Seth R. Swafford

Detection and Characterization of a Distinct Bornavirus Lineage from Healthy Canada Geese (Branta canadensis)

ABSTRACT Avian bornaviruses (ABV), identified in 2008, infect captive parrots and macaws worldwide. The natural reservoirs of these viruses are unknown. Reverse transcription-PCR (RT-PCR) was used to screen oropharyngeal/cloacal swab and brain samples from wild Canada geese (Branta canadensis) for ABV. Approximately 2.9% of swab samples were positive for bornavirus sequences. Fifty-two percent of brain samples from 2 urban flocks also tested positive, and brain isolates were cultured in duck embryo fibroblasts. Phylogenetic analyses placed goose isolates in an independent cluster, and more notably, important regulatory sequences present in Borna disease virus but lacking in psittacine ABVs were present in goose isolates.

Antiviral Susceptibility of Avian and Swine Influenza Virus of the N1 Neuraminidase Subtype

ABSTRACT Influenza viruses of the N1 neuraminidase (NA) subtype affecting both animals and humans caused the 2009 pandemic. Anti-influenza virus NA inhibitors are crucial early in a pandemic, when specific influenza vaccines are unavailable. Thus, it is urgent to confirm the antiviral susceptibility of the avian viruses, a potential source of a pandemic virus. We evaluated the NA inhibitor susceptibilities of viruses of the N1 subtype isolated from wild waterbirds, swine, and humans. Most avian viruses were highly or moderately susceptible to oseltamivir (50% inhibitory concentration [IC50], <5.1 to 50 nM). Of 91 avian isolates, 7 (7.7%) had reduced susceptibility (IC50, >50 nM) but were sensitive to the NA inhibitors zanamivir and peramivir. Oseltamivir susceptibility ranged more widely among the waterbird viruses (IC50, 0.5 to 154.43 nM) than among swine and human viruses (IC50, 0.33 to 2.56 nM). Swine viruses were sensitive to oseltamivir, compared to human seasonal H1N1 isolated before 2007 (mean IC50, 1.4 nM). Avian viruses from 2007 to 2008 were sensitive to oseltamivir, in contrast to the emergence of resistant H1N1 in humans. Susceptibility remained high to moderate over time among influenza viruses. Sequence analysis of the outliers did not detect molecular markers of drug-resistance (e.g., H275Y NA mutation [N1 numbering]) but revealed mutations outside the NA active site. In particular, V267I, N307D, and V321I residue changes were found, and structural analyses suggest that these mutations distort hydrophobic pockets and affect residues in the NA active site. We determined that natural oseltamivir resistance among swine and wild waterbirds is rare. Minor naturally occurring variants in NA can affect antiviral susceptibility.

Large-Scale Avian Influenza Surveillance in Wild Birds throughout the United States

Avian influenza is a viral disease that primarily infects wild and domestic birds, but it also can be transmitted to a variety of mammals. In 2006, the United States of America Departments of Agriculture and Interior designed a large-scale, interagency surveillance effort that sought to determine if highly pathogenic avian influenza viruses were present in wild bird populations within the United States of America. This program, combined with the Canadian and Mexican surveillance programs, represented the largest, coordinated wildlife disease surveillance program ever implemented. Here we analyze data from 197,885 samples that were collected from over 200 wild bird species. While the initial motivation for surveillance focused on highly pathogenic avian influenza, the scale of the data provided unprecedented information on the ecology of avian influenza viruses in the United States, avian influenza virus host associations, and avian influenza prevalence in wild birds over time. Ultimately, significant advances in our knowledge of avian influenza will depend on both large-scale surveillance efforts and on focused research studies.

Low Pathogenicity Avian Influenza Subtypes Isolated from Wild Birds in the United States, 2006–2008

Abstract Due to concerns that high pathogenicity avian influenza would enter into the United States, an interagency strategic plan was developed to conduct surveillance in wild birds in order to address one of the possible pathways of entry. The USDA and state wildlife agencies participated in this effort by collecting samples from 145,055 wild birds from April 2006 through March 2008 in all 50 states. The majority (59%) of all wild bird samples was collected from dabbling ducks, and 91% of H5 detections using real-time reverse transcriptase polymerase chain reaction (rRT-PCR) were in dabbling ducks. Apparent prevalence of H5 by rRT-PCR in all birds sampled was 0.38%. Most (48%) H5 detections were found in mallards (Anas platyrhynchos). Thirty-three virus subtypes were identified; H5N2 was the most prevalent subtype and accounted for 40% of all virus isolations. We present the virus subtypes obtained from the national surveillance effort and compare them with research results published from various countries.

PREVALENCE OF AVIAN PARAMYXOVIRUS 1 AND AVIAN INFLUENZA VIRUS IN DOUBLE-CRESTED CORMORANTS (PHALACROCORAX AURITUS) IN EASTERN NORTH AMERICA

Abstract Although it is well established that wild birds, such as cormorants, carry virulent avian paramyxovirus serotype 1 (APMV-1; causative agent of Newcastle disease) and avian influenza virus (AIV), the prevalence of these viruses among Double-crested Cormorants (Phalacrocorax auritus) in the Great Lakes region of North America has not been rigorously studied. We determined the prevalences of APMV-1 and AIV in Double-crested Cormorants from the interior population of eastern North America. From 2009 to 2011, oropharyngeal and cloacal swabs and serum samples were collected from 1,957 individual Double-crested Cormorants, ranging from chicks to breeding adults, on breeding colony sites in Michigan, Wisconsin, and Mississippi, USA, and Ontario, Canada, as well as on the wintering grounds of migratory populations in Mississippi, USA. Prevalence of antibodies to APMV-1 in after–hatch year birds was consistently high across all three years, ranging from 86.3% to 91.6%. Antibody prevalences in chicks were much lower: 1.7, 15.3, and 16.4% in 2009, 2010, and 2011, respectively. Virulent APMV-1 was detected in six chicks sampled in 2010 in Ontario, Canada. Only one adult was positive for AIV-specific antibodies and five individuals were positive for AIV matrix protein, but the latter were negative for H5 and H7 AIV subtypes. We provide further evidence that Double-crested Cormorants play an important role in the maintenance and circulation of APMV-1 in the wild, but are unlikely to be involved in the circulation of AIV.

Antibodies to Avian Influenza Viruses in Canada Geese (Branta canadensis): A Potential Surveillance Tool?

Traditionally, the epidemiology of avian influenza viruses (AIVs) in wild birds has been defined by detection of virus or viral RNA through virus isolation or reverse-transcription polymerase chain reaction. Our goals were to estimate AIV antibody prevalence in Canada geese (Branta canadensis) and measure effects of age and location on these estimates. We collected 3,205 samples from nine states during June and July 2008 and 2009: Georgia, Massachusetts, Minnesota, Mississippi, New Jersey, North Carolina, Pennsylvania, Washington, and West Virginia. Serum samples were tested for AIV antibodies with the use of a commercial blocking enzyme-linked immunosorbent assay. Overall, 483 (15%) Canada geese had detectable antibodies to AIV. Significantly higher prevalences were detected in geese collected from northeastern and upper midwestern states compared with southeastern states. This trend is consistent with results from virus isolation studies reporting AIV prevalence in North American dabbling ducks. Within Pennsylvania, significantly higher antibody prevalences were detected in goose flocks sampled in urban locations compared to flocks sampled in rural areas. Antibody prevalence was significantly higher in after-hatch-year geese compared to hatch-year geese. No significant differences in prevalence were detected from 10 locations sampled during both years. Results indicate that Canada geese are frequently exposed to AIVs and, with resident populations, may potentially be useful as sentinels to confirm regional AIV transmission within wild bird populations.

Avian Influenza Virus Prevalence in Migratory Waterfowl in the United States, 2007–2009

SUMMARY We analyzed 155,535 samples collected for surveillance of avian influenza viruses (AIVs), in the United States from 2007 to 2009, from migratory waterfowl (ducks, geese, and swans). The goal was to elucidate patterns of prevalence by flyway and functional groups to determine targets for future surveillance. Apparent prevalence of AIV was highest in the Pacific Flyway in 2007–2008 (14.2% and 14.1%, respectively), in the Mississippi Flyway in 2009 (16.8%), and lowest each year in the Atlantic Flyway (range, 7.3%–8.9%). Dabbling ducks had higher apparent prevalence of AIV (12.8%–18.8%) than diving ducks (3.9%–6.0%) or geese and swans (3.6%–3.9%). We observed highest apparent prevalence in hatch-year waterfowl (15.6%–18.9%). We further analyzed 117,738 of the 155,535 samples to test the hypothesis mallard (Anas platyrhynchos) had highest prevalence of AIV. We compared apparent prevalence and odds ratios for seven species of ducks and one species of goose commonly collected across the United States. Mallards had highest apparent prevalence (15%–26%) in half of comparisons made, whereas American green-winged teal (Anas creeca, 12%–13%), blue-winged teal (Anas discors, 13%–23%), northern pintail (Anas acuta, 16%–22%), or northern shoveler (Anas clypeata, 15%) had higher apparent prevalence in the remaining comparisons. The results of our research can be used to tailor future surveillance that targets flyways, functional groups, and species with the highest probability of detecting AIV. RESUMEN Prevalencia del virus de la influenza aviar en aves acuáticas migratorias en los Estados Unidos, 2007–2009. Se analizaron 155,535 muestras recolectadas para la vigilancia de los virus de influenza aviar (AIV), en los Estados Unidos desde el año 2007 al año 2009, procedentes de aves acuáticas migratorias (patos, gansos y cisnes). El objetivo fue determinar los patrones de prevalencia por vías migratorias y por grupos funcionales para determinar los objetivos de vigilancia en el futuro. La prevalencia aparente de influenza aviar fue más alta en la ruta migratoria del Pacífico durante los años 2007 y 2008 (14.2% y 14.1%, respectivamente), en la ruta migratoria del Mississippi en el 2009 (16.8%), y la más baja de cada año fue la ruta migratoria del Atlántico (rango 7.3%–8.9%). Los patos chapoteadores mostraron la mayor prevalencia aparente del virus de influenza aviar (12.8%–18.8%) en comparación con los patos buceadores (3.9%–6.0%) o gansos y cisnes (3.6%–3.9%). Se observó mayor prevalencia aparente en aves acuáticas de un año de edad (15.6%–18.9%). Posteriormente, se analizaron 117,738 de las 155,535 muestras para probar la hipótesis de que los ánades reales (Anas platyrhynchos) mostraban la mayor prevalencia de virus de influenza aviar. Se compararon la prevalencia aparente y las razones de momios para siete especies de patos y una especie de ganso comúnmente recolectados en los Estados Unidos. Los ánades reales tenían una mayor prevalencia aparente (15%–26%) en la mitad de las comparaciones realizadas, mientras que la cerceta común (Anas creeca, 12%–13%), el pato media luna (Anas discors, 13%–23%), ánade rabudo (Anas acuta, 16%–22%), o pato cuchara (Anas clypeata, 15%) tuvieron mayor prevalencia aparente en las comparaciones restantes. Los resultados de esta investigación se pueden utilizar para adaptar la vigilancia futura que se enfoque en las vías migratorias, grupos funcionales, y las especies con mayor probabilidad de detectar al virus de la influenza aviar.