Adaptive Heterosubtypic Immunity to Low Pathogenic Avian Influenza Viruses in Experimentally Infected Mallards

Naturally Acquired Antibodies to Influenza A Virus in Fall-Migrating North American Mallards

Although waterfowl are the primary reservoir for multiple subtypes of influenza A virus (IAV), our understanding of population immunity in naturally infected waterfowl is poorly understood. Population immunity may be an important driver of seasonal subtype predominance in waterfowl populations and may affect the potential for establishment of introduced IAV such as the Eurasian-like A/Goose/Guangdong/1/1996 lineage in these populations. Here, we examine the prevalence of naturally acquired antibodies to nucleoprotein (NP), hemagglutinin (H3, H4, H5), and neuraminidase (N1, N2, N6, N8) in early migrating mallards (Anas platyrhynchos) sampled in Northwest Minnesota during staging and early fall migration in September 2014, 2015, 2017, and 2018. Serologic results were compared to historic and contemporary virus isolation results from these same study sites. The prevalence of antibodies to NP ranged from 60.8−76.1% in hatch-year (HY) birds and from 86.0−92.7% in after-hatch-year (AHY, >1-year-old) mallards indicating a high level of previous infection with IAV early in the fall migration season. Neutralizing antibodies were detected against H3, H4, and H5 in all years as were antibodies to N1, N2, N6, and N8. A high proportion of NP seropositive ducks tested positive for antibodies to multiple HA and NA subtypes, and this was more common in the AHY age class. Antibody prevalence to the HA and NA subtypes included in this study were consistent with the predominance of H4N6 in these populations during all years and reflected a broadening of the antibody response with age. Additional work is needed to document the longevity of these immune responses, if and how they correlate with protection against IAV transmission, infection, and disease, and if, as detected in this study, they adequately describe the true extent of exposure to IAV or specific HA or NA subtypes.

Host Range of Influenza A Virus H1 to H16 in Eurasian Ducks Based on Tissue and Receptor Binding Studies

Dabbling and diving ducks partly occupy shared habitats but have been reported to play different roles in wildlife infectious disease dynamics. Influenza A virus (IAV) epidemiology in wild birds has been based primarily on surveillance programs focused on dabbling duck species, particularly mallard (Anas platyrhynchos). Surveillance in Eurasia has shown that in mallards, some subtypes are commonly (H1 to H7 and H10), intermediately (H8, H9, H11, and H12), or rarely (H13 to H16) detected, contributing to discussions on virus host range and reservoir competence. An alternative to surveillance in determining IAV host range is to study virus attachment as a determinant for infection. Here, we investigated the attachment patterns of all avian IAV subtypes (H1 to H16) to the respiratory and intestinal tracts of four dabbling duck species (Mareca and Anas spp.), two diving duck species (Aythya spp.), and chicken, as well as to a panel of 65 synthetic glycan structures. We found that IAV subtypes generally showed abundant attachment to colon of the Anas duck species, mallard, and Eurasian teal (Anas crecca), supporting the fecal-oral transmission route in these species. The reported glycan attachment profile did not explain the virus attachment patterns to tissues but showed significant attachment of duck-originated viruses to fucosylated glycan structures and H7 virus tropism for Neu5Gc-LN. Our results suggest that Anas ducks play an important role in the ecology and epidemiology of IAV. Further knowledge on virus tissue attachment, receptor distribution, and receptor binding specificity is necessary to understand the mechanisms underlying host range and epidemiology of IAV.IMPORTANCE Influenza A viruses (IAVs) circulate in wild birds worldwide. From wild birds, the viruses can cause outbreaks in poultry and sporadically and indirectly infect humans. A high IAV diversity has been found in mallards (Anas platyrhynchos), which are most often sampled as part of surveillance programs; meanwhile, little is known about the role of other duck species in IAV ecology and epidemiology. In this study, we investigated the attachment of all avian IAV hemagglutinin (HA) subtypes (H1 to H16) to tissues of six different duck species and chicken as an indicator of virus host range. We demonstrated that the observed virus attachment patterns partially explained reported field prevalence. This study demonstrates that dabbling ducks of the Anas genus are potential hosts for most IAV subtypes, including those infecting poultry. This knowledge is useful to target the sampling of wild birds in nature and to further study the interaction between IAVs and birds.

Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population

Understanding the epidemiological dynamics of highly pathogenic avian influenza virus (HPAIV) in wild birds is crucial for guiding effective surveillance and control measures. The spread of H5 HPAIV has been well characterized over large geographical and temporal scales. However, information about the detailed dynamics and demographics of individual outbreaks in wild birds is rare and important epidemiological parameters remain unknown. We present data from a wild population of long-lived birds (mute swans; Cygnus olor) that has experienced three outbreaks of related H5 HPAIVs in the past decade, specifically, H5N1 (2007), H5N8 (2016) and H5N6 (2017). Detailed demographic data were available and intense sampling was conducted before and after the outbreaks; hence the population is unusually suitable for exploring the natural epidemiology, evolution and ecology of HPAIV in wild birds. We show that key epidemiological features remain remarkably consistent across multiple outbreaks, including the timing of virus incursion and outbreak duration, and the presence of a strong age-structure in morbidity that likely arises from an equivalent age-structure in immunological responses. The predictability of these features across a series of outbreaks in a complex natural population is striking and contributes to our understanding of HPAIV in wild birds.

This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’. This issue is linked with the subsequent theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’.

Are Microneutralization and Hemagglutination Inhibition Assays Comparable? Serological Results from Influenza Experimentally Infected Mallard Ducks

The hemagglutination inhibition (HI) assay is commonly used to assess the humoral immune response against influenza A viruses (IAV). However, the microneutralization (MN) assay has been reported to have higher sensitivity when testing sera from humans and other species. Our objective was to determine the agreement between MN and HI assays and compare the proportion of positive samples detected by both methods in sera of mallards primary infected with the A/mallard/MN/Sg-000169/ 2007 (H3N8) virus and subsequently inoculated with homosubtypic or heterosubtypic IAV. Overall, we found poor to fair agreement (prevalence-adjusted bias-adjusted kappa [PABAK], 0.03-0.35) between MN and HI assays in serum samples collected 2 weeks after H3N8 inoculation; the observed agreement increased to moderate or substantial in samples collected 4 to 5 weeks postinoculation (WPI) (PABAK, 0.52-0.75). The MN assay detected a higher proportion of positive samples compared with HI assays in serum samples collected 2 WPI (P = 0.01). This difference was not observed in samples collected 4 WPI. Also, a boosting effect in MN and HI titers was observed when birds were subsequently inoculated with IAV within the same H3 clade. This effect was not observed when birds were challenged with viruses that belong to a different HA clade. In summary, the agreement between assays varies depending on the postinfection sample collection time point and the similarity between the antigens used for the assays. Additionally, subsequent exposure of ducks to homosubtypic or heterosubtypic strains might affect the observed agreement.

Emperor geese (Anser canagicus) are exposed to a diversity of influenza A viruses, are infected during the non-breeding period and contribute to intercontinental viral dispersal

Emperor geese (Anser canagicus) are endemic to coastal areas within Beringia and have previously been found to have antibodies to or to be infected with influenza A viruses (IAVs) in Alaska. In this study, we use virological, serological and tracking data to further elucidate the role of emperor geese in the ecology of IAVs in Beringia during the non-breeding period. Specifically, we assess evidence for: (a) active IAV infection during spring staging, autumn staging and wintering periods; (b) infection with novel Eurasian-origin or interhemispheric reassortant viruses; (c) contemporary movement of geese between East Asia and North America; (d) previous exposure to viruses of 14 haemagglutinin subtypes, including Eurasian lineage highly pathogenic (HP) H5 IAVs; and (e) subtype-specific antibody seroconversion and seroreversion. Emperor geese were found to shed IAVs, including interhemispheric reassortant viruses, throughout the non-breeding period; migrate between Alaska and the Russian Far East prior to and following remigial moult; have antibodies reactive to a diversity of IAVs including, in a few instances, Eurasian lineage HP H5 IAVs; and exhibit relatively broad and stable patterns of population immunity among breeding females. Results of this study suggest that emperor geese may play an important role in the maintenance and dispersal of IAVs within Beringia during the non-breeding period and provide information that may be used to further optimize surveillance activities focused on the early detection of Eurasian-origin IAVs in North America.

Persistence of maternal antibodies to influenza A virus among captive mallards (Anas platyrhynchos)

Wild waterfowl are maintenance hosts of most influenza A virus (IAV) subtypes and are often the subjects of IAV surveillance and transmission models. While maternal antibodies have been detected in yolks and in nestlings for a variety of wild bird species and pathogens, the persistence of maternal antibodies to IAVs in mallard ducklings (Anas platyrhynchos) has not been previously investigated. Nonetheless, this information is important for a full understanding of IAV transmission dynamics because ducklings protected by maternal antibodies may not be susceptible to infection. In this study, we examined the transfer of IAV-specific maternal antibodies to ducklings. Blood samples were collected approximately every five days from ducklings hatched from hens previously infected with an H6 strain of IAV. Serum samples were tested for antibodies to IAV by an enzyme-linked immunosorbent assay. The median persistence of maternal antibodies in ducklings was 12.5 days (range: 4-33 days) post-hatch. The majority of ducklings (71%) had detectable maternal antibodies from 4 to 17 days post-hatch, while a small subset of individuals (29%) had detectable maternal antibodies for up to 21-33 days post-hatch. Antibody concentrations in hens near the time of egg laying were correlated with maternal antibody concentrations in the initial blood sample collected from ducklings (0-4 days post-hatch). Knowledge of the duration of maternal antibodies in ducklings will aid in the interpretation of IAV serological surveillance results and in the modeling of IAV transmission dynamics in waterfowl.

NEUTRALIZING ANTIBODIES TO TYPE A INFLUENZA VIRUSES IN SHOREBIRDS AT DELAWARE BAY, NEW JERSEY, USA

Influenza A virus (IAV) infections in shorebirds at Delaware Bay, New Jersey, US, have historically included avian hemagglutinin (HA) subtypes H1-13 and H16. In a given year, infections are characterized by a limited number of HA and neuraminidase subtypes and a dominant HA subtype that often represents >50% of all isolates. Predominant HA subtypes shift between consecutive years. In addition, infection prevalence is consistently higher in Ruddy Turnstones (RUTU; Arenaria interpres morinella) compared to Red Knots (REKN; Calidris canutus rufa), despite comparable rates of exposure. To investigate a potential immunological basis for this phenomenon, a virus microneutralization assay was used to detect subtype-specific, neutralizing antibodies to H1-H12 in sera collected from RUTUs from 2012-16 and REKNs in 2012, 2013, and 2016. Neutralizing antibodies to one or more subtypes were detected in 36% (222/611) of RUTUs. Prevalence of antibodies to subtypes H6 and H11 remained high throughout the study, and these virus subtypes were isolated every year, suggesting a continual source of exposure. Antibody prevalence was intermediate for most IAV subtypes that were isolated in 2-3 of 5 yr (H1, H3, H5, H9, H10, and H12) but was low for H7 viruses, despite the isolation of this virus subtype in 3 of 5 yr. This suggests a reduced antigenicity of H7 IAVs compared to other subtypes. Antibody prevalence was low for H4 virus that was isolated once, and H2 and H8 viruses that were never isolated. Neutralizing antibodies were detected in 66% (169/257) of REKNs and subtype-specific antibody prevalences were higher in REKNs than RUTUs with few exceptions. The results suggest that population immunity influences which species is infected at Delaware Bay, indicate that IAV dynamics are subtype-dependent, and demonstrate the utility of the microneutralization assay as a supportive tool for field research.

Heterosubtypic immunity increases infectious dose required to infect Mallard ducks with Influenza A virus

Previous field and experimental studies have demonstrated that heterosubtypic immunity (HSI) is a potential driver of Influenza A virus (IAV) prevalence and subtype diversity in mallards. Prior infection with IAV can reduce viral shedding during subsequent reinfection with IAV that have genetically related hemagglutinins (HA). In this experiment, we evaluated the effect of HSI conferred by an H3N8 IAV infection against increasing challenge doses of closely (H4N6) and distantly (H6N2) related IAV subtypes in mallards. Two groups of thirty 1-month-old mallards each, were inoculated with 105.9 50% embryo infectious doses (EID50) of an H3N8 virus or a mock-inoculum. One month later, groups of five birds each were challenged with increasing doses of H4N6 or H6N2 virus; age-matched, single infection control ducks were included for all challenges. Results demonstrate that naïve birds were infected after inoculation with 103 and 104 EID50 doses of the H4N6 or H6N2 virus, but not with 102 EID50 doses of either IAV. In contrast, with birds previously infected with H3N8 IAV, only one duck challenged with 104 EID50 of H4N6 IAV was shedding viral RNA at 2 days post-inoculation, and with H6N2 IAV, only birds challenged with the 104 EID50 dose were positive to virus isolation. Viral shedding in ducks infected with H6N2 IAV was reduced on days 2 and 3 post-inoculation compared to control birds. To explain the differences in the dose necessary to produce infection among H3-primed ducks challenged with H4N6 or H6N2 IAV, we mapped the amino acid sequence changes between H3 and H4 or H6 HA on predicted three-dimensional structures. Most of the sequence differences occurred between H3 and H6 at antigenic sites A, B, and D of the HA1 region. These findings demonstrate that the infectious dose necessary to infect mallards with IAV can increase as a result of HSI and that this effect is most pronounced when the HA of the viruses are genetically related.

Lessons learned from research and surveillance directed at highly pathogenic influenza A viruses in wild birds inhabiting North America

Following detections of highly pathogenic (HP) influenza A viruses (IAVs) in wild birds inhabiting East Asia after the turn of the millennium, the intensity of sampling of wild birds for IAVs increased throughout much of North America. The objectives for many research and surveillance efforts were directed towards detecting Eurasian origin HP IAVs and understanding the potential of such viruses to be maintained and dispersed by wild birds. In this review, we highlight five important lessons learned from research and surveillance directed at HP IAVs in wild birds inhabiting North America: (1) Wild birds may disperse IAVs between North America and adjacent regions via migration, (2) HP IAVs can be introduced to wild birds in North America, (3) HP IAVs may cross the wild bird-poultry interface in North America, (4) The probability of encountering and detecting a specific virus may be low, and (5) Population immunity of wild birds may influence HP IAV outbreaks in North America. We review empirical support derived from research and surveillance efforts for each lesson learned and, furthermore, identify implications for future surveillance efforts, biosecurity, and population health. We conclude our review by identifying five additional areas in which we think future mechanistic research relative to IAVs in wild birds in North America are likely to lead to other important lessons learned in the years ahead.

Development of an influenza virus protein microarray to measure the humoral response to influenza virus infection in mallards

Avian influenza viruses pose a serious zoonotic threat, in part because current seasonal influenza virus vaccines only offer strain-specific protection, instead of heterosubtypic or universal protection against influenza virus infection. Understanding the humoral response to vaccination and natural infection in the broadest context possible is important to developing defenses against influenza zoonosis. Protein microarrays are a novel platform well suited to assaying the humoral immune response broadly and efficiently. We developed an influenza virus protein microarray (IVPM) that could be used to assay sera from many species, including humans. Waterfowl such as mallard ducks are natural reservoirs for many influenza A viruses, but their humoral immune response to infection is poorly understood. To establish this technology, we assayed sera from mallards experimentally infected with two low-pathogenic common avian influenza viruses (H3N8 and H4N5) for reactivity to influenza virus hemagglutinin (HA) by IVPM. The IVPM results correlated well with results from an established enzyme-linked immunosorbent assay, supporting the validity of the IVPM as a serological assay in influenza virus research. Interestingly, successive infection with H3N8 followed by H4N5 virus in mallard ducks induced antibodies that were broadly reactive against group 2 hemagglutinins. We also analyzed sera from wild mallards and observed serological evidence for infection in those sera. With serological information, it may be possible to infer infection history of wild avian species and gain a better understanding of the infection dynamics of influenza viruses in their natural reservoir. This might ultimately lead to interventions that enhance our pandemic preparedness.

The ecology of avian influenza viruses in wild dabbling ducks (Anas spp.) in Canada

Avian influenza virus (AIV) occurrence and transmission remain important wildlife and human health issues in much of the world, including in North America. Through Canada’s Inter-Agency Wild Bird Influenza Survey, close to 20,000 apparently healthy, wild dabbling ducks (of seven species) were tested for AIV between 2005 and 2011. We used these data to identify and evaluate ecological and demographic correlates of infection with low pathogenic AIVs in wild dabbling ducks (Anas spp.) across Canada. Generalized linear mixed effects model analyses revealed that risk of AIV infection was higher in hatch-year birds compared to adults, and was positively associated with a high proportion of hatch-year birds in the population. Males were more likely to be infected than females in British Columbia and in Eastern Provinces of Canada, but more complex relationships among age and sex cohorts were found in the Prairie Provinces. A species effect was apparent in Eastern Canada and British Columbia, where teal (A. discors and/or A. carolinensis) were less likely to be infected than mallards (A. platyrhynchos). Risk of AIV infection increased with the density of the breeding population, in both Eastern Canada and the Prairie Provinces, and lower temperatures preceding sampling were associated with a higher probability of AIV infection in Eastern Canada. Our results provide new insights into the ecological and demographic factors associated with AIV infection in waterfowl.

Evidence of Intercontinental Spread and Uncommon Variants of Low-Pathogenicity Avian Influenza Viruses in Ducks Overwintering in Guatemala

Over a hundred species of aquatic birds overwinter in Central America's wetlands, providing opportunities for the transmission of influenza A viruses (IAVs). To date, limited IAV surveillance in Central America hinders our understanding of the evolution and ecology of IAVs in migratory hosts within the Western Hemisphere. To address this gap, we sequenced the genomes of 68 virus isolates obtained from ducks overwintering along Guatemala's Pacific Coast during 2010 to 2013. High genetic diversity was observed, including 9 hemagglutinin (HA) subtypes, 7 neuraminidase (NA) subtypes, and multiple avian IAV lineages that have been detected at low levels (<1%) in North America. An unusually large number of viruses with the rare H14 subtype were identified (n = 14) over two consecutive seasons, the highest number of H14 viruses ever reported in a single location, providing evidence for a possible H14 source population located outside routinely sampled regions of North America. Viruses from Guatemala were positioned within minor clades divergent from the main North American lineage on phylogenies inferred for the H3, H4, N2, N8, PA, NP, and NS segments. A time-scaled phylogeny indicates that a Eurasian virus PA segment introduced into the Americas in the early 2000s disseminated to Guatemala during ~2007.1 to 2010.4 (95% highest posterior density [HPD]). Overall, the diversity detected in Guatemala in overwintering ducks highlights the potential role of Central America in the evolution of diverse IAV lineages in the Americas, including divergent variants rarely detected in the United States, and the importance of increasing IAV surveillance throughout Central America. IMPORTANCE Recent outbreaks of highly pathogenic H7N3, H5Nx, and H7N8 avian influenza viruses in North America were introduced by migratory birds, underscoring the importance of understanding how wild birds contribute to the dissemination and evolution of IAVs in nature. At least four of the main IAV duck host species in North America migrate through or overwinter within a narrow strip of Central America, providing opportunities for diverse IAV lineages to mix and exchange gene segments. By obtaining whole-genome sequences of 68 IAV isolates collected from migratory waterfowl in Guatemala (2010 to 2013), the largest data set available from Central America to date, we detected extensive viral diversity, including gene variants rarely found in North America and gene segments of Eurasian origin. Our findings highlight the need for increased IAV surveillance across the geographical span of bird migration flyways, including Neotropical regions that have been vastly undersampled to date.

Of Ducks and Men: Ecology and Evolution of a Zoonotic Pathogen in a Wild Reservoir Host

A hallmark of disease is that most pathogens are able to infect more than one host species. However, for most pathogens, we still have a limited understanding of how this affects epidemiology, persistence and virulence of infections—including several zoonotic pathogens that reside in wild animal reservoirs and spillover into humans. In this chapter, we review the current knowledge of mallard (Anas platyrhynchos) as host for pathogens. This species is widely distributed, often occupying habitats close to humans and livestock, and is an important game bird species and the ancestor to domestic ducks—thereby being an excellent model species to highlight aspects of the wildlife, domestic animal interface and the relevance for human health. We discuss mallard as host for a range of pathogens but focus more in depth of it as a reservoir host for influenza A virus (IAV). Over the last decades, IAV research has surged, prompted in part to the genesis and spread of highly pathogenic virus variants that have been devastating to domestic poultry and caused a number of human spillover infections. The aim of this chapter is to synthesise and review the intricate interactions of virus, host and environmental factors governing IAV epidemiology and evolution.