asia and Europe. A statistical analysis has been developed for the systematic identification and characterization of reassortant viruses. The analysis was applied to the genes of the replication complex of 152 avian influenza A viruses isolated between 1966 and 2004 from predominantly terrestrial and domestic aquatic avian species. The results indicated that reassortment among these genes was pervasive throughout this period and throughout both the Eurasian and North American lineages of the virus. Evidence is presented that the circulating genotypes of the replication complex are being replaced continually by novel genotypes created by reassortment. No constraints for coordinated reassortment among genes of the replication complex were evident; rather, reassortment almost always proceeded one segment at a time. A maximum-likelihood estimate of the rate of reassortment was derived. For significantly diverged Asian avian influenza A viruses from the period 1991-2004, it was estimated that the median duration between creation of a new genotype and its next segment reassortment was 3 years. Reassortments that introduced previously unobserved influenza genetic material were detected. These findings point to substantial potential for rapid generation of novel avian influenza A viruses, emphasizing the importance of intensive surveillance of these host species in preparation for a possible pandemic.

Global patterns of influenza a virus in wild birds

The outbreak of highly pathogenic avian influenza of the H5N1 subtype in Asia, which has subsequently spread to Russia, the Middle East, Europe, and Africa, has put increased focus on the role of wild birds in the persistence of influenza viruses. The ecology, epidemiology, genetics, and evolution of pathogens cannot be fully understood without taking into account the ecology of their hosts. Here, we review our current knowledge on global patterns of influenza virus infections in wild birds, discuss these patterns in the context of host ecology and in particular birds' behavior, and identify some important gaps in our current knowledge.

Spread of H5N1 avian influenza virus: an ecological conundrum

The role of wild birds in the spread of influenza H5N1 virus remains speculative and the ecology of influenza A viruses in nature is largely unstudied. There is an urgent need for multidisciplinary studies to explore the ecology of avian influenza viruses in wild birds and the environment to support ecological interpretation of the source of disease outbreaks in poultry.