An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology

As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken

Evolutionary pathway for the 2017 emergence of a novel highly pathogenic avian influenza A(H7N9) virus among domestic poultry in Tennessee, United States

In March 2017, a novel highly pathogenic avian influenza A(H7N9) virus was detected at two commercial broiler breeder facilities in Tennessee, United States. In this study, a wild bird low pathogenic avian influenza A virus, A/blue-winged teal/Wyoming/AH0099021/2016(H7N9), was shown to be the probable precursor of the novel H7N9 virus; this low pathogenic virus has eight possible progenitor genes sharing\u3e 99% sequence identity with the novel H7N9 virus. Phylogeographic analyses showed that viral gene constellations that formed and circulated among dabbling ducks contributed to the emergence of the novel H7N9 virus. This is in contrast to the virus that caused the 2016 H7N8 outbreak, which had more genetic contributions from viruses circulating among diving ducks. Study findings support the need for ongoing wild bird surveillance to monitor circulating viruses and to understand possible evolutionary pathways of virus emergence in poultry

Outbreak of H7N8 Low Pathogenic Avian Influenza in Commercial Turkeys with Spontaneous Mutation to Highly Pathogenic Avian Influenza

Highly pathogenic avian influenza (HPAI) subtype H7N8 was detected in commercial turkeys in January 2016. Control zone surveillance discovered a progenitor low pathogenic avian influenza (LPAI) virus in surrounding turkey flocks. Data analysis supports a single LPAI virus introduction followed by spontaneous mutation to HPAI on a single premises

Outbreak of H7N8 Low Pathogenic Avian Influenza in Commercial Turkeys with Spontaneous Mutation to Highly Pathogenic Avian Influenza

Highly pathogenic avian influenza (HPAI) subtype H7N8 was detected in commercial turkeys in January 2016. Control zone surveillance discovered a progenitor low pathogenic avian influenza (LPAI) virus in surrounding turkey flocks. Data analysis supports a single LPAI virus introduction followed by spontaneous mutation to HPAI on a single premises

Outbreak of epizootic hemorrhagic disease in captive reindeer (\u3ci\u3eRangifer tarandus\u3c/i\u3e)

In September 2020, an outbreak of epizootic hemorrhagic disease occurred in captive reindeer (Rangifer tarandus) and was associated with neurological signs and mortality. Four reindeer died or were euthanized after acute illness over a 12-day period. Affected reindeer displayed abnormal behavior, neurologic signs, lethargy, and/or lameness. The most consistent gross finding was dark red streaks throughout the adrenal gland cortices (4/4). One animal had acute hemorrhage involving the subcutis and skeletal muscles over the ventrolateral body wall and back, and abomasal serosa. Histologically, the most common lesions were adrenal gland cortical hemorrhage (4/4) with necrosis (3/4) and lymphoplasmacytic meningoencephalitis with gliosis, glial nodules, satellitosis, and nonsuppurative perivascular cuffing (4/4). The brain lesions were most frequent in the gray matter of the cerebrum, hippocampus, and thalamus but also involved the cerebellum and brainstem. Epizootic hemorrhagic disease virus serotype 6 was detected through PCR and sequencing of the spleen in all cases

H7N1 Low Pathogenicity Avian Influenza Viruses in Poultry in the United States During 2018

Here, we report three detections of H7N1 low pathogenicity avian influenza viruses (LPAIV) from poultry in Missouri (n¼2) and Texas (n¼1) during February and March 2018. Complete genome sequencing and comparative phylogenetic analysis suggest that the H7 LPAIV precursor viruses were circulating in wild birds in North America during the fall and winter of 2017 and spilled over into domestic poultry in Texas and Missouri independently during the spring of 2018. RESUMEN. Nota de investigacio´n—Virus de la influenza aviar de baja patogenicidad H7N1 en avicultura, Estados Unidos, 2018. En este art´ıculo se reportan tres detecciones del virus de influenza aviar de baja patogenicidad H7N1 (LPAIV) en avicultura en Missouri (n¼2) y Texas (n¼1) durante febrero y marzo del 2018. La secuenciacio´n completa del genoma y el ana´lisis filogene´tico comparativo sugieren que precursores de este virus de influenza de baja patogenicidad H7 circulaban en aves silvestres en Ame´rica del Norte durante el oton˜o y el invierno de 2017 y se propagaron a las aves comerciales en Texas y Missouri de forma independiente durante la primavera del 2018

Highly Pathogenic Avian Influenza Viruses and Generation of Novel Reassortants, United States, 2014–2015

Asian highly pathogenic avian influenza A(H5N8) viruses spread into North America in 2014 during autumn bird migration. Complete genome sequencing and phylogenetic analysis of 32 H5 viruses identified novel H5N1, H5N2, and H5N8 viruses that emerged in late 2014 through reassortment with North American low-pathogenicity avian influenza viruses

Highly Pathogenic Avian Influenza Viruses and Generation of Novel Reassortants, United States, 2014–2015

Asian highly pathogenic avian influenza A(H5N8) viruses spread into North America in 2014 during autumn bird migration. Complete genome sequencing and phylogenetic analysis of 32 H5 viruses identified novel H5N1, H5N2, and H5N8 viruses that emerged in late 2014 through reassortment with North American low-pathogenicity avian influenza viruses

High Rates of Detection of Clade 2.3.4.4 Highly Pathogenic Avian Influenza H5 Viruses in Wild Birds in the Pacific Northwest During the Winter of 2014–15

SUMMARY. In 2014, clade 2.3.4.4 H5N8 highly pathogenic avian influenza (HPAI) viruses spread across the Republic of Korea and ultimately were reported in China, Japan, Russia, and Europe. Mortality associated with a reassortant HPAI H5N2 virus was detected in poultry farms in western Canada at the end of November. The same strain (with identical genetic structure) was then detected in free-living wild birds that had died prior to December 8, 2014, of unrelated causes in Whatcom County, Washington, U. S. A., in an area contiguous with the index Canadian location. A gyrfalcon (Falco rusticolus) that had hunted and fed on an American wigeon (Anas americana) on December 6, 2014, in the same area, and died 2 days later, tested positive for the Eurasian-origin HPAI H5N8. Subsequently, an active surveillance program using hunter-harvested waterfowl in Washington and Oregon detected 10 HPAI H5 viruses, of three different subtypes (four H5N2, three H5N8, and three H5N1) with four segments in common (HA, PB2, NP, and MA). In addition, a mortality-based passive surveillance program detected 18 HPAI (14 H5N2 and four H5N8) cases from Idaho, Kansas, Oregon, Minnesota, Montana, Washington, and Wisconsin. Comparatively, mortality-based passive surveillance appears to have detected these HPAI infections at a higher rate than active surveillance during the period following initial introduction into the United States. RESUMEN. Altas tasas de detección del virus de influenza aviar altamente patógeno H5 clado 2.3.4.4 en aves silvestres en la parte noroeste del Pacífico durante el invierno 2014-15. En 2014, los virus de influenza aviar altamente patógenos H5N8 clado 2.3.4.4 se diseminaron a través de la República de Corea y posteriormente, se reportaron en China, Japón, Rusia y Europa. Se detectó mortalidad asociada con un virus reacomodado altamente patógeno de influenza aviar H5N2 en granjas avícolas en el oeste de Canadá a finales de noviembre. Se detectó entonces la misma cepa (con estructura genética idéntica) en aves silvestres de vida libre que habían muerto antes del 8 de diciembre del 2014 por causas no relacionadas en el Condado de Whatcom, Washington, en los Estados Unidos, en una zona contigua con la ubicación del caso índice en Canadá. Un halcón gerifalte (Falco rusticolus) que había cazado y se había alimentado de un silbón americano (Anas americana) el 6 de diciembre del 2014, en la misma zona, y que murió dos días después, resultó positivo a la presencia del virus de alta patogenicidad de origen euroasiático H5N8. Posteriormente, un programa de vigilancia activa basado en el muestreo de aves acuáticas cazadas y recolectadas en Washington y Oregón detectó diez virus de influenza aviar altamente patógena H5 de tres subtipos diferentes (cuatro del subtipo H5N2, tres del subtipo H5N8 y tres subtipo H5N1) con cuatro segmentos en común (HA, PB2, NP, y MA ). Además, mediante un programa de vigilancia pasiva basado en el muestreo de aves muertas se detectaron 18 virus de influenza aviar de alta patogenicidad (catorce subtipo H5N2 y cuatro H5N8) en Idaho, Kansas, Oregón, Minnesota, Montana, Washington y Wisconsin. Comparativamente, la vigilancia pasiva basada en la mortalidad parece haber detectado estas infecciones del virus de influenza de alta patogenicidad en un porcentaje mayor en comparación con la vigilancia activa durante este período después de la introducción inicial en los Estados Unidos

Investigation of risk factors for introduction of highly pathogenic avian influenza H5N1 infection among commercial turkey operations in the United States, 2022: a case-control study

Introduction: The 2022–2023 highly pathogenic avian influenza (HPAI) H5N1 outbreak in the United States (U.S.) is the largest and most costly animal health event in U.S. history. Approximately 70% of commercial farms affected during this outbreak have been turkey farms. Methods: We conducted a case-control study to identify potential risk factors for introduction of HPAI virus onto commercial meat turkey operations. Data were collected from 66 case farms and 59 control farms in 12 states. Univariate and multivariable analyses were conducted to compare management and biosecurity factors on case and control farms. Results: Factors associated with increased risk of infection included being in an existing control zone, having both brooders and growers, having toms, seeing wild waterfowl or shorebirds in the closest field, and using rendering for dead bird disposal. Protective factors included having a restroom facility, including portable, available to crews that visit the farm and workers having access and using a shower at least some of the time when entering a specified barn. Discussion: Study results provide a better understanding of risk factors for HPAI infection and can be used to inform prevention and control measures for HPAI on U.S. turkey farms